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Bruker SMART X2S User Manual

1. _ PY OO UF wer Acquinng Data Y i H t l cH Elapsed Tima TI Finding Structure TI Generating Report Resolution Limit Unit Call T Symmetry RI Y Crerall Progress v Acquiring Data After indexing the unit cell and finding a suitable maximum resolution data collection begins The SMART X25 integrates the data scales it and determines the Laue class during data acquisition Figure 5 5 Acquiring data Processing ylid V Dm a Avoquenng Data 9 Finding Structure Generating Report Fartolution Limit 0 84 Amgstroms Unit Coll 75 86 b 9 05 c 18 36 a 90 0 fe 80 00 yoo 00 Symmetry oP RI 7 Overall Progress DOC M86 EXS127 V4 5 3 Data Collection and Structure Solution Finding Structure SMART X2S User Manual After data collection is complete the SMART X2S solves the structure The structure solution software moves through Patterson direct and dual space methods to ensure that the structure is correctly solved Atoms are assigned using rigorous geometry checks and rigid bond tests of thermal parameters The results are then verified against International Union of Crystallography standards Figure 5 6 Finding structure Processing ylid v4 Finding Structure 2 Generating Report Resolution Limit 0 84 Angstroms Unit Coll 475 96 b 9 05 6718 36 a 90 0 fe s0 00 yon 00 Symmetry aP Rl 282 Overall Progress BE Generating Report After
2. 8 2 2 4 2 1 5 3 8 5 2 4 6 3 4 2 2 4 2 3 8 3 6 3 4 7 4 8 4 9 1 6 8 11 4 6 redundancy mode referenced documentation removing the CD removing the sample report crystal data and structure refinement report display report summary reset view button S safety issues sample return after collection scan parameters separating crystals serial ports shipping the SMART X2S crating uncrating shutdown SMART X2S correct usage features fitness for a particular purpose SMART X2S accessories kit snapshot button space group standard redundancy mode startup stop button Stopping Data Processing storage compartment structure solution structure view button functions SUM button T technical support Index 4 10 1 2 6 5 6 5 7 4 6 4 7 2 6 2 5 4 6 1 6 2 4 5 Index 3 Index temperature temperature range terms and conventions thermal ellipsoid display button time displays touchscreen and styluses interface translate buttons U ultraviolet pen light Unit Cell parameters unit cell upper cover user manual structure using the data CD with APEX2 UV curing adhesive curing problems with some crystals water soluble wetting the MicroMount V version information virus protection software W wavelength weight welcome screen X X ray safety X ray safety issues Y ylid Index 4 1 2 1 3 6 3 5 1 8 10 4 1 6 2
3. BRUKER SMART X2S User Manual Part Number DOC M86 EXS127 V4 Publication Date 25 March 2011 SC XRD Innovation with Integrity SMART X2S User Manual This document covers the SMART X2S system References to this document should be shown as DOC M86 EXS127 SMART X2S User Manual 2011 Bruker AXS Inc 5465 East Cheryl Parkway Madison WI 53711 All world rights reserved Notice The information in this publication is provided for reference only All information contained in this publication is believed to be cor rect and complete Bruker AXS Inc shall not be liable for errors contained herein nor for incidental or consequential damages in conjunction with the furnishing performance or use of this material All product specifications as well as the information con tained in this publication are subject to change without notice This publication may contain or reference information and products protected by copyrights or patents and does not convey any license under the patent rights of Bruker AXS Inc nor the rights of others Bruker AXS Inc does not assume any liabilities arising out of any infringements of patents or other rights of third parties Bruker AXS Inc makes no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose No part of this publication may be stored in a retrieval system transmitted or repr
