Home

MolWorks2.0 user`s manual

1. ccccsseeesseeenseeeteseeseseeeeseeesaeeetaneetegeeesaeesnaess 34 Hl Magniication ANG Reducida 34 I6 ADoOUE dedithag males a ceo in E oce aient eu Ee Oc M ica o dpa deci And 34 ka M aX AR e un ua UT T TL 34 HR MOVE ACON S ERR TET 34 1 MOVNO EC Lg e Roc ET a T 34 2 Movirig the selected ato sats sits cas cbe cea do 34 BUIN eh get e C mU curas 35 ELF SUDDOFECC MIG HOP Mal sis E TET 36 MPU ag o mee eee KS 36 Iie EXON AAA O O 36 R e 36 IG Properties gg ON EE 36 Groups TOF estimation hrs ege IECH 36 MPSS AA 36 Ve ORDA CIR qc A 36 o CUE ae 37 Mi A 37 1 About MolWorks MolWorks is a software tool for computer aided molecular design e Multi platform support MolWorks can be run on any platform running a Java VM Virtual machine such as Windows and Linux Redhat About modeling MolWorks can build molecules by drawing them within the Builder Panel MolWorks can handle 3D molecules You can clean up molecules by using a simple minimization algorithm You can easily change atom type and bond order for molecule You can select Wire Ball amp Stick style You can handle many molecules by using tab panels Reading molecule files and output files of computational chemistry programs and saved molecule files MolWorks can read molecule files XY Z Format File xyz amp Protein Data Bank File pdb in Version 2 0 and display molecules within the Builder Pane
2. Beveridge D L Approximate Molecular Orbital Theory McGraw Hill New York 1970 O Gaussian http www gaussian com e GAMESS http www msg ameslab gov GAM E SS GAM E SS html e MOPAC 1 Dewar MJ S Thiel W Am Chem Soc 1977 99 4899 3907 2 Dewar M J S Zoebisch E G Healy E F Stewart J P Am Chem Soc 1985 107 3902 3 Dewar M J S Stroch DM Am Chem Soc 1985 107 3898 4 Stewart J JJ P Comput Chem 1989 10 209 221 e Q Chem http www q chem com eJ oback J oback K G S M thesis in chemical engineering Massachusetts Institute of Technology Cambridge Massachusetts 1984 Please send the bug reports to following e mail address mol works abestsystems co p 37
3. ogc 12 ikera kr Dare fam coord Ti 1 b 8 In the case of reading MOPAC output file benz out Fu Hanne Hed Let apta Pbi bagel vm pire rir Lane 17 tions kr bard uam coord 13 Kran 1 b 9 In the case of reading Q Chem input file water in Lane 3 gt lor vore Aion count 1 1 b 10 In the case of reading Q Chem output file water ref Laarked 1 sra kx voter Nesen 1 b 11 The orbital energy level The orbital energy level is displayed when the output files are read and the e button in the Information Window is pressed 1 b 12 Frequency The spectrum of IR is displayed if the result of vibrational analysis is included in the output files and the mm button in the Information Window is pressed Date REA ada c D wm iv 1 c Rename Rename the selected Builder Panel Example Change the name Molecule 1 to Water Procedure 2 Change the name Molecule 1 to Water in the Rename M olecule display After clicking __ this panel is renamed Tace MEA 10 1 d Close Close the selected Builder Panel Example Close the Water Builder Panel Procedure 1 Select Close Water from the Edit menu in the Builder Panel Cep Procedure 2 Close Molecule dialog will be appeared for closing this file fier ie Boe aia Y pars Se cle cir 1 e Save As Save the molecular structure displaying in the Builder Panel Example S
4. data on right other basis set written in the text field is adopted 4 Polarization Diffuse Select the type of polarization and or diffuse function Not used Not including both polarization and diffuse 1 4t and and and 22 5 Geometry Specify the geometry type Cartesian Set up the selected molecular geometry using the XY Z format automatically Modify Geometry Frame is displayed If Save button is pushed after changing structure data within the Geometry F rame the changed structure save to the file 6 Charge Set the net charge of molecule 7 Spin Set the spin multiplicity of molecule 8 uhditscmal Keyword Display the Additional Keyword Frame Input keywords and push the Save button when you want to add other optional keywords Gaussian Make input data for Gaussian The function to convert input data Input Data Convert section and to submit a Gaussian job Run Gaussian J ob section can be used Damd Bios ric Hee 1 Pepe Leet tamm Calc Dyna Dag Cod immi mp Hamid 590 ial Da Core bg HM a ud Ct 1 Output L evel Control the volume of output file z normal terse detail 2 Calc Type Select the calculation type Single Point Optimiz F req Optimize F red Using data on right other calculation type written in thetext field is adopted 3 Calc L evel Select the calculation level RHF Restricted Hartree F ock UHF Unrestricted Hartree F ock ROHF Rest
