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ABOUT THIS USER GUIDE - The Cambridge Crystallographic Data

1. P P4 P 4 P4 m P42 2 4mm P 4 2 m P4 m mm 4m 2 pue up ce P 4 21 2 4 21 ide x P42 P42 m E 42 2 2 p 42 21 P 42 21 2 pea oe oo P41 P 41 2 2 P43 P 43 2 2 D 4 23 P41212 P 43 21 2 pr 42 mc P 4 2 c P42 m m c p e 2 6 P 4 21c P b 4 bm P 4 b 2 P4 m b m P b c 42 be P42 m b c P c 42cm P 4 c 2 P42 m PHS CH de Acc PA mcc Pos ume 42 nm P An 2 P42 m n m Pes 6 anc PA mnc Pn P4 n P4 n m m P 42 n P42 n Pn c P42 n m c Pn b P4 n b Pom b ue P42 n b c Pn c P42 n c m P qu sc 6 P4 n e c Pn n P42 n n Pn n c P4 n n c S eS 14 4 14 m 422 4mm 4 m I4 m m m 4m2 41 I41 I41 2 2 d 41 md 4 2d A e 4 cm 4 c I4 m c m c d 41 cd 41 a 141 a a d I41 am d a c d I41 ac dd Trigonal 180 DASH User Guide Pra t iS P3 P 3 P321 P3m 1 P 3 m p3 1 2 P3 1m P 3 1 P akas P31 P31 2 P31 1 2 P32 P32 2 P32 1 2 PD uu B3 sc PO d Poem zer uem Pe oec B 3G Renee zz R3 R 3 R32 R3m R 3m
2. Monoclinic a axis puc B2 1 gt Pm1 P 2 m J P 2 P eZee P 21 m 1 Pb P b P 2 b 1 P 21 b 1 1 P 21 b Pc 1 J Pc1 1 P 2 c P 21 c P 21 c 1 Pn 1 Pn P 2 n 1 P 21 n P 21 n ES C 2 C n C 2 m 1 Cn Cn C 2m B B2 Bn B 2 m 1 Bb Bb B 2 b 1 3 d LG de J Tie d I 2 c 1 Monoclinic b axis P1 1 pP T 2T P iml P 1 2 m 1 P 21 Pal 2 TL P 1 21 m 1 P a 1 P a P 2 a P 21 a P 21 a Prila eS I P ds P 1 2 c 1 P 21 c P 2176 P p l P n P 2 n P 21 n P 1 21 n C zc Calo e D demi d E C C Qu 2o q A AM cg A A 1 2 m 1 A n A n A 1 2 n 1 2 2 DASH User Guide 175 176 a 1 a 1 2 a 1 Monoclinic c axis P P 2 P m P 2 m PB 21 P 21 P 21 m P a P a P 2 a P 21 a P 21 a P b P b P 2 b P 1 1 21 c P 21 b P n P n P 2 n P 21 1 P 21 n B 1 E B 2
3. 156 31 ba c Pnm 21 157 31 cab P21mn 158 31 cba P21nm 159 31 bca Pn21m 160 31 a cb Pm2in 161 32 Pba2 162 32 cab P 2 6 5b 163 32 bca PE 2 a 164 33 Pna 21 165 33 ba c Pb un 21 166 33 cab P 2 mb 167 33 cba P21 Gon 168 33 bca Poco 2d nm 169 33 a cb Pn2la 170 34 Pnn2 171 34 cab P2nn 172 34 bca Pn2n 173 35 Cmm2 174 35 cab A 2mm 175 35 bca Bm2m 176 36 Cm c 21 177 36 ba c C cm 21 178 36 cab A2lma 179 36 cba A2lam 180 36 bca Bb21m 181 36 a cb Bm21 b 182 37 G cc 2 183 37 cab A2aa 184 37 bca Bb 2 p 185 38 Amm2 186 38 ba c Bmm 2 187 38 cab B2mm 188 38 cba C 2mm 189 38 bca Cm 2m 190 38 a cb Am 2m 1 91 39 Abm 2 192 39 ba c Bma 2 193 39 cab B 2 c mi 194 39 cba C2mb 195 39 bca Cm2a 196 39 a cb Ac2m DASH User Guide DASH User Guide 197 40 Ama 2 198 40 ba c Bbm2 1 99 40 cab B2mb 200 40 cba C2 Cm 201 40 bca GG 2m 202 40 a cb Am2a 203 4 Aba 2 204 41 ba c Bba2 205 41 cab B 2 G5 206 41 cba C S285 207 41 bca Gc Z5 208 41 a cb Ac2a 209 42 Fmm 2 210 42 cab F2mm 211 42 bca Fm2m 212 43 Fdd2 213 43 cab F2dd 214 43 bca Ed 2d 24 5 44 mm 2 216 44 cab 2mm 217 44 bca Im2m 218 45 Iba2 219 45 cab I2cb 220 45 bca lc2a 221 46 Ima2 222
4. ae P nm 21 P n m Pn2 a P n 21a P n a Pon 2b Pn b Pn2 Pn n a Pna 21 Pnam a a Pnaa a Pnab a Pnan C Pone 2 Pnom c a Pnca C Pncb C Pnen n aS Pnn2 Pnnms n a Pnna n E mn oum n Pnnn Du AR m Cmmm m C2 m NA C 2 2 21 ab Cm2a a c2m o cm e 21 E Co2ccm c ab G2 eub C E C c m 21 Comm Cc2m ab Cc 2 Comb Qc acre C oc m c ab C cca Ceep a B 2 2 2 Bmm Bmmm Bm B2m DL B2 24152 b Bm 21b Bmmb B2mb ac Bma 2 Bma B2cm Bm m ac b B2cb Bmab DASH User Guide DASH User Guide Bis cm Bbm2 Bbmm Bb 21m B D p Bb2b Bbmb B b ac Bba 2 Bbom Bb ac b Bba bb Bbac Az E LAS A222 A m Ammm Am2 A22 A21 A2122 A a Am2a Amma A 21 m A a Ama2 Amam A 2 m A a a Alaa Amaa A bc Abm2 Abmm Ac2m Acmm A bc a Ac2a Abma A bc a Aba2 Acam A bc a a Abaa A ca que ay Ae T2 212 m 2 Immm 2m 22m I ab 2a mma m 2b m m ac a 2 man I2cm men c b L2 p mc b I bc T dmi Ibmn Icm2 Iemn c a Ic2a I cma b a ba2 bam Ib a bca ES tA Se Bit 2k 22 Fmm 2 Fmmm Fm2m F2mm Fo d d F2dd Borde d Fd2d Bu Ob un Fdd2a Ed ud Fddd 179 Tetragonal
5. Number Symbol Occurrences Number Symbol Occurrences 19 P22 12 18216 4 P2 11572 1 Pl 1848 5 C2 1702 18 P222 970 92 P4 2 2 322 20 C222 393 146 R3 311 96 P432 2 290 76 P4 240 152 P3324 222 144 P3 168 173 P6 149 198 P2 3 143 169 P 132 145 P3 131 78 P43 113 154 P352 106 170 P6 90 155 R3 87 143 P3 70 80 14 56 79 14 55 23 1222 54 3 P2 53 178 P6322 47 94 P452 2 46 17 P222 43 14 4 3 D 3 Space Group Listing for DASH The Entry Number 1s an internal identifier used by DASH The corresponding space group number setting and symbol are shown in the second column of the table Within a DASH sai file the space group is stored as DASH User Guide 161 SpaceGroup entry_number sg setting symbol For example SpaceGroup or SpaceGroup 162 39 52 4 b P 1 21 1 9 53 a Entry number SG setting symbol 1 1 P1 2 2 P 3 3 a P2 4 4 a P o 2l d 5 5 al B 2 6 5 a2 G 2 7 5 a3 2 8 6 a P m 9 T al P b 10 7 a2 Pn 11 7 a3 Pe T2 8 al Bm 13 8 a2 C m 14 8 a3 m 15 9 al Bb 16 9 a2 Cn 17 9 233 E 18 9 al EE T9 9 a2 Bn 20 9 a3 b 1 21 10 a P 2 22 ll a P 21 m 1 1 23 12 al B 2 m 24 12 a2 C 2 m 25 12 a3 2 m 26 1
6. 484 190 P 6 2c 485 191 P 6 m m m 486 192 P 6 mc c 487 193 P 63 m c m 488 194 P 63 m m c 489 195 P23 490 196 F23 491 197 2 53 492 198 P 21 3 493 199 21 3 494 200 Pm 3 495 201 1 P n 3 1 496 201 2 Pn 3 2 497 202 Fm 3 498 203 1 F d 3 1 499 20332 kd 852 500 204 Im 3 501 205 Pa 3 502 206 la 3 503 207 P432 504 208 P42 3 2 505 209 432 506 210 4132 507 211 432 508 212 P 43 3 2 509 213 P 41 3 2 510 214 41 3 2 511 215 P 4 3m 512 216 F 4 3m 513 217 4 3m 514 218 4 3n 515 219 4 3c 516 220 I 43d 517 221 Pm 3 m 518 222 1 Pont 3 nel 519 222 2 Pn 3 n 2 520 223 Pm 3 n 521 224 1 Poon 3 m1 522 224 2 Pn 3 m 2 523 225 Fm 3m 524 226 E msie 174 DASH User Guide 925 227 1 F d 3 m 526 22727 F d 3 m 2 527 228 1 F d 3 es 528 228 2 F d 3 c 2 529 229 m 3 m 530 230 a 3 d 14 5 Appendix E Extinction Symbols and their Space Groups In order to use this table look up the extinction symbol returned by the space group determination program in the left hand column of the table The possible space groups for that extinction symbol are then listed in the right hand columns
7. 170 DASH User Guide DASH User Guide 361 86 1 42 n 1 362 86 2 42 n 2 363 87 4 m 364 88 1 41 a 1 365 88 2 41 a 2 366 89 422 367 90 4212 368 91 4122 369 92 41 21 2 370 93 42 72 2 371 94 42 21 2 372 95 43 2 2 373 96 43 21 2 374 97 4 2 375 98 4122 376 99 4 377 100 4b 378 101 42cm 379 102 42 nm 380 103 4cc 381 104 4nc 382 105 422 mc 383 106 42 bc 384 107 Am 385 108 4c 386 109 41 md 387 10 41 cd 388 11 4 2 m 389 12 4 28 390 13 4 21 m 391 14 4 21 392 145 4m2 393 16 4 c2 394 17 4b2 395 18 4n2 396 19 4m2 397 120 4 c 2 398 12T 42 m Sud 122 42 d 400 123 4 m mm 401 124 4 m c c 171 402 125 P 4 n b m 1 403 125 2 P 4 n b m 2 404 126 1 P 4 n n c 1 405 126 2 P 4 n n c 2 406 127 P 4 m bm 407 128 P 4 mn c 408 129 P 4 n m m 1 409 129 2 P 4 n m m 2 410 130 p An ees 411 30 2 P 4 n c c 2 412 131 P 42 m m c 413 132 P 42 m c m 414 1332 P 42 n b c 1 415 33 2 P 42 n b c 2 416 134 1 P 42 n n m 1 417 134 2 P 42 n n m 2 418 1
8. e Select which group of symmetries you would like to explore and whether a grid search is required Indexing in the triclinic crystal system may take a long time with McMaille Click Run gt Once McMaille has finished running you will be prompted to type a character and press return The results from the indexing will then be presented in a text window Closing this window will return you to DASH where you can enter your chosen cell parameters into the Unit Cell Parameter wizard window see Section 2 6 3 page 14 28 DASH User Guide 2 10 6 Importing Unit Cell Parameters DASH Wizard Results from DICYOL Import a solution into DASH by pressing an Import button re casa gt soho tte parma vane wer re A Perec 3555 as rare onmes suom sea 1766 5077 Original DICVOL output View Save As Select the appropriate solution by selecting the button next to it in the Import column lt Back Next gt Close Clicking Next gt will take you automatically to the Unit Cell Parameters wizard window DASH Wizard Unit Cell Parameters S mn x Enter crystal system trial lattice constants and space group if known ero polnt 0 0000 Browse Lattice constants 3 33383 b 8 18858 E 7 319399 ES Alpha 30000 Beta 111 187 Gamma 30000 Back Next gt Close Apply Space Group Space Group 3b P121 Crystal S
9. If you fail to select an appropriate region in which the fit will be performed e If you do not enter enough peaks to properly describe the data in the selected area If you enter far too many peaks in the selected region DASH User Guide 51 n such circumstances the peak fitting algorithm may converge to a local rather than a global minimum This is usually obvious as the calculated peaks fail to match the data It is trivial to delete a poorly fitted region and try again By way of reassurance here are some extreme examples where the peak fitting algorithm has still produced a useful result Selected range too short on the right Three closely spaced weak peaks Two very weak peaks with large esds 52 DASH User Guide DASH User Guide te at ette Selected range too short on both sides 53 54 DASH User Guide 6 INDEXING 6 1 Overview of Indexing e Correct indexing of the powder pattern i e determination of the unit cell dimensions is crucial you cannot solve the structure if the pattern is not indexed properly DASH can help you with indexing by allowing you to determine peak positions with great accuracy However DASH does not do the actual indexing itself For this you must use one of the many freely available cell indexing programs DASH does provide an interface for DICVOL see Section 6 2 6 page 58 which is convenient for many users However it is strongly recommended that
10. 114 P 42 c 289 57 Pbcm 285 86 P4 yn 215 161 R3c 271 63 Cmcm 270 76 P4 240 167 R 3c 236 205 Pa3 226 152 P3 2 222 85 P4 n 213 4 Aba2 211 147 P 3 194 31 Pmn2 188 70 Fddd 180 58 Pnnm 173 144 P3 168 52 Pnna 166 173 P6 149 45 Iba2 143 198 P2 3 143 169 P6 132 145 P3 131 8 Cm 126 87 I4 m 122 122 I 45d 114 78 PA 113 154 P352 106 165 P 3cl 100 72 Ibam 23 59 Pmmn 92 68 Ccca 92 170 P6 90 155 R3 87 142 14 acd 86 110 14 cd 85 130 P4 ncc 85 166 R 3m 84 54 Pcca 81 129 P4 nmm 19 160 R3m 78 55 Pbam 74 34 Pnn2 72 113 P 42 Im 71 143 P3 70 163 P 3 c 62 225 Fm3m 62 121 I 4 gt m 57 80 14 56 79 I4 55 81 P 4 55 217 I 43m 55 23 1222 54 3 P2 53 10 P2 m 53 186 P63mc 53 118 P 4n2 49 126 P4 nnc 49 127 P4 mbm 49 194 P63 mmc 43 26 Pmc2 48 DASH User Guide 159 P3 c 48 73 Ibca 47 178 P6122 47 94 P4522 46 136 P4 mnm 46 32 Pba2 44 17 P222 43 40 Ama2 42 14 4 2 D 2 Chiral Sohnke Space Groups Listed by Frequency of Occurrence This table lists all Sohnke space groups i e space groups in which enantiomerically pure substances can crystallise that occur at least 40 times in the Cambridge Structural Database CSD arranged in descending order of frequency Since there were over 250 000 structures in the CSD when this lost was compiled any space group not in the table is very uncommon Only the symbol for the standard setting is given for each space group in the list
11. If DASH has access to Mogul appropriate torsion angle ranges can be explored by hitting the Modal button see Section 10 4 2 page 113 Mogul is a molecular geometry database which forms part of the CSD System and is available separately from the CCDC If Mogul is not accessible modal torsion angle ranges can be defined in the Modal Torsion Angle Ranges dialogue that will appear on hitting the Modal button N3 51 C5 C5 torsion Sampling Ranges Modal Torsion Angle Ranges 2 x Recommended distribution from Mogul y z C Bimodal Y C Trimodal Torsion Angle Lower U inia 121 60911 0 00000 18000000 180 00000 to 0 00000 e o Non Modal DK Cancel The Modal Torsion Angle Ranges dialogue box allows bimodal and trimodal torsion angle ranges to be defined The radio buttons at the top of the dialogue box are used to choose whether bimodal or trimodal torsion angle ranges are required In the boxes labelled Upper and Lower enter the upper and lower bounds of a single torsion angle range thus if a bimodal search of the torsion angle space of 30 90 and 30 to 90 is required enter 30 0 in the Lower box and 90 0 in the Upper box The complementary range is automatically determined and displayed Torsion angles within both of the displayed ranges will be generated during the simulated annealing run Planar torsion angle ranges centred around 0 and 180 can be searched by defining a bimodal
12. Simulated annealing parameter bounds ETT MILI remi wt a E an ai amd aaa TOO ee ns a Jam Mogul distribution bias MDB Min hits 106 sermos V Randomise inital values Set Fragment Restraints Z matiices This will launch a dialog The user can select atoms from each fragment and a separation distance between them for 1 or more pairs of atoms either within a single fragment or between DASH User Guide fragments The user here also specifies the ideal distance between the pair of fragment atoms A default weight is specified as 100 0 DASH Wizard Distance Restraints 239 1 1 2 QOZIT i DASH User Guide 105 10 3 3 Editing a Z Matrix i di Edit Atomic Properties 2 Matrix Tia pese tenen es oce GE IS CAN IET IE je fe 39 199 jes je 3 19 E 199 3 00 1 00 000 0 nj o0 Hi Q e m acl z Z 0 O ho c e o o ce e Co O Ol Ol O Ly o o o e i na e A ea fa ce ce ce ce Co O Oo O O e ak CEE EA ES ae p NM c2 Led le Biso Occupancies 2 Bio of an non hydrogens to 3 0000 Re label Rotations Save As View Re order Save OK Cancel This window allows various atomic properties to be modified 106 View displays the edited Z matrix The list of atoms displayed allows you to delete individual atoms from the Z ma
13. Stop eem View hl Edit Solutions DASH User Guide 121 Status information Simulated annealing run number in the above example current run 3 of a set of 10 Temperature the current SA temperature value Minimum chi the minimum C for the integrated intensities 1 e the quantity that is being minimised by the SA Average chi the average value of the minimum C for the integrated intensities Profile chi the C for the diffraction profile and it is directly comparable with the c for the Pawley fit Total moves the total number of moves in the SA run so far Moves iteration the total number of moves performed NS times NT times number of parameters before a temperature reduction is applied Downhill Uphill Reject the number of downhill uphill rejected moves in last iteration of 4000 moves Buttons 122 Pausing the Simulated Annealing Run The Pause button simply pauses the DASH program to free up processor time for some other purpose Click OK to continue with DASH Starting the next Simulated Annealing Run When in a multi run the Start next button terminates the current run and starts the next Stopping the Simulated Annealing Run The Stop button stops the simulated annealing run immediately and advances to the DASH Wizard Analyse Solutions window see Section 10 9 4 page 129 Editing the Simulated Annealing Parameters The Edit button stops the simulated annealing run immediately and ret
14. and will not work well on patterns where background has been left in place In regions where intensity 1s greater than 8 times the residual background high points in the smoothed intensity are detected and peaks are assigned to these locations In cases where multiple peaks are found that are close in 2q peaks are merged Using Auto Peak is easy In the Indexing Wizard the user reaches the following window The user can click on the Auto Select Peaks button and DASH will attempt to fit ranges automatically The feature is designed not to be a black box after completion the user is encouraged to review the assignments made as the heuristics in the algorithm are not perfect 56 DASH User Guide DASH Wizard Indexing Step 1 Peak Picking The next step is indexing the pattern Select the first 20 peaks in the diffraction pattern using the mouse then press Next gt to index the pattern with DICVOL or launch a stand alone McMaille and enter found unit cell parameters by hand Alternatively if the unit cell parameters are already known they can be entered directly Hint To enable the options for external programs they must be entered in the Configuration dialogue te Index pattern C Cc C Enter known unit cell parameters lt Back Next gt Close The peaks fitted can be modified and or deleted after automatic peak fitting by hand Further the user can add in more peaks manually if they so wish Autom
15. 25 A for Cl S and 5 A per hydrogen atom So for this molecule C7H4N3035 Cl we estimate the molecular volume to be 275 J so 2 molecules per cell would need a volume approximately 550 A gt The DICVOL cell volume of 576 A suggests that we have two molecules per cell and given that the cell is monoclinic a likely space group is P2 since Z 2 for this space group 15 1 8 Stage 6 Checking the Cell and Determining the Space Group Select the top solution from the Results from DICVOL window and import this into DASH by selecting the button next to it in the Import column If only one solution is obtained it will be imported automatically into DASH Click Next gt You will see the data displayed as before but this time there are a series of tick marks at the top of the plot to indicate where the Bragg reflections corresponding to the input cell occur The first thing to do is to ensure that in general the tick marks correspond to peaks within the pattern Any unaccounted for diffraction peaks are a warning that the determined unit cell might not be correct or that there is an impurity phase present A quick glance at the Tutorial_1 xye pattern shows no unaccounted for peaks but a few excess tick marks For example 200 DASH User Guide amp theta The tick at just over 7 5 2q does not appear to correspond to anything other than background intensity which means that it probably corresponds to a systemat
16. 4G R3c R 3 Hexagonal Boe te a P6 P 6 P6 m P622 P6mm P 6 2 P6 mmm P 6 m P 63 P63 P63 m P63 2 2 BP 62 2 So P62 P62 22 P64 P64 22 BST i as P61 P61 22 P65 P65 22 Pi soy ne P 63 mc P 6 2 P63 mmc Pes se e P 63 cm P 6 c P63 mcm o P6cc P6 mcc Cubic pim e P23 Pm 3 P4 3 2 P 4 3 m Pm 3 P 21 42 P21 3 P42 3 2 P41 P41 3 2 P43 3 2 p o un P 4 3n Pm 3 E g c Pa 3 Pon Pn 3 Pn 3 Pn n Pn 3 Lem 123 m 3 432 4 32 m 3 121 3 41 141 3 2 S wd 43d a a 3 EQ a 3 MEME F23 Fm 3 F4 32 F 4 3m Fm 3 Ep F41 32 PA 56 F 4 3 c Fm 3 DASH User Guide 181 Fd 3 Fd 3m e Frida 3 C 14 6 Appendix F Using the Cambridge Structural Database The Cambridge Structural Database CSD contains gt 430 000 crystal structures for organic and organometallic molecules The CSD is part of the CSD System which also includes software for Search retrieval and analysis of structures ConQuest Crystal structure visualisation Mercury Generation of in house databases searchable alongside the CSD PreQuest Data analysis Vista The CSD System also incorporates soStar a library of intermolecular interactions containing data derived from both the CSD and PDB and Mogul a molecular geometry library For more information about the Cambridge Crystallographic Data Centre CCDC see http www ccdc cam ac uk 14 6 1 F 1 Source of Geometry for Molecular Models The se
17. 8641 76 PL ow 11317 5 P 1 217a 1 9692 32 Pad 217 6 1 11806 7 Pl a 1 9703 15 Pd n 1 8641 76 POL life X 211806 7 Pl 21 n 1 8630 93 PI amp 1 IBER Cay d 52473 4 pol 1 52473 4 Ci 1 60781 5 Gu x i 60781 5 Al 1 70921 7 T Ws I 65708 9 A1 n 1 15461 5 A1 1 170921 7 i i 1 59708 9 LOL a 1 72619 2 la 1 STEGIS 2 Al n 1 75467 5 Close the window showing the results and press lt Back in the Pawley Refinement Step 2 window A dialogue box will pop up asking whether the files generated during space group determination should be removed select Yes Now from the Space Group pull down menu select the space group determined to be the most probable P21 and press Apply Check the correspondence between the tick marks and the peak positions as before e The correct space group has been chosen and hence a Pawley refinement should be performed in this space group This step has already been performed previously and the sdi file saved Hence the structure solution process can begin e You can exit DASH at this point if you wish by selecting Exit from the File menu 15 1 11 Stage 9 Molecule Construction The crystal structure of the molecule that we are trying to solve is given below DASH User Guide 209 MH M You need to construct a 3D molecular description of the above molecule using your favourite modelling software and save it in pdb mol or mol2 format f you do not have a mod
18. Iv Unitcell V zeropoint Step size damping factor 1 0 Sigma size T Gammafsize Overlap criterion 1 0000 Sigmafstrain Gammalstrain Refinement status Cycle number 5 df 5 y Refinement number 2 135 reflections 8163 points Rwp 15 88 R exp 9 04 chi 3 087 Save as Close 8 3 5 Saving the Results of Pawley Refinement Pawley Fit files In the example shown in Section 8 3 4 page 73 the C of 3 087 is very good so you would then save the results of this refinement as the basis for structure solution Select Accept and then Save as the Save Diffraction Information for structure solution window appears into which you can enter a file name e g Example sdi click Save You can save the results of several independent Pawley refinements each in its own Pawley Fit file with extension sdi 8 3 6 Mathematical Problems with Pawley Refinement For poor quality data sets there can be problems in fitting the background with the polynomial mathematical procedure When this happens an Errors detected during Pawley fit window will appear 74 DASH User Guide Errors detected during Pawley fit E The extracted intensities are ill conditioned due to a high degree of overlap in the data set and so could be unreliable in certain ranges Full details of the problems are recorded in the fit list file polyp liz You may be able to fix the problem by decreasing the data range in theta ar by inc
19. Open I Rigid body Rietveld refinement C Rietveld refinement with GSAS Pietveld refinement with TOPAS Rietveld refinement with RIE TAN Hint Options for external programs only enabled for those given in Configuration dialogue lt Back Next gt Close Start SA After choosing the refinement package you wish to use within the Rietveld Refinement Wizard and selecting the required sdi and crystal structure files click Next gt DASH Wizard Rietveld Refinement Pawley Le Bail refinement The first step is to do a Pawley or Le Bail refinement in external refinement program with an input file generated by DASH You may wantto use a different data set or a different data range for the Rietveld refinement so DASH will first ask you for the file with the diffraction data to use In order to perform the Rietveld refinement it is necessary to do a Pawley or Le Bail fit within your chosen refinement package using an input file generated by DASH It may be advantageous to use a 142 DASH User Guide different data set or data range for the Rietveld refinement to that used for structure solution so it will now be necessary to read in the diffraction data click Next gt DASH Wizard Powder Diffraction File Diffraction data File example xye Browse Back Next Close Rebin gt Click Browse to find the diffraction data file that you want to use for Rietveld refinement and then
20. a or choosing Pawley Refinement from the Mode menu Ignore this option for the moment 2 After six peaks have been fitted DASH has sufficient information to allow a lattice parameter 4 parameters zero point refinement The results of the refinement can be seen by selecting Peak Positions from View menu This improves the lattice constants in the majority of cases and greatly improves the starting position for the Pawley refinement 3 After eight peaks have been fitted DASH has determined that the peak shape has been sufficiently well defined to allow a full Pawley refinement to be performed The Pawley Refinement Step 2 window will pop up automatically In the initial Pawley refinement only the terms describing the background and the terms corresponding to individual reflection intensities are refined using the previously refined unit cell and zero point Select Refine 3 cycles of least squares are performed This should return figures similar to the ones below or better 204 reflections 9751 points Rwp 22 25 R exp 9 38 C 5 6 Click Accept to accept the results of this refinement the fit is then displayed Now click in the main window and press Home to see how well the data are fitted The obs minus calc plot is shown in pink and emphasises any misfit in the data If you look closely at the data you are likely to see something like this DASH User Guide 205 2000 3500 3000 500 000 15
21. background subtraction the default value is eight Click Next gt to save RIETAN s ins file The pattern fitting will now be performed automatically within RIETAN Once the initial fit has been done a plot of the diffraction profile the fit and the difference profile will be shown in gnuplot graph The fitting of the pattern is a two step process closing the gnuplot window File gt Exit will start the second step of the fitting Once complete RIETAN will prompt you to save the ins file 12 6 2 RIETAN Rietveld Refinement DASH User Guide 151 DASH Wizard Rietveld Refinement with RIETAN D DASH rietan test tutoriall Example ins File name Refine options IV le DAA rerorrennerdotcet Initialisation Le Bail ORFFE Number of cycles 0E Scale Penalty parameter TK 650 00 V Background TK increasing multiplier FINC 2 0000 7 Biso Refine update ins file then call Coordinates RIETAN V Write out cif file The DASH interface for RIETAN will now guide you through the process of Rietveld refinement At any point you may view the structure e g in Mercury by clicking on View exit the refinement process by clicking on Close The right hand side of the dialogue box shows the current refinement options to start with three boxes are ticked showing that only the Scale Background and Biso terms will be refined Click on the Refine button and the ins file will be automatically updated then submitted
22. or Contes os on Tor mw osux E a eatin osux mo Tome weg 05000 uox ee ej Randomise inital values Click Next gt The resulting Simulated Annealing Protocol window that appears need not concern us here In most cases the default values will suffice See the DASH User Guide for more details Click Nex t gt The next window asks you to choose some options for the Simulated Annealing procedure It is useful at this stage to go over some of the details DASH User Guide 213 214 DASH Wizard Simulated Annealing Options Hydrogens Output C Ignore v Write out dash file at end recommended Absorb C Explicit For every run write out not recommended pdb file co file res file IV Auto local minimise F cssrfile T ci file profile Y Use hydrogens Output chi squared vs moves at end v Auto align VW Use crystallographic centre of mass Back Close Create batch file Hydrogens as the scattering power of hydrogens is low hydrogens are ignored by default to speed up the calculations The Absorb option absorbs the electrons from the hydrogen in their riding atoms For single crystal data the hydrogen atoms can be taken into account explicitly during the SA Note By default hydrogens are always included during the local minimisation at the end of each simulated annealing run During Rietveld refinement hydrogen atoms are always inc
23. x Crystal System Space Group Monoclinic b axis Lattice constants a 23332 b 8 49945 e 731801 a Alpha 30 000 Beta 111 165 Gamma 90 000 lt Back Close e Click Next gt This window allows the maximum resolution of the data to be set In most cases the default resolution of 1 75 will be appropriate DASH User Guide 153 DASH Wizard Single Crystal Step 2 Resolution Maximum resolution 1 7500 amp e Click Next gt Open the file containing the h k 1 F and s F2 values The hkl file is expected to be in SHELX format DASH Wizard Single Crystal Step 3 Reflections r Diffraction data File C Program Files CCDC DASH 3 0 Documentation T utoriall hkl Open Browse v Recalculate ESDs v Discard F squareds lower than 2 0000 sigma IV Average Friedel related pairs lt Back Close 154 DASH User Guide There are three options available for processing the data and in most cases it is appropriate to use the default values Recalculate ESDs Discard F lower than 2 0 sigma Average Friedel related pairs Click Next gt Enter the file name of an sai file where the information required for structure solution will be saved Save diffraction information for structure solution ax Save in a Data files t e E3 History El Desktop A My Documents My Computer File name Tuto
24. A with figures of merit M 22 16 1 and F 22 29 3 Whilst not fantastic figures of merit we can note that there are nearly 100 calculated peaks for this cell as against the 22 that were input This might indicate that there are a lot of systematic absences or it may indicate that the cell is DASH User Guide 245 wrong 15 4 7 Stage 5 Stop and Think Does the cell make sense In this case given that the molecule may well adopt a planar configuration it is difficult to estimate the likely molecular volume Assuming 4 molecules per cell and dividing 1800 A by 4 we get 450 which is certainly enough to accommodate the molecule s backbone of 24 carbon atoms 15 10 fluorines 10 A 460 So the cell is worth checking 15 4 8 Stage 6 Checking the Cell and Determining the Space Group It is clear that there are a great many excess tick marks indicating probable systematic absences this means that the space group must be of substantially higher symmetry than P2 Zoom into the 10 16 region of the pattern and watch the correspondence between the tick marks and the observed reflections as you scroll through some of the possible space groups You will see that many of the space groups can be ruled out immediately for example the primitive cells predict many peaks that are not observed A centred cell is therefore likely and so C2 c is a likely choice see Appendix D in the DASH User Guide Select this group and examine th
25. Another advantage of this approach is that it is not necessary to include the atomic resolution data so that the background and peak shape parameters from the Pawley refinement can be used Rietveld refinement can also be carried out in a semi automated way using the DASH interface to one of three external programs TOPAS GSAS and RIETAN These three interfaces prepare the reflection data for the external programs set up the refinement input files and facilitate refinement in a series of pre defined steps in order to carry out a basic structural refinement DASH User Guide 137 The interface between DASH and the refinement packages will only become available once the relevant sections of the Configuration Window Choose Options gt Configuration from the main toolbar in DASH have been completed see Section 2 8 page 19 12 1 2 Starting Rietveld Refinement There are two ways to start the Rietveld refinement using the solution from a simulated annealing run with the crystal structure from e g a cif ora res file The first option is recommended Note that it is possible to save all solutions from the simulated annealing and to read them back in at some other time see Section 10 9 4 page 129 DASH Wizard Analyse Solutions cil ee view Toss cs me caos Resor me AAA e E ee E qr L Se ee E IN 1 5 73 45 Atom labels for overlay Atom colours for overlay C Element solution B
26. As View Save Cancel The DASH Wizard will also confirm that you now have 15 independent degrees of freedom Click Next gt to continue 15 6 14 Stage 12 Setting up the Full Model Structure Solution n the Parameter Bounds window we now want to use the information gained during the preliminary solution to fix the coordinates of the heavy atom positions The Zr atom as found earlier sits on the origin Fragment 1 corresponds to the free Zr atom so we can change the initial x frag1 y fragl and z frag1 values to 0 0 and click on the checkbox in the F column for each of these rows to fix the coordinates Fragments 2 and 3 correspond to the two O W O fragments and we can fix the coordinates of the W atoms by simply putting in the initial values of x y and z for fragments 2 and 3 as the W atom corresponds to the origin coordinates for the fragment Choose the coordinates of fragment 2 to be 0 6 0 6 0 6 fragment 3 to be 0 3412 0 3412 0 3412 and set these parameters to be fixed as well using the checkboxes in the F column The 266 DASH User Guide rows for these fixed parameters should now all be greyed out see figure below DASH Wizard Parameter Bounds Simulated annealing parameter bounds ital Lower Upper F Modal is toa INE II wen III IET A FI y 0 f 0 E ams om onen conor 0 0 ass u amp xm v CwWegy 89 E E toa osx uses O x aden oso on Tor gt y Z m
27. B 1 B 1 2 10 B 1 n B 1 n B 1 2 n A 1 A 1 2 A 1 A 1 2 m A a A a A 2 a 2 2 m b b 2 b Orthorhombic pow od oM E 2 Pmm Pmmm Pm2m P2m Bou ccc Pg 21 Bue WD P2 2 P 212 P2 2 PZN P 21 2 2 PAZ E P 21 2 2 P 2T 21 P 21 21 2 P 21 21 2 P 21 21 21 Pa al P 2 a P2lma P a Pi b P P 241 b P2mb P n b P uc P 21 n P21mn P n o P a 2 P am P2lam P a a P2aa P aa PU od P 27 ab P P a P2an P Base Ch P moer 21 PAZ com P cm P c a P2lca P c a DASH User Guide P se o P2cb Pm cb Pr sE P21cn Pmon Pone Pmn 21 P21nm Pmnm P nia P2na Pmna P n P 21 n b Pmnb P n P2nn Pmnn Pubs s og P b m Po by 21 Pbmm Pb a P b 21 a Pbma Pb Pb2b Pbmb Pb Pb 2n Pbmn Pb a Pba2 Pbam Pb a a Pbaa Pb a Pbab Pb a Pban PB Gs Pb sea Pbcam Pb c a Pbca Pb Cc Pbcb P b 4G Pben Pb on as Pbn 21 Pbnm Pb n a Pbna Pb n Pbnb P B Pbnn Pie m Pcm 21 Pc2m P cmm Pc a Pc2 Pcma Pic JS Pc21b Pcmb Peu Pr 2 Penn Pc a Pca 21 Pcam Pc a a Pcaa Pc a Pcab P G a Pcan Bp dx Piei Poeem PHa eta Sal Pico Peg C Bcc 5 Ber xe Pcen Pre nm Pcon 2 Pcnm Pc n a Pcna Pc n Pe mb PE Pon DASH User Guide 177 178
28. Brookhaven National Synchrotron Light Source The incident wavelength was 1 1294 and the sample was held in a 0 7 mm glass capillary 15 1 3 Stage 1 Reading the data Open DASH by double clicking on the DASH icon The DASH Wizard will guide you through the structure solution process which is performed in a series of steps Select View data determine peak positions and click Next gt Click the Browse button e Select the file Tutorial l xye from e g C Program Files CCDCIDASH 3 1 Documentation Tutoriall Data files and click Open The diffraction data will be loaded into DASH Click Next gt Check that the wavelength and radiation source have been set correctly and click Next gt DASH User Guide 191 Truncate the data to a resolution of 1 75A and click Next gt The default window size setting of 100 should be good enough for this simple background Click Next gt 15 1 4 Stage 2 Examining the Data This section of the tutorial is purely descriptive so 1f you are familiar with handling powder diffraction data skip to Stage 3 The data spans 5 to 44 2q If you open the file Tutorial_1 xye in an ASCII text editor such as Wordpad you ll see that the wavelength of 1 1294 is given on the first line The data consists of three columns 1 1294 5 000 81 96 10 952 5 004 71 25 10 284 bulk of data omitted for clarity ARO DOLOS V 44 000 68 28 3 540 192 DASH User Guide Column 1 2q position Colu
29. C is about 2 7 Proceed and refine the unit cell and zero point along with the background and the intensities You may get a warning from DASH stating that errors have been detected due to instabilities in the Pawley fit If so reject the fit and increase the Overlap criterion to 2 0 Select Refine and you should get a stable refinement with a Pawley C of about 1 9 246 DASH User Guide Accept your best Pawley fit and save it as Tutorial_4 sdi 15 4 10 Stage 8 Molecule Construction Construct a 3D molecular description of the molecule using your favourite modelling software and save it in pdb mol or mol2 format This can be done for example by importing an ISIS Draw sketch into WebLabViewer for further details see Tutorial 1 Save this as Tutorial_4 full pdb Tutorial_4 full mol or Tutorial_4 full mol2 The remainder of this tutorial is based upon a Z matrix constructed importing the above ISIS Draw sketch of the molecule into WebLabViewer and exporting it as a mol file If you do not have a model builder to hand there are files provided with the tutorial Tutorial 4 full mol2 and Tutorial 4 half mol2 15 4 11 Stage 9 Setting up the Structure Solution Run Continue on from the Pawley fitting stage by pressing Solve gt Click on the ax icon and select Tutorial 4 full mol2 the file that you created in Stage 8 a Z matrix file called Tutorial 4 full l zmatrix will be generated automatically e Read in the Tutorial 4 fu
30. DASH across the GRID are available from the DASH page of the CCDC website http www ccdc cam ac uk products powder_diffraction dash along with further documentation 11 5 Post Processing of Results After running DASH in batch mode or in GRID mode there will usually be a large number of dash results files output In order to process these results it is generally easier to combine all of the files into one large dash file There are two ways of doing this Open a command prompt and navigate to your results directory then type C Program Files CCDC DASH 3 11DASH exe MERGE D 1Results Directory output dash This will automatically merge all the dash files in the directory D Results Directory to produce the file output dash Open a command prompt and navigate to your results directory then type C Program Files CCDC DASH 3 1 DASH exe MERGE A window will then appear which will allow you to navigate to your results directory and give the name for your merged dash file DASH User Guide 135 136 DASH User Guide 12 RIGID BODY RIETVELD REFINEMENT 12 1 Rietveld Refinement in DASH Rietveld refinement is a technique for minimising the differences between the modelled crystal data and the experimental powder pattern This means that it is a very useful method for validating DASH solutions and for producing publication quality crystal structures There are currently a large number of different programs available for perf
31. Each line lists a file or some data that is identified by a keyword TIC Tick mark file with hkl and 2q positions of extracted intensities e HCV Extracted hkl intensities and reflection correlations PIK Background subtracted profile RAW File name for the original data file DSL Data type wavelength and peak shape parameters Cell the unit cell parameters SpaceGroup Space group selected for the Pawley refinement PawleyChiSq c fit achieved by the Pawley refinement An example of the file Act20 sdi 1s given below TIC S HSLZDIEIE HCV NAhot20 hev HCV hct20 hkl PIK hct20 pik RAW hct20 raw DSL hct20 ds1 Cell 9 93861 8 49849 31 731 90 0000 111 1896 90 0000 DASH User Guide 11 SpaceGroup 38 4 b P1211 PawleyChiSq 2 41 2 6 Viewing Data Attributes Peaks and Crystal Symmetry After you have proceeded with the cell indexing step and choice of space group there are options for viewing the current peak list etc These items are selected from the top level menu button View as follows Diffraction Setup Type of data wavelength etc see Section 2 6 1 page 12 Peak Positions 2q for fitted peaks see Section 2 6 2 page 13 Cell Parameters Cell dimensions space group etc see Section 2 6 3 page 14 Peak Widths Parameters describing peak shape see Section 2 6 4 page 15 2 6 Viewing Diffraction Setup Structural Information Diffraction Setup Peak
32. Guide 145 12 4 1 Preparation of Data for TOPAS Rietveld Refinement DASH Wizard Background Subtraction Subtract background Number of background terms for TOPAS 20 El Complete the steps of data preparation given see Section 12 3 page 141 The final step before sending the pattern to TOPAS is the Background Subtraction This can be done within DASH but it is usually better to allow TOPAS to perform the background subtraction using 20 background terms as default Click Next gt A dialog will inform you when the first inp file has been written and hence is ready to be loaded into TOPAS 1 TOPAS inp file 1 has been written Once TOPAS is open launch the Kernal Mode Launch gt Kernal Mode and set the inp file to the inp file written by DASH Launch gt Set INP file To run the refinement hit the play button 146 DASH User Guide circled in red in the following screenshot in the window called Launch Mode gt Launch Mode C Program Files CCDC DASH 3 1 Example Example inp OX EX bl Gi i Loading C Topas3 topas inc Loading C Topas3 interface inc Launch Mode C Program Files CCDC DASH 3 1 Example Example inp Once the cycle is complete TOPAS will ask you whether you wish to update the inp file with an out file Hit No and return to DASH 12 4 2 TOPAS Rietveld Refinement The DASH interface for TOPAS will now guide you through the process of Rietveld refinement At any point y
33. Guide 59 60 Each indexing program has its own strengths and weaknesses We have found DICVOL TREOR and ITO to be useful when indexing organic crystal structures but this is not to say that other programs will not be equally successful Frequently one program will successfully index a pattern where another has failed It 1s therefore always worth trying at least two indexing programs on each problem Before running an indexing program 1t 1s useful to get some idea of the size of cell you might expect given the molecular formula For example a molecule comprising 20 non hydrogen and 25 hydrogen atoms will occupy about 450 A allowing 20 A for each of the non H atoms and 2 A for each of the H atoms Therefore a good starting point would be to search for cells of up to 2000 A in volume as a cell of this size will accommodate four molecules i e Z 4 a likely number when dealing with organic structures You can always increase this size limit later if you do not get any reasonable cells from the initial runs The majority of indexing programs were designed for use with relatively small unit cells Advances in structure solution mean that people are tackling larger and larger crystal structures thus stretching indexing programs to their limits and beyond For example it is not unheard of for TREOR to suggest that a unit cell is too large and that the data should be checked even when the cell is correct A useful trick here is to sim
34. Programs for Building 3D Molecules Popular choices are Chem3D Ultra http www cambridgesoft com products e WebLabViewer http www accelrys com viewer Cerius http www accelrys com cerius2 index html e SYBYL http www tripos com software sybyl html e SPARTAN http www wavefun com software software html e CORINA http www2 ccc uni erlangen de software corina e CONCORD http www tripos com software concord html It must be emphasised that you should examine the model created by such programs carefully It 1s quite possible to build a model that has poor bond lengths and angles which actually prevent you from solving the structure If in doubt always check the Cambridge Structural Database 14 3 Appendix C Definitions of DASH Figures of Merit Figures of merit in DASH Figures of merit for the Pawley fit to the profile DASH User Guide 157 mle Son y i i obs ical Su i wp i i ob3 J i bach Weighted profile R factor role N P C RE W y lt y 2 obs bach Expected profile R factor Where N P C number of observations number of parameters number of constraints f wos Jesl ii N P C Profile c Figures of merit for the Simulated Annealing Run f fl de f Jv bn daf C for the integrated intesities where Ip x is the extracted intensity from a Pawley refinement of the diffraction pattern Vy is the covariance m