4. 3 7 7 2 5 1 7 2 8 3 1 1 77 3 7 3 3 3 2 3 4 1 2 8 16 7 9 2 3 4 2 1 6 Z zoom buttons Z value SMART X2S User Manual 6 2 1 2 DOC M86 EXS127 V4
5. 7 1 The Crystallographic Report When the data CD is inserted into a computer with a CD ROM drive the crystallographic report automatically opens in your default web browser The report contains four sections e Report Summary Molecule Viewer Detailed Report e Alerts DOC M86 EXS127 V4 The Data CD SMART X2S User Manual 7 1 1 Report Summary Section The Report Summary gives information about the experiment and its results Information includes e Crystal information color name dimensions mounting method e Radiation information monochromatization method wavelength generator power Experiment parameters temperature scan parameters detector distance and swing angle e Unit cell parameters space group and Z value e Structure parameters and results integration absorption correction least squares and electron density and Version information for the various software modules used inside the SMART X2S Figure 7 1 Report summary section Structure determination of ylid with the Bruker SMART X2S benchtop crystallographic system A yellow crystal of ylid with the dimensions of 0 50 mm x 0 50 mm x 0 60 mm mounted on a Mitegen Micromount was automatically centered on a Bruker SMART X2S benchtop crystallographic system Intensity measurements were performed using a monochromated Doubly Curved Silicon Crystal Mo K radiation 0 71073 A from a sealed MicroFocus tube Generator settings were 50 kV 1 mA Da
6. microscope Figure 3 2 Proper crystal mounting Inner Surface Correct Outer Surface Incorrect When the crystal is in the crystal aperture and on the inner lf the crystal is positioned on the outer surface of the surface of the MicroGripper the SMART X25 will align MicroGrpper the SMART X25 will be the crystal precisely to the center of the instrument unable to position the crystal The aperture size will be readable The aperture size will appear backwards 3 2 1 Reusing Bruker Spine Pins Bruker Spine pins may be reused The ultraviolet curable glue dissolves in hot water 3 2 DOC M86 EXS127 V4 SMART X2S User Manual Sample Preparation and Mounting 3 3 Sample Preparation Procedure 3 3 1 Identifying Suitable Crystals Begin by using the microscope to look for a suitable crystal in the bulk sample The ideal crystal should be Uniform in color Free of cracks and inclusions e Without attached crystallites and e isometric i e the same dimensions in all directions The ideal crystal is about 0 5 mm in all directions Figure 3 3 Bulk crystals on microscope slide Problems Mounting Certain Crystals NOTE Some water soluble crystals may not work with the ultraviolet curable adhesive Super Glue may be used in such cases DOC M86 EXS127 V4 3 3 Sample Preparation and Mounting SMART X2S User Manual 3 3 2 Separating the Crystals 1 Isolate suitable crystals from the bulk sample and