5. el MR EE 22 PAROLE M a EE 22 PPP A 22 4 e E leegen H E e 22 COME NT LT I NU PE 23 OSC INGE OS MEET 23 ISP sarc rmm 23 SU a 23 NECI IIa TO T S t mak ais Gas eet sae 23 bro ges 23 2 Calc Dados 23 Re re 7 aa 23 4 BaSIS EE 24 5 e al Zac Oly DIMUS METTI TTL 24 s EGe pcd M mr P 24 IENIGE m 24 a N 24 TO Input Data Conversion siria 24 DD nun AUSSI I OO E 24 DT SP So M 24 DEAC WO E 24 2 ODUMI ZEC YC 25 3 ODIUImize Predio 25 Ey ANC Y MDC 25 SREL e ue E 25 D BOSIS EE 25 H POZA RTT E 25 SIAB aiT c CT 25 ST Un EE 25 A e e AREE E E EE E 25 iMDre 25 AR e m P EF 25 IONS LO 25 RAS Zi o D 25 TECATE E OG MENT ERE eii 26 xs 26 CCo de 26 a Cale VEER 26 OFS CONN W mm O nn O OE To A 27 OD VY OF DU ege e e ss 27 EAR elei redo p MONTRER UU
6. pushed after changing structure data within Geometry F rame the changed structure save to the file 6 Basis Set Select the basis set STO 3G 3 21G 4 31G 6 31G 6 311G Using data on right other basis set written in the text field is adopted 7 Polarization Select the type of polarization function not used p for H He dO f for Li CI pd dl p d f 8 Diffuse Select the type of diffuse function not used s for hydrogen s p for heavy atoms s p for all atoms 9 TimeLimit Set the maximum time of calculation minute 10 Memory Set the maximum memory used for calculation 11 Charge Set the net charge of molecule 12 Spin Set the spin multiplicity of molecule 13 Ate Keyword Display the Additional Keyword Frame Input keywords and dick the Save button if you want to add other optional keywords MOPAC Make input data for MOPAC6 and MOPAC7 25 WE p RR PU hps nr n dint rt fie mess seg Oe INT F D gm Nm fa e Dag E 5 pm egest F FA 87M iia Fay O 1 Calc Method PM3 AM1 MNDO MINDO 3 2 Calc Type Optimizd Frequencied Thermo Dat Keyword other calculation type written in the text field in the Calc Type Parameters is adopted 3 Geometry Specify the geometry type XY Z auto Set up the selected molecular geometry using the XY Z format automatically Modify Geometry Frame is displayed If Save button is pushed after changing structure data within the Geometry F rame the changed
7. sal ion E op Ligai Papas E AR 18104 Lri iml Solo oe El 114 0 Xu Ds ipa Frets bar a gp ERIT L sizie fei bod ge Ode rae cele 7 fee ILe Esrlar Melbod omega 8 II Crilical Bols lcr gt 155 3 fic EAR Pra datado lFurametar Acern rir Factor Deri be Eri imei Le Lal SX Igi cad gt Q0 REEIS Fried sic Beth zeen 2 B Pree Ter Bele le bs Gel leh im dg ced d ns Gd Lee fesier Method come T A ug 2 Fade ege Prepara DFE Laa DE p Ar LISAT Feira mb ud Hal of parigi Lan al ER Calima s AOT e Hei Gerectte Extimallos fat 288 Looideibhl 7 17 285507 Per Res Melboo Carril pret S i Eke Ererqy Eral mal Te N AS AAA o Lal Ud f Ha al Farma iva Eolo ll Lire Pel re Getto Meet of Yeeorerahion al BP olmo ld SERA bi Vier Crest delete Lal FD Gee al Las Cy ern ai Lead 141 2821 Da Did Dieser Par ea ii L i E a be al Sita Er let ie 58 7 AVE d Weil Perth Far ein idee 4 HERHIE TI LN Volume Fei ies ica 711 2 35 2 20004 Eto Seen EET was Ha Lei A joel Bee L L 32 4 Graph Select the property for plotting the graph Only the vapor pressure is supported in version 2 0 4 a Show Display the graph of selected properties vs temperature AE 7 fe Pree eee ahr g AA a a INNER ATC Il PVT Draw the PVT Pressure Volume Temperature graph m m c eg Calculate 1 First Molecule Specify the first molecule and conditio
8. shell the setup is available whenever the shell is started This can be used when executing M olWorks from a command line If the above mentioned procedures are described to login file C shell or bash profile file BA shell the setup is available whenever a user logs in This can be used when executing MolWorks by the double click of a mouse 3 b Windows Before starting the MolWorks it is necessary to add the directory where the Gaussian is installed ex C G98W to an environment variable PATH 28 10 CNDO 2 Window Execute the CN DO 2 calculation M axi mum of atoms 100 M axi mum of orbitals 300 77 cuna at BI uen Minder nde lla A rot eee ET ee ee Input Parameters 1 SCF convergency This parameter decides the precision of SCF calculation thresh hold of the difference of molecular orbital energies Default value is set to 0 000001 2 Max Cycles This parameter decides the maximum number of iteration of SCF calculation Default value is set to 100 3 Charge Set the net charge of molecule 4 Spin Set the spin multiplicity of molecule only the singlet state is supported in version 2 0 Results 1 Number of Cycle Display the actual iteration number of SCF calculation 2 Energy Difference a u Display the maximum value of the difference of molecular total energies in the iteration 3 Energy a u Display the total energy of the molecule IT Dipole Results 1 Dipole debye Display