35. The overlay check boxes allow you to select the solutions for which the crystal structures are to be shown overlaid in a single unit cell C Element solution Original atom labels DASH User Guide 129 Any of the simulated annealing solutions can be Rietveld refined by clicking the appropriate Rietveld button Usually this will only be done for the best solution Save allows you to save the solutions as pdb cssr ccl cif res and pro You can also save the final values of the SA parameters and the c progress Save solutions enables you to save all solutions plus the diffraction pattern and the Pawley fit in one binary file with the extension dash Load solutions enables you to load solutions with the extension dash Resume SA allows you to resume the simulated annealing where it left off New runs will be appended to the existing one Delete last run enables you to delete the last solution listed in the summary window A dash file saved after solutions have been deleted will not include the solutions deleted Selecting a solutions Restart button starts the simulated annealing with this solution s parameters as the initial parameters The initial parameters are not randomised and existing runs are overwritten 10 9 5 Reproducibility of Solution A good indicator is the reproducibility of the structure solution using different starting seeds If the process keeps converging to the same minimum a
36. Treatment of Stereoisomers If a molecule has several possible stereoisomers you may need to try simulated annealing with each in turn e g cimetidine shown here there are possible cis or trans positions of the CN group e Sometimes of course you may be able to infer the probable stereochemistry from the chemical DASH User Guide 97 synthesis or from spectroscopic evidence You will not be able to determine absolute configuration from powder data 9 8 Molecule Translation and Rotation Special Positions Molecules will normally be allowed to translate and rotate freely in the unit cell subject of course to the constraints of space group symmetry This normally adds six degrees of freedom for each chemically discrete entity in the asymmetric unit so solving structures with Z gt 1 is much harder than solving structures with Z 1 Rotation is expressed as quaternion numbers O0 O3 Rotations can be restricted to a single axis see Section 10 3 4 page 107 There are four of these but they are not mutually independent and actually contribute only three degrees of freedom to the problem see Appendix H References page 189 Fixed positions are sometimes required for molecules that occupy a special position in a space group A common example is when a centrosymmetric molecule has its centre at the origin in a centrosymmetric spacegroup This has to be handled by introducing a dummy atom into the Z matrix For example a m
37. a nicely crystalline sample data by permission of Dr L Smrcok The background counts are higher and the profile generally noisier than the example synchrotron pattern but the background to noise ratio is still reasonable The profile is significantly worse than the synchrotron example at high angle but peaks are still sufficiently well defined to produce useful information for structure solution 40 DASH User Guide 4 2 3 Example of a Poor Profile This is laboratory data 1 54056 wavelength for a rather poorly crystalline sample data by permission of Dr J P Attfield the peaks are fairly broad and background is high with little diffracted intensity beyond about 25 DASH User Guide 41 5000 4500 4000 3500 3000 bserved profile 2500 S n M E 2000 As REN nent y PE 8 3 10 11 12 12 14 15 16 qug 18 2 theta 11000 10000 9000 39000 7000 6000 5000 4000 3000 2000 Observed profile Note The above data were actually sufficient to solve a problem involving 7 variable torsion angles Remember that weak peaks provided that they are sufficiently well determined are just as powerful a constraint on the solution as strong peaks 4 3 Initial Assessment of Esds The error bars on the data points should look similar to those shown in the example profiles If they look significantly bigger then there could be a problem with the esds If you have been given a d
38. adding in fact 4 torsion angles per molecule 8 torsion angles for the total SA search This does not work in this case as we have reached the present limit of the method with this data but it is worth trying in less complex structures DASH User Guide 259 15 5 15 Stage 13 Conclusion DASH can solve structures with two molecules per asymmetric unit The CSD should be consulted with regard to conformations of flexible rings Models with markedly wrong ring conformations will not give the correct solution 15 5 16 References DICVOL Program D Louer amp M Louer 1972 J Appl Crystallogr 5 271 275 A Boultif amp D Louer 1991 J Appl Crystallogr 24 987 993 Model Builder PC Spartan Pro Version 1 0 5 16 8 2000 Copyright 1996 2000 Wavefunction Inc Visualiser Mercury provided with DASH has good H bonding features RPluto has H bond graph set analysis features CCDC 1999 RPluto is freely downloadable for non commercial purposes from http www ccdc cam ac uk prods rpluto index html Single crystal structure CSD reference code BEURIDIO E A Green R D Rosenstein R Shiono D J Abraham B L Trus R E Marsh 1975 Acta Crystallogr B31 102 107 15 6 Tutorial 6 Solving the Structure of an Inorganic Compound 15 6 1 Introduction The object of this tutorial is to guide you through the process of solving an inorganic crystal structure using the compound ZrW5Og as an example This compound zirco
39. also choose to write out a file at the end of each simulated annealing run that contains the coordinates of the best solution obtained 1 e the solution with the lowest C value This file will be given a default name using the Pawley fit File name selected e g sucrose55 sdi will produce a file sucrose55 pdb for example The structure files also contain the intensity and profile c values of the solution Options for file formats are pdb Additional information contained in this file includes the DASH simulated annealing parameters as well as the translations Q rotations and torsion angles e cssr a file is written in cssr format e ccl a file is written in cc1 format e cif a file is written in cif format res a file is written our in res format pro when selected a file with the extension pro is written out which contains 2q the observed profile the calculated profile for the best solution and the original esds The file is written out in ASCII format and can be imported into a spreadsheet package such as Excel Output Chi squared vs moves at end when selected a graph of the profile C versus moves is written out to a file in ASCII format with the extension chi at the end of the simulated annealing This can be imported into a spreadsheet package such as Excel Output parameters at end when selected a tbl file is written at the end of the simulated annealing run this file contains the translations the Q
40. and find the location of your installation of the Mogul executable If a standard installation of Mogul has been performed DASH should automatically pick up the path to Mogul from the Windows Registry 228 DASH User Guide CCDC Mogul Beta 1 1 EE ioj xl File Searches Help Build query Results and analysis View structures Results Navigator All hits 47 Accepted hits 47 Showing hits with R factor all Relevance Number Cortibuon amp v 1 00 47 100 0 Mogul search Torsion angle 20 value in query A A A A Numberof hits 45 30 135 180 Torsion angle View diagrams Click to de select bars click and drag to de select a range Statistics Total 47 Selected 47 Furio plat Select all hits in histogram Id min l 0 033 Displayed hits 47 R factor filter Selected hits 47 Deselect all hits in histogram All fragments Histogram click in bar to deselect click again to reselect Right click For options 47 hits for the torsion angle have been found by Mogul and these can be viewed by clicking on the View Structures tab in the Mogul window If individual bars of the histogram are selected deselect all hits in histogram and then click on the histogram bars of interest only these structures are displayed in the View Structures window For example
41. bond Remember that in the majority of cases hydrogen atoms will have been placed in assumed positions and will not be subject to adjustment other than as a consequence of adjustments made to the main backbone of the molecule Hence an O H group that does not appear to H bond might well do so if the H atom is rotated to a new position Finally remember to check the molecular conformation does it compare well with similar molecules in the Cambridge Structural Database 10 9 4 Files saved from multiple runs of SA If multiple runs of the SA procedure have been requested see Section 10 6 page 119 the program will keep a record for each run of the lowest c found and the name of the corresponding solution co ordinate file The solution files names are created from the given name of the run with the text suffix 001 002 The solutions are sorted into ascending order of Profile Chi squared in the display DASH Wizard Analyse Solutions I Run Dyer ome ren neces Reve penes me E E EE IA IE JA e 5e 3 ae 1 1 pom 5 e e O Atom labels for overlay ae colours for overlay C By solution number Save solutions By element Load solutions Save Resume S Delete last run E Select solutions Bl through se Invert Selection Show overlay Selecting the View button for a specific solution allows you to view the crystal structure and the calculated profile
42. click on Next gt to read the data into DASH DASH User Guide 143 144 DASH Wizard Diffraction Setup Radiation type Wavelength for angle dispersive ray data in A C LebxXray Radiation Ka 1 12940 v Monochromated e Synchrotron C OW Check that the radiation type and wavelength specified are correct If the data are monochromated ensure that the Monochromated check box is ticked If you are going to use GSAS for the refinement you have the opportunity to load in a GSAS ins file You may want to do this if you have measured instrument parameters that you would like to use in the refinement Check the Load ins file check box and browse to the location of the file Click Next gt to continue DASH User Guide DASH Wizard Profile Range Please note thatfor maximal performance ofthe background subtraction algorithm the diffraction pattern should not start or end at a Bragg peak Start lv Truncate data to start at 2 theta 5 000 End 7 Truncate datato end at 2 theta or atthe equivalent maximum resolution The data range to be used can be modified at this point but it is usual to utilise as much of the diffraction pattern as possible during Rietveld refinement hence the data truncation option has been switched off by default If you wish to truncate the data enter the range to be used Click Next gt to proceed 12 4 Refinement using TOPAS DASH User
43. da a a 01 Optionally the wavelength can be included in the file as the very first line 2 4 Inspecting Diffraction Data The main window shows the diffraction data plotted as observed counts versus 2q There are numerous keyboard and mouse facilities for selecting ranges of 2q scaling of peak height and generally zooming into a region of the profile for closer examination see Section 4 page 37 The next stage for consideration is removal of the background from the data see Section 2 4 1 page 9 2 4 1 Removing the Background from Diffraction Data It is recommended that the background is subtracted through the Wizard see Section 2 10 page 21 Alternatively the background can be subtracted choosing the following icon from the menu bar Ju The method of background removal is a Monte Carlo low pass filter which has advantages of being mathematically robust It is recommended that you let DASH take care of the background subtraction at this stage If you choose to leave the background fitting to later it will be included in the Pawley fitting process using a shifted Chebyshev polynomial see Section 8 5 1 page 79 Note If your data set is of laboratory origin or there is noticeable non uniform background then it is best to remove the background using the Monte Carlo method Poor quality data sets that are not background subtracted at this stage i e sets where the discrimination between peaks and background is poor can give ri
44. dbf files and the dash files when the jobs are finished will be named using this filename as the base along with a number corresponding to the particular SA run package 11 3 Using DASH in Batch Mode 11 3 1 Drag and Drop Running Individual dbf files can be dropped on to the DASH executable or the shortcut icon on your desktop In this mode DASH will run in the background without any displayed user interface Multiple SA packages can be run concurrently in this manner but no progress or final results will be shown The output files will be sent to the directory where the input files were residing see Section 11 5 page 135 11 3 2 Multi Core Processing with MDASH For computers with multi core processors there is also a currently unsupported tool called MDASH which allows the controlled distribution of sets of SA runs across the system The tool provides an interface displaying the progress of the SA runs and will pop up the DASH program to show the results when completed For further information on MDASH see the MDASH documentation within 134 DASH User Guide the DASH 3 1 Unsupported Extras directory 11 4 Using DASH in GRID Mode For users with access to a GRID enabled network of computers DASH can also be run in GRID mode To achieve this it is necessary to set up the client PCs and the GRID servers for distributed DASH This application of DASH is not currently fully supported but installers to set up the computers to use
45. for a bond length to a preceding atom a bond angle to two preceding atoms and finally a torsion angle to three preceding atoms In Stage 10 you ran a program which converted the Cartesian model of Stage 9 into a Z matrix The program further identified by examination of the chemical atom types that only one torsion angle should be treated as variable namely N3 51 C5 C6 The SA run explored the search space with all other parameters of the Z matrix fixed which we have seen this gives a chemically sensible result in our solution The Rietveld refinement allows variation of any of the Z matrix parameters for the chosen solution The first stage of the Rietveld refinement is to keep all parameters fixed except the global isotropic temperature factor scale This allows the initial guess of the Biso values for each atom in the Z matrix to be adjusted by a global scale factor the default values set by DASH are Biso 3 0 for all non hydrogens and 6 0 for hydrogens When the scale factor K is refined then the Biso for each atom is simply K Biso as input in the Z matrix file In single crystal X ray refinement it is usual to set the value for Biso for hydrogens to about 1 25 times the parent heavy atom In the case of powder data for this size of molecule there will be little observable effect if we set all H atoms to have the same value The starting Biso hydrogen value of 6 0 may be considered rather too large and could be adjusted to say 4 0 H
46. in to isolated single peaks working from low to high 2q see Section 4 1 page 37 Fit the peaks using the right mouse button as described in Section 5 1 page 47 Continue picking peaks remembering that you need to sample a total of about 8 over the whole 70 DASH User Guide 2q range When 8 peaks have been fitted a Pawley Refinement Status window appears see Section 8 3 3 page 71 8 3 3 Pawley Refinement Interface The Pawley Refinement Status window appears by clicking the icon in the main window or by selecting Pawley Refinement from the top level Mode menu DASH Wizard Pawley Refinement Step 2 CE Xx M Refinement control Intensities Y Re use intensities Iv Background M back 2 E Iv Unit cell lv Zeropoint Step size damping factor 1 0 I Sigmafsize Gammafsize Overlap criterion 1 000 Sigmafstrain Gammafstrain Refinement status Cycle number 5 of 5H Refinement number EE 83 reflections 6951 points A wal 1253 dm exp Sun chi 2532 Refine Save as Accept The options available are Refined variables Intensities all Pawley refinements treat the reflection intensities as variables in a least squares fit Re use refined intensities DASH utilises the intensities extracted from the previous cycle as a starting point for the next cycle Deselection of this option causes DASH to ignore the previous values and generat
47. is a pre set minimum of 1000 moves 10 5 5 Random Number Seeds e Simulated annealing is a random process that depends on computer generated random numbers Random number generators use a set of seeds which determine the sequence of random numbers used within the program Changing the seeds will change the sequence and thus alter the route taken by the algorithm through c space Different seeds used for otherwise identical runs will generate different paths Conversely keeping the same set of seeds between otherwise identical runs will result in identical paths This can be useful in demonstrating situations as a set of random seeds that produces an answer quickly can be noted and used again Note that when you ask for multiple runs DASH automatically calculates a new set of random seeds for each run 118 DASH User Guide 10 6 Simulated Annealing Options DASH Wizard Simulated Annealing Options Hydrogens m Output C Ignore Iv Write out dash file at end recommended Absorb C Explicit For every run write out not recommended pdb file cd file restile IV Auto local minimise cssrfile M cif file profile v Use hydrogens Output chi squared vs moves at end IV Auto align Output parameters at end LR A AIR Y Use crystallographic centre of mass lt Back Close Create batch file gt Hydrogens The Absorb option default takes account of the electron density of hydrogen atoms by incr
48. of reflections is treated as a single variable with the resultant intensity partitioned equally between the component reflections Look at the output file polyp lis to get information about which reflections have been merged together in this way The file also lists the total number of reflections and other diagnostic information 8 7 Hints for Improving the Pawley Fit Once a reasonable initial Pawley fit has been obtained it can usually be improved by Adding into the refinement the cell dimensions and zero point see Section 8 7 1 page 86 Refining some or all of the peak shape parameters see Section 8 7 2 page 86 DASH User Guide 85 8 7 1 Cell Dimension and Zero Point Refinement An initial Pawley fit can almost always be improved by adding into the refinement the cell dimensions and zero point The cell dimensions will now be refined against the whole of the profile rather than the small number of peaks you chose initially The zero point origin of 2q axis may have been measured experimentally for the instrument on which data were collected but it is always desirable to refine 1t anyway A refined absolute value of 0 01 would not be atypical An error in the zero point may manifest itself on the profile difference plot by a systematic shift in peak positions 8 7 2 Peak Shape Refinement 86 Unless and until the peak shape parameters are explicitly included in the Pawley refinement their values wi
49. one should use at least two indexing programs The freely available CRYSFIRE suite of Shirley provides a rudimentary interface to most of the popular indexing programs e g DICVOL and ITO and is currently available for download from http www ccp14 ac uk The steps involved in indexing are Selecting the first 20 or so low angle peaks and measuring their positions for input to the indexing program Of course only the positions of the lines are important for indexing not their intensities It therefore follows that weak peaks carry just as much weight as strong ones in the indexing process see Section 6 2 page 55 Indexing the pattern to find a plausible set of cell dimensions see Section 6 3 page 59 Checking for possible cells of higher symmetry see Section 6 4 page 61 Checking the cell in DASH by comparing observed and calculated peak positions see Section 6 5 page 61 6 2 Selecting Peaks for Indexing 6 2 1 Overview of Peak Selection for Indexing You should select the lowest angle peaks available regardless of their intensity to ensure that the indexing program has a chance to find the correct cell In general you should pick the first 20 peaks or so including shoulders trying not to miss any As long as a peak is clearly present you should pick it even if it is weak but if you are not sure the peak is significantly above the background you can leave it On balance if you are at all uncertain ab
50. page 47 Fitting multiple peaks and shoulders see Section 5 3 page 49 Common problem situations see Section 5 4 page 51 5 1 How to use the Interface to Select Peaks Zoom in to the area around the peak Sweep out an area using the right mouse button in this example move to about 6 85 2q click right and hold down as you sweep right to about 7 05 before releasing the right button The hatched area now covers the peak and enough background either side to allow an accurate estimate of the peak parameters If you are not happy with the area that you ve swept out simply put the mouse cursor inside the hatched area and select the Delete key on the keyboard to remove the current selected area then try again 5 2 Basic Peak Fitting When you first read experimental data into DASH it will be displayed in the resizable graph DASH User Guide 47 window Identify the first peak in the diffraction pattern and zoom in on it remembering to include a little baseline either side of the peak if possible Sweep out a selection area by clicking and holding the right mouse button remembering to include a little baseline either side of the peak if possible To fit the peak in a hatched area either press Return or Enter with the cursor positioned inside that area or press the following Fit peaks button from the toolbar 48 DASH User Guide Selecting this button will fit all areas that have not yet been fitted The p
51. parameters simultaneously It s a good idea to examine the values of the peak shape parameters Select Peak Widths from the View menu and refine only the parameters that have large coefficients as these are the ones that impact upon the profile fit In the case of cimetidine refining just Gamma strain and setting the number of cycles to 10 rather than the default value of 5 produced a C of 20 0 Your final Pawley c should be in the range 20 25 If the c increased considerably after a refinement select Reject and try refining with a different peak shape parameter Accept your best Pawley fit making a note of the c and save it as Tutorial 3 sdi 15 3 10 Stage 8 Molecule Construction Construct a 3D molecular description of the molecule using your favourite modelling software and save it in pdb mol or mol2 format If you do not have a model building program to hand there is a file supplied with the tutorial Tutorial 3 cis mol2 This model for the cis isomer was created using the Spartan program using default minimisation settings Select the file Tutorial 3 cis mol2 DASH User Guide 237 15 3 11 Stage 9 Setting up the Structure Solution Run Start DASH as before and select Simulated annealing structure solution from the Wizard e Select the Tutorial 3 sdi file Click on the ax icon and select Tutorial 3 cis mol2 the file that you created in Stage 8 a Z matrix file called Tutorial 3 cis zmatrix will be generated
52. position in 2q Esd the estimated standard deviation of the position in 2q Tick the 2q position calculated from unit cell once entered Diff the difference between the observed position and the tick mark hkl after unit cell indexing these are the Miller indices assigned to the peak Prob probability of correctness of assignment Lattice parameters and Zero point these fields are filled in after a Pawley refinement or when an on the fly cell refinement has been performed These are display fields only The DICVOL button can be used to create an input file ready for the DICVOL indexing program after fitting a number of peaks see Section 6 page 55 DASH User Guide 13 2 6 3 Viewing Unit Cell Parameters Structural Information Space Group Crystal System Triclinic Zero point 0 01 Apply Lattice constants a 7 08936 b 10 59343 e 19 2071 o Alpha 100 109 Beta 93 747 Gamma 101 564 Volume 1383 674 The above Structural Information window appears after selecting Cell Parameters from the View menu This example shows a cell and space group ready for input to the Pawley Refinement a b c unit cell lengths in units of Angstroms Alpha beta gamma unit cell angles degrees Volume calculated volume of the unit cell cubic Angstroms e Zero point zero point error of the powder pattern in degrees 2 theta if known Crysta
53. range such as 20 to 20 The complementary range determined and displayed will be 160 to 160 If a trimodal range is chosen then torsion angles will be sampled from the defined space and two further ranges at 120 To accept the defined torsion angle ranges press OK This will return you to the main Parameter Bounds dialogue box and the torsion angle to which modal ranges have been applied will be highlighted in red Hitting Cancel will result in all edits since the last accepted modal range being ignored Hitting Non Modal will return you to the Parameter Bounds dialogue box and the full 360 torsion angle range will be applied A non modal torsion angle range is shown in black DASH User Guide Torsion angles may be fixed at a value Click the F box and then type in the required value in the initial box e g 0 0 When all parameter ranges are set click Next gt see Section 10 3 7 page 110 10 4 2 Using DASH with Mogul If DASH has access to Mogul appropriate torsion angle ranges can be explored using this program Mogul is a molecular geometry database which forms part of the CSD System and is available separately from the CCDC If Mogul has been installed in the default location DASH should automatically find the path to the executable and this path will be displayed in the Configuration window see Section 2 8 page 19 However if DASH does not find the path to the Mogul executable it is possible to enter a pat
54. rather than the correct occupancy which should be 1 3 as they each reside on the 3 fold axis was not a problem because the ratios of the atomic occupancies are correct The incorrectly high occupancies used are compensated by changes in the scale factor Once the oxygens are included it will become important to use the correct occupancies of 1 3 for the Zr and W atoms The fit to the experimental diffraction pattern still shows a lot of differences as we have not found the positions of the oxygen atoms We can now use these positions that we have determined for the heavy atoms in the next cycle of the structure solution in order to find the light atom positions The coordinates of a general position on the 3 fold axis can be written as x x x we have seen that the Zr atom resides at the position 0 0 0 The positions of the two W atoms can be found by clicking in Mercury on More Info gt Atom List Inspection of the W coordinates should DASH User Guide show that the average positions of the two atoms are 0 6 0 6 0 6 and 0 3412 0 3421 0 3412 respectively Click lt Back to return to the DASH Wizard welcome window and select Simulated annealing structure solution Click Next gt to continue 15 6 13 Stage 11 Building the Full Model In order to fully solve the structure and determine the light atom positions we now need to set up a more complicated structural model We will continue to use a free Zr atom and use a tetr
55. scans and sum them together using the data reduction software rather than collecting a single long run For example four one hour runs are preferable to one four hour run Prepare each sample fresh in order to reduce preferred orientation 3 1 10 Choice of Step Size Ideally you should have plenty of points across every peak in the diffraction pattern in order to accurately describe the underlying peak shape f you use a step size that is too large you risk missing subtle features such as peak shoulders that may be critical at the indexing stage Ifthere is any doubt it is better to collect data on a finer grid since a coarser grid can always be constructed later by re binning the data the converse is obviously not true 3 1 11 How Long to Count For Obviously the longer the time spent on collecting data the more closely it will resemble the true diffraction pattern e For each doubling of the collection time the estimated standard deviations are improved by a factor of 21 Eventually a stage 1s reached where substantial increases in collection times are required in order to achieve modest improvements in the signal to noise ratio DASH User Guide 33 Asa general guide the data should be collected sufficiently long that reflections can be clearly distinguished from the background at around 1 5 spatial resolution Not all samples will diffract strongly to this resolution but 1t remains a useful rule of thumb 3
56. search is performed using a simulated annealing algorithm This section covers The basics of simulated annealing see Section 10 2 page 101 Using the interface for structure solution see Section 10 3 page 102 Simulated annealing parameters see Section 10 5 page 117 Monitoring the progress of structure solution see Section 10 8 page 124 Assessing the final answer see Section 10 9 page 127 Troubleshooting see Section 10 10 page 130 Final Rietveld refinement see Section 10 11 page 130 Limitations of DASH see Section 10 12 page 131 10 2 Fundamentals of Simulated Annealing The algorithm starts by assigning random values to the parameters molecular position orientation and conformation Agreement between calculated and observed Pawley intensities is assessed by computing a c goodness of fit statistic One of the parameters is randomly altered and the c value recalculated The algorithm accepts the new parameter value if the c value has gone down i e the fit has been improved If the c value has gone up then the new value is either rejected or accepted subject to a Boltzmann distribution The probability of accepting such an uphill move depends on the current temperature of the system the higher the temperature the more likely it is that an uphill move will be accepted This procedure is repeated many times each parameter being altered in turn At the end of a predetermined set of moves the t
57. simulated annealing run Default values are provided which are usually satisfactory To accept these values simply click the Next gt button The meaning of these parameters is discussed in Section 10 5 page 117 Maximum number of SA runs the default setting is 10 runs It is generally advisable to try several SA runs using different random number seeds this is done for you automatically if you specify the number here The best solution from each run is stored in suitably numbered files see Section 10 9 4 page 129 Maximum number of moves per run the default setting is 10 000 000 When this number of moves is reached the run is terminated whatever the value of c see Section 10 5 4 page 118 Profile chi squared multiplier the default setting is 5 0 This means that if the SA profile c falls below a value 5 0 times that of the Pawley fit C7 and the minimum number of moves has been exceeded the run is terminated see Section 10 5 4 page 118 The Print button will pop up a text editor window containing a summary of the current simulated annealing parameters This text file can be edited saved and printed 10 4 Setting torsion angle ranges 10 4 1 Manually entering torsion angle ranges Torsion angles are not normally fixed and will have a range of 360 However upper and lower DASH User Guide 111 112 bounds can be entered here to define a single torsion angle range to be searched such as 10 to 10
58. the DASH User Guide 257 axial directions a and c because of defined origin choice on a screw axis and the b axis origin position 1s indeterminate Refcode BEURIDIO 15 5 14 Stage 12 Experiments with the Ring Conformation When the molecular model was built it was stressed that the ribose ring is puckered with the 3 carbon out of the plane of the rest of the ribose ring and on the same side as the 6 membered ring Build a model where the conformation of the ribose ring is different for example where the 3 carbon of the ring points away from the 6 membered ring the other four atoms of the ring defining a plane If you do not have access to a model building package a file Tutorial_5 2 mol2 1s included in the data 258 DASH User Guide files Repeat the Simulated Annealing stage you can use DASH Wizard but this time import Tutorial_5 2 mol2 and then read in the newly created Tutorial 5 2 l zmatrix file as before Proceed with the solution stage You will find that a good solution is not found and molecules may appear tangled with close contacts An example result is shown below It should also be mentioned that you can experiment in DASH with flexible ring systems only by a rather crude method whereby one takes the molecular model in the model building program and breaks a bond in the ribose ring say C2 C3 and then export as a MOL2 file Importing this into DASH then causes the rings to be treated as flexible chains
59. the Exact Peak Positions Select the first 20 peaks using the method described in the first tutorial Here is a guide to the approximate positions 2q of the first 20 peaks 16 7803 19 3916 21 6881 23 7869 27 5389 29 2538 30 8623 32 4090 35 5199 36 7033 DASH User Guide 261 39 3372 40 5986 41 8329 43 0303 44 2036 45 3575 46 4954 48 6816 49 7570 50 8086 15 6 6 Stage 4 Indexing A typical run of DICVOL ifthe selected peaks were very close to those given in the previous stage should return a cubic cell as the best fit with a b c 9 1547 A V 767 23 A Figures of merit M 24 160 1 F 24 154 6 A number of other possible cells are likely to appear with lower symmetry Select the cubic cell as this should give the best figures of merit 15 6 7 Stage 5 Stop and Think Does the cell make sense There is a very approximate method of estimating molecular volume using 15 A per C N O atom and 25 for heavier atoms So for this compound ZrW 5Os we estimate the formula unit volume to be 195 so 4 formula units per cell would need a volume of approximately 780 A The DICVOL cell volume of 767 A suggests that we have roughly four formula units per cell 15 6 8 Stage 6 Checking the Cell and Determining the Space Group The space group that is automatically selected for the cubic crystal system is P23 A quick scan of the diffraction pattern and tick marks for the predicted reflections should show that the majority of tic
60. the choices with the arrow keys until a good match between the tick marks and peak positions is obtained A very good correspondence is achieved with space group P 1 2 1 number 4 b Thus we need to attempt structure solution in P2 254 DASH User Guide with 2 independent molecules in the asymmetric unit 15 5 9 Stage 7 Extracting Intensities Pick 8 peaks which are isolated using the method described in Tutorial 1 Stage 7 When 8 peaks have been chosen the Pawley Refinement Status window will pop up automatically The initial 3 cycles of the least squares refinement only involves the terms corresponding to the background This should give a Pawley C of 3 or better accept these three cycles The next 5 cycles of the least squares refinement should bring the Pawley C down to about 1 5 Accept your best Pawley fit making a note of c and save the file as 7 utorial 5 sdi 15 5 10 Stage 8 Molecule Construction Construct a 3D molecular description of the molecule using your favourite modelling software and save it in pdb mol or mol2 format Care must be taken with the conformation of the ribose ring The five membered ribose ring is not planar four atoms of the ring define a plane and the 5t atom will be found either above the plane on the same side as the 6 membered heteronuclear ring or below the plane If we search the CSD for molecules very similar to uridine we find that the torsion angle defined by O C4 C3 and C2 is ei
61. the high angle estimates where the peaks are weak Select Accept if satisfactory DASH now subtracts the background from the data as will be seen in the updated display 10 DASH User Guide 2 5 Pawley Fit Files DASH keeps a record of progress while one is working on a chosen set of diffraction data When you start a new project the only item in the directory will be your diffraction data file After indexing the cell and extracting intensities by the Pawley fit procedure DASH creates a file with extension sdi that 1s then known as the Pawley Fit file see Section 2 5 1 page 11 This contains all the information needed for the last stage of the DASH process 1 e structure solution using a molecular model The default name is based on the diffraction data file e g for a compound called hydrochlorothiazide we might have a data file hcf xye producing a Pawley Fit file hct sdi If you had a second set of experimental data for hydrochlorothiazide e g hctnew xye and chose this as the input file DASH would create a new Pawley Fit file called by default hctnew sdi but you can choose the names as you wish 2 5 1 Pawley Fit File an Example The Pawley Fit file contains the full file names for various types of data that are created by DASH as the result of the Pawley refinement It is not essential to know the details of these files but it is important to be aware of the data files that are used by the structure solution process
62. themselves widen and thus no advantage is gained In situations where it is possible to select a wavelength e g at a synchrotron it should be chosen to maximise the incident flux unless compelling reasons such as absorption dictate otherwise 3 1 6 Data Collection Geometry Transmission geometry is recommended with the sample in a rotating capillary e It is also possible to collect diffraction data in transmission mode when the sample is held as a thin film in a suitable attachment Reflection geometry may be used but there is a high risk of preferred orientation having a significant impact on the diffraction pattern Whilst a small degree of preferred orientation can be tolerated in a structure solution it is a complication that is best avoided 3 1 7 Background Reduction You should endeavour not to introduce any additional background scattering For example it may be appropriate to use borosilicate capillaries rather than glass or quartz in order to avoid seeing the amorphous scattering from the capillary manifest itself as a background hump 3 1 8 Zero Point Calibration Although it is possible to refine instrumental zero point errors in the whole pattern fitting stage it is always preferable to calibrate the instrument prior to a structure solution using a well defined standard sample e g NBS silicon 32 DASH User Guide 3 1 9 One Long Scan versus Several Short Scans It is generally better to perform several short
63. to RIETAN for the first step of refinement When the cycle of refinement has completed you will be prompted to save the ins file before being returned to the DASH interface The Refine options will have been updated to include the atomic coordinates for the final cycle of refinement Click Refine to complete the refinement Note Default values for the Number of cycles Penalty parameter TK and TK increasing multiplier FINC are provided but can be altered Note Output from RIETAN is written toa 1st file should you wish to look up the reported Rwp and Rp values for the refinement cycles 152 DASH User Guide 13 PREPARATION OF SINGLE CRYSTAL DATA If you have poor single crystal data then it may be possible to solve the structure within DASH using the simulated annealing protocol This is often successful in cases such as limited hkl ranges from high pressure cells or just poorly diffracting crystals which do not give enough data for direct methods phasing DASH requires a file containing the h k 1 F ands F2 values in the SHELX format and a molecular model Once the hkl data have been read in the structure solution proceeds as for powder diffraction Select Preparation of single crystal data from the first DASH Wizard see Section 2 10 page 21 and click Next gt Enter the crystal system space group and unit cell parameters in the boxes provided DASH Wizard Single Crystal Step 1 Unit Cell Parameters b R it f ri
64. to the acceptor N on the imidazole ring 238 DASH User Guide 15 3 13 Stage 11 Examining the Output Structure View the structure using the View button in the Results from Simulated Annealing window All should look reasonable there should be no abnormal close contacts between molecules except perhaps for some H atoms The H atoms contribute such a small percentage of the total scattering power of the molecule that they have very little effect on the value of c The positions of methyl H atoms in particular are poorly determined as they have been placed in calculated positions and not allowed to rotate There is a crystal structure for this cis isomer in the CSD CIMEDTO3 the H bonding scheme matches this exactly There may appear to be an extra H bond to the cyano N in your solution but this will be just within the arbitrary limit set for distance scanning for H bonds in the visualiser The Mercury visualiser allows you to easily examine the H bond network just by clicking on the H bonds 15 3 14 Stage 12 Experiments Altering the cis trans Isomer It is interesting to do the experiment of trying to solve the structure with the trans isomer You can either build a model with the trans configuration save it as Tutorial_3 trans mol2 a trans isomer model file is provided with this Tutorial as Tutorial_3 trans mol2 or use a more advanced feature of DASH to allow the model to rotate about the relevant C N double bond You will find t
65. values before starting the simulated annealing When Randomise initial values is not selected the values shown in this dialogue window will be used allowing a previous run to be restarted where it left off If the first simulated annealing cycle is a dummy cycle to determine the initial temperature the values will be reset at the start of the second cycle e Set any of the molecular translation parameters x Fragl y Fragl z Fragl as fixed by clicking F box if required by the space group e g in P2 we can fix the y translation for the first molecule given Generally it is not necessary to fix any of the molecular rotation parameters Q0 O1 Q2 Q3 Torsion angles are not normally fixed and will have a range of 360 However upper and lower bounds can be entered here to define a single torsion angle range to be searched see Section 10 4 page 111 10 3 7 Starting the Simulated Annealing Run You will reach the DASH Wizard Simulated Annealing Protocol window from the parameter range menu see Section 10 3 6 page 109 110 DASH User Guide DASH Wizard Simulated Annealing Protocol Simulated Annealing Termination criteria TO Cool NI N2 Number of SA runs DE 0 00 0 020 20 25 Max number of 1 0000 x10 E moves run Profile chi sqd multiplier 5 0000 Moves each T Random iis E 4000 seeds El lt Back Close Print This allows the user to set the variables that control the