7. 3 C8 C9 1 4076 C9 C10 1 383 3 C10 C11 1 505 2 C2 S1 C1 105 18 9 CHSLCT 106 86 11 C1 S1 C7 99 88 11 Cool 111 29 16 C3 C2 S1 126 15 14 ciie si 122 41 13 01 C3 C2 129 51 17 01 C3 C4 124 52 17 C2 C3 C4 105 95 15 C5 C4 C10 12135 17 C5 C4 C3 13025 18 C10 C4 C3 108 38 15 C4 C5 C6 118 2 2 C8 C6 C5 120 6 2 C6 C8 C9 121 7 2 C10 C9 C8 116 9 2 C9 C10 C4 121 22 17 C9 C10 C11 129 40 18 C4 C10 C11 109 36 15 02 C11 C2 130 12 16 2 C11 C10 124 91 16 C2 C11 C10 104 95 15 DOC M86 EXS127 V4 The Data CD SMART X2S User Manual Anisotropic Displacement Parameters Figure 7 6 Anisotropic displacement parameters Table 4 Anisotropic displacement parameters x10 for ylid The anisotropic displacement factor exponent takes the form 2x7 h a Ul _ 2hka b U2 vH U2 u33 u v3 Iu S1 41 1 35 1 40 1 41 9 1 5 1 O1 45 1 49 1 57 1 13 1 2 1 11 1 02 60 1 45 1 521 91 8 1 17 1 C1 49 1 38 1 63 1 1 1 13 1 9 1 c 41 1 35 1 34 1 4 1 3 1 1 1 C3 36 1 34 1 39 1 0 1 2 1 4 1 C4 40 1 36 1 35 1 4 1 2 1 7 1 C5 43 1 52 1 50 1 4 1 8 1 6 1 C6 66 1 56 1 48 1 7 1 24 1 13 1 C7 90 2 54 1 38 1 1 1 4 1 5 1 C8 9202 48 1 40 1 1 1 20 1 14 2 c9 74 391 391 31 5 1 2 1 C10 51 1 32 1 33 1 3 1 3 1 5 1 C11 45 1 320 351 1 1 1 1 2 1 Hydrogen Coordinates and Isotropic Displacement Parameters Figure 7 7 Hydrogen coordinates and
8. 8 1 2 1 8 10 7 6 2 4 8 15 6 3 3 6 4 1 4 1 6 3 8 10 1 12 5 1 Bruker Spine Pin reusing brukersupport com C Caution notice defined CD inserting retrieving using with APEX2 CD burning CD R media types CE Declaration of Conformity checking quality CHK button choosing your crystal s shape choosing your crystal s size cleaning the SMART X2S clearance closed beam design compound name length limit computer compartment consumable items cooling completely air cooled cooling displays 3 2 1 2 1 3 4 2 6 5 7 7 6 5 4 2 8 26 5 2 5 3 4 5 4 8 4 9 8 10 2 4 2 1 4 4 8 3 8 25 2 1 2 6 Index 1 Index coordination compounds CPK colors crystal selection criteria size crystal information area D Danger notice defined data resolution specifications Deletion of collected data detailed report section detector distance Detector Frame Display detector specifications detector swing angle DHCP dimensions discard report button discard report dialog documentation revision numbers E electron density entering your sample s formula environment requirements equivalent terms Ethernet port extended redundancy mode F finding structure forward button forward to CD burning button 2 1 6 1 3 3 3 3 1 3 2 4 8 15 7 4 7 2 5 1 2 4 7 2 8 16 4 5 2 4 1 3 8 16 4 10 5 2 5 4 4 1 4 1 frequently used elements in formula screen 4 6
9. 8 1 3 SMART X2S Compartments 0 0 ee 8 3 8 2 Moving the SMART X2S 00 0 ce ee 8 4 8 2 1 Moving the SMART X2S over Short Distances 8 4 8 2 2 Crating the SMART X2S for Shipping 2 2000 eee 8 5 8 2 3 Uncrating the SMART X2S 2 0 00 ns 8 9 8 3 Preventive Maintenance and Inspections 8 10 8 3 1 Cleaning the SMART X2S 2 2 llle 8 10 8 3 2 Replacing the Lithium Battery 0 0 00 2 eee 8 10 8 3 3 Surveying the SMART X2S for Radiation Leakage 8 11 8 4 The SMART X2S Archival and Deletion Routine 8 15 8 5 Remote Access to the SMART X2S Frames Directory 8 16 8 5 1 Connect the Computer to the SMART X2S 22 222 8 16 8 5 2 Check that the SMART X2S Has a Dynamic IP Address 8 16 8 5 3 Connect the SMART X2S to the Isolated Private Network 8 17 8 6 Connecting to WebESX 3 asien ml E X Pado Oe Rea ee 8 17 8 6 1 Connecting to WebEx without a SMART X2S Service CD 8 17 8 7 Updating the SMART X2S Software es 8 18 8 7 1 Preparing for the Software Update llle 8 18 8 7 2 Replacing the Compact Flash Card 0 0 00 cece aes 8 22 8 7 3 After Updating the Software 0 0 ee 8 24 8 8 Consumable tems ss dg v XR ar 8 25 8 9 CE Declaration of Conformity 0 0 ee 8 26 Ig Er