9. structure save to the file 4 Calc Type Parameters 4 a Optimize Algorithm Select the algorithm for geometry optimization This button becomes active only in the case that Optimize is selected in Calc Type EF Eigenvector Following BFGS 4 b Thermo Data aiii Bi ed meen ete Oe OT F lupa amd Iren T Dag E ra mj F FA RH acd ue Fry es a de 4 b 1 Initial Temp Specify the initial temperature This field becomes active only in the case that Thermo Data Is selected in Calc Type 26 4 b 2 Final Temp Specify the final temperature This field becomes active only in the case that Thermo Data is selected in Calc Type 4 b 3 Step Number Specify the step size of temperature This field becomes active only in the case that Thermo Data is selected in Calc Type 4 b 4 Symmetric Number Specify the symmetric number of geometry This field becomes active only in the case that Thermo Data is selected in Calc Type Point group Syrrrretric pole aa Synmetric its dcin Symmetric EY nio Marte ihe ee r eea 6 1 1 C2 Cx Cn 2 D3 D3 Dn 6 Dh RESCH BT Ca Ca Cn 4 De Deg Don 12 On 24 Ce Ca Cn 6 S 3 4 c Interatomic Distance Check Write the keyword GEO OK ON or not OFF GEO OK override the job termination which is due to that two atoms are within 0 8 A of each other 4 d Orbital output Specify which the enable or disable to display the information of molecular orbita
10. the absolute value of dipole moment 2 X debye Y debye Z debye Display the component of dipole moment along X Y and Z direction IV Ces Execute the CNDO 2 calculation V M s Display the MO Control Window and the shape of highest occupied molecular orbital HOM O in the Builder Panel This button becomes active only in the case that the CNDO 2 calculation 29 is converged VI mee Calculate and display the absolute value of dipole moment and its component along X Y and Z axes This button becomes active only in the case that the CNDO 2 calculation is converged 11 Display MO Window Control the displaying mol ecular orbital resulted by CNDO 2 calculation Camrrnit Pla n Enero Leseel dai 0 01 Energy Level pev 11127 Change Eras Current Energy Level Display the energy of selected orbital indicated by red arrow I1 Change Level Up or down the level of molecular orbital displayed within the Builder Panel Ill S Scale Multiply or reduce of S orbital component of molecular orbital displayed within the Builder Panel IV P Scale Multiply or reduce of P orbital component of molecular orbital displayed within the Builder Panel V Show MO Set the molecular orbital displayed within the Builder Panel to HOMO or LUMO Example The LUMO of ethylene 30 1 Highest Occupied Molecular Orbital 2 Lowest Unoccupied Molecular Orbital VI MOLevel All of the molecular orbitals are displa
11. A 27 2 0 9 aac le E 28 HO CNDOJ 2 WIM COW ERA ERAN 29 Ke JEE EE 29 RECH OOV TOT T m 29 EA IA ee vag 29 J I ll Tc M 29 DS as 29 a Ei RE O O O 29 LV NISL E oT TEILEN 29 2 E r oy Difference ta ais doo 29 ER at do eet D EMT o O o e 29 IB Rit e Ke EI ara 29 DE DONG YC m 29 2 A depyel Y ACD VE Z QeDVE cesinsrosk xabenzant vn ad EIRENE AEE AEO D ed DN e 29 FA E 29 V WEE 29 UM P M H PM 30 BABERE EORUM o 30 I Current Energy Leva E 30 A A T UR 30 IM ct 30 buco 30 Pe RE E o 30 A ae 31 RAR Gg leg Hate ee WIA le EE 32 l PULE e e RE 32 Be zeit NET UR TET Oe ITUR 32 2 Palat Tieber s iesu c sene ut RE ey ME MM E II re RU M E DID IE D DE ME 32 AAA A A A 32 DON ae 33 UERN NUDO UN A CP MEE 33 UB ecu IMO CCUG TTE CETTE E T SEEMS 33 2 S96 cond Medill mI IT I TET 33 ca SN FBgANSZ S4 LLL UU 33 13 IFuncilonal GROUPS WINdOW rr 34 LA Messages VV ele TEE 34 ESIR OWN OUSE TOU SO rediere minus a amc A EE eae 34 Ms E ER 34 Il Rotation Z axis perpendicular tO tHE window
12. MolWorks Version 2 0 Manual Wel come to M ol Works Releasing Version 2 0 on September 29 2003 MolWorks is developed by Best Systems Inc Best Systems Inc and MolWorks are trademarks of Best Systems nc All Rights Reserved Best Systems Inc HM VP SOUT MONOS EE 1 2 System Regui nn E 1 Rl nts s TO Seo gl U e M teclas dto 2 AT IDISDlay Se EET TTC tU EO 3 Puis me eee 4 oA US asec e E A o O OE E oA 4 ZIN AN iia 12 SIMON ota 12 AI PrOD SS naaa a a 12 SI lee ce aa UIT 12 A ia 13 We Maln Kl leen sit A cia 14 IN Status Dai AA A o den centu ences ii 14 SI MOCC WIA GC OW RE 14 PEOPLE UU LET 15 LE up eec E 15 SS o a a 16 Eo ne Mm Ku A 17 Re RENTE ER N NEE ES IE E ASEE ORC T PERTH 18 5 SION C PM 18 Li TROON Ecl A A e oro a ESE 19 GIP we eleng Tope ite Te eme 19 Ed Eilegoiiizebcrsndiae WV COW c e TUM 20 Selecting the Q Chero e Dn H ss iios doy ie iS ed a Pu events Kv FE pM FE ea CE eU CL ORE VER Y rU RSEN CEU a YR 20 ao WEE 20 I Selecting the Gaussian button NENNEN 20 hg BE 20 Hi Serectina the GAMIESS e ia Osiris 21 ng PECES O 21 LV Selecting the MOPAC DUEEOD is ie iia 21 h 0 SE 21 V Q Chem Gaussian GAMESS MOPAC NNN 21 Sl iO WINOON AERE 22 Beie EE EE 22 NG