66. 0 starts maximum number of moves 10 million random seeds 315 159 was performed with the modal torsion angle ranges recommended by DASH Of the 10 runs 8 had a value of profile C below 10 and the average number of moves required was 646 750 A similar run performed without modal torsion angles resulted in 7 10 solutions with a profile C below 10 and the average number of moves required was 1 828 450 Using DASH with the CSD ConQuest and Vista If you have access to the Cambridge Structural Database CSD Conquest and Vista you can perform the following torsion angle searches for yourself If not results for the searches are given The first torsion angle listed in the Parameter Bounds dialogue box is S8 N11 C12 013 and it has an initial value of 0 25 Draw an appropriate fragment in Conquest and define the torsion angle of interest A screenshot of a query used is given below DASH User Guide 231 fal File Edit Atoms Bonds 3D Options Help 3 Click on atoms bonds to select 3D Parameters A Click and drag to select groups of atoms DRAW EDIT ERASE ADD 3D pa 5i Options Delete Contacts Se RingMaker Search Store Templates Cancel By viewing in Vista the torsion angles returned it is clear that this torsion angle is well described by a bimodal distribution at 160 to 160 and 20 to 20 232 DASH User Guide Return to the Parameter Bounds dialogue box in DASH hit the Modal button in the row
67. 0 to 120 and 60 614 to 120 C17 C16 C15 N14 178 54 Trimodal 160 to 160 b40 71 to 80 and 40 to 80 a This initial value is determined from a sketched model and is reasonably far from the true angle for this structure If the bimodal ranges indicated are entered and Ok is pressed a dialogue box will pop up and inform you that the initial value does not fall within the defined ranges To proceed change the initial value of this torsion angle to for example 70 00 DASH User Guide 233 Enter the above torsion angle ranges and start the simulated annealing process In our hands a simulated annealing run started with random seeds 159 and 314 gave 10 10 solutions in an average of 1199250 moves when no restraints were applied 3 10 solutions had a profile c value below 10 0 With the above restraints applied and therefore the search space reduced 10 10 runs starting with the same random seeds solved and the average number of moves required was 796250 There were 10 solutions found with a profile c below 10 0 Thus if you have a problem that is proving difficult to solve with no restraints applied during simulated annealing it may be valuable to see if there are torsion angle ranges that can be defined from a search of the CSD to reduce the search space 15 2 15 Stage 13 Conclusion Global optimisation processes may locate local minima particularly if a Z gt 1 or b the data are of limited res
68. 00 1000 500 22 0 22 10 22 8 22 08 84 BS BEL er Een BSG 0 6 eT 2B theta The fit is very good but the tell tale sinusoidal misfit indicates that the unit cell and zero point are in need of some further refinement Going back to the Pawley window note that the program has anticipated this and has flagged the unit cell and zero point for refinement Select Refine to perform a Pawley refinement for 5 cycles in which the background intensities unit cell and zero point are all refined The fit should improve to for example 204 reflections 9751 points Rwp 16 2 R exp 9 38 c 3 0 The figures of merit have improved select Accept to see the improvement in the fit 206 DASH User Guide 4000 3500 3000 500 D TL M A m Ton rm d 1500 1000 500 EE 22 07 BSR SEE mn DI HE SAL aa BELG Dr Bale theta Examine the whole profile If you have achieved a c of around 3 the fit to the data will be excellent Click Save as to save the refinement results to disk as a DASH Pawley Fit File sdi called Tutorial 1 sdi 15 1 10 Stage 8 Revisiting Space Group Determination Now that Pawley fitting and refinement has been introduced it is an appropriate point to try an alternative way of determining the space group Select Back in the Pawley Refinement Step 2 window to return to the Unit Cell Parameters window This time select Space Group DASH User Guide 207 DASH Wizard Unit Cell P
69. 0541 174090243 042636861 348446047 055644157 157264365 069792204 852291799 1 703096616 825562143 211062816 092210833 1 127281963 352239204 797847048 544242324 395989867 819438688 259879230 672914357 440188292 208123004 913234641 000000 000000000000 0000 0 0 Lecul jecul Lecul Lecul Legui Lecul Lecul Lecul Lecul Lecul Lecul lecul Lecul Lecul Lecul Lecul lecul e001 e001 e001 e001 e001 e001 e001 e001 e001 e001 e001 e001 e001 e001 e001 e001 e001 185 18 H18 19 H19 20 H20 lt TRIPOS gt BOND 1 1 2 4 3 2 4 2 5 3 6 1 7 5 8 6 9 3 10 4 11 11 12 1 13 11 14 14 1 5 13 16 2 17 17 18 17 1 19 17 2 20 16 Z Matrix file created by DASH from the input MOL2 file YOU WADA BPOWBENAANTDOWA OY O1 On Bs 1 085947683 0 655864517 0 114861688 vo pp m e E Br hs RB PRLREPRPRPRPRNDNERPRRRPR EP m Zmatrix generated by Mercury 1 0 1 0 1 0 90 0 90 20 0 Q NS QOO BO noQ om ox 0 1 3962050 1 4009359 1 0863878 1 3974412 1 4788489 1 3954068 1 0849666 1 3975310 1 0869166 1 1042872 1 3055687 1 3672807 1 0877015 1 3908269 0000000 4222555 9753443 1 0950410 1 0949880 1 0942323 oooooooo0o0coco00o00o00o00o000000 0 90 0 0 0 120 120 6071742 8266674 2386237 8853515 8880618 8934394 7967855 9435928 0945149 7165368 3670309 9284636 3143121 188445
70. 1 12 Optimising Use of Data Collection Time Fora given data collection time the question arises of how to optimise the use of that time A common formula is Time per step expt duration in seconds 2Qmax 2Gmin step size This scheme gives equal weighting to all data points and takes no account of the fact that the diffracted intensities at low angle will be much stronger than those at high angle In many cases this may be sufficient but a more sophisticated data collection strategy is described in J Mater Chem 1997 7 569 572 Implementing such a data collection scheme is a simple matter and is strongly recommended when using scintillator detectors on a laboratory or a synchrotron source 3 1 13 Neutron Data DASH does not currently handle neutron diffraction data 3 2 Hints for Treating Data 3 2 1 Lorentz Correction DASH always corrects the data for Lorentz effects so no correction should be applied to the data in advance 3 2 2 Polarisation Correction e In the case of synchrotron data DASH assumes that the incident radiation is vertically polarised and provided that the Synchrotron radiation option is turned on when the radiation wavelength is entered no pre processing of the data is necessary e In the case of laboratory X ray data DASH applies an appropriate polarisation correction provided that the Laboratory radiation option is turned on when the radiation wavelength is entered and no pre processin
71. 15 54 15 56 15 56 theta This is the 7 peak selected thus we have accurate peak shape descriptors and peak positions for 7 peaks throughout the pattern This is sufficient information for a least squares cell refinement to be performed on this monoclinic cell and DASH will do this automatically A sign that lattice parameter refinement has commenced is that the tick mark above the peak jumps closer to the peak after fitting this indicates that the cell has been updated to incorporate the latest peak position DASH has automatic settings that determine the best point at which to attempt a full Pawley refinement At this time it automatically displays the Pawley Refinement Status window In this example the window is not yet displayed so we continue picking peaks DASH User Guide Further up the pattern there is another isolated peak which is easily fitted Now with a total of 8 8 6 8 6 1 peaks fitted the Pawley Refinement Status window is displayed automatically Observed profile HH tat Mut Hit Hn uet Y Mgr u Prts ty y Het iu 15 95 16 00 16 05 16 10 16 15 16 20 16 25 16 20 2 theta Initial Pawley Fitting of Intensities and Background Once enough peaks have been selected and the program has stable estimates of the cell dimensions and peak shape parameters you can perform an initial Pawley fit of the reflection intensities and the background This will be indicated by the appearance of a pop up window Usuall
72. 2 1155213 7617586 PRPrPRPP PR 0000000 0000000 2814856 6861954 1 491802143 1 935183860 0 961941388 0 0000 0 90 9009 0 000000 CO oO Oo 1 0000000 0000000 0000000 8814973 5745262 4571818 6027188 6006996 5806770 179 146 178 17 9 1 19 3 6874795 LUTO 61 124 117 2769860 8411988 8979722 9304618 3664126 8330576 8034053 2946259 4607417 7913565 5 793237167 5 604477331 6 977167021 OGO GOG 0 FO 0 0 02 00 0 o o o0c O O 0 0 JO 0010 Y0ONNRA RR CO vo 12 13 15 16 16 16 DOWNNNNFFRFRFNNY OC OO Y 12 13 13 T3 nd moo 00 10 CO PO PO t E E io r2 9201 C0 C0 OO OO O03 030 C000 OY C0 C0 CO ON WA C0 C0 C0 OY uy CO 0 09 900 OO CX C2 2 O 0 0 90 00 Oro Molecule001 Molecule001 Molecule001 C3 CO 403 OO 00 0 00 0 0 0 0 0 O09 CS N H O 00001 1 5 iO C0 PO OUT O wN HK d a HH C c3 cl C6 H7 C4 O ol C H2 CO 00 UMN 5 C3 C3 Cl C3 Cl C6 Cl C3 C6 C11 C1 C3 C4 CZ C6 C3 C1 N13 016 014 c17 C17 C17 H10 C6 C3 C2 CS C4 Cl C3 H8 C4 Cl C5 Hl2 CLT Cl C3 136111 HT2 16 C2 C6 C3 9 C5 C4 Cl cil Cl C2 C6 N13 C11 O16 C2 O16 H18 O16 H18 The Z Matrix format is commonly used in molecular modelling see Appendix H References page 189 In this format we describe the molecular co ordinates in terms of internal co ordinates namely the bond lengths bond angles and torsion a
73. 243 15 4 2 Data The data set Tutorial 4 xye is a laboratory X ray diffraction data set collected by Dr Lubo Smrcok The incident wavelength was 1 789 15 4 3 Stage 1 Reading the Data Open DASH and select the directory where the data resides Select View data determine peak positions and click Next gt Select the file Tutorial 4 xye using the Browse button Click Next gt Check that the wavelength and radiation source have been set correctly and click Next gt 15 4 4 Stage 2 Examining the Data and Removing the Background The data spans 4 to 61 2q Remember that this data has been collected at a relatively long wavelength and so the real space resolution of the data is only 1 8 Truncate the data to 2 0 resolution 244 DASH User Guide Having examined the data we really want to strip out the background This is because the data whilst good are nowhere near as good as the synchrotron data sets that you examined in Tutorials 1 and 2 If we defer background modelling until the Pawley fit stage we have an additional set of parameters to worry about at that stage With the weaker data at higher angles there is always a chance that correlations between the weak peaks and the background parameters may cause instabilities in the fit These can be avoided by removing the background at this stage Select Preview using the default value of 100 for the filter window size Examine the background fit carefully a
74. 3 Here is a guide to the positions 2q of the first 23 peaks 4 84 6 63 7 07 7 51 7 81 9 70 10 51 10 56 10 77 10 91 11 12 11 40 11 98 12 11 12 21 12 52 12 77 13 22 13 28 13 74 14 10 14 30 14 42 Click Next gt Select Run to run DICVOL or use another indexing program as described in Tutorial 1 15 5 6 Stage 4 Indexing If you have selected peaks which are very similar to those given in the previous stage the DICVOL program returns a monoclinic cell with a 13 8703 A b 14 7167 A c 4 9207 A beta 95 70 and cell volume 999 47 A with figures of merit M 23 74 8 and F 23 374 8 Other cells are suggested with beta greater than 96 but it is customary to choose the cell with the smallest angle This turns out to be in very good agreement with a single crystal structure reported in the Cambridge Structural Database CSD reference code BEURIDIO 15 5 7 Stage 5 Stop and Think Does the cell make sense In this case we estimate the molecular volume to be 17 x 15 A 9C 2N and 60 12 x 5 12 H 315 If there were 2 or 4 molecules in the unit cell we thus estimate volumes of 630 or 1260 A respectively The estimate for 4 molecules per cell is more likely allowing for the fact that there is likely to be extensive H bonding which will tend to make the cell smaller in volume 15 5 8 Stage 6 Checking the Cell and Determining the Space Group You should check through the space groups scrolling through
75. 3 a1 Po2 b 1 27 13 a2 P 2 n 28 13 a3 P 2 c 1 29 14 al P 21 b 30 14 a2 P 21 n 31 14 a3 P 21 c 32 15 al B 2 b 11 DASH User Guide DASH User Guide 33 15 a2 2 n 34 15 a3 2 0 35 15 al 2 c 36 15 a2 2 n 37 157 83 2 b 38 3 b 2 39 4 b 21 1 40 5 b1 2 41 5 b2 2 42 5 53 2 43 6 b m 44 7 b1 c 45 7 b2 n 46 L2b3 a 47 8 b1 m 48 8 b2 m 49 8 b3 m 50 9 b1 c SL 9 b2 n 52 9 b3 a 53 9 pi a 54 9 b2 n 55 97b3 C 56 10 b 2 m 57 11 b 1 21 m 1 58 12 b1 2 m 59 12 b2 2 m 60 12 b3 2 m 61 13 b1 2 c 1 62 13 b2 2 n 63 T343 2 a 1 64 14 b1 21 c 65 14 b2 21 n 66 14 b3 21 a 67 153p1 2 03 68 15 02 2 n 1 69 15 53 2 a 1 70 15 b1 2 a 1 T 15 b2 2 n 1 72 153 b3 2 c 1 73 Se Lag 163 164 74 4 c 2 75 Szal 2 76 5192 3 77 5 c3 2 78 ee m 79 7 c1l a 80 dec n 81 PEGS b 82 8 c1 m 83 8 02 m 84
76. 35 P 42 m b c 419 136 P 42 m n m 420 137 1 P 42 n m c 1 421 13752 P 42 n m c 2 422 138 1 P 42 n c m 423 138 2 P 42 n c m 2 424 139 I 4 m mm 425 140 I 4 m cm 426 41 1 41 am d 427 Ad 41 a 2 428 42 1 41 ac d 429 142 2 41 a 2 430 143 P 431 144 P 432 145 P 32 433 146 H R 37H 434 147 Pi 3 435 148 H R 3 H 436 149 MESA 437 50 P321 438 151 P 3 2 439 152 P 31 2 440 53 P 32 2 441 154 p 32 2 442 159034 R 32 H 172 DASH User Guide DASH User Guide 13 156 P 3m 144 157 P 3 m 145 158 P 3 G 146 159 B 3 147 160 R3m 148 161 BR See 149 62 P 3 m 150 163 P G 151 164 P 3m 152 L65 P A 153 166 H R 3m 154 167 H B3 d 155 L46 R R 3 R 156 L48 R R 3 R 157 155 R R 32 R 158 160 R R 3 m R 159 161 R R 3 ER 160 166 R R 3 m R 161 167 R R 3 ER 162 168 P6 163 169 P 61 164 70 P 65 165 171 P 62 66 72 P 64 167 T3 P 63 168 174 P 6 169 75 P 6 m 170 76 P 63 m 171 NN P622 172 78 Pot 2 2 173 79 Pe5 22 174 180 P 62 22 175 181 P64 22 176 82 P6322 177 183 P6mm 178 184 P6cc 79 185 P 63 cm 180 186 P 63mc 181 187 P 6m 2 182 188 P 6c2 182 189 P 62m 173
77. 46 ba c Ibm 2 223 46 cab I2mb 224 46 cba 2cm 225 46 bca Ic2m 226 46 a cb m 2 a 227 47 Pmmm 228 48 1 P n n Ts 229 48 2 Pnnn 2 230 49 Pre Em 231 49 cab Pmaa 232 49 bca Pbmb 233 50 Pban 234 50 2 Pban 2 235 50 1cab Boobs 236 50 2cab Dime bz 2371 50 1bca Pe mas 167 238 50 2bca Penaz 239 51 Pmma 240 51 ba c Pmmb 241 51 cab Pbmm 242 517 Cba Pcmm 243 Silsbee P m cem 244 51 a cb Pmam 245 52 Pnna 246 52 ba c Pnnb 247 52 cab Pbnn 248 52 cba Pre mon 249 52 bca Pnon 250 52 a cb Pnan 251 53 Pmna 252 53 ba c Pnmb 293 53 cab Pbmn 254 53 cba Penm 255 53 bca Pnom 256 53 a cb Pman 257 54 Pe era 258 54 ba c PG eb 259 54 cab Pbaa 260 54 cba Pcaa 261 54 bca PB eb 262 54 a cb Pob ab 263 55 Pbam 264 55 cab Pmcb 265 55 bca Pcma 266 56 Eco 267 56 cab Pnaa 268 56 bca Pbnb 269 57 Pbom 210 57 ba G P oc aum 271 57 cab Pmca 272 57 cba Pmalb 243 57 bca Pbma 274 57 a cb Porm 21D 58 Pnnm 276 58 cab Pmnn 277 58 bca Pnmn 278 59 1 Pmmn l 168 DASH User Guide DASH User Guide 279 59 2 Pmmn 280 59 1cab Pnmm 281 59 2cab Pnmm 282 59 1bca Pmnm 283 59 2bca Pm
78. 7 16 70 17 65 18 27 18 66 18 72 18 93 19 45 19 51 19 72 20 00 20 35 22 92 e Click Next gt Select Run to run DICVOL or use another indexing program as described in Tutorial 1 15 3 6 Stage 4 Indexing If the selected peaks were very close to those given in the previous stage then the DICVOL program returns a monoclinic cell with a 10 3846 A b 18 7995 A c 6 8201 A beta 106 44 and volume 1277 04 A with figures of merit M 20 80 4 and F 20 198 7 Only one other cell was suggested also monoclinic with almost identical volume b and c axes and alternative a 10 687 and beta 111 29 15 3 7 Stage 5 Stop and Think Does the cell make sense In this case we estimate the molecular volume to be 320 from the fact that there are 17 non Hydrogen atoms in the molecule each volume approximately 15 and 16H each approximately 5 A so 17 x 15 16x 5 323 A gt Therefore given the unit cell volume of 1277 A we know from this very rough approximation that the cell is most likely to accommodate 4 molecules At this point your knowledge of space group frequencies should suggest that P2 c is a strong possibility 236 DASH User Guide 15 3 8 Stage 6 Checking the Cell and Determining the Space Group The space group P2 will automatically have been selected Although the most likely space group is number 14 you should now check through the systematic absences by scrolling through all the space gr
79. 75 Sometimes the powder pattern will not contain useful data to this high angle In such cases it is better to cut the data down to lower resolution e g 2 0 or even 2 5 Examples are provided illustrating some suitable cut off points for A high resolution profile see Section 8 4 1 page 76 A medium resolution profile see Section 8 4 2 page 77 A low resolution profile see Section 8 4 3 page 78 8 4 4 Truncating High Resolution Data an Example Synchrotron dataset with an incident wavelength of 1 1 thus data were collected to maximum 2q 60 equating to 1 1 spatial resolution 6000 4 dH t LIN MI II LIN ee 5500 5000 4500 4000 3500 3000 2500 43 2000 4 1500 1000 500 4 Observed profile 10 15 20 25 20 25 40 45 50 55 50 2 theta There are 418 reflections in this data range which is slightly more than DASH will handle by default However a significant proportion nearly 25 of these reflections occur in the last 5 of data 76 DASH User Guide 220 3 11 mm IE HIE IEEE HE MALI WII INGI Wr Inn grt 200 150 160 140 Observed profile 120 100 80 Although the crystal is still diffracting quite strongly at this point sufficiently well for the information content to be useful in structure refinement it is clear that the extent of reflection overlap is high If we cut the data limit back 5 to 55 we simplify the problem by reducing the number of re
80. 8 c3 m 85 9 cl a 86 9 02 n 87 9 03 b 88 giic b 89 9 c2 n 90 9 c3 a 91 10 c 2 m 92 Tic 21 m 93 12 c1 2 m 94 12 c2 2 m 95 1263 2 m 96 loc 2 a 97 13 c2 2 n 98 13703 2 b 99 14 c1 21 a 100 14 c2 21 n 101 14 c3 21 b 102 Tel 2 a 103 15 02 2 n 104 15 03 20 105 15 cl 2 b 106 15 82 2 n 107 15 c3 2 a 108 16 2 2 109 17 2 21 10 17 cab 21 22 11 17 bca 2 2 12 18 DI T3 18 cab 2 pu 14 18 bca 23 7205 DASH User Guide DASH User Guide 15 19 p 21 21 21 16 20 C22 21 17 20 cab A21 2 2 18 20 bca B 2 21 2 19 21 G 2 252 120 21 cab A222 121 21 bca BZ Ze 2 122 22 F222 123 23 2 2 2 124 24 21 21 21 125 25 Pmm 2 126 25 cab P2mm 127 25 bca Pm2m 128 26 Pmc 21 129 26 ba c Beca 21 130 26 cab P2lma 131 26 cba P 21am 1 32 26 bca Pb21m 133 26 a cb Pm21pb 134 27 BEAZ 135 27 cab Pp Z aa 136 27 bca Pb 2 1b 137 28 Pma2 137 28 ba c Pbm 2 1 39 28 cab P2mb 140 28 cba P 2 06 m 141 28 bca Poc 2 m 142 28 a cb Pm2a 143 29 Pca 27 144 29 ba c P b c 21 L45 29 cab P 21l ab 146 29 cba P2lca 147 29 bca Per 21 75 148 2923 Cchb Pb2la 149 30 Pan EZ 150 30 ba c Pen2 TSL 30 cab B 2 5 a 152 30 cba P2an 153 30 bca Pb2n 154 30 a cb Pn2b 1 55 31 Pmn 21 165 166
81. ABOUT THIS USER GUIDE This user guide is a practical guide to solving crystal structures from powder diffraction data using DASH It includes instructions in using the Windows Interface as well as providing help on the scientific issues relevant to structure solution It is intended for readers who already have some crystallographic experience but perhaps with single crystal rather than powder techniques Use the navigational buttons above to move between pages of the user guide and to access the full table of contents TOC and index An extensive set of tutorials are also available for DASH Tutorial 1 will guide you through the process of structure solution in considerable detail subsequent tutorial examples will be more concise but will introduce other new aspects of the structure solution process Tutorials can be accessed by clicking on the Tutorials see page 191 link on the bottom of this page The DASH user guide is divided into the following sections Introduction see page 3 General Features of the Windows Interface see page 5 Data Collection and Data Treatment see page 31 Preliminary Inspection of Profile see page 37 General Hints on Selecting Fitting and Measuring Peaks see page 47 Indexing see page 55 Space Group Determination see page 65 Pawley Fitting see page 69 Building and Constraining Molecules see page 93 Structure Solution see page 101 Running DASH in Grid Mode or Batch Mode see page 133 Rigid b
82. ASH see Section 9 5 page 96 9 5 Reading Molecules into DASH and Defining Rotatable Bonds DASH reads molecules as Z matrices These can be created externally or created internally by DASH when it reads a mo1 or mo12 file see Section 9 4 page 95 The number of copies of a Z matrix can be entered in the column labelled Number DASH automatically recognises all flexible torsion angles in the molecule for non hydrogen atoms By default the torsion angles around single acyclic bonds will be varied through the full range of 180 to 180 during simulated annealing However it is desirable to limit the number of variable parameters and their allowable ranges since this will reduce the search space and increase the chances of structure solution This is frequently possible with torsion angles For example a search of the Cambridge Structural Database shows that acyclic esters are invariably within 10 of the trans conformation Thus the O C O C torsion angle can be constrained to a range of say 10 to 10 or even fixed at 0 Do not vary torsion angles that only affect the positions of H atoms e g the torsion angles of OH NH and CH groups The data will not be sensitive to changes in these angles Many other torsion constraints can be inferred from the Cambridge Structural Database The best choice of constraints may depend on the quality of the data For example it is usually sensible to allow amide
83. ASH to allow cis trans as a variable torsion angle giving the correct solution The accuracy of the molecular model does matter 15 3 18 References DICVOL Program D Louer amp M Louer 1972 J Appl Crystallogr 5 271 275 A Boultif amp D Louer 1991 J Appl Crystallogr 24 987 993 242 DASH User Guide Model Builders WebLabViewerLite Version 3 20 12 8 98 Copyright 1998 Molecular Simulations Inc PC Spartan Pro Version 1 0 5 16 8 2000 Copyright 1996 2000 Wavefunction Inc Single crystal structure cis cimetidine CSD reference code CIMETDOS R J Cernik A K Cheetham C K Prout D J Watkin A P Wilkinson B T M Willis 1991 J Appl Crystallogr 24 222 226 Single crystal structure trans cimetidine CSD reference code CIMETDO1 L Parkanyi A Kalman B Hegedus K Harsanyi J Kreidl 1984 Acta Crystallogr C40 676 679 15 4 Tutorial 4 Handling a Structure in Which There is a Space Group Ambiguity 15 4 1 Introduction The object of this tutorial is to guide you through the structure solution of decafluoroquaterphenyl DFQP It assumes that you have completed the previous tutorials In this tutorial you will learn how to Handle a structure solution in which there is a space group ambiguity Deal with a structure that has a potential centre of symmetry Deal with a more prominent background than you have encountered so far Handle a difficult Pawley fitting problem DASH User Guide
84. Box The Rigid Body Rietveld Refinement dialogue box can be accessed from the Analyse Solutions dialogue box after a simulated annealing run DASH User Guide 139 Rigid Body Rietveld Refinement Mal ES Translations and orientations Torsions Anales Bonds Te V oes f oo pasa plo ec ess F p ues TF E eser ies Fi 2 p f caco erf sacr pores T m fara meo jasa caca nass F m owes TF or jasa we oe F Dwsecr foss eses ses m osse T a ew Fy osszcr uses ms je T ej 0 IV Hide rings 0 v Hide H amp 0 v Hide H 0 ns an Clear E Set All Clear E Set All Clear Set All Clear Set All Refinable parameters are positions and orientations of all Z matrices torsion angles valence angles e bond lengths global isotropic temperature pre factor preferred orientation if used during simulated annealing In order to refine a variable its check box must be selected The check boxes for positions orientations torsion angles valence angles and bond lengths are labelled V for variable and can be switched on and off either individually or as a group by using the Clear and Set buttons Due to the low x ray scattering power of Hydrogen torsion angles valence angles and bond lengths involving one or more Hydrogen atoms are hidden by default and not refined The global isotropic temperature pre factor is a factor that pre multiplies the isot
85. Browse r Molecular Z matrices i Fi of degrees of freedom llename 1 Example_1 zmatrix zl View E dit TERRAE si E Back Next gt Close Convert Re label Pref Orient gt e Select the Pawley Fit file with extension sdi saved after the Pawley refinement Either type in the file name or browse for files with extension sdi The main window now displays the diffraction data with tick marks Proceed to input Z matrix files for the molecule s see Section 10 3 1 page 103 10 3 1 Input of the Z Matrices Click on the ax icon This will display all files available with the extension zmat rix JnOl2 mol ml2 pdb cssr CLf OP res Select the file and click Open When a Z matrix file is successfully read in the number of parameters set up is displayed to the right of the open folder button The first molecule should show that at least 6 parameters are created Each rotatable torsion angle adds 1 to the total parameters Ifthere is more than one molecule in the asymmetric unit repeat the loading process for the next Z matrix file Select View to view a Z matrix Flexible torsion angles can be colour coded by ticking the Colour flexible torsions check box under Options Configuration Select Edit to edit a Z matrix see Section 10 3 3 page 106 Click on the ax icon to clear a Z matrix you have loaded but do not want to use
86. C Mogul 1 1 2 mogul exe Browse DICYOL Browse McMaille C Program Files McM aille McMaille exe Browse TOPAS Browse EXPGUI Tel C gsas expguiltcl84 exe Browse RIETAN C Program Files RIETAN 2000 programs rietan exe Browse Colour flexible torsions iv write CIF for viewer Write wavelength to xye files j Run single instance of built in Mercury Viewer the viewer used for viewing Z matrices and solutions The viewer will display crystal structures from cif pdb or mol2 files e Arguments for viewer If using built in Mercury the command line argument to load all files is supplied by default This ensures that when cif files are written for structures to be overlaid all structures are loaded and displayed simultaneously If Mercury CSD is used to view structures supplying the command line argument client will load each structure selected into a single instance of MercuryCSD If within MercuryCSD the Multiple Structures check box is ticked the structures will be displayed simultaneously Mogul If access to Mogul is available then enter the path to the Mogul executable here or click on the Browse button e DICVOL If DICVOL 4 is available for indexing then enter the path to the DICVOL executable here or click on the Browse button McMaille If McMaille is available for indexing then enter the path to the McMaille executable here or click on the Browse button TOPAS If TOPAS i
87. DB 180 00000 180 00000 18000027105000000002 14 Here the parameter s start value is first followed by the control keyword MDB Subsequently we have the maximum amp minimum value range for the parameter followed by the number of bins in the associated histogram Finally we have the histogram itself Clearly the histogram DASH User Guide could easily be altered to reflect say the range of torsion angles observed in a conformational analysis for the associated molecule 10 5 Simulated Annealing Parameters 10 5 1 Starting Temperature e Ifthe search space is complex i e contains many local minima the starting temperature must be high so that the algorithm will make many uphill moves in the early stages This will ensure that the search space is explored thoroughly e Setting 70 to zero in the interface instructs DASH to select the starting temperature automatically This is recommended at least in the first simulated annealing run until you get a feel for the problem DASH selects the starting temperature by performing a brief simulated annealing run at high temperature and monitoring the variance of the C value as random moves are made in parameter space Based on the results the starting temperature is set to a value that will allow the algorithm to escape deep local minima at the outset of the search 1 e the higher the variance in c the higher the starting temperature The optimum starting temperature is very data depen
88. H User Guide Simulated Annealing Press W H Flannery B P Teukolsky S A and Vetterling W T Numerical Recipes 1986 Cambridge University Press Cambridge ISBN 0521308119 274 277 amp 326 331 Simplex Method of Optimisation Press W H Flannery B P Teukolsky S A and Vetterling W T Numerical Recipes 1986 Cambridge University Press Cambridge ISBN 0521308119 289 293 Two molecules in the Asymmetric Unit Bell A M T Smith J N B Attfield J P Rawson J M Shankland K and David W I F 1999 New Journal Of Chemistry 23 565 567 Z matrix Leach A R Molecular Modelling Principles and Applications 1996 Longman ISBN 0582239338 1 3 DASH User Guide 189 190 DASH User Guide 15 TUTORIALS 15 1 Tutorial 1 Step by Step Structure Solution of Hydrochlorothiazide 15 1 1 Introduction The object of this tutorial is to guide you through the process of structure solution using the molecule hydrochlorothiazide as an example Tutorial 1 goes through the process in considerable detail subsequent tutorial examples will be more concise but will introduce other new aspects of the structure solution process This tutorial will take a novice user about 2 hours to complete and experienced powder crystallographers considerably less time MH M NH NH sg d EN A XQ o o 15 1 2 Data The data set Tutorial l xye is a synchrotron X ray diffraction data set collected at 20 K on Beamline X7A of the
89. Hint To enable the options for external programs they must be entered in Configuration dialogue Index pattern C External DICYOL 04 or later Stand alone McMaille C Enter known unit cell parameters After you have picked some peaks for indexing Selection of the check box Index pattern will take you to an interface to DICVOL91 Selection of the check box External DICVOL 04 or later will take you to an interface to DICVOL04 peaks from impurities allowed e Selection of the check box Stand alone McMaille will take you to an interface to McMaille e Click Next gt If you already know the cell parameters then Selection of the check box Enter known unit cell parameters will take you to the Unit Cell Parameters window where the parameters can be entered Click Next gt DASH User Guide 25 2 10 3 Interface to DICVOL91 DASH Wizard Indexing Step 2 DICYOL DICVOL Settings Mas mum 3000 0 Minimum Volume ii 0 0 ab c 0 0 30 0 30 0 125 0 M Orthorhombic v Monoclinic Triclinic pen I Cubic v Tetragonal IY Hexagonal lt Back Run gt Close If known enter the experimental zero point error Experimental zero point 0 0000 0 020 0 0 0 0 ar En Tor 1 0000 Peak position error Measured density Molecular weight Minimum Figure of merit Scale factor Previous Results gt Select the appropriate crystal systems Note that Tricl
90. Positions Cell Parameters Peak Widths Pawley SA Radiation type r Profile range 5 000 2 le min xmax 32 800 7 min 21 Ymax 9617 Synchrotron Wavelength for angle dispersive X ray data in A C Civ neutron radiation 1 12940 C TOF neutron on S M Time af liahtmeutran Apply Flight path mj 2 theta The above Structural Information window appears after selecting Diffraction Setup from the View menu Information can be entered on e Radiation type Laboratory or Synchrotron DASH does not yet handle neutron data e Profile Range this is for information only 12 DASH User Guide Wavelength the radiation wavelength used is entered here For a synchrotron data set you must enter the wavelength in the entry field For laboratory data you can either type the wavelength or use the pull down menu to select the appropriate radiation type 2 6 2 Viewing Peak Positions Structural Information Diffraction Setup Peak Positions Cell Parameters Peak Widths Pawley SA Jr ea re I 0 TIER E IE LE AO saf ip Sp som E IO IS A IE i i v som i LEI II SO ip of num Lo IAE eme ome E i i s vom an refinement E Alpha Beta Gamma Zero point SSS ERE nsum il The above Structural Information window appears after selecting Peak Positions from the View menu This example shows a list of peaks fitted ready for cell indexing Position the peak
91. SH an example image is shown here of the best solution found for cimetidine see Tutorial example 4 It is easy to display hydrogen bonds for quick checking and here it can be seen that all expected donors and acceptors are satisfied By clicking on the ends of H bonds one can see the connected molecules and assess the H bond networks pattern It is important here also to check quickly for any impossibly close contacts between atoms The 3D visualiser is not automatically kept up to date with the best solution In order to look at the latest solution you must click View again DASH User Guide 123 The choice of visualiser is controlled via Configuration which can be selected from the Options menu bar 10 8 Monitoring the Progress of Structure Solution As a simulated annealing run proceeds DASH displays a number of diagnostic statistics the most important of which are Various C statistics see Section 10 8 1 page 124 The current temperature the total number of moves made so far the number of downhill moves and the number of uphill moves that are accepted or rejected see Section 10 8 2 page 125 Whether or not to stop a Simulated Annealing run see Section 10 8 3 page 125 Monitoring the progress of structure solution see Section 10 8 4 page 126 DASH simulated Annealing Status Ea Simulated annealing run number 3 of 10 Temperature VERE capu A Minimum chi Average chi 2 Profile chi To
92. Then click Next see Section 10 3 6 page 109 DASH User Guide 103 10 3 2 Atom tethering 104 DASH features the ability to apply tethers between unassociated atoms in the solution process The main function for atom tethering is to allow a user to break a ring in a molecule to make it flexible A tether can then be used to make the code force ring closure while allowing the rings internal torsion angles to vary The intensity C is biased by the tether Two atoms A and B are separated by a distance of d Ap if the ideal distance of separation is d idea and there is a permitted tolerance of t then the modified C is given by c c qW MAX 0 0 dideat dagl t Y Where W is a user supplied weight and q is an annealing factor the annealing factor scales linearly from 0 to 1 as the simulated annealing progresses It is also possible to tether atoms in different z matrices to one another to allow the user to input information regarding the presence of a given interaction Atom tethering of independent z matrices will rarely improve the success rate of the solution search for good quality data and in certain cases may even degredate performance due to the addition of barriers into the monte carlo search process but may be useful with poorer patterns where there is higher uncertainty in the reflection intensities To use click the Set Fragment Restraints in the Parameter Bounds window DASH Wizard Parameter Bounds
93. affected The two most likely remaining candidates for refinement are the valence angles and the torsion angles The temperature factors tend to correlate with all other parameters and it therefore best not to refine the temperature factors in combination with other parameters Therefore the next step is to deselect the Global isotropic temperature factor check box and to click on the Set button for the valence angles which will select all angles except those involving Hydrogens to be refined Next deselect all angles by pressing the Clear button then select all torsion angles Set and refine those Depending on how much the Chi sqd values have changed it may now be necessary to refine the positions and orientations of the Z matrices again keeping all bond lengths angles and torsion angles fixed Depending on the quality of your data it must be good and the quality of your initial model 1f you have reason to suspect it contains errors you may try to refine some or all of the bond lengths Depending on how much the Chi sqd values changed you can return to the isotropic temperature factor again and repeat the whole cycle 12 3 Preparation of data for Rietveld Refinement using TOPAS GSAS or RIETAN DASH User Guide 141 DASH Wizard Rietveld Refinement SDI file C Program Files CCDC DASH 3 1 Example Example sdi Open Browse Crystal structure C Program Files CCDC DASH 3 1 Example Example mol2
94. ahedral geometry for the tungstate moieties As the W atoms are each on a 3 fold axis the rest of the tungstate tetrahedra must be represented by one partially occupied O atom on the 3 fold axis and one fully occupied O atom lying off the 3 fold with the remaining two O atoms generated by symmetry For the tungstate tetrahedra we can therefore use O W O fragments generated with ideal O W bond lengths and an ideal tetrahedral O W O bond angle These fragments can be generated using your preferred model building software or using a file supplied with the tutorial Tutorial_6 atoms mol2 The structure solution window will still show the same sdi file as used previously along with the atom z matrices which we used in the preliminary solution Click on the es icons to remove each of the atomic z matrices Next click on the as icon and select Tutorial 6 frags mol2 three Z matrix files will be automatically generated We also need to edit the occupancies of the atoms on special positions To do this click Edit in the row for the z matrix The atoms Zrl W1 Ol W2 and O2 should be set as an occupancy of 0 3333 and the remaining two atoms O3 and O4 should be left with a occupancy of 1 0 e g see below DASH User Guide 265 Edit Atomic Properties Z Matrix a io to tio NC A a 2m fee fe ew 9 5 raj IE p m 155 Biso Occupancies Set Biso of Allnon hydrogens Y to 3 0000 Re order Re label Rotations Save
95. arameters Enter crystal system trial lattice constants and space group if known ero polnt 0 0000 Lattice constants a 93332 b 8 49945 e 731801 a Space Group 3b P121 Crystal System Monoclinic b axis Alpha 90 000 Beta 111 185 Gamma 90 000 lt Back Close Apply Space Group gt In order to furnish the space group determination program with a required set of reflections and intensities a Pawley fit to the profile has to be obtained in the most general space group of the crystal system under study On pressing Space Group gt DASH automatically selects the correct space group Select Clear Peaks from the Pawley Refinement Step 1 Peak Picking window and proceed through the Pawley fitting process as before Once a good Pawley fit to the data has been achieved press Run gt to launch the space group determination program The console window of Extinction Symbol will appear and once the calculations have finished press Enter on the keyboard to view the results The space group P21 should be the most probable space group found for the data and hence will be listed first with the highest probability in the right hand column of the results table 208 DASH User Guide File Edit Search Listed as in cryst sorted table handbook Pdi 1 0 Pl 211 10 8291 Fa iad 10 8291 PI 1 0 Pl a 1 9703 15 P 1 21n 1 8630 93 P 1 21 a 1 9692 32 ei n 1
96. arch program ConQuest allows one to retrieve all molecular fragments specified by drawing chemical diagrams The chemical environment of the fragments can be specified very precisely using a variety of attributes such as number of hydrogens per atom cyclicity of bonds etc The geometry of these fragments may be saved as a list of geometric parameters defined by the user and displayed as histograms and scattergrams by the program Vista DASH provides a direct link to Mogul a molecular geometry database which forms part of the CSD System and is available from the CCDC Searches for molecular fragments bond lengths bond angles and torsion angles can be performed quickly and easily 14 6 2 F 2 Checking of Best Solutions against CSD Packing Motif The ConQuest program is also able to search for intermolecular interactions and store parameters in the same way as for intramolecular geometry for examination by Vista a statistical analysis package Examples of such useful information are H bonds and chloride ion interaction with charged nitrogen The packing motifs of the retrieved structures can be examined using the visualiser Mercury or Pluto These programs are particularly useful for easy exploration of H bonding motifs The soStar library of intermolecular interactions is also provided with the CSD system This is an extensive library of scattergrams of the intermolecular crystal environment of a set of well known chemical groups Each gro
97. ata set and you suspect that the esds are incorrect then you can always replace them with the square roots of the counts or delete them from the input file and let DASH calculate them 4 4 Initial Assessment of Background Shape Backgrounds may be largely flat sloping or rising and falling as illustrated in the example 42 DASH User Guide profiles During data input a Monte Carlo background estimation routine gives you the chance to fit and remove the background You should normally use this background removal option During Pawley fitting a 24 order polynomial is then sufficient to represent the background If you did not take the background subtraction option then a higher order polynomial will be used The more complex the background the more terms might have to be used in this polynomial 4 5 Initial Assessment of Peak Shapes DASH is able to fit the majority of peak shapes that you will encounter in diffraction from organic compounds including asymmetry at low angles due to axial divergence Asymmetry due to axial divergence at low angle 6000 5500 5000 4500 4000 3500 3000 2500 2000 1500 1000 500 Observed profile 4 75 4 60 4 85 4 90 4 95 5 00 5 05 5 10 5 15 5 20 5 25 2 theta Symmetric peaks at moderate resolution Observed profile 14 25 14 40 14 45 14 50 14 55 14 60 14 65 2 theta DASH User Guide 43 When visually assessing a diffraction pattern it is useful to remember that at l
98. atic peak picking is not perfect and as such should not be treated as a black box often the peaks picked are sufficient for indexing purposes but still the user should review the results carefully after use The following caveats exist 6 2 4 Shoulders on peaks are rarely detected by the current algorithm Occasionally a single actual peak can be assigned 2 or more peak positions particularly when said peak is broad e g a t low 2q Unfitted background renders the algorithm useless We occasionally miss weaker peaks Some strong pairs of peaks are sometimes misinterpreted as a single peak This case is a bug in the code which remains unresolved at time of writing Only the first 20 peaks are fitted this means the results for the 18 204 peaks can appear strange when the 20 peak overlaps with other higher angle peaks it can appear that the algorithm has missed the higher angle peaks as they will lie in the fitting range but in fact the algorithm has decided to ignore the higher angle peaks How to View Peak Positions Switch to viewing peak positions by selecting Peak Positions from the View menu DASH User Guide 57 Structural Information Diffraction Setup Peak Positions Cell Parameters Peak Widths Pawley SA pee es me ow DID n IE BE IO IAE Wd af EA IE II ICE EZ v i s vm 3 es ooo A IE i i v vom M Ter A i i s vom a dia refinement E Alpha Beta Gamma Zero point a Pe s