13. anamy 2 2257 i ca na em sm tuf oa Th ma oe sa mn e jur 19 7 Simplified Setting Window TheSimplified Setting Window is the basic window to createthe input files for Q Chem Gaussian GAMESS and MOPAC When you want to set any parameters please dick Amemcen Then the MO Window will be displayed Selecting the Q Chem button Coren Shbeerzdr Moleculn 1 Save the Q Chem input file for geometry optimization by RHF STO 3G Example H20 comment H 20 end rem J OBTYPE SP EXCHANGE HF BASIS STO 3G end molecule 01 O 4 4300385 1 6507636 0 6619955 H 3 4728384 1 6507636 0 6619955 H 4 669702 1 6507636 1 5887065 end Selecting the Gaussian button Chem Gaussian GAMESS Hier d ER Save the Gaussian input file for geometry optimization by RHF STO 3G Example H20 P RHF STO 3G OPT Comment line H20 01 O 0 0 0 0 OO H 0 96 0 0 0 0 H 0 282 0 918 0 0 20 IT Selecting the GAMESS button Coren rg jr Molncaie 1 OC bom Gmussiae GAMES MODAL 1 Sage Input Fite Savethe GAMESS input file for geometry optimization by RHF STO 3G Example H20 CONTRL SCFTYP RHF RUNTYP OPTIMIZE COORD CART ICHARG 0 MULT 1 END BASIS GBASIS STO NGAUSS 3 END GUESS GUESS HUCKEL END DATA Comment line H20 Cn1 O 8 00 0 0 OO H 1 096 0 0 0 0 H 1 0282 0 918 0 0 END IV Selecting the MOPAC button 7 Simplified Sorting P Carpe Vinierir Motecu
14. ave the geometry of acetaldehyde as test xyz file Procedure 1 Select SaveAs from Edit menu in the Builder Panel Omen tinea tegt ncn stelle Eni Procedure 2 The browser for Save file will be appeared After changing the file name acetaldehyde xyz to test xyz press a nn Cl pts a aa ee I7 cartabrpdrate ac EC i Wi E C rop DT P 1 end KC pa pide_d mm paphia i 17 caer IN acta dated 387 he ENE L File mame desde Sne mon vi rom NY Formal Files Can Cen Procedure 3 If the same file name already exists there following message dialog will 11 be displayed wy Save Fila As 1 f Exit Display the Exit dialog 2 a Molecule Display the Molecule Window When the Molecule Window is already displayed it comes to the front of the display 2 b Periodic Table Display the Periodic Table Window When the Periodic Table Window is already displayed it comes to the front of the display 2 c Messages Display the Messages Window When the Messages Window is already displayed it comes to the front of the display 3 MO 3 a Interface Display the Simplified Setting Window for creating input files for Q Chem Gaussian GAMESS and MOPAC 3 b Calc Display the CNDO 2 Window for CNDO 2 calculation 4 Properties Estimation 4 a Estimation Display the Estimation Window 5 Window Molecula Periodic Tae K Already existed Esta
15. el e g Atom count 8 Modeis displayed here Draw or Select 5 Molecule Window TheMolecule Window consists of the M enu Bar Tool Bar and Builder Panel n the Builder Panel you can operate several molecules using tab panels In the bottom of the window the methods to Builder Panel Mesue t Amae ers drag Magi sh gb an plena ditate legt an 14 Menu Bar 1 Edit Clean 1 a Undo Undo the previous editings 1 b Redo Redo the editings 1 c Cut Cut the selected atom s 1 d Copy Not supported in Version 2 0 1 e Paste Not supported in Version 2 0 1 f Delete Delete the selected atom s 1 g Select Ali Men Box Element Type Boma 1 g 1 All All atoms in the selected Builder Panel will be selected 1 g 2 Atom The dicked atom s will be selected unselected 1 g 3 Box The white line box will be shown from the clicked point All atom s in the white line box will be selected unselected 1 g 4 Element Type All atom s being a same element type with the clicked atom will be selected unselected 1 g 5 Bond The clicked bond s will be selected unselected 15 1 h Atom Type Choose the element type for drawing Hydrogen Carbon Nitrogen Oxygen Fluorine Sulfur Chlorine Bromine lodine 1 i UnSelect When the selected atom s and or bond s are existed this command becomes active When you choose this all selected atom s and or bond s will be uns
16. elected LI Draw Set the draw mode 1 k Add Hydrogens Adding the hydrogen atoms automatically considering the bond orders distances angles and dihedral angles 1 1 Clean Execute a simple geometry optimization If the energy is under 0 5 a u or the number of calculation cycles achieve 300 calculation is finished If you open the new Builder Panel or select other Builder Panel during the calculation optimization is stopped 2 Measure Distance Ctrl D Angle Ctrl A Dihedral Ctrl H 2 a Distance Measure the distance between two selected atoms and display the value in the Status Bar Q Example Measurement of the C O distance in acetaldehyde Procedure 1 Select Distance from the Measure menu Then the following message appears in the Status Bar jeleci z atoms from fie Molecule window Procedure 2 Select two atoms in the Builder Panel The distance is displayed in the Status Bar Distance OU3I C 1 2 1 2751003568324301 A 16 2 b Angle Measure the angle between three selected atoms and display the value in the Status Bar Q Example Measurement of the O C C angle in acetaldehyde Procedure 1 Select Angle from the Measure menu Then the following message appears in the Status Bar Selec 3 atoms from the Molecule verdor Procedure 2 Select three atoms in the Builder Panel The angle is displayed in the Status Bar nngle 3 010221 20 001811 30753317 2 c D
17. files are read the molecular structure with the results of calculation are displayed Lowk ine samples sl ju ft SE ES carbormdrata w Love A rni Lig ganii AB Faes Ci pecido d iE Formal Files dzee Cipsi Protein Data Bank File ad CO zcgwert oC been kung Eee pn bk Py iscetalterr uu Ehem Dm File nut Aog ie gt Gaussian input Hie com pk TT Fihi name Gaussian Output Ale cut ka Open Files uf pi WY Ponmat Files oa Am ed 1 b 3 In the case of reading Gaussian input file h20 com Motorka Laarked 3 gem kr hic Bim teun J 1 b 4 In the case of reading Gaussian output file h20 log Fe hio Morh Pis Men HO ppi nene furis Ed Mazout Bos Late epis Ae eee E bg Lasel 3 ars Er hib Bkm Cu I Kecka 1 b 5 In the case of reading GAMESS input file h20 inp c0 T a es MO eee eee Heli Frit imus Dos Label pias AS ee Chur mjaf idh F Set NIT EIL EJ DR RH pan trum J Dna 1 b 6 In the case of reading GAMESS output file E Mo Wor ks ARA Dis Ven BH Prapertion Weien Hiei EE me 3 NE E S NI Wm E E mg O UN ER A AP mg Madorola DR Meapse Deel ae H Ark lhak opps Choos Lifted akerra P TGo oc cout 1 TM 1 b 7 In the case of reading MOPAC input file benz dat bp imas marta
18. ification and Reduction When you move a cursor to the right on the Builder Panel holding on the shift button the molecule is magnified When you move a cursor to left on the Builder Panel holding on the shift button the molecule is reduced 16 About dealing molecule s Max atoms 1000 atoms Il Move atom s 1 Moving all atoms You should click the left button of mouse and drag the pointer to the place where you want 2 Moving the selected atom You should dick the right button of mouse and drag the pointer to the place you want 34 IT Building the molecule Procedure 1 If you select New from File of the menu bar new molecule panel is shown When you dick on the Builder Panel one carbon atom is displayed Carbon is the default atom Procedure 2 When you move mouse pointer the white lineis drawn from the first carbon Procedure 3 If you click the point you want to place the second carbon C C bond is drawn Procedure 4 If you want to change the selected atom from carbon to oxygen you should click O on the Periodic Table Window or selecting Edit gt Atom Type gt Oxygen from menu bar of the Molecule Window Procedure 5 When you click the second carbon and move a pointer the white line appears from the second carbon When you click the point you want to place the oxygen the C C O is drawn Procedure 6 H ydrogen s are added by clicking Add Hydrogens from the Tool Bar or selecting Edit gt Add Hydrogens fr
19. ihedral Measure the angle between four selected atoms and display the value in the Status Bar Example Measurement of the O C C O dihedral angle in acetaldehyde Procedure 1 Select Dihedral from the Measure menu Then the following message appears in the Status Bar Select 4 atoms fom the Molecule wende Procedure 2 Select four atoms in the Builder Panel The dihedral angleis displayed in the Status Bar 0 L riedral aca c TczZF H 5zD D 3 Bond Serie Double Triple 3 a Single Double Triple Change bond order of the selected bond to single double or triple 17 4 Label Element Syrian Serial Numbers Charge 4 a Element Symbols Display the element of each atom 4 b Serial Numbers Display the serial number of each atom 4 c Charge Display the partial atomic charge of each atom after the results have been obtained from the CNDO 2 calculation Element Symbols Serial Numbers and Charge can be displayed simultaneously 5 Display HM Ball amp Stick mo Wn Fiane Moseme nt Home po Hin Cente 5 a Wire Display the molecule as a wire frame style 5 b Ball amp Stick Display the molecule as a ball and stick style 5 c MO Display the molecular orbital if the CNDO 2 calculation has already finished 5 d Wire Frame Movement Translation rotation and zoom of the molecule will be performed using the wire frame style although the molecule is displayed in ball amp stick sty
20. l 4 e Time Limit Set the maximum time length of calculation by the selected unit 4 f Charge Set the net charge of molecule 4 g Spin Set the spin multiplicity of molecule 4 h Aidiitional Keyword Display the Additional Keyword Frame Input keywords and push the Save button when you want to add other optional keywords 9 Setup Window O M0 Sat up Buca safe mite sitim 1 Work Directory Set a default directory for saving a Gaussian input data file 2 Application Set the executable file of Gaussian In the case of Gaussian98 it is set to g98 Linux or g98 exe Windows The above two items are set using the Search button If OK button is pushed the setup 27 becomes effecti ve 3 Other setup In addition to a setup on the Setup Window the following setup is necessary for submitting Gaussian jobs The method for setting up in the case of using Gaussian98 is shown as an example Please refer to the Gaussian manual for details 3 a Linux Before starting the M olWorks a setup of an environment variable g98root and execution of a script is required In the following examples it is assumed that the Gaussian is installed at opt g98 In the case of C shell setenv g98roct opt source 998root g98 bsd g98 l ogi n In the case of BA shell export g98root opt source 998root g98 bsd g98 profi e If the above mentioned procedures are described to cshrc file C shell or bashrc file BA