99. atrices Relabel Vi 1 lt Back Close _Relabel ew Click Next gt to continue n the Simulated Annealing Protocol window choose a lower Profile chi sqd multiplier for example 1 5 or 2 0 this time as we expect the fit to the experimental data to be even better now as we are modelling the full structure Also the O atoms have so few electrons compared to the Zr and W atoms which means that the O atom positions only have a small effect on the diffraction pattern so the correct solution is harder to find Click Next gt and then Solve gt to start the Simulated Annealing process This SA run is also likely to take a while as the differences between correct and incorrect solutions are quite small in terms of the effect on the profile 15 6 15 Stage 13 Examining the Final Structure The Analyse solutions window will now show the results of the SA runs The runs may not all have reached the same structural minimum and this can be seen by the range of final Profile chi sqd values for the runs Correct solutions should be identified by the lowest Profile chi sqd and Intensity chi sqd values Take a look at the solutions found by DASH for the full structure by clicking on the View button for one of the top few solutions Using the Packing feature of Mercury turned on it should be possible to see that the tungstate moieties have formed into nicely shaped tetrahedra although the O1 and O2 atoms may be slightly off t
100. atrix from the Pawley refinement c is the scale factor and F x is the calculated structure factor from the current trial structure 158 DASH User Guide 14 4 Appendix D Frequency of Occurrence of Space Groups This appendix lists space groups by their frequency of occurrence in organic and organometallic crystal structures 14 4 1 D 1 Space Groups Listed by Frequency of Occurrence This table lists all space groups that occur at least 40 times in the Cambridge Structural Database C f ws 5 us d 1 N P C Profile c CSD arranged in descending order of frequency Since there were already over 250 000 structures in the CSD when this list was compiled any space group not included in the table is very uncommon Only the symbol for the standard setting is given for each space group in the list Number Symbol Occurrences Number Symbol Occurrences 14 P2y c 73151 2 P 1 41639 19 P2 2 32 18216 15 C2 c 15150 4 P2 11572 61 Pbca 7768 33 Pna2 y 3157 62 Pnma 3128 9 Cc 2075 1 Pl 1848 60 Pbcn 1841 3 C2 1702 29 Pca2 1474 11 P2 ym 1350 13 P2 c 1064 12 C2 m 1053 148 R 3 1044 18 P2 2 2 970 7 Pc 760 56 Pccn 720 43 Fdd2 684 88 14 a 671 92 P4 2 2 522 20 C222 393 36 Cmc2 362 64 Cmca 334 82 I 4 330 176 P63 m 325 146 R3 3ll 96 P442 2 290 DASH User Guide 159 160
101. automatically e Read in the Tutorial 3 cis zmatrix file Atthis point DASH will confirm that there are 14 independent parameters These parameters are listed when you click on Next gt There are 3 parameters describing the positional coordinates 4 of which 3 independent describing the molecular orientation within the unit cell and 8 variable torsion angles Note that in this model we are keeping the cis configuration fixed Click Next gt to proceed to the Simulated Annealing Protocol window Leave the parameters set at the default values click Next gt again then click Solve gt This will take a little longer than the earlier Tutorial examples as there are more torsion angles allowed to vary 8 compared with 6 in Tutorial 2 15 3 12 Stage 10 Monitoring Structure Solution Progress The progress of the structure solution can be followed by monitoring the profile C and the difference plot At some point in the run you should see a dramatic fall in the c value from about 1000 to around 200 At this point you can investigate if a local minimisation produces an improvement the answer will almost certainly be Yes so accept this improved point Have a look at the structure with the View button You should see that the H bonding of groups is now quite plausible always look first for unsatisfied H donor atoms You will see also that the molecule has coiled around to form an intra molecular H bond from the NH near the end of the chain
102. bably solved Note however that sometimes the profile c may be up to 10 times the value of the Pawley n and the structure is still basically correct The exact ratio depends upon many factors such as accuracy of the input model and extent of preferred orientation 10 8 2 Interpreting Current Temperature and Number of Moves A great many moves perhaps several million may be needed for the structure solution of a large flexible molecule and it is not unreasonable to leave DASH running overnight Ideally you should get about an equal proportion of uphill downhill and rejected steps early on in the annealing Ifthe starting temperature was too low you will find that the number of accepted uphill moves is small even though the profile C for the structural model is still much higher than the Pawley es This means that the search is trapped in a local minimum and you should stop the run and restart at a higher starting temperature 10 8 3 Deciding Whether to Stop a Simulated Annealing run The Pawley fit c can be viewed by selecting Pawley SA from the View menu Use of the Local minimisation button at any time during structure solution activates a simplex minimisation from the current best position This allows you search the area around the current minimum in order to assess the best attainable c in the vicinity of the current well 1 e the minimum in search space that is currently being explored You should normally onl
103. be narrowed by editing the Upper bounds box DASH User Guide e In the case of torsion angle C76 C15 N14 C12 DASH cannot process the torsion angle distribution returned from Mogul as it does not recognise the shape of the distribution Modal torsion angle ranges can either be entered manually in the Sampling Ranges boxes for example a lower bound of 50 and an upper bound of 180 could be used or no torsion angle ranges need be applied In this case click the Non Modal button e For torsion angle C3 C4 58 N11 a bimodal distribution is recommended by DASH 45 to 135 This covers the majority of the torsion angle distribution returned from Mogul However if this range is accepted and OK is clicked a warning will pop up stating that the initial value of the torsion angle is not within the defined ranges In this case it is acceptable to change the initial value of the torsion angle to for example 50 Clicking OK now will apply the torsion angle ranges e For torsion angle C17 C16 C15 N15 the histogram of Mogul shows peaks at approximately 60 and 180 indicating a trimodal distribution Upon closing the Mogul window DASH recommends a trimodal distribution with ranges 150 to 150 30 to 90 and 30 to 90 These ranges are appropriate so click on OK to accept them e Out of the 6 torsion angles modal ranges have been set for 5 of them Proceed through the simulated annealing as before A simulated annealing run with 1
104. benefits manifest themselves best with nicely crystalline samples where peaks that are overlapped in the laboratory X ray pattern become well resolved in the synchrotron pattern The collection of synchrotron X ray powder diffraction data is indicated when laboratory data has failed to provide a solution or when a precise high resolution structure solution is required 3 1 2 Choice of Detector Type Of the two common types of detector scintillation detectors give better resolution but linear PSDs position sensitive detectors offer vastly better counting statistics Use of either is likely to yield good results If the sample line widths are well matched to the resolution of the PSD there is little to be gained by switching to a scintillation detector Most high resolution powder diffractometers at synchrotrons currently use one or more scintillation detectors Increasingly though image plates are being used to shorten data collection times and provide better counting statistics The choice of which to use depends very much upon the prevailing instrumental set up the station scientist 1s in the best position to advise you on such matters 3 1 3 Required Resolution Global optimisation methods of structure solution do not require data collected to such a high angle as do direct methods of structure solution Typically if data can be collected to approximately 1 5 resolution then structure solution will be feasible Note that we are spea
105. ct with good H bond patterns and torsional geometry close to the CSD This gives us some confidence that the solution of structure with 8 torsion angles can be carried out with a good likelihood of success It is interesting that Model A which had not been subjected to energy minimisation still gave correct solutions but with a higher C than the other solutions You should try a multiple run with your own constructed cis isomer model file 15 3 16 Stage 14 Rietveld Refinement In order to demonstrate the utility of the built in rigid body Rietveld refinement module a refinement on simulated annealing solutions generated from Model B will be outlined A similar process could be carried out using one of the interfaces to an external refinement package Model B was generated in PCSpartan Pro and a simple energy minimisation performed and therefore can be expected to have bond angles and bond lengths that are only roughly in agreement with the crystal structure values Carry out multiple simulated annealing runs with the molecular model described by Tutorial 3 ModelB zmatrix and random seeds 314 and 159 Once the simulated annealing is complete and the Analyse Solutions dialogue box is displayed click on the Rietveld button corresponding to the best solution The refinement of the best solution from these simulated annealing runs should take the structure DASH User Guide 241 towards the solutions obtained for a refinement on Model C th
106. d length C2 C7 from 1 4297 to 1 4397 changes Chi sqd by typically from 28 42 to 28 73 4 01 to 4 03 Changing the position of a heavier atom e g chlorine in C11 C4 generally produces a larger change to Chi sqd for a shift of 0 01 in the bond length 15 1 16 Using maximum resolution If this were a real example of refinement of an unknown structure you would try to refine against the maximum resolution data that the DASH intensity extraction can handle This tutorial example so far was carried out at a resolution of 1 75A using 135 extracted intensities The current version of DASH can use a maximum of 350 reflection intensities In order to do this you must go back to Stage 1 and read in the data with a higher truncation value in 2q e g 44 0 degrees corresponding to 1 507A resolution This gives a Pawley fit of about 2 35 for 204 extracted reflections When one ruins the SA there are typically solutions with Chi sqd about 7 04 The Rietveld refinement following the order of refinement a Global Temperature Factor b Translations and Rotations gives a temperature factor scale 0 211 and Chi sqd 28 42 Profile Chi sqd 4 01 DASH User Guide 221 15 1 17 To refine from another SA solution Close the Rietveld window with Close this returns you to the main DASH window Click on the Mode pull down menu then select Analyse Solutions This returns you to the list of solutions form your last SA run Note that if you exit completely from DASH this Anal
107. d read in the Tutorial 1 mol file or the Tutorial_1 mol2 file DASH will generate the internal format Z matrix that 1t uses to describe the molecular conformation DASH analyses the molecule and automatically selects rotatable torsions In this case the bond connecting the benzene ring to the SO NH group is the only rotatable torsion in the molecule Read in the newly created Z matrix by clicking on the ax icon in the Molecular Z Matrices window and selecting the file Tutorial l zmatrix DASH User Guide Note that DASH has determined that there are 7 independent degrees of freedom to be determined if the crystal structure is to be solved i e 3 positional coordinates for the centre of mass of the molecule 3 parameters describing the orientation of the molecule within the unit cell and 1 internal torsion angle describing the molecular conformation DASH now has the information it needs concerning the molecule so click Next gt The following menu allows you to fix or bound parameters In this particular example we are allowed to fix the y coordinate of the centre of mass of the molecule at any position as P2 is a polar space group Do this by clicking on F short for fix in the line corresponding to the y coordinate of the molecular fragment y fragl DASH Wizard Parameter Bounds Simulated annealing parameter bounds osa em T uem r ves BET TEE BCE oue BR I DEE IIS BE BT BR la FE aes aso concn
108. data However a preliminary visual inspection of the data is always worthwhile as 1t may give clues about possible problems Things to look out for are 4 1 Signal to noise ratio see Section 4 2 page 38 Esds see Section 4 3 page 42 Background shape see Section 4 4 page 42 Peak shapes see Section 4 5 page 43 Balance of peak intensities see Section 4 6 page 44 and see Section 4 7 page 45 Useful 2q range see Section 4 8 page 45 How to Use the Interface to Inspect a Profile When you input a diffraction data file to DASH the default display is of the complete data set over the full range of 2q There are several methods for examining chosen areas of the data set 4 1 1 How to Zoom in to a Chosen Area The simplest way to zoom is to use the left mouse button ensure that you are in Zoom mode this is the default mode by selecting Default from the Mode menu or depressing the icon on the menu bar Click and hold the left mouse button and drag out a rectangle around the area that you want to zoom in on To zoom out simply select the Home key on the keyboard This example shows the effect of zooming in on two peaks that lie just either size of 10 2q You will see that DASH plots both the intensity and the error bars DASH User Guide 37 A useful keyboard short cut for zooming in on the 2q axis is to select Shift Selecting Shift will zoom out on the 2q axis A useful command to re scale the
109. data range obtained in a powder diffraction experiment is to take all the data from the lowest 2q value to the highest value at which Bragg peaks are still clearly discernible from the background There is little point in including data in the Pawley refinement that is above the useful range it will merely slow the refinement down without adding useful information In extreme cases it may actually hinder structure solution as unreliable information has been introduced into the problem Structure solution does not normally require as much data as structure refinement Diffraction data up to 1 5 resolution are normally sufficient for a successful structure solution though in many cases data to 2 0 or even lower resolution will suffice DASH will handle up to a total of around 600 refinable intensities during the Pawley fitting process DASH User Guide 45 46 DASH User Guide 5 GENERAL HINTS ON SELECTING FITTING AND MEASURING PEAKS Selecting peaks in DASH is necessary for two different reasons Firstly it is necessary for measuring accurate positions of low angle peaks for input to a cell indexing program Secondly it is necessary to fit the shapes of a number of peaks across a wide 2q range before performing a Pawley refinement This section is applicable to both situations and gives some general advice on How to use the interface to select peaks see Section 5 1 page 47 The basics of peak fitting see Section 5 2
110. dent it could be 25 K in a good case a simple response surface with few local minima but much higher gt 1000 K for a complex problem 10 5 2 Cooling Rate e DASH typically uses a fixed conservative cooling rate of 0 02 K i e the rate at which the temperature is reduced for the annealing process The temperature reduction is applied at the end of each cycle of annealing The cooling rate is not constant as the annealing proceeds If DASH detects large fluctuations in c implying that the algorithm is in an interesting region of parameter space it automatically reduces the cooling rate to ensure a thorough search The slower the cooling rate the more thorough the search of parameter space and the greater the chances of finding the global minimum However a slow cool obviously takes longer 10 5 3 Number of Moves The values of N and N2 determine the number of moves random parameter changes that are made at each temperature Specifically if there are N variable parameters positional rotational conformational the simulated annealing performs N N2 N moves at each temperature Default values are NZ 20 and N2 25 these will only need to be increased in difficult cases DASH User Guide 117 10 5 4 Convergence Criteria How does DASH know when it has a correct answer and thus when to stop the annealing process The c obtained from the Pawley fit represents very much the best fit that can be obtained from the data al
111. e plenty of points across each peak The fall off in diffracted intensity with increasing angle due to the Lorentz effect and thermal effects The increasing number of peaks per unit angle with increasing angle The excellent signal to noise ratio even at the maximum diffraction angle i e peaks can still be clearly discriminated from background 15 1 5 Stage 3 Fitting the Peaks to Determine the Exact Peak Positions We need accurate estimates of the 2q positions of the first 20 or so peaks in the diffraction pattern in order to index the diffraction data i e determine the unit cell and hence the Laue class of the crystal DASH makes this process quick and easy by fitting entire peaks accurately It is important to emphasise that we are only interested in peak positions not peak intensities at this stage so weak peaks are every bit as important in indexing as strong ones The first peak in the diffraction pattern is at just under 7 To fit this peak Zoom in to the area around the peak e Sweep out an area using the right mouse button i e move to about 6 85 2q click the right hand mouse button and hold down as you sweep right to about 7 05 before releasing the right button The hatched area now covers the peak and enough background either side to allow an accurate estimate of the peak parameters If you are not happy with the area swept out e g if your finger slipped as you were sweeping simply put the cursor inside t
112. e H bonds is quite common This is what we see below using the Mercury visualiser with Packing and H bond switched on If you have time try doing several SA solution runs and compare the results This is easy to do in DASH notice that in the Simulated Annealing Protocol window there is the option to start a set of runs each with a different seed for the random number sequence If you identify that reasonable termination criteria would be Max number of moves run 2 000 000 and Multiplier for Pawley c as 3 5 the runs will terminate either at move number 2 000 000 or when the profile C falls below a value of 3 5 times the c for the Pawley fit The best solution files are stored in sequence if you called your run fit the output files are fit 001 pdb fit1 002 pdb etc 226 DASH User Guide The accuracy of the solution can be assessed by comparing these independent solutions An example is given here of an output structure red a final profile c of only slightly higher than the lowest c solutions found in a set of runs In this case it is a structure that differs only slightly from the correct structures corresponding to a local minimum with a profile c only slightly higher than that of the correct crystal structure The H bonding scheme is correct but there are small differences in the terminal side chain torsion angles 15 2 14 Stage 12 Applying Modal Torsion Angle Restraints In the following section the use of
113. e Small ions H bond motifs intra and intermolecular 9 4 Converting Molecules to Z Matrix Format Molecules built in third party programs can be read by DASH and converted automatically into Z matrix files see Section 9 4 1 page 95 By default the DASH will assign every single acyclic bond as being rotatable meaning that it will be varied during simulated annealing This can be over ridden either by editing the Z matrix file or in DASH at the time of setting variable parameters for SA structure solution see Section 10 3 6 page 109 9 4 1 Using the Interface to Create Z Matrix files Select Structure Solution either from the Mode menu or by clicking the icon Selecta sdi file from the Molecular Z Matrices window that appears by clicking on the Browse button DASH Wizard Molecular 2 Matrices fel xi SDI file C Program Files CCDC DASH 3 0 Example Example sdi Open Browse r Molecular Z matrices i ES of degrees of freedom ls BB peces ll view cm 7 i at ves em D 7 Bla ve e y PA Bg ve ee Back Next gt Close Convert Re label Pref Orient gt i i The allowed input formats for molecular model files are res cssr pdb mol2 or DASH User Guide 95 mol liebe ax icon e Select from displayed files in working directory Click Open This has created a file with extension zmatrix which can then be used by D
114. e a new set from scratch Unit Cell when selected the unit cell parameters are refined Zeropoint when selected the zero point correction for the diffraction data is refined Background when selected a polynomial of order shown is fitted to the background see Section 8 6 1 page 83 N back the number of terms to be used in the polynomial Sigma size when selected the peak shape parameter sigma 1 is refined see Section 8 6 2 page 85 DASH User Guide 71 Sigma strain when selected the peak shape parameter sigma 2 1s refined see Section 8 6 2 page 85 Gamma size when selected the peak shape parameter gamma 1 is refined see Section 8 6 2 page 85 Gamma strain when selected the peak shape parameter gamma 2 is refined see Section 8 6 2 page 85 Fixed Parameters Overlap Criterion this controls when closely overlapping peaks are treated as a single variable in the Pawley fit rather than as discrete variables The default value of 1 0 is sufficient for fitting most data sets Damping Setting this factor to a value of e g 0 1 might help stabilise very unstable refinements Refinement Status The lower section of the window displays the current status of the refinement Cycle number the spinner gives control over the maximum number of cycles of refinement that are performed upon selecting the Refine button Refinement number this simply records a sequential number for each refinement t
115. e asymmetric unit see Section 9 9 page 98 9 2 Building Molecules in Third Party Programs There are several programs available for building 3D models of molecules so DASH does not provide this capability see Appendix B Programs for Building 3D Molecules page 157 Points to remember when building molecules are Ensure that the bond lengths bond angles and ring conformations have reasonable values since they will not normally be allowed to vary during simulated annealing This is most easily achieved by using a fast force field type minimisation in a modelling package Tables of standard bond lengths may be found in Volume C of nternational Tables for X Ray Crystallography Torsion angles around single acyclic bonds can usually be set to any value since they will be varied during the simulated annealing process Stereochemistries will not be altered during simulated annealing so if a molecule has more than one chiral centre it is important that the relative stereochemistries are correct If you do not know what is correct there may be no choice other than to try simulated annealing with each possibility in turn Absolute stereochemistry does not matter The positions of hydrogen atoms will make little difference to fitting X ray powder patterns so DASH User Guide 93 protonation states and torsion angles involving H atoms are not critical In practice you may often omit H atoms entirely Write molecules out as
116. e crystal system and unit cell parameters have been entered click on Space Group in the DASH Wizard Unit Cell Parameters window DASH automatically sets the space group to the most general for the crystal system chosen Proceed to the Pawley Refinement window see Section 8 2 page 69 Select 6 10 individual peaks distributed over the whole 2q range of the pattern Once DASH has stable values for the unit cell and peak shape parameters the DASH Wizard Pawley Refinement Status window will automatically pop up Obtain a good Pawley fit to the data by refining the background unit cell and zero point parameters When satisfied with the fit launch the space group determination program by pressing the Run gt button The console window for Extinction Symbol appears Once the program has finished running the results of the extinction symbol determination they can be viewed by pressing Enter on the keyboard The most probable extinction symbols along with their probabilities are displayed in descending order in the right hand column When the results window is finished with close the window In the Pawley Refinement window click lt Back The files that have been generated during space group determination including the table of results can be removed at this point by clicking Yes in the Confirm dialogue box The files will not be deleted if No is chosen The space group associated with the most probable extinction symbol can now be sel
117. e model generated from a single crystal structure In the runs performed here the best solution had a profile C of 52 88 and an intensity C of 41 70 After allowing all the sets of parameters to refine individually for example Global isotropic temperature factor then torsion angles then angles then bond lengths and zmatrix the profile C and intensity C had reduced to 34 48 and 21 14 respectively The following table lists selected angles in Model B solutions before and after Rietveld refinement The values found in the single crystal structure are also given for comparison It can be seen that the solution for Model B is moving towards the single crystal structure during Rietveld refinement Angle Before RR After RR Crystal Structure N11 C1 N5 111 53 117 54 123 89 N11 C1 N2 127 43 124 36 117 52 N2 C3 N4 176 98 170 13 170 34 N25 C24 C30 129 70 120 79 121 81 C20 S19 C16 96 47 99 07 105 50 Not many refinement cycles are performed before changes in the C values become very small Like Tutorial 1 small changes can be brought about in the value of intensity c by repeatedly refining the bond angles and bond lengths for example However given the resolution of the data these changes do not represent an improved set of coordinates for this structure 15 3 17 Stage 15 Conclusion One can clearly distinguish between cis and trans isomers in this case tis possible to use D
118. e of the space groups can be ruled out immediately for example face centred and body centred lattices leave some peaks unaccounted for Many of the primitive lattice space groups appear likely from the tick mark positions In this situation where more than one possible space group exists it is logical to begin with the most frequently occurring space group In this case the most frequently occurring orthorhombic space group is P2412121 so select this number 19 confirm visually that it matches the data and click Next gt 15 2 9 Stage 7 Extracting Intensities Choose 7 isolated peaks from across the pattern Fit these peaks using the method described in Tutorial 1 and then carry out the Pawley refinement The initial 3 cycles of least squares refinement only involve the terms corresponding to the background and to the individual reflection intensities accept these three cycles The next 5 cycles of least squares refinement involve the terms describing background intensities unit cell and zero point These refinement details will be suggested automatically by DASH When these cycles are complete check the difference line this should be almost flat by this point The final Pawley c should be between 3 and 4 224 DASH User Guide Accept this Pawley fit and save it as Tutorial_2 sdi Exit from DASH if you wish at this point in the tutorial 15 2 10 Stage 8 Molecule Construction Construct a 3D molecular description of the molecule u
119. e pattern closely Things look good at low angle but the peak at 24 5 is misplaced Altering the setting to 2 a results in excellent agreement throughout the pattern so this appears to be the best choice Note however that Ja has the same systematic absences as 2 a and therefore gives exactly the same level of agreement Using the table in Appendix D of the DASH User Guide the centrosymmetric space group 2 a C2 c is about 7 times more common than the non centrosymmetric space group Ja Cc As the molecule possesses a molecular centre of symmetry in the middle of the bond between the two central rings 2 a is certainly the more likely choice 15 4 9 Stage 7 Extracting Intensities Pawley fitting this pattern in either 2 a or Ja will give identical results the absences are the same and so we will fit Ja We want to delete the last group of 3 peaks as they are highly overlapped in the region of 35 sweep this range and select the Delete key The program now detects that it has peaks available for unit cell refinement and so the Pawley Refinement Status window appears automatically as the peaks widths for all the indexing peaks that you fitted earlier are still available to DASH Select Refine The initial 3 cycles of least squares refinement only involve the two terms corresponding to the linear background and to the individual reflection intensities accept these three cycles Using the cell constants listed in Stage 4 the Pawley
120. e refined from your initial estimates in order to give the best fit to the data Now you simply repeat this until we have 20 accurate peak positions Listed below are 2q ranges and the number of peaks contained in them as a guide DASH User Guide 197 Region 2q below 13 5 13 5 to 14 6 14 6 to 16 4 16 4 to 17 5 17 5 to 18 5 18 5 to 20 20 to 20 9 20 9 to 21 3 Peaks in region 5 3 N wo A N Cumulative peaks 5 8 12 13 15 19 22 24 e Here are the first 24 peak positions as returned by DASH viewed by selecting Peak Positions from the View menu 6 9822 13 6925 15 7753 19 0501 20 6314 9 4942 13 7905 15 9581 19 1452 20 7735 10 3453 14 0003 16 8146 19 3479 21 0639 12 1847 15 2696 17 7552 19 7249 21 1688 12 2228 15 6883 18 0107 20 5468 The only peak you might have struggled to see was the one at 17 75 2q as it is very weak 198 DASH User Guide sel 00 150 160 5 17 50 17 55 17 90 q9 55 as ae 13 2 theta 15 1 6 Stage 4 Indexing Having selected 20 or so peaks we now want to index the pattern There are an number of options at this point you can choose to index the pattern using the installed version of DICVOL use an external program McMaille or DICVOL0A4 or enter known unit cell parameters Index pattern is already selected so click Next gt to index using the internal version of DICVOL Ensure that all crystal systems except Triclinic are selec
121. eak is fitted and the fit displayed as a solid green line The peak position is indicated by a vertical blue line The program will tell you if you select too small an area for peak fitting If you select a larger area than is necessary for defining the baseline around a peak no harm is done as long as you do not stray into the next peak along The fitting process simply takes longer as more points have to be considered in the fit 5 3 Fitting Multiple Peaks and Shoulders More than one peak can be fitted at once Select an area and give the program the position of the first peak in the region by moving the cursor over the top of the first peak and selecting 1 on the keyboard Move on to the top of the second peak and select 2 Alternatively new peak positions can be added by pressing the Insert key Continue until all the peaks you think are present are accounted for Upon selecting Enter all peaks are fitted and their true positions indicated DASH User Guide 49 50 Selecting an area containing several diffraction peaks but fitting only one peak i e the default fit results in a poor fit This can range from the obvious 1 e an entire independent peak is missed out DASH User Guide to the more subtle 1 e a shoulder on a peak is missed 5 4 Common Peak Fitting Problems There are a few circumstances in which you might obtain a poor fit to the data If you are trying to fit a very weak peak with large esds
122. easing the occupancy value of their riding atom by the appropriate amount Alternatively since the scattering power of hydrogen atoms is low contributions from hydrogens can be ignored If you wish to take account of the hydrogen positions directly then the Explicit option can be used Auto Local Minimise when selected the c of each final solution is minimised using a simplex algorithm before the solution is written out If Use Hydrogens is selected hydrogens are included in the local minimisations of the final solutions Auto Align when selected the molecules of the final solution are aligned before the solution is written out Use crystallographic centre of mass when selected each atom is assigned a weight of Z when the molecular centre of rotation is calculated where Z is its number of electrons Otherwise no weights are applied Create batch file Click this button to write files that can be submitted to a grid or to write files that can be used to run DASH in batch mode see Section 11 2 page 133 Options for saving files are as follows Write out dash file at end enables you to save all solutions plus the diffraction pattern and the Pawley fit in one binary file with the extension dash This file is written once the simulated DASH User Guide 119 annealing run is complete The dash files can be reopened within DASH to view solutions obtained from previous runs of DASH see Section 10 9 4 page 129 You may
123. ected usually 8 to 10 and stable estimates of these parameters have been obtained an initial Pawley refinement of the background and reflection intensities can be performed Guidelines for peak selection are If possible choose strong well defined reflections that collectively span a broad 2q range They should include at least one or two peaks at low 2q so that any low angle peak asymmetry is well described in the refinement of the peak shape parameters If possible isolated reflections should be chosen These can be identified by looking at the tick marks at the top of the display which show the reflection positions calculated from the cell and space group you have specified However it is valid to fit multiple peaks if necessary As selection of peaks proceeds DASH will update peak shape parameters and then cell parameters and then indicate that it is ready to perform the initial Pawley refinement 8 5 1 Choosing Peaks Prior to Initial Pawley Fitting an Example see page 79 8 5 1 Choosing Peaks Prior to Initial Pawley Fitting an Example The following example of peak selection for Pawley refinement illustrates some of the situations you will encounter Fitting the first three peaks in the pattern These peaks are all fairly strong and well separated and can be fitted easily Inclusion of these peaks helps subsequent cell refinement as they correspond to low order reflections and gives a good parameterisation o
124. ected from the Space Group drop down menu Occasionally there will be a choice of space groups for the extinction symbol returned DASH User Guide 65 7 2 66 For guidance a table listing the extinction symbols with their associated space groups 1s available see Appendix E Extinction Symbols and their Space Groups page 176 It may be also be useful to refer to the table of most probable space groups when deciding which space group to try first see Appendix D Frequency of Occurrence of Space Groups page 159 Check the agreement between the calculated Bragg reflections of the chosen space group as shown by the tick marks and the peak positions of the experimental pattern Please note that the purpose of Extinction Symbol is to provide guidance in identifying the space group it is not a substitute for good judgement Perform a Pawley Refinement in the chosen space group as normal Identifying Systematic Absences with DASH Systematic absences can be identified in DASH by comparing for different possible space groups the observed peak positions with those calculated from the cell and postulated space group These are represented by tick marks at the top of the profile display Even if you already have clues about the space group it is probably best to start by selecting the primitive space group of the appropriate crystal system with no systematic absences e g P2 for monoclinic Look to see if the gaps in the pattern match the
125. el by taking accurate CSD values than to trust results from force field energy minimisation Indeed for metal complexes the CSD examples are almost essential for good model building Torsion angle distributions may be easily obtained from the CSD using the ConQuest program and searching on the appropriate fragments or by using the direct link to Mogul a molecular geometry database from DASH Mogul forms part of the CSD System which is available from the CCDC The user may decide to reduce the flexibility of the model in DASH during the solution search by placing limits in the torsion angle ranges or even fixing at certain values as in cases of intramolecular H bonding e In cases of ions such as chloride there is much information in the CSD knowledge base soStar of intermolecular group group interactions This can be used in certain cases to predict the likely distance of an 10n from a group in the main molecule and can greatly improve the chances of solution H bonding motifs may be important in certain structures with more than one molecule per asymmetric unit It may be possible to find examples in CSD which would allow one with confidence to fix the relation ship of the second molecule to the first by H bonding e g carboxylic acid centrosymmetric dimers or chains with expected geometry In summary use the CSD to check 94 DASH User Guide Bond lengths Bond angles Torsion angles ranges Ring conformations
126. elated integrated intensities SA based search 1 e DASH David W I E Shankland K and Shankland N 1998 J Chem Soc Chem Commun 931 932 Extinction Symbol Program Markvardsen A J David W I F Johnson J C Shankland K 2001 Acta Cryst A57 47 54 Large pharmaceutical molecule structure solution telmisartan two polymorphs Dinnebier R E Wagner M Peters F Shankland K and David W I F 2000 Z Anorganische Und Allgemeine Chemie 626 1400 1405 Mercury visualisation and analysis of crystal structures Macrae C F Edgington P R McCabe P Pidcock E Shields G P Taylor R Towler M van de Streek J 2006 J Appl Cryst 39 453 457 Mercury 2 0 New features for the visualisation and investigation of crystal structures Macrae C F Bruno 1 J Chisholm J A Edgington P R McCabe P Pidcock E Rodriguez Monge L Taylor R van de Streek J Wood P A 2008 J Appl Cryst in press Pawley Refinement Pawley G S 1981 J Appl Cryst 14 357 Retrieval of Crystallographically Derived Molecular Geometry Information Bruno I J Cole J C Kessler M Luo J Motherwell W D S Purkis L H Smith B R Taylor R Cooper R I Harris S E Orpen A G 2004 J Chem Inf Comput Sci 44 2133 2144 Rotation of molecules Quaternions Leach A R Molecular Modelling Principles and Applications 1996 Longman Harlow ISBN 0582239338 382 385 188 DAS
127. elling package to hand there is a model file named Tutorial I1 mol2 provided with the tutorial taking the co ordinates from the Cambridge Structural Database reference code HCSBTZ If you are using this model rather than creating your own you can now skip to Stage 10 For the purposes of the tutorial we ll assume that the molecule was sketched as indeed it was using the freely available ISIS Draw sketching package Furthermore we will assume the 2D to 3D conversion will be performed using the widely available WebLabViewer Once the molecule is sketched within ISIS Draw select the whole molecule and copy it to the clipboard using Ctrl C Within WebLabViewer ensure that the following Import options accessed from the View menu are enabled 210 DASH User Guide eret PORTET EGITTO EIE ET nl ESSO ES Iv v LI LI Li LI v Paste the 2D model into WebLabViewer using Ctrl V After pasting the molecule into WebLabViewer the 2D chemical sketch is converted into a 3D molecular model in ball amp stick display mode DASH User Guide 211 Save the molecule coordinates in mol format as Tutorial_1 mol 15 1 12 Stage 10 Setting up the Structure Solution Run 212 Start DASH as before and select Simulated annealing structure solution from the Wizard Click Next gt Browse for the DASH project file that you saved at the end of Stage 7 and load the file that you saved e g Tutorial_1 sdi Click on the icon an
128. ematic absences is to perform a Pawley fit in the space group with no systematic absences At the end of the Pawley fitting procedure the output file polyp hkl can be examined for systematic absences and the space group deduced from these absences DASH User Guide 7 3 Identifying Systematic Absences an Example The tick marks in the following figure correspond to the space group P2 i i la ala aa it rt DN PVAUM stl Pa EIQUE The peak around 7 6 2q appears to be absent If the user changes the space group to P 1 2 1 a likely choice the graph is updated with a new set of tick marks CMT VOYWNE Sr a CET 1 VIT v FA wr ng EIA y VIR CAPIT APA P ROPA ON RES ATA The predicted peak at 7 6 is an absence in P 1 2 1 other predicted peaks are consistent with the observed data and so the fit can be performed in P 1 2 1 DASH User Guide 67 If you pick the wrong space group it is often obvious The following display results ifthe space group is changed to P 1 c 1 This choice of space group is clearly wrong since the strong peak at about 7 0 would need to be systematically absent bserved profile 2 theta 7 4 Space Group Ambiguities 68 If it is difficult to decide which of two space groups is a better match to the pattern you can try toggling between them several times to identify subtle differences between the calculated peak positions For example you might find a point at