21. l In addition it can read input output files of Gaussian GAMESS MOPAC and Q Chem and can analyze and visualize the results MolWorks also can write molecule files only XYZ Format File xyz in Version 2 0 and input files for the programs see next O Pre and Post processors for quantum mechanics programs MolWorks has interfaces for Q Chem Gaussian GAMESS MOPAC MolWorks include a CNDO 2 calculation engine and can display the MO Molecular Orbital within the Builder Panel MolWorks can convert a Gaussian input data into a Q Chem input data and create an input data file for Q Chem MolWorks can submit a Gaussian job only when Gaussian program is installed locally Properties Estimation MolWorks can estimate molecular properties using Group Contribution Methods and Principle of Corresponding States You can estimate molecular properties and squeeze down the target molecule from the list MolWorks can display diagram of Equation of the State for the molecular mixtures 2 System Requirements Windows 98 2000 NT 4 0 XP Pentium M MX 233MHz and above Linux Redhat 45MB hard disk space including J ava VM 32M B RAM 64M B recommended 256 color VGA monitor 800x600 or greater Ethernet Card or Ethernet Board is necessary 3 How To Start Up e Windows Users Execute the M olWorks from the Start Menu e LinuxUsers E xecute the command MolWorks from the command line in the window While the Star
22. le 5 e Axis Display the XY Z axes on upper left corner of the Builder Panel 5 f Home position Change the molecular direction to the one of the axes above and move the center of mass of the molecule to the center of the Builder Panel 18 5 g Center M ove the center of mass of the molecule to the center of the Builder Panel Il Tool Bar Add Hyirogens gem ice Cut button This button becomes active when one or more atoms are selected on the Builder Panel The selected atoms are deleted when this button is pressed 2 Copy button Not supported in Version 2 0 Paste button Not supported in Version 2 0 Undo button Undo the previous editings Redo button Redo the editings Add Hwirngens Add Hydrogen button Adding the hydrogen atoms automatically considering the bond orders distances angles and dihedral angles Clean Clean button E xecute a simple geometry optimization 6 Periodic Table Window In draw mode element types can be selected by clicking the appropriate button Also clicking on the required element can change selected atoms in the Builder Panel The background color of each element is adopted in the Builder Panel Also atomic number mass of element IUPAC melting point boiling point specific heat and density are displayed at the top of the window Parindic Tatio omui ee EE m m Mon Seu Humber p vues 12 001 100 Melina Ped ISALI Buling Point 4077 4 pacific Haai 1 741 D
23. ln 1 o CUNEO ESCONDE mmo ER mr Anc Save the MOPAC input file for geometry optimization by PM3 Example H20 PM3 XYZ PRECISE Comment line H20 Comment line O 00 100 10 01 H 0 96 100 1001 H 0 282 10 918 10 01 V Q Chem Gaussian GAMESS MOPAC After clicking aewescea the MO Window is displayed 21 8 MO Window TheMO Window consists of four tabs concerned the four programs Q Chem Gaussian GAMESS and MOPAC Q Chem Make input data for Q Chem 1 Calc Type Select the calculation type Single Point Optimize Frequencies Transition Structure Using data on right other calculation type written in the text field is adopted 2 Calc Level Select the calculation type RHF Restricted Hartree F ock UHF Unrestricted Hartree F ock ROHF Restricted open shell Hartree F ock MP2 2nd order Moller Plesset perturbation CCD Coupled Cluster with Doubles CCSD Coupled Cluster with Singles and Doubles QCISD Quadratic Configuration Interaction OD Optimized Orbital Coupled Cluster Doubles BLYP Becke exchange LYP correlation B3LYP Becke s Three Parameter Hybrid Method Using the LYP Correlation B3PW91 Becke s Three Parameter Hybrid Method Using the PW91 Correlation EDF1 Empirical Density Functional 1 Using data on right other calculation type written in the text field is adopted 3 Basis Set Select the basis set STO 3G 3 21G 4 31G 6 31G 6 311G Using
24. n 1 a Molecule Select molecule in the Builder Panel 1 b Mol Ratio Set the ratio of mixture 1 c Exp Boiling P Set the experimental boiling point if you already know If you set it the estimation is more accurate If you don t set this estimated boiling point from J oback parameter is used 2 Second Molecule Specify the second molecule and condition The descriptions of the settings for second molecule are same as above 3 Calculate Estimate properties and draw PVT graph using condition in First and Second Molecule 33 13 Functional Groups Window This window displays the groups and the number of each group used for properties esti mation 14 Messages Window Display the messages of M olWorks Conse wtf dor i address US DEO ABTESBSZBE gading from fie CP rogram F ilesiWolinrks 1 515 amplaestetblenie ep oaded atoms for efrdena 15 How to use mouse Rotate ctri drag Magnify shift drag d plange Rotate ctri shift drag Rotation When you move a cursor to right or left on the Builder Panel with holding on the control button the molecule will be rotated by Y axis When you move a cursor to up or down on the Builder Panel holding on the control button the molecule rotate by X axis I Rotation Z axis perpendicular to the window When you move a cursor to right or left on the Builder Panel with holding on the control button and the shift button the molecule rotates on Z axis III Magn
25. om menu bar of the Molecule Window Procedure 7 The molecule cleaned up by clicking Clean from the Tool Bar or selecting Edit gt Clean from menu bar of Molecule Window 35 17 Supported file format Import XY Z Format Files xyz Protein Data Bank File pdb Q Chem Input File in inp Q Chem Output File out log ref Gaussian Input File com inp Gaussian Output File out log GAMESS Input File com inp GAMESS Output File out log MOPAC Input File dat MOPAC Output File out Export XY Z Format Files xyz AY Z type Comment First line Atom type X coordinate 18 Properties Estimation Groups for estimation in this program CHa non ring gt CH 2 non ring gt CH non ring gt C lt non ring CH 2 non ring CH non ring C lt non ring C non ring CH non ring cC non ring Il Properties 1 J oback J oback Method Boiling Point K C CH2 ring gt CH ring gt C lt ring CH ring C lt ring F CI Br OH alcohol Y coordinate Z coordinate After the second line OH phenol O non ring O ring gt C 0 non ring gt C 0 ring O CH aldehyde COOH acid COO ester O except as above NH gt A e Am J oback Method Freezing Point K C J oback Method Critical Temperature Tc K C J oback M e
26. on is pushed after editing input data on the Gaussian tab the conversion is carried out 11 Run Gaussian J ob If Run button in Run Gaussian J ob section is pushed the Gaussian program is executed At first input data edited in the Gaussian tab is saved at a file then the Gaussian job is submitted To use this function the Gaussian need to be installed locally And some setup is required at Setup Window Ill GAMESS Make input data for GAMESS The General Atomic and Molecular Electronic Structure System 1 Calc Type Select the calculation type 24 Single Point Gradient Optimiz Frequencie Using data on right other calculation type written in thetext field is adopted 2 Optimize Cyde Specify the maximum number of iteration for geometry optimization This button becomes active only in the case that Optimize is selected in Calc Type 3 Optimize Precision Specify the precision of geometry optimization This button becomes active only in the case that Optimize is selected in Calc Type 4 Calc L evel Select the calculation level RHF Restricted Hartree F ock UHF Unrestricted Hartree F ock ROHF Restricted open shell Hartree F ock Using data on right other calculation level written in thetext field is adopted 5 Geometry Specify the geometry type XY Z auto_ Set up the selected molecular geometry using the XY Z format automatically Modify Geometry Frame is displayed If Save button is
27. ricted open shell Hartree F ock CCD Coupled Cluster with Doubles CCSD Coupled Cluster with Singles and Doubles QCISD Quadratic Configuration nteracti on MP2 2nd order Moller Plesset perturbation BLYP Becke exchange LYP correlation B3LYP Becke s Three Parameter Hybrid Method Using the LYP Correlation Using data on right other calculation level written in the text field is adopted 23 4 Basis Set Select the basis set ST O 3G 3 21G 4 31G 6 31G 6 311G Using data on right other basis set written in the text field is adopted 5 Polarization Diffuse Select the type of polarization and or diffuse function Not used Not including both polarization and diffuse 4 44 and and and 6 Geometry Specify the geometry type XY Z auto_ Set up the selected molecular geometry using the XY Z format automatically Modify Geometry Frame is displayed If Save button is pushed after changing structure data within the Geometry Frame the changed structure save to the file 7 Charge Set the net charge of molecule 8 Spin Set the spin multiplicity of molecule Q Arhiitional Keyword Display the Additional Keyword Frame Input keywords and push the Save button when you want to add other optional keywords 10 Input Data Conversion Convert the input data for Gaussian into the input data for Q Chem and save the converted data to file as a Q Chem format If Save button in Input Data Conversion secti