129. emperature is lowered thus decreasing the chances of acceptance of uphill moves the above process is then repeated The algorithm terminates when the system converges to a minimum hopefully global in c space or when a maximum number of moves is reached DASH User Guide 101 In essence the algorithm tries to move downhill in C space but occasionally allows uphill moves in order to let the system escape from local minima 10 3 Using the Interface for Structure Solution In order to use the interface for structure solution you can either Call the Wizard by clicking on the following icon Either select Simulated Annealing Structure Solution Or select Structure Solution from the top level Mode menu e Or click on the following icon x This will bring up the DASH Wizard Molecular Z Matrices window shown below which you can use to Input Z matrices see Section 10 3 1 page 103 e Edit Z matrices see Section 10 3 3 page 106 e Edit Z matrix rotations see Section 10 3 4 page 107 e Look at preferred orientation see Section 10 3 5 page 109 e Check and set parameter ranges see Section 10 3 6 page 109 e Access Mogul if available via the Parameter Bounds window see Section 10 4 2 page 113 e Start the simulated annealing run see Section 10 3 7 page 110 102 DASH User Guide DASH Wizard Molecular 2 Matrices Ma ES SDI file C Program Files CCDC DASH 3 0 Example Example sdi Open
130. eoisomers Investigate the success rate with different sources of molecular models Learn a bit more about the Pawley fitting process There are possible cis trans stereoisomers and we will refer to cis when the cyano group is on the same side of the C N double bond as the sulphur chain 15 3 2 Data The data set Tutorial 3 xye is a synchrotron X ray diffraction data set collected on Station 8 3 of the Daresbury SRS The incident wavelength was 1 5285 15 3 3 Stage 1 Reading the Data Open DASH and select the directory where the data resides Select View data determine peak positions and click Next gt Select the file Tutorial 3 xye using the Browse button DASH User Guide 235 Click Next gt Check that the wavelength and radiation source have been set correctly and click Next gt 15 3 4 Stage 2 Examining the Data The data spans 8 01 to 56 0 2q Truncate the data to 2 0 A resolution and subtract the background using the default window value of 100 You can examine the background curve green in detail in the usual way by zooming in on regions of the profile Since this data has a very uniform low level background there are no problems click Next gt 15 3 5 Stage 3 Fitting the Peaks to Determine the Exact Peak Positions Select the first twenty peaks using the method described in Tutorial 1 Here is a guide to the positions 2q of the first 20 peaks 9 33 9 97 12 84 13 42 14 20 14 58 16 37 16 5
131. equally valid Structure solutions of this complexity using DASH take so little time to execute that it is worth investigating the various possibilities in order to be certain that you have the correct answer The final fit to the data is not that great but the chemical sense of the structure is such that there is no doubt that the structure is correct The published Rietveld refined structure Smrcok et al for this molecule confirms this Accordingly note that it is entirely possible to obtain a profile C that is a factor of 10 higher than the Pawley c and still have the correct structure DASH User Guide 251 Some remarks on Rietveld Refinement are in order The published structure reported the results of an unrestrained Rietveld refinement which shows quite severe distortion of the benzene rings This is a natural consequence of allowing too many variables to be optimised against the rather limited data especially this set of laboratory data of lower accuracy than synchrotron A tradition has grown up of allowing unrestrained refinement of all atomic positions in order to prove that the crystal structure is correct This certainly proves that the atoms all fit well with the low resolution electron density represented here by only 174 reflections which are extracted by Pawley fit corresponding to the complete data set in 2q corresponding to 1 763A resolution However a more realistic model for the real crystal structure is obtained if one us
132. equivalent maximum resolution lt Back Next gt Close Apply DASH User Guide 23 Enter the 2q angle at which the pattern should be truncated at the beginning This gives the possibility to remove the part of the pattern affected by the beam stop Enter the 2q angle at which the pattern should be truncated at the end This gives the possibility to truncate the data to a certain resolution see Section 8 4 page 75 e Click Next gt DASH Wizard Background Subtraction Subtract background Number of iterations ak Window 100 Fe iv Use Monte Carlo for background correction Smooth Window 100 H e Adjust the width of the window to match the curvature of the background e Smooth Checking this box will smooth the profile before the background is subtracted using a window size of x data points where x is specified in Window The intensity at point I will be recalculated to be the average intensity of points I x to I x where x is the window size e Click Next gt 24 DASH User Guide 2 10 2 Selecting an Indexing Package DASH Wizard Indexing Step 1 Peak Picking The next step is indexing the pattern Select the first 20 peaks in the diffraction pattern using the mouse then press Next gt to index the pattern with DICYOL or launch a stand alone McMaille and enter found unit cell parameters by hand Altematively ifthe unitcell parameters are already known they can be entered directly
133. es the DASH Rigid group Rietveld refinement It has be seen in the previous section 12 that the low resolution data gives an unreasonably long value for the central C C bond 1 60A when we refine with a half molecule in 2 a A better model for the full crystal structure is to use the constrained full molecule placed with its centre of mass on the crystallographic 2 fold axis at 0 0 y 0 25 If the DASH Rietveld refinement is applied to the data available to 1 763A resolution in space group Ja we obtain typical solutions with Chi sqd of about 86 and Profile Chi sqd of 11 3 An example refinement of the global isotropic temperature factor scale followed by refinement of Translations y only and Rotations gave values of 0 6717 and Chi sqd of 85 87 11 30 A check of the shortest inter molecular contacts shows shortest C H 2 60A F F 2 56A and H41 F16 2 09A This latter value is rather closer than expected being 0 5A shorter than the van der Waals radii sum but the other short contact values can be seen in CSD single crystal structures 15 4 16 References DICVOL Program D Louer amp M Louer 1972 J Appl Crystallogr 5 271 275 A Boultif amp D Louer 1991 J Appl Crystallogr 24 987 993 Model Builders WebLabViewerLite Version 3 20 12 8 98 Copyright 1998 Molecular Simulations Inc Crystal structure of decafluoroquaterphenyl L Smrcok B Koppelhuber Bitschnau K Shankland W I F David D Tunega and R Rese
134. et to 10 The data has been truncated to a resolution of 2 0 In the initial Pawley refinement only the terms describing the background and the terms corresponding to individual reflection intensities are refined using the previously refined unit cell and zero point When you select Refine 3 cycles of least squares are performed This should return figures similar to the ones given below 89 reflections 6950 points Rwp 33 52 Rexp 9 22 c 13 210 Select Accept to accept the results of this refinement the fit is displayed Now click in the main window and select Home to see how well the data are fitted The observed minus calculated plot is shown in pink and emphasises any misfit in the data If you look closely at the data you are likely to see something like this 30 6 30 9 31 31 1 31 2 31 3 30 7 2 theta DASH User Guide 73 The next stage is to refine Background Intensities Unit Cell and Zeropoint DASH assumes that after the initial background and intensities fit you will automatically want to refine the unit cell and zero point Accordingly tick marks are automatically set in the menu boxes Normally 5 cycles of refinement are sufficient Click the Refine button and then the Accept button to store the results of refinement The Pawley Refinement Status window now looks like this DASH Wizard Pawley Refinement Step 2 Refinement control F Intensities v Re use intensities VV Background N back 2 E
135. eter bounds when you click on Next gt Note that each atom is free to move anywhere in the unit cell and that each atom has a full occupancy As DASH does not have anti bumping constraints multiple atoms are free to move to the same site Click Next gt to access the Simulated Annealing Protocol window Change the Profile chi sqd multiplier to 6 0 leave the remaining variables at their default values click Next gt and then click Solve gt This set of SA runs will take a little while but should converge eventually to a solution with a profile C in the region of 5 75 Ideally each SA run should produce a solution with approximately the same value of ome suggesting that this is the correct solution and is reproducible DASH User Guide 263 15 6 12 Stage 10 Analysis of Preliminary Solution 264 Take a look at the solutions found by DASH individually by clicking on the View buttons for each row in the Analyse solutions table It should be obvious that the Zr atoms are aggregating on the origin or one of the symmetry equivalent positions to the origin in each case e g 0 0 5 0 or 0 5 0 0 5 etc The W atoms are also seen to aggregate but these sit on the 3 fold axes of the unit cell This can be seen by turning on the symmetry elements in Mercury click Display gt Symmetry Elements The 3 fold axes should be shown as green vectors with no arrows on In this case the fact that the atoms were each assigned full occupancy
136. exing see Section 6 page 55 and space group determination see Section 7 page 65 Extraction of reflection intensities by Pawley fitting see Section 8 page 69 Building and constraining the molecules see Section 9 page 93 Use of simulated annealing to solve the structure see Section 10 page 101 DASH User Guide 3 DASH User Guide 2 GENERAL FEATURES OF THE WINDOWS INTERFACE 2 1 Overview of the Windows Interface The DASH Windows interface enables you to carry out all the necessary steps for structure solution This section explains the layout of the main window and the various input and output files This is an example of the main window after reading in an X ray diffraction pattern of laboratory data for Decafluoroquaterphenyl Smrcok L et al Z Kristallogr 2001 216 63 66 DASH L Of x File Mode View Options Help ee a X Sg 7 lle el ole els 1 14000 12000 10000 sooo 6000 Observed profile 4000 2000 10 15 20 25 30 35 2 theta C Program Files CCDC DASH 3 0 Documentation Tutorial4 Data files Tutorial_4 xye 21 904 11094 5 There are three ways of accessing most functions in DASH Through the Wizard use of the Wizard is highly recommended From the top level menu File Mode View Options and Help Using the Icon buttons which provide access to functions with one mouse click The main window displays the experimental diffraction profile and w
137. f any asymmetry DASH User Guide 79 80 present 1400 1200 1000 800 600 400 Observed profile 200 fpe y 0 i polo 5 40 5 45 5 50 5 55 5 60 5 65 5 70 5 75 5 60 5 85 5 90 5 95 6 00 2 theta Looking further up the pattern there is a strong peak that could be selected but it has a weak satellite peak to the right which would need to be fitted simultaneously The weak peak is not strong enough to provide useful peak parameterisation information in its own right but it is strong enough to affect parameterisation of the strong peak so would have to be included in the fit There are almost certainly better choices at other points in the pattern so do not use these peaks 3000 2500 2000 1500 1000 500 10 25 10 20 10 35 10 40 10 45 10 50 Still further up the pattern there is a strong isolated peak that can easily be used The triplet and the doublet on either side of it could be selected too but we really want to sample peaks throughout the 2q range in order to parameterise the peak shape right across the pattern By fitting the triplet we simply get three peaks telling us about the local peak shape around 2q 11 37 Fitting the single peak at 11 56 gives us exactly the same information DASH User Guide 1400 1200 1000 800 600 400 200 2 theta Even further up the pattern there is a nicely isolated pair of fairly strong peaks We could fit these reflections individually b
138. first 16 rather than the first 20 peaks Or try deleting very weak peaks or dubious shoulders It is important to realise that DICVOL is more tolerant of missing lines than it is of spurious lines Most importantly try another program Searching for Cells of Higher Symmetry Once a plausible cell has been obtained from an indexing program it is worth performing cell reduction using a program such as TRACER to check whether it corresponds to a cell of higher symmetry Searching for cells of higher symmetry is particularly important when the cell from the indexing program is triclinic This is especially true when the indexing program lists a lot more calculated than observed peaks since this suggests systematic absences Cell reduction is also useful for identifying equivalent solutions i e cells from the indexing program that appear to be different but actually correspond to the same reduced cell Checking the Cell in DASH Once a pattern has been indexed and a preliminary cell identified you can return to DASH and input the profile and the cell You will need to specify a space group start with the space group of the crystal system that has no systematic absence e g P2 for monoclinic The pattern is displayed with tick marks indicating the reflection positions predicted from the input cell and space group DASH User Guide 61 62 DASH User Guide The first thing to do is to check that the tick marks actually correspond to t
139. fit of the background and reflection intensities see Section 8 6 page 83 Improving the fit by refining the cell zero point and possibly peak shape parameters see Section 8 7 page 85 Assessing the quality of a Pawley fit see Section 8 8 page 87 Dealing with numerical instabilities see Section 8 9 page 90 8 2 Sequence of Operations in Pawley Fitting The usual sequence of operation in Pawley fitting as implemented in DASH is Truncate the data to a suitable range for structure solution see Section 8 4 page 75 Specify a space group and initial values for the cell parameters see Section 7 page 65 The Pawley fit can be performed in the default space group i e a group with no systematic absences of the appropriate crystal system or in the true space group if it is known e Select about 8 peaks from across the 2q range choosing as far as possible strong single reflections see Section 8 5 page 79 As the peaks are selected DASH automatically refines the cell dimensions and the peak shape parameters Note that the automatic cell refinement does not DASH User Guide 69 commence until sufficient reflections with non zero values of h k and have been sampled Once the program is satisfied with the stability of these parameters it allows simultaneous refinement of a a polynomial representing the background and b the reflection intensities The cell parameters zero point and peak shape parameter
140. flections to be refined to only 323 at the cost of only 0 1 A loss in spatial resolution In fact this structure can easily be solved from data extending to 1 0 A resolution 43 2q and the total number of reflections in this range is then only 163 g 8 4 2 Truncating Medium Resolution Data an Example Synchrotron dataset with an incident wavelength of 0 85 so 1 5 resolution equates to around 2q 33 2200 2000 1800 1600 1400 1200 1000 Observed profile tis clear that diffraction is still strong at the high angle end DASH User Guide 77 There are around 350 reflections in the full data range and this can easily be fitted so truncation 1s not necessary 8 4 3 Truncating Low Resolution Data an Example Synchrotron dataset with an incident wavelength of 1 15 A thus 1 5 A spatial resolution equates to a 2q value of 45 However it is clear that the diffraction data is fading long before this point t t H t e Given the poor signal to noise ratio there is little point in fitting the data beyond about 30 which equates to about 2 2 resolution this is sufficient to solve the structure 78 DASH User Guide Observed profile 21 22 22 24 25 26 27 26 29 20 2 theta 8 5 Choosing Peaks Prior to Initial Pawley Fitting The first step in Pawley fitting is to select some peaks for refining the peak shape parameters and the unit cell dimensions Once enough peaks have been sel
141. fter multiple simulated annealing runs you can have increasing confidence in the solution 10 10 Things to Try When Structure Solution Fails Review the original data e g do the esds look reasonable have all corrections been applied Review the indexing and the Pawley fit if necessary try solving the structure in a different space group Check the molecular stereochemistry or ring conformation or whatever else might be relevant Might there be solvent present and are you sure of the molecular structure Have you frozen any torsion angles around single bonds If so consider releasing them Conversely if the number of parameters is large try reducing the search space by fixing torsion angles to likely values or at least to smaller ranges Try altering the non hydrogen atom temperature factors Persevere if the data are reasonably good Z 1 and the number of rotatable torsions is lt 10 DASH should be able to solve the structure with ease 10 11 Final Rietveld Refinement 130 The solution found by DASH may be verified by Rietveld refinement using a program such as TOPAS GSAS FullProf or RIETAN DASH provides an interface to TOPAS GSAS and RIETAN DASH User Guide tis also possible to do a rigid body Rietveld refinement in DASH see Section 12 1 page 137 Initially try refining only the scale factor and a global temperature factor Following this if necessary you can attempt to use highly constrained R
142. g in Mercury by clicking on View switch to using EXPGUI for refinement by clicking on Launch an EXPGUI exit the refinement process by clicking on Close The right hand side of the dialogue box shows the current refinement options to start with only two boxes are ticked to show that only the Scale and Background terms will be refined e Click on the Refine button and the exp file will be automatically updated then submitted to GSAS for the first step of refinement When the cycle of refinement has completed you will be returned to the DASH interface The Refine options have been updated such that a Uiso parameter will be refined in the next cycle of refinement Continue this process of refinement until all the checkboxes have been ticked The final cycle of refinement will be followed by output of the final structure in cif format Note Default values for Weights on Restraints FACTR are provided but can be altered 12 6 Refinement Using RIETAN 150 DASH User Guide 12 6 1 Preparation of Data for RIETAN Rietveld Refinement DASH Wizard Background Subtraction M Subtractbackgraund Number ofiterations 20 H Window 100 H Iw Use Monte Cano for kackaraund correction a Smooth Number of background terms for RIETAN Complete the steps of data preparation given see Section 12 3 page 141 The final step before sending the pattern to RIETAN is to choose the number of terms to be used by RIETAN for the
143. g Structure Solution Progress The progress of the structure solution can be followed by monitoring the profile C and the difference plot The molecule and crystal packing can be examined using the View button 15 5 13 Stage 11 Examining the Output Structure View the structure using the View button in the Results from Simulated Annealing window All should look reasonable there should be no abnormal close contacts between the atoms In particular check the formation of H bonds The picture below is taken from the Mercury visualiser for a SA good solution In order to get a simple view of H bonds we suggest clicking Show hydrogens off and H Bond on 256 DASH User Guide In the CSD it is found that in nearly every case H bond donor atoms will be satisfied so you should check all the OH groups and the NH Most of the O acceptor atoms will also take part in H bonds except for the ribose O which is often found not to accept Note that in DASH the torsion angles involving H atoms are fixed by default at whatever value was input from the model this means that the H atoms do not necessarily point in the correct direction to form optimal H bonds in these SA solutions For comparison an H bond picture from Rpluto is given below for the single crystal structure BEURID10 which shows the same H bond pattern The directions of the axes may be inverted as absolute configuration cannot be determined from powder data There is an ambiguity of 0 5 in
144. g of the data is necessary 34 DASH User Guide The exact form of the polarisation correction applied is suitable for instruments equipped with a primary monochromator Whilst not exactly correct for different instrumental geometries it is still a good enough approximation to be useful tis always possible to fully correct for the polarisation effects of particular geometries if your data processing software allows it before inputting the corrected data into DASH Within DASH the data should then be treated as having been obtained using monochromatic synchrotron radiation A Lorentz correction should never be applied in advance 3 2 3 Kao Stripping DASH is able to handle data collected using monochromatic radiation only The use of more than one incident wavelength is a serious complication that should be avoided when tackling problems of structure solution e However it is possible that your diffractometer software may provide suitable K4 stripping routines that allow you to export a data file from which the K gt contribution has been removed algorithmically In such cases the exported file may be treated within DASH as a monochromatic laboratory X ray data set NB Stripping algorithms inevitably introduce some degree of uncertainty into the data 3 2 4 Esds Each 2q count data point must be accompanied by an estimated standard deviation esd Ideally the diffraction data set input into DASH should consist of th
145. g so that the bulk of its scattering power is concentrated within a few hkl planes Weak peaks provided that they are sufficiently well determined are just as powerful a constraint on the structure solution as strong peaks The distribution of intensities may be indicative of preferred orientation 1 e the crystallites in the powder sample were not randomly oriented with respect to the incident radiation but tended to be aligned along a certain direction Preferred orientation is not usually a big problem if transmission capillary data has been collected Whilst in principle the direction and extent of preferred orientation within the sample can be determined as part of the structure solution process in the current version of DASH only the extent of the preferred orientation can be optimised during the simulated annealing In rare cases a large peak may turn out to be an instrumental artefact e g a spike in the detector electronics Such rogue points can normally be edited out by hand 44 DASH User Guide 4 7 Flattened Peak Tops If strong peaks in your diffraction pattern appear to have flattened tops it is likely that the detector has been saturated during the data collection If the flattening has seriously truncated the height of the peak you will not be able to obtain an accurate intensity value for the peak during Pawley fitting 4 8 Initial Assessment of Useful 2q Range e A simple rule of thumb for assessing the useful
146. gaps in the tick marks Zooming the picture helps a lot when assessing whether a peak is matched by a tick mark Do not worry about tick marks that are not matched by peaks in the profile they could be systematic absences or weak peaks However peaks with no corresponding ticks are a warning If you do see a peak in the profile with no matching tick mark the cell is probably wrong though impurities or instrument spikes should not be ruled out Having examined the space group with no absences you can now try space groups of higher symmetry to account for any systematic absences in the pattern Browse through the space groups comparing calculated and observed peak positions A useful technique is to cycle through space groups with just one cause of systematic absence e g 42 B2 C2 12 etc since this may enable you to eliminate a complete set e g all C centred space groups quickly It is necessary to look separately at different settings of the same space group e g P21 c P21 n and P21 a since the cell from the indexing program could correspond to a non standard setting Although you are looking mainly for peaks in the observed pattern that do not have matching tick marks since this virtually eliminates that space group do remember to look for the opposite discrepancy If there are a lot of calculated peaks that are not observed you may be looking for a space group with more systematic absences Another way of identifying syst
147. ght 1996 Science 272 90 92 DIAMOND Program Version 3 0 Crystal Impact Crystal Impact GbR Postfach 1251 53002 Bonn Germany 2004 DASH User Guide 269
148. h to Mogul in the Configuration window Once a path to Mogul is present in the Configuration window hitting the Modal button will launch Mogul and a histogram of the distribution of angles obtained from structures within the CSD for the chosen torsion angle will be displayed It should be noted that the Mogul histogram displays all torsion angles positive and negative on a positive axes i e 0 180 The structures that contribute data to the histogram can be examined by clicking on the View Structures tab in the Mogul window DASH User Guide 113 CCDC Mogul Beta 1 1 E inl x File Searches Help Build query Results and analysis View structures Results Navigator Mogul search Torsion angle All hits 30 Accepted hits 30 10 Showing hits with A factor all Relevance Nunber Contibuion H 1 00 30 100 0 B E See E heen EE m VERRERERE A hadenn Numberof hits Le 45 90 Torsion angle View diagrams Click to de select bars click and drag to de select a range Statistics Total 30 Selected 30 Histogram display Select all hits in histogram ld min 0 005 Displayed hits 30 Rfactor filter Selected hits 30 Deselect all hits in histogram All fragments Histogram click in bar to deselect click again to reselect Right click For options Upon closing the Mogul window the Modal Torsion Angle Ranges dialogue will be disp
149. has the disadvantage of significantly increasing the number of variables and so increases the complexity of the problem Ways of avoiding this include Ignore one of the molecules if you have two molecules one of which is relatively small and so responsible for less than say 10 of the scattering i e only 10 or less of the sum of all the electrons in the asymmetric unit are in the smaller molecule then DASH may be able to find a 98 DASH User Guide reasonable solution for just the larger residue Typical examples would include leaving out water of crystallization or an ethanol molecule in presence of a large molecule like a steroid If this succeeds i e produces a solution with a profile c slightly higher than that expected from a complete solution with all atoms present the resulting model can be converted into a new Z matrix DASH can then be instructed to use the first atom in the molecule as an anchor point all the torsion angles being constrained to the values found in the simulated annealing run A second structure solution can then be attempted optimising only the rotational orientation of the main molecule and both the position and the position and orientation of the small molecule If certain H bonds can be assumed to be present it may be possible in fact to tether a water molecule to be at a certain distance from a donor or acceptor atom on the main molecule Sometimes it is possible to guess the location of a small i
150. hat has been run The bottom line of boxes reports the results of a refinement run Reflections this is the number of extracted reflection intensities Points this 1s the number of profile data points used Rwp this is the weighted profile R factor see Appendix C Definitions of DASH Figures of Merit page 157 R exp this 1s the expected profile R factor see Appendix C Definitions of DASH Figures of Merit page 157 Chi this is the profile C see Appendix C Definitions of DASH Figures of Merit page 157 Buttons 12 Refine start the Pawley refinement Close close the window Accept accept the results of the refinement that has just completed Reject reject the results of the refinement that has just completed Save as save the refinement results as a Pawley Fit file ready for structure solution see Section 8 3 5 page 74 DASH User Guide Solve proceed to the Structure Solution stage see Section 10 page 101 8 3 4 Pawley Refinement an Example Using the Example xye file the unit cell parameters and space group information and having selected 8 peaks see Section 8 3 2 page 70 you will arrive at a window as shown in Section 8 3 3 page 71 100 200 300 In this example we have assumed that the background has been fitted by the Monte Carlo background subtraction routine Ifthe background had not already been subtracted the only difference would be that N back would be automatically s
151. hat if you take a trans isomer model the SA solution process will not get very far Using the multiple run feature of DASH a typical set of 5 runs had final C of 367 452 647 975 624 with hopelessly tangled close contacts You can modify the previous cis cimeditidine model to cover both cis and trans configurations To do this you need to make one small change to the Z matrix file Tutorial 3 cis zmatrix Look at the DASH User Guide 239 labelling of the source molecular model provided with this Tutorial Tutorial_3 cis mol2 shown below hydrogens omitted 240 The relevant torsion angle we now want to vary is C3 N2 C1 N11 If you examine the Z matrix you will see the line that specifies this torsion angle looking at the labels on the right count up 15 from bottom The torsion angle column 6 is set at 1 4448765 the number 0 that follows is a control indicator to tell DASH that this is a fixed torsion angle if you change this to 1 this indicates a variable torsion angle Make this change and save your Z matrix as a new file e g cistrans zmatrix Now begin a structure solution run loading this new matrix look down the list of parameters in the Parameter Bounds window This angle is now freely variable from 0 to 360 and the total DASH parameter count is now 15 Go to the Simulated Annealing Protocol window where there is the option of performing multiple runs If you do a set of 5 runs as before with the maximum number of mo
152. he current annealing temperature In MDB the maxwellian distribution is modified to favour moves to torsion angles into regions of space that are heavily populated in the corresponding mogul distribution This is summarised below The maxwellian is binned and multiplied by the respective bin in the mogul The mogul distributions are first modified so that no bin contains zero hits this ensures that no parameter space is completely excluded from the maxwellian 6 4 ll MEM 0 d T T T T 0 5 100 50 0 50 100 100 50 4 t 100 100 50 0 50 100 20 MDB can have benefit but on occasion can detract from the solution process By using MDB the user is assuming that the torsion angles in the correct solution lie within the most commonly observed ranges of torsion angles In some structures this clearly will not be the case in such situations MDB will tend to bias the search algorithm away from the correct answer Tactically it is best to use MDB in initial runs If however the structure fails to solve still consider re DASH User Guide 115 running the solution SA without MDB as a fall back in case your structure contains an unusual torsion angle The drawbacks are mercifully rare MDB has a beneficial effect in gt 90 of the test cases that we use it for either in speeding up the search by reaching the global minimum more quickly In some large s
153. he 3 fold axes The ZrOg moieties are also formed into undistorted octahedra The following figure shows an image of the solved structure in Mercury and the equivalent view displayed using ZrOg and WO polyhedra in the DIAMOND structural visualiser DASH User Guide 267 Clicking on the Show overlay button in the Analyse Solutions window should also show that the solutions fit with each other very well which suggests that the solution is reproducible In order to refine the structure in a meaningful manner there is a built in rigid body Rietveld refinement module see Section 11 1 of the DASH User Guide To start a Rietveld refinement from one of the structure solutions simply click on the Rietveld button for that row of the Analyse Solutions table and choose the refinement package that you wish to use Careful refinement of the bond angles and bond distances should cause the tungstate moieties to assume a better shape 15 6 16 References DICVOL Program D Louer amp M Louer 1972 J Appl Crystallogr 5 271 275 A Boultif amp D Louer 1991 J Appl Crystallogr 24 987 993 Extinction Symbol Program Markvardsen A J David W I F Johnson J C Shankland K 2001 Acta Cryst 457 47 54 Model Builder WebLabViewerLite Version 3 20 12 8 98 Copyright 1998 Molecular Simulations Inc Powder crystal structure ZrW Og ICSD code 83267 268 DASH User Guide T A Mary J S O Evans T Vogt amp A W Slei
154. he hatched area and press the Delete key on the keyboard to remove the current selected area then try again 194 DASH User Guide BO nunt With the cursor in the hatched area press the Return or Enter key to fit the peak The solid green line indicates the fit to the data whilst the vertical blue line indicates the peak position Selecting Peak Positions from the View menu shows the exact peak position DASH User Guide 195 Diffraction Setup Peak Positions Cel Testen em y Do not worry if you do not have the exact same position however it should be very close to this value e Fit the next two peaks at around 9 5 and 10 3 2q in the same way Zoom in on the doublet at 12 17 2q It is clear from the shape of the peak that there are two contributing reflections here Sweep out an area covering the two peaks using the right mouse button anii 7000 5000 3000 2000 3000 000 1000 12 05 12 10 12 15 12 20 Ag gr 12 30 theta Now you need to give two initial estimates for the peak position This is easily done by moving the cursor close to the top of the first peak and pressing 1 on the keyboard to insert the first estimate then moving to the top of the second peak and pressing 2 to insert the second estimate 196 DASH User Guide 5000 4 5000 2000 Then with the cursor inside the hatched area press Return or Enter as before to fit the two peaks Note that the peak positions ar
155. he pattern i e that the unit cell is correct The correspondence shown below is very good indicating that the cell is probably correct The excess tick marks are probably systematic absences indicating that the correct space group has a higher symmetry than the one currently being assumed 1400 1200 1000 600 600 Observed profile 400 200 DASH User Guide 63 64 DASH User Guide 7 SPACE GROUP DETERMINATION Once the pattern has been indexed you have a putative cell and crystal system The next step is to determine the space group Probabilistic approach to space group determination see Section 7 1 page 65 Identifying systematic absences see Section 7 2 page 66 e An example of identifying systematic absences see Section 7 3 page 67 Dealing with space group ambiguities see Section 7 4 page 68 7 1 Probabilistic Approach to Space Group Determination DASH provides an interface to Extinction Symbol a program that identifies the most probable space groups for a set of reflections and their intensities see Appendix H References page 189 In order to furnish Extinction Symbol with the required information a Pawley fit to the diffraction data must be obtained in the most general extinction group of the crystal system under consideration For more information about the Extinction Symbol program please look at the product manual which includes a reference to the published research paper Once th
156. hen applicable the background any selected peaks the calculated profile the difference profile and the cumulative c with various colour coding conventions The path to the current diffraction data file is shown at the bottom left of the status bar The coordinates of the current mouse cursor position and the h k values of the peak nearest to the mouse cursor are shown at the bottom right of the status bar 2 2 Input of a Powder Diffraction File To input a powder diffraction file it is recommended that you use the option View data determine peak positions from the main Wizard window see Section 2 10 page 21 Alternatively you can use DASH User Guide 5 the Wizard option Preparation for Pawley refinement or click on the following icon E This leads to a pop up window that shows all files in the selected directory with an extension that match those of the file types that can be read by DASH These include e raw Bruker more information about this file type is given below e raw STOE more information about this file type is given below e rdand sd Philips e udf uxd e xye cpi Sietronics mdi Materials Data Inc pod Daresbury x01 Bede txt ThermoARL asc Rigaku Simply Click on the file icon filename this places the filename in the box Click on Open When a Bruker raw file is opened DASH scans the file for data ranges When only one is found it
157. ic absence for the true space group of the crystal The tick at just over 9 5 2q may be another absence although there is just a hint of a shoulder present on the stronger peak We already guessed that a likely space group is P2 so let us see if increasing the symmetry from P2 to P2 eliminates likely absences whilst leaving no unaccounted for peaks Inthe Unit Cell Parameters window select P2 from the Space Group pull down menu DASH User Guide 201 DASH Wizard Unit Cell Parameters Enter crystal system trial lattice constants and space group if known ero polnt 0 0000 Lattice constants a 93332 b 8 49945 e 731801 a Crystal System Monoclinic b axis Space Group 3b P121 Alpha 90 000 Beta 111 185 Gamma 90 000 lt Back Close Apply Space Group gt Using the down arrow cursor key move down the list and watch the tick marks update to show the reflection positions corresponding to the currently selected space group Alternatively you can use the mouse to scroll down and select individual space groups It s pretty obvious that choices such as P 1 c 1 eliminate major peaks and clearly cannot be 202 correct DASH User Guide Tick marks with space group P 1 c 1 Alternatively P 1 2 1 eliminates the tick at 7 5 2q whilst leaving one at just over 9 5 Tick marks with space group P 1 2 1 DASH User Guide 203 Examining the re
158. ietveld refinement of the atomic positions and isotropic temperature factor and or refine preferred orientation You should consider using all the available data for the Rietveld refinement There are a great many packages capable of performing Rietveld refinement of an output structure Many of these are commercial and are shipped with diffractometers so consult your diffractometer manufacturer for details There are also several freely available packages such as DBWS CCSL GSAS and FullProf A good starting point is to visit http www ccp14 ac uk where many of the programs can be downloaded together with examples and tutorials 10 12 DASH Limitations Generally given reasonable data DASH is routinely successful on structures containing one molecule in the asymmetric unit and up to 10 flexible torsion angles With more flexible molecules or with structures containing two molecules in the asymmetric unit the solution is often found if care is taken Hard limits 300 atoms 600 reflections 15000 data points Although DASH is at the heart of the structure solution process it is not completely stand alone You will need to use some other programs all of which can be obtained easily and with little or no expense Specifically you will need programs for Checking for possible unit cells of higher symmetry see Appendix A Programs for Indexing and Cell Reduction page 157 Building molecules in 3D see Appendix B Programs for B
159. if the bars around 180 are selected and the structures viewed then Refcodes QERXUK TOHBUN and TOHBUNO1 are displayed Returning to the histogram in the Results and analysis pane it is clear that the torsion angle is most often found to be around 0 with a very small percentage of structures found with torsion angles of 180 It should be noted that the Mogul histogram displays all torsion angles positive and negative on a positive axes i e 0 180 Close the Mogul window select File from the top level menu and click on Exit in the pull down menu DASH User Guide 229 230 The Modal Torsion Angle Ranges window of DASH will now be displayed DASH performs a very simple analysis of the distribution of torsion angles returned from Mogul and if it recognises the torsion angle distribution will recommend a range of torsion angles to be searched during the simulated annealing these are displayed in the Sampling Ranges section of the window Modal Torsion Angle Ranges l B x Torsion Angle rs amp N11 C12 013 torsion Sampling Ranges Lower Upper Initial 0 25178 20 00000 0 00000 0 00000 to 20 00000 to Non Modal OK Cancel These ranges are only a recommendation and can be edited and altered To alter the torsion angle ranges type the new value in the boxes labelled Lower and Upper DASH will calculate the other torsion angle ranges depending on whether the torsion angle has been chosen to be bimodal o
160. ing the keyboard command Ctrl H The following features are available DASH Help allows you to view a copy of the current user guide and also provides access to the Tutorials DASH Tutorials allows you to view a set of Tutorials for DASH Clicking on any of the tutorials will cause a window to pop up prompting the user to supply a directory in which to save the files for the specific tutorial Clicking on the feature will cause the browser to go up a level within the directory structure for navigation purposes 20 DASH User Guide Directory to save tutorial files CADASH_FILES Cancel About DASH gives the DASH version number 2 10 The DASH Wizard DASH Wizard irn 3 Welcome to the DASH Wizard This wizard leads you through the DASH options ranging from viewing diffraction data to full molecular structure solution using simulated annealing DASH options View data determine peak positions C Preparation of single crystal data C Simulated annealing structure solution C Analyse solutions C Bietveld refinement The DASH Wizard has been designed to guide you through the structure solution process which is performed in a series of steps View data determine peak positions see Section 2 10 1 page 22 Preparation of single crystal data see Section 13 page 153 DASH User Guide 21 Simulated annealing structure solution see Section 10 page 101 Analyse solutions see Sect