28. rmatian windowtCs mo 5 a Already existed window s Checked window brings to the front of the display 12 6 Help System information 6 a System I nformation MolWorks displays the System Information dialog box 6 b About MolWorks TheAbout MolWorks dialog box is displayed MolWorks 2 baal out Pe Mokke Verbe 2 0 001 250562003 Copyright 22008 2003 Best System bsc OS Veron andows 2000 D AN rights resene OS chiese c5 MaP forks ls a registered trademark JD rado Buri Maria pil ME ESAS Jm elen unn 09 13 Il Main Window For the following windows Molecule Window Periodic Table Window Simplified Setting Window MO Window MO Setup Window CNDO 2 Window Estimation Window Pure Properties Window Properties Graph Window Functional Groups Window PVT Window and M essages Window are displayed with in Main Window To minimize the window dick the button The minimized window will be displayed at the bottom of the Main Window While the E button is shown you can change the size of the window To maximize the window click the E button To dose the window click the El button I Status Bar Choose the Status Bar from the View menu The following status bar is displayed at the bottom of the Main Window D O Messages are displayed here 2 The element type and the serial number of the atom are displayed here e g C 1 Display the number of total atoms in the Builder Pan
29. thod Critical Pressure Pc bar atm J oback Method Critical Volume Vc cm3 mol Edmister Method omega From J oback Parameter Acentric F actor Lee Kesier Method omega From J oback Parameter Acentric F actor Critical Compressibility factor Zc Yen Woods Method Density g cm3 Reidel Method Vapor Pressure mmH g Vetre Method Heat of Vaporization at boiling point cal mol L J Collision Diameter for Chemkin program A L J Well Depth for Chemkin programY mol 36 2NH non ring gt NH ring gt N non ring Na non ring N Xring CN NH SH S non ring S ring 2 Modified J oback Modified J oback Boiling Point K C Modified J oback Critical Temperature K C Modified J oback Critical Pressure bar atm Modified J oback Critical Volume cm3 mol Edmister Method omega L ee K esler Method omega Critical Compressibility factor Zc Density Estimation at 298K g cm3 Yen Woods Density Estimation g cm Riedel Vapor Pressure at 298K mmHg Vetre M ethod H eat of Vaporization at boiling point cal mol Heat Capacity Estimation at 298K cal mol K Gibbs Energy kcal mol H eat of Formation kcal mol Thermal Conductivity at 298K mW mK of Gas Thermal Conductivity at 298K mW mkK of Liquid Molecular Surface Estimation A2 Molecular Volume Estimation A3 Surface Tension Estimation at 298K dyne 19 References e CNDO 2 Pople J A
30. tup Window is displayed several modules are loaded Then Initial Display will be appeared on the screen Startup Window Initial Display MolWorks 2 0 ear Coman 2300 1009 Erit Ed esa d Is A epa rd 4 Display Contents Thelnitial Display consists of the Main Menu Main Window Status Bar Initial Display ki Iw Main Window Status Bar Main Menu 1 File E Fit 1 a New In the case of the Molecule Window and Periodic Table Window are opened in the Main Window If the Molecule Window is already displayed new Builder Panel will be added I TEE PE P In ta Wi m LU T mr aree me Preis Urianir 1 1 b Open The browser for open file will be appeared Select a molecular coordinate file and press opm The molecular structure will be displayed in the Builder Panel 1 b 1 File name Display the selected file name bere cc E prm coh Hi 7 samples wt Cal Es CH ira x 3 carbohydrate LE Es manoma CH organi Gig opiida d 3 peptide 3 solvent a eer a Open Fina nf rau KY Forma Fllers ae h 1 ent 1 b 2 Files of type Specify the reading file type In version 2 0 it can read XYZ Format File xyz Protein Data Bank File pdb and input and output files of Gaussian GAMESS MOPAC and Q Chem When the input files are read the molecular structure with the options and parameters for the calculation are displayed and when the output
31. yed The red arrow points the level of selected orbital If the orbital set that the difference of orbital energies is below 0 0001 hartree is existed i e degenerated orbitals are existed it displays as right hand below 3l 12 Estimation Window Pure Properties 1 Molecule All molecules displayed in the Molecule Window are listed in the pull down menu When certain molecule is selected in the pull down menu this molecule is displayed in the Builder Panel automatically And when certain molecule is selected in the Builder Panel this molecule is displayed in this menu automatically 2 Parameter Select the parameter for estimation 2 a J oback Joback K G S M thesis in chemical engineering Massachusetts Institute of Technology Cambridge Massachusetts 1984 2 b Modified J oback Use oback parameters determined by us with some modification 3 Calculate Estimate the pure properties of molecule using selected parameter And display the Pure Properties Window and the Functional Groups Window the groups and the number of each groups using in the calculation are displayed within this mugen Poe Propet iaa raras SC Dista dabis mark A mprres Fur Pipa kiat iini uw Pies d imp Palri JU 124 AE cla c m bled LE tet biet Bal lira Pale r 311 22111 HAAG UK Kack Malbos Freccior Fais kr 115 94 Erit ver ami 7 e DK C pe IER AR LU Dsg ND Lri kel Primmuribar Ach Mathes Critica Pronet a Col

MolWorks2.0 user`s manual

Contents

Download Pdf Manuals

Related Search

Related Contents