161. ing this control Show peak fit difference display of the difference between measured and fitted peaks may be toggled on and off using this control Show Error Bars on Difference Profile display of the error bars on a data point in the difference profile may be toggled on and off using this control Error Multiplier Used to control the value of the multiplier applied to error bars Divide difference by ESDs when ticked the points of the difference curve are divided by the ESDs of the observed number of counts and multiplied by the average ESD Show cumulative chi sqd display of the cumulative chi sqd during Pawley refinement and simulated annealing may be toggled on and off using this control DASH User Guide 17 Colours these buttons may be used to alter the default colours used by DASH for display of the profile Selecting any one of the buttons brings up a colour chooser from which you may select a colour by clicking on the appropriate square Color Basic colors A Mama EEEN T Custom colors qa ARA A 18 EEE Hue 13 60 Red o Sat 240 Green o Define Custom Colors gt gt Coloris alid Lum 20 Blue 255 OF Cancel Add to Custom Colors 18 DASH User Guide 2 8 Configuration Configuration Viewer C Program Files CCDC Mercury CSD 2 0 mercury exe Browse Arguments for viewer iw Use built in Mercury Mogul C Program Files CCD
162. inic might take a long time Click Run gt Clicking on Previous Results will return you to the Results window showing parameters obtained from a previous indexing 26 DASH User Guide 2 10 4 Interface to DICVOL04 DASH Wizard Indexing Step 2 External DICVOL External DICVOL Settings Minimum Maximum Volume A 0 0 4000 0 ab c 0 0 30 0 p 90 0 125 0 I o iv Orthorhombic iv Monoclinic Triclinic Max impurity lines iv Cubic iv Tetragonal iv Hexagonal Experimental zero point 0 0 Peak position error 0 030 Measured density 0 0 Molecular weight Minimum figure of merit 5 0000 scale factor 1 0000 Estimate zero point dad iv Refine zero point IT Exhaustive search DICVOLIB f known enter the experimental zero point error Previous Results gt f known enter the maximum number of impurity lines to be tolerated Select the appropriate crystal systems Note that Triclinic might take a long time Click Run gt Clicking on Previous Results will return you to the Results window showing parameters obtained from a previous indexing DASH User Guide 27 2 10 5 Interface to McMaille DASH Wizard Indexing Step 2 Stand alone McMaille Option for black box mode Monte Carlo on all symmetries Ngrid 3 C Monte Carlo on all symmetries but withouttriclinic search Ngrid 3 C Monte Carlo an all symmetries grid search Ngrid 4
163. intensity axis to the maximum peak height in the selected range is to select Ctrl 4 1 2 How to Zoom Out to the Full Data Set To zoom out and display the full data set simply select the Home key on the keyboard 4 1 3 How to Move the View Window Left Right or Up Down You can use the left and right cursor keys to move up left or right through the data in 2q the horizontal axis Selecting the Shift key in conjunction with the left or right cursor keys allows the same movement but with a smaller step size The up and down cursor keys allow you to move the window up and down in the intensity range the vertical axis 4 2 Signal to Noise Ratio How easy is it to distinguish the Bragg peaks from the background Obviously the noisier the data the less certain we can be of obtaining a definitive crystal structure The following examples should help give you some idea of what good average and poor quality diffraction patterns look like 4 2 1 Example of a Good Profile This is synchrotron data from a nicely crystalline sample with an incident wavelength of 0 6 The background is low and the peak to background ratio is excellent even at high angles Individual esds of each point displayed as vertical bars are relatively small showing that data have been collected for a sufficiently long time 38 DASH User Guide 39 DASH User Guide 4 2 2 Example of an Average Profile This is laboratory data 1 7889 wavelength for
164. ion 10 9 4 page 129 Rietveld refinement see Section 12 1 page 137 It may be called up at any time by clicking the z icon in the main window 2 10 1 View Data Determine Peak Positions Select the first option View data determine peak positions and click Next gt DASH Wizard Powder Diffraction File Diffraction data File C AProgram Files CCOCADASHA 3 0 E amp ample E ample ve Open Browse lt Back Next gt Close Rebin gt Click Browse Select a data file e g Example xye and the diffraction data will be loaded into DASH and displayed You are given the opportunity to rebin the data by choosing Rebin gt otherwise click Next gt 22 DASH User Guide DASH Wizard Diffraction Setup Radiation type Wavelength for angle dispersive X ray data in A C Lab Xray Radiation cu Kal 7 1 12940 Iv Manachramated Synchrotron C EW neutron x Time ofAliahtneutron C TOF neuton SUR fightpath mi 2 thet Check that the radiation type and wavelength have been set correctly Click Next gt DASH Wizard Profile Range Op x Please note that for masimal performance of the background subtraction algorithm the diffraction pattern should not start or end at a Bragg peak Start I Truncate data to start at 2 theta 5 000 End Truncate data to end at 2 theta 32 800 7 Convert 2 0001 A or at the
165. is loaded but when more than one is found the data ranges to be summed can be selected through the following dialogue window 6 DASH User Guide Select Data Range x This file contains more than one data range Please selectthe ranges to be summed No Start End Step Time 0 50 1 00 2 00 4 00 8 00 55 005 65 019 0 014598 16 00 Intensities and ESDs will be re scaled to counts per second OK Cancel By default all data ranges are selected and clicking OK reads in all data ranges DASH sums the data ranges as follows 1 Per 2q value data point the number of raw counts and the number of seconds that has been counted for is stored 2 The combined list of 2q values from all data ranges is sorted in ascending order 3 If two 2q values are closer together than the smallest 2q step used in any of the patterns being summed they are merged by summing their raw numbers of counts summing their counting times and averaging their 2q values This process is repeated until the original smallest step size is restored 4 The intensities are scaled to Counts Per Second by dividing the total raw number of counts per 2q value by the total number of seconds counted for that 2q value The esds are calculated as total raw number of counts 2i total number of seconds counted for It is possible to implement an optimised data collection strategy see Section 3 1 12 page 34 using multiple data ranges in Bruker raw files I
166. ity This is a warning sign although it could always be due to an impurity an instrument spike or preferred orientation At high angle there may be a reasonable fit to the data but an overall mismatch of intensities due to an incorrect overall isotropic temperature factor Systematic forfeiting of the high angle data implies that the temperatures factors for the atoms have been set too low whilst underfitting implies that the temperature factors B are too high The DASH default values of B 3 0 for non hydrogen atoms and B 6 0 for hydrogen atoms are normally sufficiently close to allow structure solution These defaults can always be altered in the input Z matrix 10 9 3 Inspecting the Crystal Packing An important indicator of whether a solution is correct is the network of interactions that are formed in the structure 128 DASH User Guide Check that there are no unreasonably close intermolecular contacts in the crystal An occasional marginally short contact e g an H H distance of just under 2 may be expected given that the structure is effectively of low resolution but anything more extreme indicates that the solution is at least partially wrong Large void spaces are equally unlikely unless you suspect the presence of e g solvent which has been left out of the calculation Check that likely interactions are formed for example it is extremely rare for an N H or O H group not to be involved in a hydrogen
167. k marks correspond to observed peaks This suggests that the space group is either correct or quite close to the correct one Try selecting some of the other space groups in the list for the cubic crystal system and looking at the correlation between tick marks and peaks You will see that the majority of space groups produce regions where there are no tick marks but there are observed peaks e g F23 123 1243 Fm 3 Pa 3 The correct space group for this crystal structure is actually P2 3 Have a look at the predicted peak positions for this space group and check that these correspond to the observed peaks To check that this is correct run the space group determination tool This should confirm that the space group is primitive and that the only systematic absences present indicate a 2 screw axis which only leaves two possible space groups P243 and P4532 The structure will not solve however in P4532 262 DASH User Guide 15 6 9 Stage 7 Extracting Intensities Select a series of isolated peaks across the diffraction pattern e g 16 77 21 69 32 41 45 36 51 85 62 50 as shown in previous tutorials The peak picking algorithm may continue to the Pawley refinement step after you have only chosen 5 or 6 peaks if it deems the peaks chosen acceptable The initial 3 cycles of refinement should give a Pawley C of around 1 2 accept these three cycles The next five cycles of least squares refinement should bring the Pawley C value down
168. king here of spatial resolution within the data set The 2q value corresponding to this resolution can be easily calculated from 291 sq 2 sin I 3 0 A Data should be collected to as low a 2q value as possible since the low resolution reflections help with the indexing process Generally this low angle limit is imposed by the diffractometer because there is a risk of damage to the detector from the straight through beam at 2q values close to zero DASH User Guide 31 3 1 4 Obtaining Monochromatic Radiation in the Laboratory The radiation source should ideally be monochromatic n decreasing order of preference monochromatisation can be achieved by Use of a primary monochromator i e one that lies between the X ray tube and the sample For a copper X ray tube this eliminates CuKg2 and CuKy leaving only CuK Use of a secondary monochromator i e one that lies between the sample and the detector These usually eliminate only CuKp leaving both CuK 4 and CuK45 The CuK contribution then needs to be stripped out algorithmically which is a complication best avoided The use of filters to achieve monochromatisation is considered to be inappropriate for structure solution work 3 1 5 Choice of Wavelength e It is doubtful if any particular wavelength offers an advantage when dealing with organic powder samples Whilst longer wavelengths spread out the pattern and would seem to decrease the chances of peak overlap the peaks
169. king the Set button below this column This specifies refinement of the translation parameter for the molecule centre of mass and the orientation of the molecule In this space group P21 the position along the y axis is arbitrary so switch off the y check box and click Refine You will see the Chi sqd values drop to 42 58 and 5 48 with slight change of temperature scale to 0 13059 This is perhaps as far as is reasonable to refine this structure for publication You can now output a CIF file using the Save as button e g with filename Tut Rietveld Biso and choose output file type cif from the list of file formats You can check that the Rietveld refinement is stable by allowing all torsion angles to vary click the Set button at the bottom of the Torsions column deselect the Global isotropic temperature factor and clear the Translations and Orientations by using the Clear button underneath the column There will be very little change in the parameters with almost no reduction of the Chi sqd values DASH User Guide Asa further experiment you can also switch off refinement of the Translations and Orientations and Torsions by using the Clear button underneath each column and deselect the Global isotropic temperature factor box Now allow all bond angles to vary You see a small shift in coordinates with a small reduction in Chi sqd to 36 82 and 5 22 You can compare this refined structure to the starting value when you entered the Rie
170. l 6 2 5 How to Cut and Paste Peak Positions to External Programs Note that if you want to copy the set of peak positions into the notepad for feeding to other programs you can easily get the peak positions out of DASH and into a file as follows Select View from the Peak Positions menu and then click on the word Position at the top of the peak position column This selects the entire column Use Ctrl C to copy the entire column to the clipboard Once inside an appropriate editor such as Notepad or Wordpad use Ctrl V to paste the column into a file 6 2 6 How to create a DICVOL91 input file Switch to viewing peak positions by selecting Peak Positions from the View menu Create an input file for DICVOL using the DICVOL button see below Fill in the information required on maximum values allowed for cell axes and volume e Click Save DICVOL File button Give a file name e g Actpeak21 dat Run the DICVOL program with this file as input 58 DASH User Guide The menu for creating a DICVOL91 file is shown here In the example below values have been entered such that minimum cell volume 0 A maximum cell volume 3000 The maximum cell axial length is set to 30 and the maximum monoclinic cell angle is 125 All crystal systems except triclinic will be searched and the wavelength has been set as 1 1294 As it is synchrotron data DASH has set the peak position error to 0 02 by default 0 03 for labora
171. l 2001 Z Kristallogr 216 63 66 15 5 Tutorial 5 Dealing with Two Molecules in the Asymmetric Unit 15 5 1 Introduction The object of this tutorial is to guide you through the structure solution of uridine It assumes that you have completed Tutorial 1 In this tutorial you will learn 252 DASH User Guide How to handle two molecules in the asymmetric unit To appreciate the importance of a good molecular model HO CH HO Y Y 15 5 2 Data The data set Tutorial 5 xye is a synchrotron X ray diffraction data set collected on BM16 at the ESRF at 130K The incident wavelength was 0 85075 15 5 3 Stage 1 Reading the Data Open DASH and select the directory where the data resides Select View data determine peak positions and click Next gt Select the file Tutorial 5 xye using the Browse button Click Next gt Check that the wavelength and radiation source have been set correctly and click Next gt 15 5 4 Stage 2 Examining the Data The data spans 4 to 30 2q Truncate the data to 2 0 resolution The background can be removed DASH User Guide 253 at this stage so proceed to do so The default value for the window parameter of 100 is appropriate When you are satisfied that the background fit green line is reasonable click Apply and then Next gt 15 5 5 Stage 3 Fitting the Peaks to Determine the Exact Peak Positions Select the first 23 peaks using the method described in Tutorial 1 Stage
172. l System a list of the crystal systems Space Group a list of space group symbols in various settings Clicking on the following icon clears the unit cell parameters ES 14 DASH User Guide 2 6 4 Viewing Peak Widths Structural Information IE x Diffraction Setup Peak Positions Cell Parameters Peak Widths Pawlep SA Sigma Gamma HPSL HMSL Equations Fw Hm The ray lineshape is modelled as a convolution of Gaussian Lorentzian and axial divergence asymmetry terms The angular dependences of the peak shape variables are given in the panel below c of sec A o2 tan B Gaussian IP scf D tang Lorentzian detector sample height APS MS a detector to sample distance The above Structural Information window appears after selecting Peak Widths from the View menu There are six tabs that allow you to access details of the peak description parameters These fields are for display only The fields are populated once a few peaks have been fitted as reliable peak shape parameters have been calculated by this stage Inspection of the values can be useful in deciding which peak shape parameters 1f any need to be varied in a Pawley refinement see Section 8 6 2 page 85 DASH User Guide 2 6 5 Viewing Pawley SA Structural Information IE x Diffraction Setup Peak Positions Cell Parameters Peak Widths Fawley S Sigma size 0 0065 Gamma size 0 0165 HFSL 0 0111 Sigma st
173. l intensities are treated as being variables in the least squares process and so if DASH comes close to achieving this profile C in the annealing process there is a good chance that the answer is correct There are a number of reasons as to why you will not obtain as good a fit in the structure solution process as you did with the Pawley fit Your input model is based on a number of chemical assumptions some of which may not be entirely accurate the assumption is that all non H atoms have fixed temperature factors There may be some preferred orientation in the sample Accordingly DASH realises that if the profile c comes within a preset multiple default value 5 0 of the Pawley c then there is a good probability that this structure is worth examining For example with the default multiplier setting 1f you achieved a Pawley C of 3 7 then the SA process would terminate when the SA profile C fell below a value of 18 5 The multiplier setting is user controllable via a field on the SA control panel There is always a chance that the SA process may become trapped in a local minimum with a profile C value above the pre set cut off In such circumstances the SA could in principle run forever For that reason there is a pre set maximum of 10 000 000 SA moves in DASH The majority of structures will solve well before this number of moves is reached You can reduce the maximum number of moves if required but note that there
174. l of 10 background terms were used and the Pawley fit returned R 5 9 Rexp 2 5 and C 5 6 Some misfit though not much is evident between the peaks at high angles Observed profile eser s EE EE E rs s a Increasing the number of background terms to 15 brings about a significant improvement with Rwp 5 65 Rexp 2 5 and c 5 15 DASH User Guide 2100 PoP HE P OHETIE A A TI a u D LI 2000 1900 1800 1700 TOU raises on atre at art tt 1500 1400 1300 1200 1100 T7 LTS 18 18 5 19 19 5 20 2 theta A further increase to 20 background terms improves the fit slightly but the high angle plot is oth virtually indistinguishable from that with 15 parameters so the gains in going to 20 order are not worth it In fact the fit with a 10 order polynomial is sufficient to solve the structure 8 6 2 Reflection Intensity Fitting n fitting the individual reflection intensities a peak shape description function is centred at the calculated 2q of each reflection The parameters used in the function S S2 gj 9 have already been determined from the initial set of peaks you selected and should not be varied at this stage They can be refined later once the unit cell and zero point have been fully optimised The fitting procedure not only estimates the individual reflection intensities but also their covariances e Ifa group of reflections are too close together then the observed intensity for that clump
175. layed and if the torsion angle had a distribution that DASH recognised a recommended range of torsion angle values will be shown in the Upper and Lower sample range boxes It is recommended that the user check that the suggested ranges are appropriate before accepting them The lower and upper bounds on the ranges can be edited if different ranges are thought to be more suitable To accept the defined torsion angle ranges press OK This will return you to the main Parameter Bounds dialogue box and the torsion angle to which the modal ranges have been applied will be highlighted in red Hitting Cancel will result in all edits since the last accepted modal range being ignored Hitting the Non Modal button will return you to the Parameter Bounds dialogue box and the full 360 torsion angle range will be applied A non modal torsion angle range is shown in black 114 DASH User Guide 10 4 3 Mogul Data Biasing Mogul data biasing MDB is an alternative way of using MOGUL to improve retrieval of correct answers in searching MDB uses Mogul distributions to bias the sampling in searching to tend to favour regions of space where Mogul indicates there is a high likelihood The underlying code works by modifying the Maxwellian distribution used for each step In simulated annealing each trial move is calculated by first taking a number at random from a maxwellian distribution The maxwellian tends to favour particular moves dependent on t
176. lecule was allowed to roam freely throughout the unit cell Ifthe space group truly is 2 a then the centre should lie either on the origin or on the 2 fold axis Accordingly we can Constrain the centre of mass to lie at 0 0 0 Constrain the centre of mass to lie on 0 25 y 0 and repeat the structure solution runs in a to see the fits that are obtained 248 DASH User Guide How to constrain the molecule to lie on special positions To constrain the centre of the molecule to lie on the origin of the cell stop the current annealing run by pressing Stop and return to the Parameter Bounds window Enter values of 0 0 for the initial values of x fragl y frag1 and z frag1 and then click the F check box for each of these variables in order to fix the x y z position of the molecule within the unit cell at the fractional co ordinates 0 0 0 Note that by default DASH uses the centre of mass of the molecule as the x y z reference point and for the DFQP molecule this corresponds to the midpoint of the central bond You can now proceed with the simulated annealing run knowing that the centre of mass of the molecule will always be constrained to lie at 0 0 0 e Similarly for the SA in which we wish to hold the centre of mass on the 2 fold axis return to the Parameter Bounds window Following the same procedure as just outlined fix x frag at 0 25 leave y frag1 to vary and fix z frag1 at 0 0 Fixing the centre of mass at 0 0 0 causes
177. ll be based only on the few peaks you chose when setting up the initial refinement Normally you should not need to refine the peak shapes further However if you notice that certain peaks are not well fitted it may be worth including them directly in the peak shape estimation process Sweep out an area to select the peak and fit as before The overall peak shape description will be updated and you can re run the Pawley fit with the updated parameters The peak shape used within DASH is a full Voigt function a convolution of a Lorentzian and a Gaussian function which uses 2 parameters S and S to describe the angle dependent Gaussian component s s sec q sj tan q and 2 parameters gj and 9 to describe the angle dependent Lorentzian component g gi sec q g tang There are also two asymmetry parameters HPSL and HMSL but these are fully defined by the peak fitting procedure and cannot be refined during the Pawley fitting The refined values of the peak shape parameters may be seen by selecting Peak Widths from the View menu The values should all be positive though small negative values are occasionally obtained There may be some cases usually those that involve some anisotropic line broadening in which it is useful to refine the peak parameters within the least squares of the Pawley fit In general only peak shape parameters of sizeable magnitude should be refined there is little to be gained by refining a single
178. ll zmatrix file which has three moveable torsion angles At this point DASH will confirm that there are 9 independent parameters These parameters are listed when you click Next There are 3 parameters describing the positional co ordinates 4 3 of which independent describing the molecular orientation within the unit cell and 3 variable torsion angles All F boxes are unticked by default indicating that all 10 parameters are allowed to vary during structure solution Click Next gt leave the parameters set at their default values click Next gt again then Solve gt the simulated annealing process begins 15 4 12 Stage 10 Monitoring Structure Solution Progress The progress of the structure solution can be followed by monitoring the profile C and the difference plot The profile C should fall fairly quickly to below 20 and the fit to the data should look not bad with the residual misfits distributed throughout the pattern 15 4 13 Stage 11 Examining the Output Structure View the structure using the View button in the Results from Simulated Annealing window The molecular conformation and the packing look reasonable However we have still only explored a DASH User Guide 247 15 4 14 Stage 12 Exploring the Possibility of 2 a A Space Group Ja There is a quick and easy way to explore whether or not the true space group is a or 2 a whilst performing all SA runs in a In the previous run the centre of mass of the mo
179. luded Use crystallographic centre of mass when selected each atom is assigned a weight of Z when the molecular centre of rotation is calculated where Z is its number of electrons Otherwise no weights are applied Auto local minimise when selected the c of each final solution is minimised using a simplex algorithm before the solution is written out If Use hydrogens under Auto local minimise is selected hydrogens are included in the local minimisations of the final solutions Auto align when selected the molecules of the final solution are aligned before the solution is written out This only applies when more than one run has been selected Output pdb when selected the crystal structure of the final solution is written out in pdb format Output cssr when selected the crystal structure of the final solution is written out in cssr format Output cel when selected the crystal structure of the final solution is written out in ccl format Output pro when selected a file with the extension pro is written out which contains 2q the observed profile the calculated profile for the best solution and the original esds The file is written out in ASCII format and can be imported into a spreadsheet package such as Excel Output cif when selected the crystal structure of the final solution is written out in cif format DASH User Guide Output res when selected the crystal structure of the final solution is written out in res forma
180. mn 2 diffracted intensity counts Column 3 estimated standard deviation of the intensity If you zoom in on the diffracted data as it is displayed in DASH you will see that DASH displays both the intensity and the error bars The simplest way to zoom is to use the left mouse button Click and hold the left mouse button and drag out a rectangle around the area that you want to zoom in on To zoom out simply press the Home key on the keyboard Note that there are other ways to zoom in on the data see the DASH User Guide for details Try zooming in on the two peaks that lie just either side of 10 2q gun Ton 600 son 400 300 00 100 a HEN 25 Uc 9 5 2 theta You can use the left and right cursor keys to move up and down the data in 2q Some other useful keyboard shortcuts whilst examining data are Shift Zoom in Shift Zoom out Ctrl Rescale the y axis to the maximum in the current range Whilst browsing the data note the following features The peak asymmetry elongated tails to the left hand side of the peaks in the low angle peaks due to axial divergence The flat background indicative of a lack of amorphous content The sharp peaks indicating a good crystalline sample DASH User Guide 193 The excellent instrumental resolution See for example the doublet of peaks around 12 17 2q The use of a small step size commensurate with the instrumental resolution and the narrow peaks 1
181. modal torsion angle ranges during the Simulated Annealing stage is demonstrated using DASH and also how this can be facilitated using the CSD System software which now includes Mogul Mogul is a molecular geometry database which forms part of the CSD System and is available separately from the CCDC Press lt Back from the Solution Summary dialogue to return to the introductory Wizard Window Choose the option Simulated annealing structure solution Reload the z matrix file for Tutorial 2 and then proceed to the Parameter Bounds dialogue box as before DASH User Guide 227 Two methods of accessing torsion angle distributions from the CSD are provided Using DASH with Mogul see page 228 Using DASH with the CSD ConQuest and Vista see page 231 Using DASH with Mogul If DASH has access to Mogul the distributions of each torsion angle in the CSD will be examined using Mogul and restricted ranges will be determined from these data will be applied Scroll down the parameters until the torsion angles are visible e The first torsion angle listed in the table is S8 N C12 013 Click on the Modal button If the correct path to Mogul is present in the DASH Configuration window access this from the top level menu by selecting select Options then Configuration then a histogram of the Mogul hits for the selected torsion angle will appear If a path to Mogul is not present in the Configuration window hit the Browse button in this window
182. mol or mol2 files These can then be read into the DASH program for conversion into the Z matrix format that DASH requires see Section 9 4 1 page 95 Check the geometry of similar molecules in the CSD see Section 9 3 page 94 9 3 Using the Cambridge Structural Database CSD to Check Models Most molecular model building programs start from a user created 2D diagram with bond types from which to construct an approximate 3D model This 1s then minimised from this starting point using various force fields at whatever level of sophistication is available in the program For many molecules there will be no ambiguity as to the final 3D model as regards the rigid portions and the settings of any flexible torsion angles will not matter as DASH will recognise these and automatically set these as variable parameters in the structure solution search However when ring systems are involved or unusual combinations of elements in functional groups the user is strongly advised to check for similar molecules in the Cambridge Structural Database CSD using the ConQuest search program For example this may reveal that a particular ring conformation is favoured in the experimental structures and so one can adjust the 3D molecular model accordingly e tis worthwhile checking the bond lengths and bond angles for any unusual groups for significant deviation from the CSD average It is probably wiser in such cases to construct the first trial mod
183. n Packing lower left The single axis of rotation is specified by the origin of rotation of the molecule and one other vector which can be any of the following The vector between two atoms Just enter the numbers of the atoms An easy way of finding out what the number of an atom is is to relabel the atoms first using Re label and then displaying the atom labels in Mercury Fractional co ordinates e g 0 0 1 would restrict the rotation of the molecule to be parallel to the c axis e Normal to a plane defined by three atoms in the molecule Just enter the numbers of the atoms An easy way of finding out what the number of an atom is is to relabel the atoms first using Re label in the previous screen and then displaying the atom labels in Mercury OK returns you to the Edit Atomic Properties Z Matrix window keeping the changes that have been made Note that clicking Cancel in the Edit Atomic Properties Z Matrix window will also cancel changes made in the Edit rotations Z Matrix window Cancel returns you to the Edit Atomic Properties Z Matrix window discarding the changes that have been made View displays the Z matrix The unit cell axes are included allowing you to check the origin and initial orientation of the molecule To display the unit cell axes when using Mercury select Show cell axes lower right rather than Packing lower left 108 DASH User Guide 10 3 5 Preferred Orientation DASH Wizard Additi
184. n an optimised data collection strategy data points at higher 2q which on average have less intensity are measured longer than data points at lower 2q The Variable Counting Time scheme used for the above file would have been DASH User Guide 7 2q range counting time seconds per step 5 0 15 0 0 5 15 0 25 0 1 0 25 0 35 0 2 0 35 0 45 0 4 0 45 0 55 0 8 0 55 0 65 0 16 0 The third step is performed to smooth the seams between two adjacent data ranges but it also allows reading in of data that has been collected using the following Variable Counting Time scheme entirely equivalent to the previous one 2q range counting time seconds per step 5 0 65 0 0 5 15 0 65 0 0 5 25 0 65 0 1 0 35 0 65 0 2 0 45 0 65 0 4 0 55 0 65 0 8 0 2 3 Format of Diffraction Data DASH recognises two formats of diffraction data within the file type with extension xye the file should be a normal ASCII text file 2q counter reading estimated standard deviation of the count 2q counter reading If no standard deviation is given in the input file DASH recognises this and sets the standard deviation to be the square root of the count The start of an example file where the diffractometer step size is 0 004 degrees 2q is given below 8 DASH User Guide 2000 81 96 10 952 004 71 25 10 284 008 72 40 10 343 012 76 87 10 661 016 63 58 9 695
185. ne Stop Stops the simulated annealing run immediately and returns you to the first Simulated Annealing Protocol window Click Edit to end a simulated annealing run and change parameters Local minimisation Invokes a simplex optimisation that takes the structure to the deepest minimum in the vicinity of the current best structure Click View to visualise the crystal structure of the best solution obtained so far for the current run DASH User Guide 215 Click Solutions to analyse the solutions found so far On a modestly specified PC e g Pentium III 300 MHz the structure solution process should take less than 30 seconds to reach a profile c of around 12 by which point the structure is solved to a high degree of accuracy this is an ideal value the actual number you get may differ from this The profile C is 12 05 less than four times that of the Pawley profile C i e solved DASH Simulated Annealing Status Bii 2 xj Simulated annealing run number 1 of 10 Temperature 118 17 a AE Minimum chi 2 3213 66 Average chi 4004 98 Profile chi 2 m 216 07 Total moves TE 204000 moesten W ere Downhill Uphill Reject 4000 Start Next Stop Local View minimisation Edit Solutions Examine the difference plot 216 DASH User Guide The fit is excellent even at high angle Remember also that we have effectively only refined a scale factor to get to this poi
186. ngles The molecule is assembled by building up the molecule atom by atom and placing each atom at a given bond length bond angle and torsion angle with reference to the earlier atoms Each atom line effectively gives the instructions for adding another atom to the molecule The atoms in this Z matrix file are referred to by their sequence 186 DASH User Guide numbers I J K L in this list In the example above there are 20 atoms which is specified as the first item on line 2 of the file NAT Note that the atoms are presented in a different order from the input Cartesian co ordinate file in mol2 or pdb format Line 1 Title line Line 2 Is ignored Line 3 NAT the number of atoms following in the atom list IAT the atom number to use as origin for DASH rotation parameters 0 is taken as using centre of mass as origin Line 4 Atom lines These atoms are given sequence number I 1 to NAT Item 1 EL Element type Item 2 BL Bond length in Angstroms to connect this atom to atom J item 8 on line Item 3 FB Flag to signal fixed 50 or variable 71 Item 4 BA Bond angle in degrees for angle I J K where K is item 9 on line Item 5 FA Flag to signal bond angle fixed variable Item 6 BT Torsion angle I J K L where atom L is item 10 on line Item 7 FT Flag to signal torsion angle fixed variable Item 8 J atom number for bond I J Item 9 K atom number for angle I J K Item 10 L atom number for torsion angle I J K L Item 11 Temperature fact
187. nium bis tungstate contains zirconium ions pink and tungstate tetrahedra green with oxygen atoms shown in red For this tutorial it is assumed that you have already completed Tutorial 1 In the process of this tutorial you will learn how to e Solve the structure of an inorganic compound Handle multiple structural fragments as separate z matrices Cope with the complications of high symmetry space groups 260 DASH User Guide 15 6 2 Data The data set Tutorial 6 raw is a laboratory x ray diffraction data set collected at room temperature by John Evans The incident wavelength was 1 54060 15 6 3 Stage 1 Reading the data Open DASH and select the directory where the data resides Select View data determine peak postions and click Next gt Select the file Tutorial_6 raw using the Browse button Click Next gt Check that the wavelength and radiation source have been set correctly and click Next gt The default settings shown in the Background Subtraction window are good enough for this simple background Click Next gt 15 6 4 Stage 2 Examining the Data This data set is very clean with a very low background and sharp reflections so we do not want to throw away any of the high resolution reflections Change the settings to truncate the data to a resolution of 1 0 Subtract the background using the default window setting of 100 Click Next gt 15 6 5 Stage 3 Fitting the Peaks to Determine
188. nm 284 60 Beben 285 60 ba c Pc an 286 60 cab Pone 287 60 cba Pnab 288 60 bca Pbna 289 60 a cb B cou 290 61 Pbca 291 61 ba c Pcab 292 62 Pnma 293 62 ba c Pmnb 294 62 cab Pbnm 295 62 cba Penn 296 62 bca P Gn 297 62 a cb Pna 298 63 Cc mc 299 63 ba c C c 300 63 cab An a 301 63 cba Ama 302 63 bca Bbn 303 63 a cb B m b 304 64 C ca 305 64 ba c Cemb 306 64 cab Ab a 307 64 cba Aca 308 64 bca B D 309 64 a cb B ab 310 65 e m 311 65 cab Amm 312 65 bca Bmm 313 66 Cue e 314 66 cab Amaa 315 66 bca Bb b 316 67 Cn a 317 67 ba c Cmm b 318 67 cab Abmm 319 67 cba A nm 169 320 67 bca Bm com 321 67 a cb Bmam 322 68 1 Goo er 323 68 2 Cre Caiz 324 68 1ba c Cccb 329 68 2baec C c c bi2 326 68 1cab Abaa 327 68 2cab Aba a 2 328 68 1 cba A caa 329 68 2 cba Aca a 2 330 68 1bca Buba b 331 68 2bca Bbcb 2 332 68 la cb Bba b 333 68 2a cb Bb a b 2 334 69 Fmmm 3 35 TO E d didel 336 70 2 ES daad 337 el mmm 338 72 bam 339 72 cab m cp 340 72 bca cma 341 73 bca 342 73 ba c cab 343 74 mma 344 74 ba c mm bpb 345 74 cab bmm 346 74 cba cmm 347 74 bca mem 348 74 a cb Imam 349 75 P 4 350 76 P 41 351 77 P 42 352 78 P 43 3539 79 I4 354 80 I 41 355 81 P 4 356 82 I 4 357 83 P 4 m 358 84 P 42 m 359 85 1 P 4 n 1 360 85 2 P 4 n 2
189. now told the program that the SA must now be performed in space group 2 a consult the DASH User Guide Appendix D 3 for an explanation of the format of the Space Group line whilst leaving the pointers to the existing Pawley fit files Next as we are now in 2 a we only require half a molecule to fill the asymmetric unit Construct a Tutorial 4 half mol file based on the above diagram and read it into DASH The resultant Tutorial 4 half_1 zmatrix file only has a single torsion angle the torsion angle between the two halves of the full molecule is automatically determined by the orientation of the molecule within the unit cell Using the Wizard load the new Tutorial_4 half sdi file and the Tutorial 4 half I zmatrix file Do not fix any of the variable parameters 1 e allow the molecule to roam the unit cell and start a SA run The profile C should fall rapidly to around 20 Viewing the molecule shows that the space group symmetry is indeed constructing the whole molecule though the central bond is not displayed on screen the distance C C can be measured to be about 1 6 A 250 DASH User Guide There is therefore no doubt that this molecule crystallises in space group 2 a Note that the molecule is sitting on a 2 fold rotation axis and not the centre of symmetry 15 4 15 Stage 13 Conclusion This tutorial has shown that there are several ways to solve the crystal structure of DFQP using global optimisation all of them
190. nt and the structure is clearly solved Click View to see the solution in the 3D visualiser 15 1 14 Stage 12 Examining the Output Structure DASH can output 5 coordinate file formats describing the final answer output from simulated annealing see the Configuration window Here we assume that the project filename was Tutorial l sdi Tutorial l pdb protein data bank format file containing a Cartesian coordinate description of the SA solution Tutorial l cssr Cambridge Structure Search and Retrieval format file containing a fractional coordinate description of the SA solution Tutorial l ccl Cambridge Crystallographic Subroutine Library format file containing a fractional co ordinate description of the SA solution e Tutorial l cif Crystal Information File format file containing a fractional coordinate description of the SA solution e Tutorial l res SHELX format file containing a fractional coordinate description of the SA solution DASH User Guide 217 The Mercury visualiser supplied with DASH has options to display Packing and H bonds Using these options your answer should look like that given below You can see that all donors and acceptors are satisfied Remember that the exact location of your molecule along b depends upon where you anchored the molecule In the above picture the molecule was fixed at y 0 5 The solution obtained is in excellent agreement with that reported for hydrochlorothiazide at ro
191. ody Rietveld refinement see page 137 Preparation of Single Crystal Data see page 153 Appendices see page 157 Tutorials see page 191 So lA Un d WN m p p je pah je je Nh WN DASH User Guide DASH User Guide 1 INTRODUCTION 1 1 The DASH Program DASH solves crystal structures from powder diffraction data It assumes that the molecular formula of the compound being studied is known and that the unit cell and space group can be determined by indexing the powder pattern It constructs a trial crystal structure by placing a 3D model of the compound inside the unit cell This 3D model will generally consist of rigid units connected by links having unknown torsion angles 1 e an accurate description of the molecule but with an unknown molecular conformation The chances of choosing the correct conformation and positioning the model at the correct point in the cell with the correct orientation are very small However DASH checks how close a trial solution is to the correct structure by calculating diffraction data and comparing 1t with the measured diffraction data DASH uses simulated annealing to adjust the trial structure until it agrees well with the measured data thereby solving the crystal structure directly from the powder diffraction data 1 2 Basic Steps for Structure Solution The basic steps involved in solving structures from powder data are Data collection and data treatment see Section 3 page 31 Cell ind
192. of observed and calculated profiles figures of merit which pertain to the entire pattern do not highlight local problems such as peaks that might not be fitted at all e g impurity peaks The following example shows a good fit The pink difference plot shows no marked areas of misfit DASH User Guide 87 88 The same is true at high angle 1 i r Wi I r P t i Hur n gn gui 1 a VLLL AN H H DASH User Guide 220 200 150 160 140 120 100 80 60 40 20 Ifthe positions of calculated and observed peaks do not match well e g because the zero point and unit cell are not properly refined there is a characteristic sinusoidal difference plot In this example the problem is solved by refining the cell and zero point DASH User Guide 89 Slightly too narrow peak widths result in a rise dip rise difference plot This is often seen as a weak trace around very strong peaks A small misfit in tails is not serious you should start to worry if the misfit is somewhere approaches one third of the peak height e Ifa dip rise dip difference signature is seen the calculated peak is too wide 8 9 Numerical Instability in Pawley Refinement Sometimes a Pawley refinement will diverge and DASH will display an error message Possible ways of removing the numerical instability include 90 DASH User Guide Truncating the data a bit more see Sec
193. of the S8 N11 C12 013 torsion angle The Modal Torsion Angle Ranges dialogue box will pop up and it is here that the determined ranges can be entered In the Lower box enter 20 00 and in the Upper box enter 20 00 Since the Bimodal radio button is active at the top of the dialogue box the complementary bimodal range at 160 00 and 160 00 will be determined and displayed Once you are satisfied that the correct ranges are displayed press OK This will return you to the Parameter Bounds dialogue box and the row of the S8 N C12 O13 torsion angle will be displayed in red indicating that modal ranges are active Should you wish to define a trimodal torsion angle range enter the upper and lower bounds of a single range in the Upper and Lower boxes for example 160 to 160 Hitting the Trimodal radio button will generate two further torsion angle ranges at 120 from the initial range you have specified for example at 40 to 80 and 40 to 80 The following table details the results of searches performed in the CSD v5 24 for all the six torsion angles of this molecule Torsion Angle Initial value Mode Modal Ranges Number of Observations S8 N11 C12 013 0 25 Bimodal 160 to 160 and 97 20 to 20 C15 N14 C12 N11 179 72 Bimodal 160 to 160 and 254 20 to 20 C4 S8 N11 C12 65 08 Bimodal 50 to 90 and 50 412 to 90 C16 C15 N14 C12 179 37 Cannot define 43 C3 C4 S8 N11 27 90 Bimodal 6
194. olecule can be constrained to sit on a centre of symmetry by including a dummy atom of any element type but with a very low site occupation factor e g 0 00001 This atom is positioned on the inversion centre 0 0 0 0 0 0 and anchored there by clicking the fixed box in the translation parameter list A bond must be input from this dummy atom to any atom in the molecule to allow the concept of the Z matrix to be maintained Rotations will still be allowed for this molecule using this atom as the molecular origin reference point The easiest way to create the Z matrix is to build a model with a model building program place a dummy atom at the centroid and draw a bond to the nearest normal atom The input this model file mol2 or pdb format in the normal way to the DASH Z matrix conversion program Then examine the Z matrix file and edit the file to set this dummy atom to be the origin reference atom for the molecule see Appendix G Z matrix format page 185 There are cases where one might want to specify a certain fixed distance to be maintained between a small molecule or ion see the example in Section 9 9 page 98 9 9 Structures with gt 1 Molecule per Asymmetric Unit If the structure contains more than one chemically bonded unit molecule or ion in the asymmetric unit each must be built separately and input to DASH However although you can vary the positions of more than one molecule or ion in the simulated annealing process this
195. olution Looking at the above example of a false minimum it is clear that superficially they can look chemically sensible This is hardly surprising as they lie at a point on the c hypersurface very close to the global minimum of the crystal structure Accordingly it is always prudent to run a structure solution multiple times with different random number seeds to ensure that a consistent minimum is reached 15 2 16 References DICVOL Program D Louer amp M Louer 1972 J Appl Crystallogr 5 271 275 A Boultif amp D Louer 1991 J Appl Crystallogr 24 987 993 Model Builder WebLabViewerLite Version 3 20 12 8 98 Copyright 1998 Molecular Simulations Inc Single crystal structure CSD reference code BEDMIG C H Koo S I Cho Y H Yeon 1980 Arch Pharm Res 3 37 Retrieval of Crystallographically Derived Molecular Geometry Information Bruno 1 J Cole J C Kessler M Luo J Motherwell W D S Purkis L H Smith B R Taylor R Cooper R I Harris S E Orpen A G in press 15 3 Tutorial 3 Handling cis trans Isomerism 15 3 1 Introduction The object of this tutorial is to guide you through the structure solution of cimetidine exploring the problems of different molecular models and cis trans isomerism this tutorial assumes that you have 234 DASH User Guide completed Tutorial 1 In this tutorial you will learn how to Handle a structure solution where the molecule has different ster
196. om temperature by Dupont amp Dideberg 1972 15 1 15 Stage 13 Rietveld Refinement There are several options for Rietveld refinement in DASH including interfaces to external refinement packages and a built in module for refinement For the purposes of this example to refine the structure in a meaningful manner we will use the built in rigid body Rietveld refinement module see Section 11 1 of the DASH User Guide This implementation uses the extracted intensities with their correlation matrix from the Pawley refinement stage and is thus limited to the resolution chosen in 2q in Stage 1 Up to now the default setting in DASH has been used which truncated the data to 2q of 37 65 corresponding to a resolution of 1 75 e Examination of the Pawley refinement carried out in Stage 7 will show the actual number of 218 DASH User Guide extracted intensities e g 135 The Pawley refinement result values may be examined using the View menu and then selecting Pawley SA The low resolution of the data means that we cannot expect to refine coordinates of this molecule in an unconstrained manner and obtain physically reasonable values The information is just not there However it is meaningful to fit the molecule as a sequence of rigid body fragments which is the meaning of the Z matrix description The Z matrix consists of instructions for constructing the molecule atom by atom each atom in this case being added according to the values given
197. on relative to a larger one For example in the following ion pair it is highly likely that the chloride will be hydrogen bonded to the N H group Examination of the CSD database presented in IsoStar for an NH central group approached by a CT ion shows an average distance of 3 1 A The method of constraining such an ion in the DASH SA procedure is best explained by this example Using a model building program construct a Cl atom at the required position relative to the N atom draw a dummy bond to the N atom and output asa mol2 or pdb file On reading into the DASH Z matrix conversion program this produces a single Z matrix file where the Cl atom is now tethered to the N atom The actual distance from N to Cl can of course be modified by directly editing the Z matrix file as can a dummy bond angle In this case the torsion angle involving Cl is not meaningful and can be set as fixed in the parameter list DASH User Guide 99 100 DASH User Guide 10 STRUCTURE SOLUTION 10 1 Overview of Structure Solution DASH solves structures by altering the positions orientations and where appropriate conformations of the molecules in the unit cell subject to the constraints of space group symmetry until a good match is obtained between calculated and observed intensities This process is a search for a global minimum in a multi dimensional parameter space the parameters being positions rotations expressed as quaternions and torsion angles This
198. onal SA Parameters a b ES Iv Include preferred orientation axis 0 E 0 E 1 E lt Back Next gt Close The March Dollase preferred orientation correction can be used The direction of the preferred orientation must be entered in this window the magnitude is optimised during the simulated annealing All preferred orientation parameters are written out to all molecular output files 10 3 6 Checking and Setting Parameter Ranges You arrive atthe DASH Wizard Parameter Bounds window after loading the Z matrix files as in see Section 10 3 1 page 103 DASH User Guide 109 DASH Wizard Parameter Bounds CU E3 Simulated annealing parameter bounds sta T eme upper Tr moss Pais IEEE IO IO lo Weg oj ooo 1umx r weg usw noox iur uweg ooj 00000 iumx r Geg sxx 00000 iunx r Gag ooj aoo BB I mweg s 100000 vowx r sl v Randomise inital values m Re label View ho x lt Back Next gt Close e The purpose of the menu is to allow you to control which parameters are variable or fixed Each parameter has a starting value a lower limit and an upper limit The box F is ticked for fixed or unticked for variable parameter control respectively Ifthe Randomise initial values check box is selected the starting values for the parameters that are varied during the simulated annealing step will be set to random
199. or to be used in DASH structure factor calculation Item 12 Occupancy factor of atom in range 0 0 to 1 0 Item 13 Original number Item 14 Label of atom I in input Cartesian file Item 15 Label of atom J in input Cartesian file Item 16 Label of atom K in input Cartesian file Item 17 Label of atom L in input Cartesian file Notes The flags FT for torsion angles are set as fixed or variable by the Z Matrix generation program using the chemical knowledge of the bond type and hybridisation state It is possible to over ride these settings by locating the torsion angle with the help of the input atom labels e g O14 C11 N13 C1 There may be a case where one wishes to make this a variable torsion angle although described as a double bond by setting FT 1 and thus effectively allowing exploration of cis and trans isomers in the search Only those torsion angles flagged with FT 1 are displayed as parameters in the Simulated annealing parameter setup window see Section 10 3 6 page 109 DASH User Guide 187 14 8 Appendix H References Original authors of the DASH program before CCDC took over onward development and distribution of the program David W I F Shankland K Background estimation using a robust Bayesian Analysis David W I F D amp Sivia D S 2001 J Appl Cryst 34 318 324 Correlated integrated intensities GA based search Shankland K David W I F and Csoka T 1997 Z Kristallogr 212 550 552 Corr
200. orming Rietveld refinement Within DASH there s a built in rigid body refinement module and interfaces to three external programs TOPAS GSAS and RIETAN These interfaces are designed to facilitate the transfer of structural data to the external program and allow an inexperienced user to carry out a basic structural refinement Each of the interfaces will not necessarily provide the best route through a refinement for any specific structure but are intended to offer a starting point for using the particular program No support is provided for the external programs which are supported to differing extents by their own developers The interfaces from DASH to each program along with the built in rigid body refinement module will be supported Web links for external programs e TOPAS http www bruker axs de index php id topas GSAS http www ccp14 ac uk solution gsas e RIETAN http homepage mac com fujioizumi rietan angle dispersive angle dispersive html 12 1 1 Options for Rietveld Refinement in DASH There are currently four available options for Rietveld refinement in DASH Firstly there is a built in module for performing rigid body Rietveld refinement which uses the rigid bodies Z matrices from the simulated annealing stage The use of rigid bodies imposes a large number of constraints on the atomic coordinates which makes it more likely that the Rietveld refinement will result in a chemically reasonable crystal structure
201. otron data M 20 values of 50 or more and F 20 values of 100 or more are encouraging Values for laboratory data will be generally lower an M 20 of say 20 or more might be considered reasonable and worthy of pursuit McMaille reports a number of figures of merit for its solutions and even suggests cells that it judges to be worth investigation Multiple solutions 1 e several possible unit cells are a common occurrence especially when DASH User Guide 6 4 6 5 the input data are not especially good However even when the data are good a program may report two or more unit cells that apparently match the data In such circumstances the solutions should be closely examined If all the cells have almost identical cell volumes then they are likely to be alternative settings of the same cell and any one of them could be used This can be checked by cell reduction If however the cells are markedly different in volume then they are likely to be unrelated and each one needs to be examined more closely If you find several cells all with good figures of merit the correct cell is likely to be the one of highest symmetry A large number of low figure of merit solutions is normally a bad sign it indicates that the input positions are sufficiently vague that a number of cells match to within experimental error If you have trouble finding a cell it is sometimes worth deleting the last 3 or 4 peaks from the input e g try with the
202. ou may exit the refinement process by clicking on Close DASH User Guide 147 DASH Wizard Rietveld Refinement with TOPAS C Program Files CCDC DASH 3 1 Example Example inp File name Refine Jv Use DASH recommendation V Anisotropic broadening penalties_weighting_K1 5 El Scale Weight on restraints wscale Background Distance 10000 Prel Angle Biso Flatten 1000000 Coordinates Include ESDs in output Write new inp file reads out file Save profile v Write out cif file The Rietveld Refinement with TOPAS wizard window will be displayed with the Anisotropic broadening check box ticked This is the first parameter to be refined Hit Write and a new inp file will be written ready to be loaded into TOPAS Return to TOPAS and hit the play button of the Launch Mode window You will be asked whether you wish to update the inp file with the out file Hit No and return to DASH Repeat the above cycle until all the parameters have been refined six inp files should be written for a standard refinement In the final cycle a cif file of the solution will be written by TOPAS Note Default values for Weights on Restraints are provided but can be customised 12 5 Refinement Using GSAS 148 DASH User Guide 12 5 1 Preparation of Data for GSAS Rietveld Refinement DASH Wizard Background Subtraction Subtract background Number of iterations 20 H Iv Use Monte Ca
203. oups b axis unique which have Z 4 You will have to decide which setting of space group 14 is correct P2 a P24 c or P2 n For example look at the peaks in the region 12 to 15 P2 n creates a tick mark at 13 8 where there is no peak and has no tick mark at 13 42 where there definitely is a peak P2 c also has no tick mark at 13 42 but creates a tick mark at 8 1 where there is no intensity You should examine other peaks and tick marks to confirm the choice of space group as P2 a 15 3 9 Stage 7 Extracting Intensities Choose 8 isolated peaks from across the pattern e g 9 33 12 84 14 58 17 65 18 27 19 72 23 63 26 10 Fit these peaks using the method described in Tutorial 1 then carry out the Pawley refinement The initial 3 cycles of least squares refinement only involve the terms corresponding to the background which actually has been removed so notice only 2 polynomial terms are used This should give a Pawley C of about 76 accept these three cycles The next 5 cycles of least squares refinement involve the terms describing background intensities unit cell and zero point This should bring Pawley the c down to about 35 Up to this point the Peak Shape parameters have not been refined To refine these you fill in the tick boxes Sigma size Sigma strain Gamma size Gamma strain it is best to try these options just one at a time DASH does not allow you to refine both sigma parameters simultaneously or both gamma
204. out a peak or shoulder it is probably better to include it in the first instance You can easily edit it out of the peak list later if the pattern fails to index As successive peaks are selected DASH will refine the peak shape parameters e Submit these peaks to a cell indexing program such as DICVOL or McMaille in order to obtain a preliminary unit cell and crystal system DASH User Guide 55 6 2 2 How to Use the Interface to Select Peaks for Indexing Zoom in to well resolved single peaks working from lowest 2q upwards Pick the peak using the right mouse button as described in Section 5 1 page 47 Continue picking peaks the peak count appears beside the blue peak position line Finish peak picking when you have between 20 25 peaks 6 2 3 Auto peak picking for indexing DASH contains a heuristic algorithm for automatic peak picking The algorithm first smoothes the powder pattern by window integration in a fixed 2q range of 0 012 around each point in the profile The window width has been determined by experimentation with several sample patterns it seems that this width offers a good trade off between effective smoothing for patterns collected at narrow 2q step sizes and masking of peaks in patterns collected with broader step sizes e Next the pattern is scanned for regions where the intensity is greater than 8 times the residual background Auto peak selection is habitually applied after background subtraction in DASH
205. ow angles peaks appear broadened by asymmetry At high angles peaks begin to overlap Thus it is probably best to assess the overall peak sharpness from the low to mid range section of the diffraction pattern where the probability of diffraction peaks being the result of individual Bragg reflections is much higher than at high angle Sharp diffraction peaks are obviously preferable because the sharper the peaks the less overlap there will be between adjacent peaks in the pattern The most obvious reason for broad peaks in a diffraction pattern is that the compound under study possesses intrinsically broad peaks Frequently recrystallisation of the sample can improve matters but normally we are stuck with the sample as is and must accept the broader peaks tis always possible that peaks that appear broad are actually doublets i e closely spaced pairs of peaks f any of the peaks are noticeably sharper than the others this can indicate hk dependent line broadening i e some classes of reflections are sharper than others If only relatively few reflections are affected and the broadening is not excessive this will not preclude structure solution 4 6 Patterns Dominated by a Few Strong Peaks If your diffraction pattern is dominated by just a few very strong peaks the following possibilities exist The distribution of intensities may be correct For example this type of pattern will result if a planar molecule is lyin
206. owever the value of Biso for non hydrogen atoms is typical for this size of molecule at room temperature Choose the first solution in the Analyse Solutions dialogue box click on the Rietveld then select Rigid body Rietveld refinement and click on Next gt this will launch the following window DASH User Guide 219 220 Rigid Body Rietveld Refinement ES l Y lg xi Translations and orientations Torsions Angles Bonds Se mens ene res TF sac irr esr 5207 ac 0 53882 E y pes Fr pas F F en f cac rios im pum T wee es m or F ss s f fas uos y Nisz iex 0 v Hide rings 0 v HideH 0 v Hide H 4 0 Clear E Set All Clear Set All Clear Set an Clear Set All IV Global isotropic temperature factor 1 0000 Calculate Save as Compare Intensity ei 107 67 J Preferred orientation 1 0000 Refine Close View Profile Chi sqd 8 04 Le You will see that the check box for Global isotropic temperature factor is selected click Refine The starting value of 1 000 with Chi sqd 100 72 and Profile Chi sqd 8 01 will change to 0 13902 43 49 and 5 53 respectively This very low value of the temperature factor scale corresponds to the unusually low data collection temperature of 20K Keep this temperature factor fixed by deselecting the check box Now switch on the check boxes marked V for the left hand column Translations and orientations by clic
207. page 129 Reproducibility of solution see Section 10 9 5 page 130 10 9 1 Assessing the Final Profile c The first thing to look at is the profile C for the structural model As a rough guide a good solution should have a profile c of around 2 3 times the value of the Pawley c Accurate models will give small multiples of the Pawley c but if your starting model is not particularly accurate you may still get the correct answer but with a much higher multiple Ifthe profile C for the structural model is much more than 10 times the Pawley c then the DASH User Guide 127 structure is almost certainly wrong even though there may be elements of truth in it The c value can be forced up by a variety of effects e Your data may have a systematic problem e g preferred orientation K45 contributions for laboratory data You may not be modelling all of the scattering in the unit cell e g there might be a solvent or perhaps the compound is not exactly what you think it is You may have truncated the data at the wrong point You may have fixed parts of the molecule in the wrong conformation Your estimates of particular bond lengths angles may be significantly in error 10 9 2 Visual Comparison of Observed and Calculated Profiles Visually compare the observed and calculated profiles Are there any peaks that are very poorly fitted For example a strong peak for which there is little or no calculated intens
208. parameter that is very close to zero as its contribution to the overall magnitude of the composite width will be negligible Refinement of small peak shape DASH User Guide parameters may lead to numerical instabilities 8 8 Assessing the Quality of the Pawley Fit The quality of a Pawley fit must be judged in two different ways both of which are important How good are the goodness of fit parameters see Section 8 8 1 page 87 How do the observed and fitted profiles compare visually see Section 8 8 2 page 87 8 8 1 Interpreting Pawley Fit Parameters The parameters R Rex and C are a guide to the quality of a Pawley fit see Appendix C p wp exp g Definitions of DASH Figures of Merit page 157 Ideally Rwp should be close to Rexp and C should be close to 1 0 However this ideal is often not met in practice particularly before the cell and zero point have been refined and particularly with laboratory data For example four recent Pawley fits in a laboratory gave c values of about 1 5 15 and 30 These were all synchrotron data sets generally you should expect higher c values with laboratory data AC 1 0 indicates that the esds on the data set are not quite correct specifically they have been overestimated You should not rely solely on the fit parameters visual inspection of the fit is essential 8 8 2 Visual Assessment of Pawley Fit There is no substitute for examining by eye the fit
209. ply divide all the line positions by two and try again The cell that results will be 8 times too small but you simply double the axial lengths to recover the correct cell DASH offers this option through the use of a scale factor By default DASH creates a DICVOL input file in which the axis lengths is limited to 30 A or less Since organic structures may contain a cell axis of length gt 30 you may need to alter this default if initial indexing fails Similarly you may need to increase the volume limit beyond 3000 A if you are dealing with a large structure or a centred cell The majority of organic crystal structures crystallise in monoclinic orthorhombic and triclinic space groups and you should check these symmetries first Within DICVOL and McMaille the crystal symmetries are searched in order from highest to lowest symmetry As the symmetry falls the cell searches take longer to execute It can take quite a while possibly 2 3 hours even on a fast processor to find triclinic cells using DICVOL or McMaille This is the main reason why triclinic cells are not searched by default so don t forget to try triclinic if your initial indexing attempts fail Some indexing programs e g TREOR will report if they have located a non primitive unit cell whereas other simply report the equivalent primitive cell Like most indexing programs DICVOL gives two figures of merit M lines and F lines for identifying the best solution For synchr
210. r trimodal these ranges are displayed in the grey boxes To accept the torsion angles displayed click on OK To reject modal torsion angle ranges click on Non Modal Clicking Cancel will remove any edits made to the torsion angle ranges since OK was last clicked In this case the suggestion of torsion angle ranges of 20 to 0 and 0 to 20 is appropriate and the ranges suggested by DASH should be accepted by clicking on OK The Parameter Bounds dialogue box will be displayed and the torsion angle S8 N11 C12 013 will be displayed in red indicating that modal torsion angle ranges have been applied Next click on the Modal button for the next torsion angle C 5 N 4 C12 N 1 Again a histogram generated by Mogul will appear and this time it will show a very clear distribution of torsion angles around 180 When the Mogul window is closed the Modal Torsion Angle Ranges dialogue box will be shown with a recommended torsion angle distribution of Bimodal around 180 degrees The torsion angle ranges displayed in the Sampling Ranges boxes are satisfactory so click OK This procedure should be repeated for all torsion angle ranges For torsion angle C4 58 N11 C12 the histogram displayed in Mogul shows a cluster of data around 50 to 100 Upon closing the Mogul window DASH recommends a bimodal torsion angle range of 45 to 135 This range adequately covers the distribution returned by Mogul and can be accepted by clicking OK If you wish the range can
211. ra My Network P Save as type Diffraction information files sdi y Cancel Zi This will bring up the DASH Wizard Molecular Z Matrices window Proceed with entering a molecular model and setting up simulated annealing runs as for normal powder data see Section 10 page 101 DASH User Guide 155 156 DASH User Guide 14 APPENDICES 14 1 Appendix A Programs for Indexing and Cell Reduction A good starting point for acquiring programs and advice is the Collaborative Computational Project Number 14 CCP14 http www ccp14 ac uk In particular http www ccp14 ac uk solution indexing lists available software for powder indexing One simple way to cover all of the tried and tested indexing approaches is to retrieve and install the CRYSFIRE indexing suite which packages together a number of indexing programs under a common interface The CHEKCELL program may prove a useful tool for discriminating between multiple solutions returned by an indexing program In our experience DICVOL has proven to be a highly effective program for indexing powders Note however that 1t 1s not especially tolerant of spurious input lines For example the insertion of a single spurious line into an otherwise accurate set of input lines can cause the solution to be missed In contrast the absence of one or two correct lines from the input file does not necessarily mean that the indexing solution will not be found 14 2 Appendix B
212. rain 0 0001 Gamma strain 0 0112 HMSL 0 0071 Resolution 2 0001 A 83 reflections 63951 points Fawley chi 2 510 The above Structural Information window appears after selecting Pawley SA from the View menu This example shows several pieces of information about the last Pawley refinement It is possible to manually enter values that will be used for subsequent Pawley refinements but this should not usually be necessary 2 7 Plot Options for Graphics The DASH Plot Options window appears after selecting Options from the top level menu 16 DASH User Guide DASH Plot Options x El Character size Iv Show error bars on observed profile 0 5 Symbol size V Show background TUNES V Connect data points Divide difference by ESDs V Show peak fit difference Show cumulative chi sqd Show error bars on difference profile Error multiplier 1 0000 Colours Observed Profile Calculated Profile Difference Profile Axes Tick Marks Peak Fitting OK Character size not currently active e Symbol size not currently active Show Error bars on Observed Profile display of the error bars on data point may be toggled on and off using this control Show Background display of the calculated background may be toggled on and off using this control Connect data points display of lines connecting the data points of the powder pattern may be toggled on and off us
213. reasing the overlap criterion OF Views Fit list ie View fit list file shows the output of the fitting program If you look at the last few lines of this file there are messages as to why the procedure failed Do not accept the results of this refinement Check the following 8 4 2q range consider if there is really any useful data above a certain 2q and truncate see Section 8 4 page 75 Overlap Criterion it is always worthwhile re running the refinement with a larger value of the Overlap Criterion see Section 8 3 3 page 71 For heavily overlapped weak data a value of 2 0 may suffice to stabilise the refinement Truncating the Data DASH limits the number of reflections that can be refined in a Pawley refinement to around 350 This is all that you will need to solve the majority of organic structures Accordingly it may be necessary to truncate the data 1 e throw away counts above a certain 2q value The actual truncation of the data must be done before the Pawley refinement stage either by manually editing the input data file or by using the Wizard You must judge the point in the profile at which the significant information ends As a general rule if data can be used up to 1 5 A there will generally be enough information to solve most organic structures i e for CuK radiation wavelength 1 54056 A q sin 1 1 2d Therefore q sin 1 1 54056 2 1 5 B0 Therefore 2q 0 DASH User Guide
214. ree columns of data lt 2q gt count estimated standard deviation Many diffractometers will output such a listing However if only lt 20 gt lt count gt are available in the input file DASH will automatically calculate the esd values from counting statistics 3 2 5 Background Subtraction e Some diffractometer software may offer the possibility of background subtraction However it is better to leave modelling of the background to DASH unless there is a good reason to do otherwise e g if you have an appropriate physical model for the background and therefore can remove the background with confidence DASH provides a robust Monte Carlo background fitting option that is recommended for use with most data sets DASH User Guide 35 3 3 36 Checklist for Diffraction Data Use synchrotron or monochromatic laboratory X ray radiation If possible collect data to at least 1 5 A resolution Use transmission capillary geometry Do not apply Lorentz or polarisation corrections or subtract the background before entering DASH DASH will assume raw data and perform these steps itself Esds are preferable in the input file 1 e lt 2q gt count estimated standard deviation gt If only 2q count is available DASH will automatically calculate esds DASH User Guide 4 PRELIMINARY INSPECTION OF PROFILE Unfortunately it is not possible to guess whether a structure will solve just by looking at the diffraction
215. rial 2 xye using the Browse button Click Next gt Check that the wavelength and radiation source have been set correctly and click Next gt 15 2 4 Stage 2 Examining the data Note that this data set was collected quickly at the end of a day s beamtime and so only extends to 22 2q Hence the data set extends to a resolution of only 2 A Truncate the data to start at 1 5 to remove the data points affected by the beam stop and then subtract the background using the default window value of 100 and click Next gt 15 2 5 Stage 3 Fitting the peaks to determine the exact peak positions Select the first twenty peaks using the method described in Tutorial 1 Here is a guide to the positions 2q of the first 20 peaks 3 4383 6 1080 6 8792 8 5344 8 9466 9 4316 9 9800 10 1033 10 2499 10 3269 10 7041 11 1635 11 3767 11 5027 12 2579 12 3053 13 3092 13 4047 13 5143 13 5696 Click Next gt e Select Run to run DICVOL or use another indexing program as described in Tutorial 1 15 2 6 Stage 4 Indexing Y our indexing program may reveal a number of possible unit cells The unit cell with the highest figures of merit should be orthorhombic with a volume of 1266 DICVOL for example returns an orthorhombic cell with a 26 66826 A b 9 08435 A c 5 22571 A and volume 1265 999 A with figures of merit M 20 107 1 and F 20 506 6 DASH User Guide 223 Closer inspection of the other unit cells that are suggested b
216. rlo for background correction F Smooth Window 100 H Number of background terms for GSAS 8 E Preview Complete the steps of data preparation given see Section 12 3 page 141 The final step before sending the pattern to GSAS is the Background Subtraction This can be done within DASH but it is usually better to allow GSAS to perform the background subtraction using eight background terms as default e Click Next gt to save the GSAS exp file The Pawley fit will now automatically be performed within GSAS follow the on screen instructions when prompted Once the fit has been done a plot of the diffraction profile the fit and the difference profile will be shown Close this plot by clicking on File gt Quit Return to DASH where you can continue with the GSAS Rietveld Refinement 12 5 2 GSAS Rietveld Refinement DASH User Guide 149 DASH Wizard Rietveld Refinement with GSAS D DASH gsas test tutoriall Example exp File name iv Use DASH recommendation Number of cycles 3 E Weight on restraints FACTA Distance 1000 IV Background Refine options Initialisation Pawley VW Scale 0 Angle 100 00 zu Planar group 100 00 iso Coordinates Write out cif file Refine update exp file then call GSAS View Launch an EXPGUI lt Back Nes Close The DASH interface for GSAS will now guide you through the process of Rietveld refinement At any point you may view the structure e
217. ropic temperature factors of the individual atoms This allows different atoms e g different elements to have different isotropic temperature factors Buttons Calculate calculates the powder pattern with the current parameters without refinement Save as allows you to save the current crystal structure to a pdb res cssr ccl or cif file and allows you to save the current powder pattern both experimental 140 DASH User Guide calculated to a pro file Compare displays the original crystal structure and the Rietveld refined crystal structure superimposed Refine performs a Rietveld refinement Close closes the window View displays the Rietveld refined crystal structure Axis allows you to specify an axis to include the March Dollase preferred orientation model Relabel pressing Relabel relabels all atoms in all Z matrices This is useful for identifying e g torsion angles 1f a molecular model used for building a Z matrix did not have unique atom labels Note that it is possible to manually enter values for all refinable variables These values will be effective immediately 12 2 2 Rigid Body Refinement Steps When the Rigid Body Rietveld Refinement dialogue box is launched the Global isotropic temperature factor check box is automatically selected and hitting Refine will carry out the first step of the Rietveld refinement This step will not change the crystal structure only the thermal parameters are
218. rotations and the torsion angles of all solutions This can be exported into a spreadsheet package such as Excel f you wish to keep the results for several runs started with different values of the parameter ranges see Section 10 3 6 page 109 or simulated annealing protocol see Section 10 3 7 page 110 you are given the option to input a new name for each run This occurs in a popup menu immediately on the first display of the Simulated Annealing Status window see Section 10 7 page 121 120 DASH User Guide Overwrite Output Files 2 Do you wish to overwrite existing files Current base for filenames Example Hit Mo to enter a new filename For example you might want to do separate runs keeping torsion angles 3 or 4 fixed and give file names like this sucrose tor3fixed sucrose tor4fixed etc which will output best solution files sucrose tor3fixed pdb sucrose tor4fixed pdb etc 10 7 Status Display of Simulated Annealing Run You will reach this menu after clicking Solve gt in the Simulated Annealing Protocol window see Section 10 3 7 page 110 It enables you to monitor the progress of the Simulated Annealing Run DASH simulated Annealing Status E Simulated annealing run number 3 of 10 438 58 341 04 Temperature Minimum chi Average chi 2 5174 75 Profile chi 14 76 Total moves ss 16000 movestiteration WENN P Downhill Uphill Reject 4000 Pause
219. s are kept fixed during this stage of the procedure see Section 8 6 page 83 Ifthe fit looks promising then it is usual to run more cycles of refinement allowing the cell parameters and zero point to vary see Section 8 7 page 85 Finally some or all of the peak shape parameters may be refined though this is rarely necessary see Section 8 8 page 87 The results of the Pawley refinement crucially the reflection intensities and their covariances can then be saved for use in structure solution see Section 10 page 101 8 3 How to Use the Interface for Pawley Fitting There are two methods for setting up the information needed for the Pawley Refinement The DASH Wizard which will help ensure that items are not forgotten see Section 2 10 page 21 The main Window option for more experienced DASH users see Section 8 3 1 page 70 8 3 1 Using the Main Window to Prepare for Pawley Refinement Load an X ray diffraction powder pattern see Section 2 2 page 5 Subtract the background see Section 2 4 1 page 9 Select View from top level menu Select Diffraction Setup from tab bar Input type of data e g Synchrotron Wavelength etc see Section 2 6 page 12 Click Apply Select Cell Parameters from tab bar Fill in details of the cell dimensions and space group Click Apply Click OK Proceed to pick peaks see Section 5 1 page 47 8 3 2 Picking of Peaks for Pawley Refinement Zoom
220. s available for Rietveld refinement then enter the path to the TOPAS DASH User Guide 19 executable or click on the Browse button EXPGUI Tel If GSAS is available for Rietveld refinement then enter the path to the tc184 exe in the expgui folder here or click on the Browse button RIETAN If RIETAN is available for Rietveld refinement then enter the path to the RIETAN executable here or click on the Browse button Colour flexible torsions when selected flexible torsion angles are colour coded when viewing a Z matrix Write wavelength to xye files If checked the wavelength entered or selected when reading in a powder pattern will be automatically written to the xye file Write CIF for Viewer If checked individual cif files will be written for all structures chosen to be overlaid If using built in Mercury these files will be automatically displayed simultaneously If MercuryCSD is used the cif files will be loaded but to display the structures simultaneously the Multiple Structures dialog has to be invoked Run single instance of built in Mercury When ticked only one copy of built in Mercury will be opened and all structures will be loaded into that instance of Mercury Unticking the check box will cause a fresh copy of built in Mercury to be opened each time a structure is selected for viewing 2 9 Online Help 7 The online version of this user guide is available by clicking the Help button the El icon or by us
221. s of 10 SA runs each this will produce 50 packages Each package is represented by a dbf file which gives DASH the instructions for that set of SA runs A gra file is also created which lists the filenames for each of the separate packages For running DASH across a GRID it is recommended to use packages containing just one SA run each this allows greater flexibility when assigning packages to different nodes of the network DASH User Guide 133 DASH Wizard Generating GRID batch files Total number of SA runs to perform 500 E Split runs into packages containing 10 SA run s each You will be prompted for the directory and name of a grd file The base name for dbf and dash files will be taken from the file name that you choose dbf and dash files will be called base name nnn dbf and base name nnn dash respectively where nnn is the node number e g base name 078 dash The dbf files that are created store all of the parameters defined for the SA runs so if a particular option is chosen in the Simulated Annealing Options window then it will be adhered to in batch mode Note The dbf files are in simple text format and can be edited using a basic text editor such as Notepad or Wordpad in order to for example modify one parameter then re run a set of SA runs To generate the input files click on the Write gt button At this point you will be prompted for the output directory and the filename for the gra file The
222. s some flexibility by setting a range of 10 to 10 for the central torsion angle C N C 0 However if the data is poor it is probably better to fix the torsion at exactly Zero tis sometimes useful to make repeated attempts at structure solution with torsion angles constrained to various likely ranges 9 6 Treatment of Rings Rings can be handled in two ways in DASH Youcan input a likely ring conformation obtained by looking at examples in the Cambridge Structural Database or by minimising in a modelling package and keep the ring geometry fixed 96 DASH User Guide 9 7 during simulated annealing If the structure fails to solve you can then try an alternative ring conformation You may have to postulate the positions of ring substituents too For example in the molecule below 1 4 dichloro 1 4 dinitroso cyclohexane it is not only necessary to set the ring conformation presumably chair but also to decide whether the substituents are axial or equatorial ON Cl El MH Alternatively you can break one of the ring bonds and treat the resulting chain as a sequence of rotatable acyclic torsion angles This technique might be necessary if the ring is unusual and you have no idea about its probable conformation However it increases the number of variables significantly and also means that you are not taking advantage of the constraints imposed by ring closure Thus effectively you are making the search space much larger
223. se to problems at the Pawley Fitting stage due to correlation between the polynomial background and the very weak intensities DASH User Guide 9 Background fitting using a Monte Carlo low pass filter E Please adjust the number of iterations and the window size until a suitable background iz obtained Number of iterations 2 Window oJ Y Use Monte Carlo for background correction OF Cancel Preview The pass filter value is set at 100 by default Select Preview to run the fitting the display now shows the background fitted as a green line Check that it looks reasonable and is not removing any significant intensity from the peaks A close up view of a fitted background on a laboratory data set is given below i m t f e Neh E di mati _ Ifyou are not happy with the background you can try smaller or larger values of the Low pass filter window size This value 1s related to the number of data points per degree and larger values tend to give a smoother more featureless background whilst smaller values allow the program to give a varying background more accurately A closer look at the above example shows that whilst the background estimate is excellent there are a few ripples in the background line Increasing the low pass filter window size and applying it will smooth out these ripples Select a value that suits your data remembering to look closely at
224. sing your favourite modelling software and save it in pdb mol or mol2 format This can be done for example by importing an ISIS Draw sketch into WebLabViewer see Tutorial 1 for further details Save this as Tutorial 2 pdb Tutorial 2 mol or Tutorial_2 mol2 If you do not have a model building program to hand there is a file supplied with the tutorial Tutorial 2 mol2 15 2 11 Stage 9 Setting up the Structure Solution Run e Start DASH as before and select Simulated annealing structure solution from the Wizard e Select the Tutorial 2 sdi file Click on the ax icon and select either Tutorial 2 pdb Tutorial 2 mol or Tutorial 2 mol2 the file that you created in Stage 8 a Z matrix file called Tutorial 2 l zmatrix will be generated automatically Read in the Tutorial 2 l zmatrix file and click Next gt Note that as Z 4 for P24242 it follows that Z 1 because we know from Stage 5 that the cell is most likely to accommodate 4 molecules Therefore only one Z matrix is required At this point DASH will confirm that there are 12 independent parameters These parameters are listed when you click on Next gt There are 3 parameters describing the positional co ordinates 4 of which 3 independent describing the molecular orientation within the unit cell and 6 variable torsion angles All F boxes are unticked by default indicating that all 13 parameters are allowed to vary during structure solution Click Next gt to proceed to
225. slightly further Refinement of the peak shape parameters is unlikely to improve the refinement for this data set Your final c parameter should be in the region of 1 0 1 2 Accept your best Pawley fit making a note of the c value and save it as Tutorial 6 sdi 15 6 10 Stage 8 Building the Preliminary Model In order to solve the crystal structure we need to define a starting model The oxygen atoms have much less electrons than the Zr and W atoms and therefore scatter x rays more weakly This means that it is sensible to determine the positions of the heavy atoms first before attempting to determine the light atom positions A starting model for the heavy atom structure solution can therefore be defined as simply free Zr and W atoms These can be set up using your preferred model building software or using a file supplied with the tutorial Tutorial 6 atoms mol2 15 6 11 Stage 9 Setting up the Structure Solution Run e Start DASH as before and select Simulated annealing structure solution from the Wizard e Select the Tutorial 6 sdi file Click on the ax icon and select Tutorial 6 atoms mol2 the file that you created in Stage 8 three Z matrix files will be automatically generated Atthis point DASH will identify that there are 9 independent parameters three parameters each for the positional coordinates of the three atoms 1 Zr atom and 2 W atoms The parameters will be then be listed along with their initial values and param
226. st of the pattern the correspondence between tick marks and peaks is excellent and we can conclude that the peak at just over 9 5 2q is a very weak diffraction feature of a crystal whose space group is P24 b axis unique Click Apply in order to select the space group P2 Click Next gt 15 1 9 Stage 7 Extracting Intensities Initially this is much like the indexing phase We are aiming to model the entire diffraction pattern and so we need to be able to fit peaks We are confident that we have a reasonably accurate cell and the correct space group The criteria for peak fitting are slightly different from the ones used in indexing and we need to Fita number of preferably isolated reflections e Sample peaks across the pattern in order to parameterise the peak shape across the pattern Ensure that any peak asymmetry is modelled at the start of the pattern From the Pawley Refinement Step 1 Peak Picking window select Clear Peaks Some suitable peaks for this pattern are given below Fit them by sweeping out areas over the peaks with the right mouse button as before in the order they are given Peak Approx Location Note 1 6 97 2 9 49 3 14 0 lOption to Pawley refine 4 16 8 5 20 78 6 22 75 21 parameter refine starts 7 8 27 8 31 85 Pawley window appears 1 After three peaks have been fitted you are given the chance to go to profile refinement directly by pressing the following icon 204 DASH User Guide
227. t Output chi squared vs moves when selected a graph of the profile C versus moves is written out to a file in ASCII format with the extension chi at the end of the simulated annealing This can be imported into a spreadsheet package such as Excel Note that when more than 1 simulated annealing run 1s requested the above options pertain to every run This can generate quite a number of files Each option except Use hydrogens can be switched on and off while the simulated annealing 1s running Click Solve gt The simulated annealing run now starts 15 1 13 Stage 11 Monitoring Structure Solution Progress Full details of all the output from the structure solution run are given in the DASH User Guide For this tutorial you need only watch The Profile c e The obs calc plot i e the difference plot shown by default in pink The profile c is on the same scale as the Pawley fit profile c that you obtained when fitting the data in Stage 7 So if the current profile C is close to the value of the Pawley profile 0 you ve probably solved the structure DASH runs the SA process until the user intervenes by pressing one of the following buttons on the SA output panel Pause Pauses the SA run until you hit OK This can be useful to free up the processor temporarily as DASH is computationally intensive Start next When in a multi run the Start next button terminates the current run and starts the next o
228. t all points in the pattern but especially at the low and high angle regions The fit is excellent with only a marginal underestimation at low angle Try altering the window size to 50 and select Preview Note the better fit at low angle and also the increased flexibility in the background shape that decreasing the window size has brought about Although you could proceed with either value as both give an excellent fit return to the less structured background by changing the window size back to 100 and click Apply to strip off the background The background subtracted pattern is displayed Examine it closely before proceeding to the next stage 15 4 5 Stage 3 Fitting the Peaks to Determine the Exact Peak Positions Select the first 22 peaks using the method described in Tutorial 1 Here is a guide to the positions 2q of the first 22 peaks 8 7661 17 3011 18 7498 20 7870 21 3166 21 5902 23 6311 24 4517 24 9854 25 4535 27 1252 27 7534 28 1742 29 1876 30 7017 33 5830 33 7804 34 1816 34 7082 34 9715 35 2415 35 4262 Click Next gt e Select Run to run DICVOL or use another indexing program as described in Tutorial 1 15 4 6 Stage 4 Indexing Y our indexing program may reveal a number of possible unit cells The unit cell with the highest figures of merit should be monoclinic with volume 1794 A gt The DICVOL program returns a monoclinic cell with a 24 04678 A b 6 15668 A c 12 42973 A and beta 102 753 Volume 1794 80
229. tal moves N 16000 movestiteration WENN M ML Downhill Uphill Reject 4000 Pause Stop E View bl Edit Solutions 10 8 1 Interpreting c Statistics DASH displays the minimum and average values of the correlated integrated intensities C and the best value of the profile C for the structural model The Pawley fit c can be viewed by selecting Pawley SA from the View menu 124 DASH User Guide The minimum correlated integrated intensities C is the quantity that 1s actually being minimised This is the minimum value obtained so far of the C statistic that measures the fit between the reflection intensities calculated from the structural model and the intensities extracted from the Pawley fit The average C is the average value of the correlated integrated intensity C at the current temperature The profile C for the structural model measures the fit between the powder profile calculated from the best structural model so far and that observed experimentally This C value is on the same scale as the Pawley fit C7 which makes it the most useful statistic for assessing how close the structure solution is to the best fit possible Ifthe profile C for the structural model is well above the c obtained from the Pawley fit the structure is some distance from the true crystal structure Ifthe profile C for the structural model is close to the Pawley c within a factor of 2 5 the structure is pro
230. tations of a Z matrix are handled during simulated annealing It is recommended that the sdi file has been loaded first so that the unit cell parameters are available for visualisation of the centre of rotation and the initial orientation The origin of rotation can be specified in the same manner as in the zmat rix file see Section 9 8 page 98 and can be checked visually by pressing View and switching on the display of the cell axes in your viewer When using Mercury select Show cell axes lower right rather than Packing lower left The rotations of molecules that lie on a rotation axis or in a mirror plane can be restricted to that DASH User Guide 107 rotation axis or to the axis perpendicular to the mirror plane When restricting rotations to a single axis the initial orientation of the molecule with respect to the unit cell needs to be specified This can be done by entering the Euler angles or quaternions Ifthe axis of rotation is specified either as the line through two atoms or as the normal to the plane defined by three atoms i e if the axis of rotation can be specified from the molecule alone it is also possible to choose the initial orientation such that the axis of rotation is aligned with an axis specified in fractional coordinates The initial orientation can be checked by pressing View and switching on the display of the cell axes in your viewer When using Mercury select Show cell axes lower right rather tha
231. ted Select Run gt to run the DICVOL indexing program See the lists of available software for powder indexing at http www ccp14 ac uk solution indexing For other Indexing Programs you can easily get the peak positions out of DASH and into a file by e Selecting Peak Positions from the View menu and then clicking on the word Position at the top of the column containing the peak positions This selects the entire column e Use Ctrl C to copy the entire column to the clipboard Inside an appropriate editor such as Notepad or Wordpad use Ctrl V to paste the column into a file e Save the line positions into a file with the correct format for your favourite autoindexing program Your indexing program should return a monoclinic unit cell of volume 576 S A typical run of DICVOL if the selected peaks were very close to those given in the previous stage DASH User Guide 199 returns a monoclinic cell with a 9 9388 A b 8 49954 A c 7 31875 A b 111 19 V 576 453 A Figures of merit M 24 131 F 24 446 With figures of merit as good as these there is little doubt that the cell has been correctly indexed It is possible to change this cell into one with a conventional setting but for the moment we will proceed with the cell as it is returned by DICVOL 15 1 7 Stage 5 Stop and Think Does the cell make sense There is a very approximate method of estimating molecular volume using 15 A per C N O atom
232. the profile C is still very high then the search is probably trapped in a local minimum You should stop it and start again at a higher starting temperature Note that DASH can spend a long time apparently stuck at one C value but remember that it is continually sampling parameter space so as long as uphill moves are being accepted at a decent rate be patient For very large molecules it may be necessary to leave the program running overnight to achieve solutions 10 8 4 Monitoring the Progress of Structure Solution A graph of Profile c vs Number of Moves is plotted as the simulated annealing runs progress The end point of the simulated annealing run the product of the Pawley C and the multiplier chosen in the Simulated Annealing Protocol window is shown on the graph as a horizontal line The graph can be zoomed in on using the left mouse button and the Home key resets the view to full scale 126 DASH User Guide 54 Run Progress Mei x Profile Chi squared Number of Moves 100000 10 9 Assessing the Solution Important questions to ask are has the data been fitted and subsequently does the structure make sense You therefore need to examine The profile c see Section 10 9 1 page 127 The visual match between calculated and observed profiles see Section 10 9 2 page 128 The crystal packing see Section 10 9 3 page 128 The files saved from multiple simulated annealing runs see Section 10 9 4
233. the Simulated Annealing Protocol window The default values can be used for this example so click Next gt then Solve gt to begin the simulated annealing NB Keen chemists should resist the urge to restrict the torsional rotations pertaining to the two bonds around the carboxyl group 15 2 12 Stage 10 Monitoring Structure Solution Progress The progress of the structure solution can be followed by monitoring the profile C and the difference plot Once a profile c of a roximately 10 12 or less is reached you can be sure that a very good p pp structure has been found as this value is only 3 times the Pawley c value Finalise the solution by selecting the Local minimisation button and accepting the answer DASH User Guide 225 If your final profile C is a bit higher than 10 you are clearly close and perhaps only a single atom at the end of the chain is slightly misplaced Take a close look at the output structure and read the section below 15 2 13 Stage 11 Examining the Output Structure View the structure using the View button in the Simulated Annealing Status window The structure should be chemically reasonable in terms of molecular conformation and intermolecular distances The potential for H bonding is obvious We can examine similar structures in the Cambridge Structural Database and observe that where there are more acceptors O than donors NH firstly the donors must be satisfied and secondly bifurcation of th
234. the structure solution to stick at a very high profile ome around 130 In contrast after constraining the centre of mass of the molecule to lie on the 2 fold axis the profile C falls rapidly to around 20 and local minimisation reduces this still further to around 18 The packing motif is identical to that obtained in a Note that a 2 fold rotation of the molecule about the b axis does not give an exact mapping from one half of the molecule to the other as in a there is no constraint upon the torsion angles to produce this However it is so close to doing so that it is safe to conclude that the molecule crystallises in space group 2 a and that a Rietveld refinement with only half a molecule in the asymmetric unit will be successful B Space Group 2 a You can if you want re fit the diffraction data using the same unit cell and selecting space group 2 a but there is in fact an easier way of running the SA in 2 a As stated previously a and 2 a have the same systematic absences and so Pawley fitting in either space group will give the same result Accordingly we can use the Pawley fit files already created and simply modify the Tutorial 4 sdi file to inform the SA that we now wish to solve in 2 a Copy Tutorial 4 sdito Tutorial 4 half sdi and open the file in a text editor Look for the following line SpaceGroup 52 9 b3I1a1 and change it to SpaceGroup 69 15 b3 I 1 2 a 1 DASH User Guide 249 and then save the file You have
235. ther between 0 and 30 C3 lies below the plane or C3 lies above the plane torsion angle between 0 and 40 In uridine C3 lies above the plane and to start with your molecular model should copy this Later you will run through the simulated annealing process with a molecular model of a different ring conformation If you do not have access to a molecular modelling package a mol2 file created by SPARTAN is included for the tutorial Tutorial 5 mol2 15 5 11 Stage 9 Setting up the Structure Solution Run Continue on from the Pawley fitting stage by selecting Solve gt Click on the ax icon and select Tutorial 5 mol2 the file that you created in Stage 8 a Z matrix file called Tutorial l zmatrix will be generated automatically Read in the Tutorial 5 l zmatrix file Asthere are two molecules in the asymmetric unit read in the Tutorial 5 zmatrix file again At this point DASH will confirm that there are 16 independent parameters These parameters are listed when you click on Next gt There are 3 parameters describing the positional co ordinates 4 of which 3 independent describing the molecular orientation within the unit cell and 2 variable torsion angles for each molecule Click on Next gt leave the Simulated Annealing Protocol window with the default values click Next gt again and then click on Solve gt The structure should solve reasonably quickly DASH User Guide 255 15 5 12 Stage 10 Monitorin
236. tion 8 4 page 75 Reducing the number of background parameters Taking advantage of the automatic background subtraction that DASH offers see Section 2 4 1 page 9 DASH User Guide 91 92 DASH User Guide 9 BUILDING AND CONSTRAINING MOLECULES 9 1 Overview of Building and Constraining Molecules DASH solves structures by taking a model of the molecule or molecules in the asymmetric unit and moving it them around subject to the constraints of space group symmetry until it finds a good match between calculated intensities and those derived from the Pawley fitting If necessary rotatable torsion angles in the molecule s are allowed to vary either through a complete 360 range or through a smaller range defined by the user Ifthe asymmetric unit contains more than one molecule they are moved independently of one another A requirement for solving structures therefore is to input appropriate 3D models of the molecule s Important things to consider are Building molecules in third party programs see Section 9 2 page 93 Converting molecules to Z matrices see Section 9 4 page 95 Reading molecules into DASH and defining the ranges through which bonds can be rotated see Section 9 5 page 96 Treatment of rings see Section 9 6 page 96 Treatment of stereoisomers see Section 9 7 page 97 Molecules on special positions see Section 9 8 page 98 Structures with more than one molecule in th
237. tory data The other values have been left at their default setting and will not affect the DICVOL result Create indexing file Unit cell limits Minimum Maximum 3 y Experimental Details Wavelength A 1 12940 Volume A 0 0 3000 0 Experimental zero point 0 0000 a 0 0 30 0 Use fixed error 0 020 b A 0 0 30 0 c 0 0 30 0 C Use errors from DASH H9 90 0 125 0 Measured density optional 0 0 Molecular weight a m u optional 0 0 r Crystal systems to search Triclinic M Tetragonal Other Settings M Monoclinic IV Hexagonal Minimum figure of merit 5 0000 IV Orthorhombic M Cubic leer 1 0000 Run DICYOL Save DICVOL File Close Alternatively indexing may be performed using the Wizard see Section 2 10 1 page 22 6 3 Running the Indexing Program DASH provides an automated interface to DICVOL91 just click Run DICVOL DASH also provides an interface to DIC VOL04 and later and McMaille The interfaces to these programs can be accessed through the Peak Picking wizard window see Section 2 10 1 page 22 There is no automated interface between DASH and indexing programs other than DICVOL91 DICVOL04 and McMaille i e it is necessary to set up the input files for the programs by hand However this task is facilitated by copying the peaks from the DASH Peak Positions listing into the notepad see Section 6 2 5 page 58 DASH User
238. trix and allows you to change the label element Biso and occupancy of each individual atom Biso s and occupancies can be changed for groups of atoms using the Set button Re order re orders the atoms carbon atoms first followed by the remaining elements in alphabetical order and hydrogen atoms last Re label re labels the atoms as element sequential number e g C7 and Br24 Rotations displays the Edit rotations Z matrix dialogue box see Section 10 3 4 page 107 Save As allows saving of the edited Z matrix with a new name DASH User Guide Save saves the edited Z matrix OK returns you to the DASH Wizard Molecular Z Matrices window keeping all changes If atoms have been deleted DASH will try to assemble a new Z matrix from the remaining atoms Cancel returns you to the DASH Wizard Molecular Z Matrices window discarding all changes 10 3 4 Editing Z Matrix Rotations Edit Rotations 2 Matrix Drigin for rotations Use molecular centre of mass C Use atom number 18 v Restrict rotation around a single axis r Axis direction C Line through atom numbers 1 E and 2 H Fractional co ordinates 0 0000 0 0000 1 0000 Normal to plane defined by atom numbers Bana m Initial orientation Align with axis 0 0000 0 0000 1 0000 Euler angles 0 0000 0 0000 0 0000 Re abel OK Cancel View This window allows full control over the way orien
239. tructures we find that MDB makes the solution process succeed in more runs than without MDB MDB can be enabled by clicking the Set MDB button in the Parameter Bounds wizard window The choice of distributions to use can be controlled by increasing or decreasing the minimum hits the higher the number of hits the more populated a mogul distribution has to be to be used in MDB The default of 10 observations may seem a little low Note however that due to the nature of the algorithm used using distributions with low numbers of observations in fact makes little difference to the solution process as the weight of bias to the maxwellian distribution is in proportion to the number of hits in the distribution A distribution with only 10 observations in will not really change the sampling for a given torsion by a great amount DASH Wizard Parameter Bounds Simulated annealing parameter bounds ind Lower Upper F Modal METE 1000000 A a A ME E A la sse 18000000 reno Mogul distribution bias MDB Min hits 106 SetMDB Y Randomise inital values Set Fragment Restraints Paice DASH also supports reading SA input settings directly from DBF files This in principle could 116 allow the user to set up searches with data distributions from other sources A given torsion angle can be biased by specifying a parameter amp range for the given torsion in the input DBF file in the following form 65 95955 M
240. tveld window by clicking Compare The Mercury display shows that there have been very small shifts in the coordinates use the Zoom in feature The resulting coordinates are not more significant than the previous coordinates saved as the CIF file but they do confirm that the refinement is stable and you are in a local minimum of the Chi sqd surface e Similarly you could refine all the bond lengths and achieve a further small reduction in Chi sqd but this is cannot be interpreted as an improved set of coordinates for this solution There 1s simply not enough data to justify these fine variations from the starting values of bond lengths and bond angles Another way of looking at the calculation is that you could achieve the same low Chi sqd values with a range of slightly different molecular models At present you have no information of the estimated standard deviations of the coordinates Note As an experiment that if you attempt to refine the Global isotropic temperature factor together with a significant number of the torsions angles or distances that the procedure takes a considerable time to converge e g 2 3 minutes showing that the temperature factor is highly correlated with the other parameters e Some insight may be obtained as to how individual parameters affect the calculated Ch sqd by manually setting any parameter value in the menu box and clicking on Calculate This simply calculates Chi sqd at that point e g changing the bon
241. uilding 3D Molecules page 157 DASH User Guide 131 132 DASH User Guide 11 RUNNING DASH IN GRID MODE OR BATCH MODE 11 1 Overview of DASH in Batch GRID Mode Structure solution can now be performed by DASH using distributed processing to speed up the procedure This can be achieved in a number of ways depending on the resources at your disposal whether this consists of a single processor computer a multi core machine or an entire network of computers The use of distributed computing can be particularly helpful when individual SA runs are long due to a complex problem This section covers the following Setting up the input files see Section 11 2 page 133 Using DASH in batch mode see Section 11 3 page 134 Using DASH in GRID mode see Section 11 4 page 135 e Post processing of the results see Section 11 5 page 135 11 2 Setting up Input Files During the process of setting up a series of SA structure solution runs there is the option of creating batch files see Section 10 6 page 119 clicking on the Create Batch File button will access the Generating GRID batch files dialogue box This section of the wizard will allow you to create the input files necessary to run DASH in a distributed fashion The first step 1s to choose the total number of SA runs that are required these runs are then split into packages with a user defined number of runs in each If for example the user chooses 500 SA runs split into package
242. up termed the central group has a set of pre processed 182 DASH User Guide scattergrams of interacting groups in the CSD taking account of symmetry to produce an overall picture These scattergrams can be easily inspected using the Rasmol visualiser provided An IsoStar example is shown here of a central charged amine group NH3 approached by a chloride ion CT In the IsoStar contour view option the scatterplot has been contoured to show the preferred positions of the chloride at about 3 0 A from the nitrogen 14 7 Appendix G Z matrix format Example molecule Z 4 methoxybenzaldoxime CSD reference code AANHOX There are two variable torsion angles about bonds C2 O16 and C1 C11 DASH User Guide 183 Pa er H20 DASH User Guide 184 EXAMPLE MOL2 file PC Spartan Pro File Created by lt TRIPOS gt MOLECULE C motherwell samoxime mo2 20 20 SMALL NO_CHARGES lt TRIPOS gt ATOM 1 Ci 2 c2 3 c3 4 C4 5 c5 6 c6 q 7 8 H8 9 H9 10 H10 11 C11 12 H12 13 N13 14 014 15 H15 16 O16 17 C17 DASH User Guide 293217313 008979730 488999937 080645376 223538726 344323476 737253557 252034022 504578299 508767609 389641286 290524363 166972637 081028705 599746303 183225243 050187143 Export 250035865 027063995 978777859 364432686 250142376 088558606 865934089 327749313 121804863 061069866 420855758 18080
243. urns you to the DASH Wizard Parameter Bounds window see Section 10 3 6 page 109 Simplex Optimisation of the Best Solution This Local minimisation button pauses the run and takes the parameter values for the best DASH User Guide solution to date as a starting point for as Simplex minimisation see Appendix H References page 189 A pop up window appears giving the improved value of the C for the integrated intensities which can be compared with the minimum c in the Simulated Annealing Status window You can then continue from this improved position by clicking Yes or ignore this by clicking No Since the DASH implementation of simulated annealing varies one parameter at a time in the random path this local minimisation point can have a dramatic effect in speeding up the final stage of the process of finding the lowest c point However it will have no useful effect until the search has reached a point reasonably near to the global minimum Therefore it is generally used once a good fit to the data has been achieved in order to quickly take the structure to the best minimum in the vicinity of the current structure Viewing the 3D Structure of the Best Solution As the simulated annealing run proceeds DASH keeps a record of the best solution found to date The View button opens up the default 3D Visualiser immediately for the current version of this best solution The CCDC visualiser program Mercury is supplied with DA
244. ut as they overlap a little it is better to fit them together as a doublet 500 450 400 350 300 250 200 Observed profile 150 100 50 12 26 12 28 12 40 12 42 12 44 12 456 12 46 12 50 2 52 12 54 12 56 12 56 2 theta Note that these two peaks contribute two entries in the list of peak positions select Peak Positions from the View menu yet only a single entry in the lists of peak shape parameters select Peak Widths from the View menu as both peaks have been fitted with the same values for sigma and gamma Moving further up again there is a peak that has contributions from two Bragg reflections i e there are two tick marks close together above the peak but there are no clues as to their exact relative positions Peaks such as this are best avoided because each time a peak is fitted DASH attempts to refine the input unit cell the one you obtained by indexing and entered at the start of the Pawley fitting process In this situation the peak positions are not well defined and there is a risk that the cell could be refined away from the correct values Thus avoid DASH User Guide 81 82 15 12 15 14 15 16 15 18 15 20 15 22 15 24 15 26 15 26 15 20 2 theta Next we find a moderately strong reflection which is sufficiently isolated to allow fitting even with a narrow selection range The very weak peak on the left is not strong enough to interfere Observed profile 15 42 15 44 15 46 15 46 15 50 15 52
245. ves per run 3 000 000 and c multiplier 3 0 you will get probably about 2 or 3 correct solutions out of 5 A typical set of runs gave c 329 200 76 199 74 The low values 74 and 76 are very satisfactory solutions with variable torsion angle C3 N2 C1 N11 values around 6 0 which is the cis conformation DASH User Guide The Z matrix format is described in Appendix F of the DASH User Guide 15 3 15 Stage 13 Effect of Molecular Models on Simulated Annealing Another interesting experiment is to see how much the fine detail of the model building affects the chance of solution with DASH Experiments were carried out with three models the files are provided with this Tutorial as Tutorial_3 ModelA zmatrix Tutorial_3 ModelB zmatrix Tutorial_3 ModelC zmatrix Model A was prepared using the ISIS Draw sketcher and WebLabViewer with no energy minimisation exported as a mol file Model B was prepared using Spartan to sketch and then do a simple energy minimisation exported as amol2 file e Model C was the CIMETDOS structure taken from the CSD as a mol2 file H atom positions were recalculated at ideal geometry using Rpluto Each model was used for a set of 30 SA runs with Max number of moves run 3 000 000 and Profile chi sqd multiplier 3 0 The Pawley fit C was 22 06 The solutions had profile C as follows A 18x 149 11 x 282 1 x 443 B 19x 103 11 x 241 C 20 x 83 10 x 268 The solutions marked are corre
246. view of Pawley Fitting The aim of Pawley fitting in DASH is to fit the observed powder profile in the absence of a structural model using a a polynomial representing the background b a set of parameters describing peak shape c zero point and cell dimension parameters and d estimates of the individual reflection intensities The overall fit between the resulting calculated profile and the observed profile is displayed graphically and expressed by a number of goodness of fit statistics including C7 Provided the fit is good enough the refined reflection intensities can then be used for structure solution The final Pawley fit to the data represents the best fit to the data that you can obtain As such it serves as a reference value to aim for during the structure solution process The final Pawley fit chi squared can be viewed throughout the rest of the structure solution process by selecting Pawley SA from the View menu see Section 2 6 5 page 16 This section covers how to perform Pawley fitting of your data including An overview of the usual sequence of steps see Section 8 2 page 69 Truncating the profile 1 e identifying the 2q value beyond which there is little or no useful Bragg intensity see Section 8 4 page 75 Selecting and fitting peaks so as to obtain good estimates of peak shape and cell parameters prior to performing the initial Pawley fit see Section 8 5 page 79 Performing an initial Pawley
247. which one of the space groups has two tick marks and the other has only one If the peak underneath is unusually broad this indicates that the former space group is slightly more likely Inevitably there will be many cases where the space group cannot be determined unambiguously In this situation there is little choice other than to try each possibility in turn starting with the space group that has the highest statistical probability of occurrence see D 1 Space Groups Listed by Frequency of Occurrence page 159 In extreme cases it may be necessary to attempt Pawley fitting and even structure solution in all possible space groups Appendix D Frequency of Occurrence of Space Groups see page 159 lists space groups in decreasing order of their frequency of occurrence in the Cambridge Structural Database A separate listing is given for chiral space groups if you know that your structure is enantiomerically pure see D 2 Chiral Sohnke Space Groups Listed by Frequency of Occurrence page 161 Of course there are space groups that have identical systematic absences In such cases the powder diffraction data alone are insufficient to determine the true space group In principle the distribution of structure factors can distinguish between centrosymmetric and non centrosymmetric space groups but in practice powder diffraction data are rarely of sufficient quality to permit this distinction DASH User Guide 8 PAWLEY FITTING 8 1 Over
248. y you should keep the cell dimensions and peak shape parameters fixed in this initial refinement Allowing them to vary is likely to destabilise the refinement The following subsections cover Background fitting see Section 8 6 1 page 83 Reflection intensity fitting see Section 8 6 2 page 85 Background Fitting of Raw Data in the Pawley Refinement Note that in this example we have assumed that the background has not been fitted by the Monte Carlo background subtraction routine This is by way of illustrating use of the Pawley refinement for a raw data set Background intensity is primarily due to amorphous content in the sample and scattering from experimental components such as a glass capillary or cryostat chamber The background is fitted to a polynomial which by default has 10 terms It is undesirable to use more background terms than necessary to describe the data since high order polynomials can begin modelling genuine peak intensity This leads to high correlations between the background and peak intensities especially at high angles A polynomial with as few as 5 terms might be enough for a flat or gently curving background at DASH User Guide 83 84 the other extreme you should never have to use more than about 15 Normally the simplest policy is to try the default of 10 and accept it if the fit looks satisfactory The following example profile has a very non uniform background In this case a tota
249. y invoke this search if the current profile C is within a factor of 5 6 times the value of the Pawley c and DASH User Guide 125 you want to accelerate the final stages of the search If the simplex search brings the intensity c down significantly NB the simplex warning box currently reports the Intensity C not the profile C then the structure will have been pulled in very close to the final answer so you can accept the results of the simplex and stop the annealing If not just hit No and allow the annealing to continue from the position 1t occupied prior to the simplex DASH can automatically test for early termination Early termination testing tries to speed up searching by attempting speculative local minimisation of DASH runs when a given run s profile c gets to within a threshold of the fitted pawley C The user specifies an early termination criterion in the simulated annealing If the SA gets within twice of this threshold then new good solutions are minimised if the minimised structure has a profile C less than the specified termination criterion the solution is accepted and the SA run is terminated Ifthe c is a large multiple of the Pawley C say a factor of 10 or higher and a reasonable proportion say 1096 of uphill moves are still being accepted then the annealing has not converged and it should therefore be left running Ifthe number of rejected uphill moves is about 50 of the total moves being made and
250. y solution number Save solutions Original atom labels By element Load solutions Save Resume S Delete last run zi Select solutions 1 through se Invert Selection Show overlay In order to do a Rietveld refinement for a crystal structure that is not a simulated annealing structure from DASH choose Rietveld refinement in the main Wizard window The following window will appear 138 DASH User Guide DASH Wizard Rietveld Refinement let ES SDI file C Program Files CCDC DASH 3 1 Example Example sdi Open Browse Crystal structure C Program Files CCDC DASH 3 1 Example Example mol2 Open i Rigid body Rietveld refinement C Rietveld refinement with GSAS Pietveld refinement with TOPAS C Rietveld refinement with RIETAN Hint Options for external programs only enabled for those given in Configuration dialogue Back Next Close Start SA It is also possible at this point to start an SA structure solution run using the given crystal structure coordinates without randomisation of initial coordinates by clicking on the Start SA button Note that there can be ambiguities with respect to unit cell settings and space group settings DASH only knows one setting for P2 2 2 and loading a crystal structure file with a different space group setting will produce erroneous results 12 2 Rigid Body Refinement 12 2 1 Rigid Body Refinement Dialogue
251. y the indexing program will reveal that many of them are slight monoclinic distortions of the above unit cell with almost identical volumes and lattice parameters and beta 90 Other suggestions generally have much lower figures of merit and can be ruled out immediately Considering that the orthorhombic unit cell has the best figures of merit and that it is usually best to try the simplest option first we will proceed to the next stage assuming an orthorhombic unit cell with the lattice parameters given above 15 2 7 Stage 5 Stop and Think Does the cell make sense In this case we estimate the molecular volume to be 330 A from the formula CjgH 3N gt 03SCI and approximate volumes C N O 15 A gt S CI 2 25 A and H 5 A in the molecule Therefore given the unit cell volume of 1266 A we know from this very rough approximation that the cell is most likely to accommodate 4 molecules At this point your knowledge of space group frequencies should suggest that P2 2 2 is a strong possibility A list of space groups and their frequencies is given in Appendix D of the DASH User Guide 15 2 8 Stage 6 Checking the Cell and Determining the Space Group The space group P222 will automatically have been selected The presence of some excess tick marks indicates probable systematic absences this means that a space group of higher symmetry might be more appropriate Scroll through some of the possible space groups You will see that som
252. yse Solutions window is not recoverable 15 1 18 References DICVOL Program D Louer amp M Louer 1972 J Appl Crystallogr 5 271 275 A Boultif amp D Louer 1991 J Appl Crystallogr 24 987 993 Extinction Symbol Program Markvardsen A J David W I F Johnson J C Shankland K 2001 Acta Cryst AS7 47 54 Model Builder WebLabViewerLite Version 3 20 12 8 98 Copyright 1998 Molecular Simulations Inc Single crystal structure CSD Refcode HCSBTZ L Dupont amp O Dideberg 1972 Acta Crystallogr B28 2340 2347 15 2 Tutorial 2 Solving a Structure from a Low Resolution Data Set 15 2 1 Introduction The aim of this tutorial is to guide you through the structure solution of chlorpropamide and it assumes you have completed Tutorial 1 In this Tutorial you will learn how to Handle structures that are more flexible than hydrochlorothiazide Solve a structure from a low resolution data set See one of the potential pitfalls of global optimisation 1 e local minima O 0 cl 8 NH NH CH Et O 222 DASH User Guide 15 2 2 Data The data set Tutorial_2 xye is a synchrotron X ray diffraction data set collected on BM16 at the European Synchrotron Radiation Facility The incident wavelength was 0 800077 15 2 3 Stage 1 Reading the data Open DASH and select the directory where the data resides Select View data determine peak positions and click Next gt Select the file Tuto
253. ystem Monoclinic b axis Fill in details of the unit cell parameters and space group see Section 2 6 3 page 14 DASH User Guide 29 The unit cell parameters can also be read in at this point from a crystal structure file by clicking on the Browse button Click Next gt DASH Wizard Pawley Refinement Step 1 Peak Picking The next step is Pawlep Refinement It is recommended that you clear the peak fit ranges selected for indexing by pressing the Clear Peaks button Clear Peaks After clearing the old peak fit ranges select ca 8 peaks spanning the pattern starting at low 2 theta Peak shape parameters can be viewed selecting View Peak Widths from the menu When vou are happy with the peaks you have selected press Nest gt to run the Pawley refinement lt Back Next gt Close Proceed with peak selection for indexing as described in Section 6 2 page 55 Click Next gt Pawley refinement is the next step see Section 8 page 69 followed by structure solution see Section 10 page 101 30 DASH User Guide 3 DATA COLLECTION AND DATA TREATMENT 3 1 3 1 1 Hints for Collecting Data Synchrotron versus Laboratory Data DASH is capable of solving structures from both synchrotron and laboratory X ray data Synchrotron X ray powder diffraction stations offer better instrumental resolution and positional accuracy coupled with a vastly superior incident flux These

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