10. Conformity Figure 8 30 SMART X2S CE Declaration of Conformity we Bruker AXS Inc 5465 East Cheryl Parkway Madison WI 53711 5373 Tel 1 608 276 3000 Fax 1 608 276 3006 info bruker axs com www bruker axs com DECLARATION OF CONFORMITY Manufacturer s Name Bruker AXS Inc Manufacturer s Address 5465 East Cheryl Parkway Madison WI 53711 5373 USA Declares that the product Product Name SMART X2S Model Number 882 030500 Conforms to the following product specifications Safety EN 61010 1 2001 2 Edition EMC EN 55011 1998 with Amendment A1 1999 Group 1 Class A for ISM Equipment EN 61326 1 2006 using IEC 61000 4 2 2001 3 2002 4 2004 5 2001 6 2003 and 11 2004 EN 61326 using EN 61000 3 2 2000 A2 2005 EN 61326 using EN 61000 3 3 1995 A1 2001 A2 2005 Year in which the CE marking is aff xed 2009 Kline Wilkins Sr V P Global Operations 8 26 DOC M86 EXS127 V4 Index Copyright Notice Numerics 3D view A Aborting Data Processing absorption correction acquiring data administrator SMART X2S instrument administrator administrator key air cooled design airflow alerts section altitude limitations Archival of collected data atom label visibility buttons attaching crystal to micromount B back button back to beginning button ball and stick display button battery Beryllium safety bravais type DOC M86 EXS127 V4 6 1 5 5 1 2 5 2 5 3 1 1 8 1
11. DOC M86 EXS127 V4 8 23 SMART X2S Administrator Information SMART X2S User Manual 8 7 3 After Updating the Software 1 If your Compact Flash card slot is on the inside of the computer compartment close up the computer compartment 1 1 Using the 4 mm hex wrench attach the drawer to the computer chassis by replacing the two hex bolts that were removed in Section 8 7 1 step 4 1 2 Using the 2 mm hex wrench replace the computer compartment top cover that was removed in Section 8 7 1 step 4 2 Push in the drawer and lock it using the Administrator key 3 Power on the SMART X2S by flipping the green power switch Figure 8 28 Power switch The instrument powers up and the computer boots The software will automatically detect that a new card is present perform some configuration steps and then restart the instrument again Figure 8 29 SMART X2S startup New CF card detected screen Hen DF cand derecied After the computer has restarted the second time the software update process is finished and the system is ready to use 8 24 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 8 8 Consumable Items Part Number Quantity Description Replaceable fuse 3 15A 250V 070 003200 2 SLO BLO Replaceable battery lithium Panasonic 122 004600 1 CR2032 DOC M86 EXS127 V4 8 25 SMART X2S Administrator Information SMART X2S User Manual 8 9 CE Declaration of
12. Index 1 DOC M86 EXS127 V4 V Table of Contents SMART X2S User Manual This page intentionally left blank vi DOC M86 EXS127 V4 1 About this User Manual 1 1 The Structure of this User Manual This User Manual describes the SMART X2S and its functions and illustrates the steps required to perform a structure determination e Introduction to the SMART X2S describes the system its specifications and its functions Sample Preparation and Mounting discusses separating a crystal from the bulk sample and attaching it to the micromount e Setting Up Data Collection starts the data collection by entering crystal information and then inserting the blank CD and sample e Data Collection and Structure Solution describes the steps in the SMART X2S automatic data collection and structure solution phase e Structure View Report Display and CD Burning describes the SMART X2S results after collecting and solving the structure e The Data CD describes the report and files on the CD which contain all the information necessary to publish the structure or if desired work further with it in Bruker s APEX2 software suite and SMART X2S Administrator Information discusses procedures and operations to be carried out by the SMART X2S Administrator i e an on site person responsible for the instrument s security safety and function DOC M86 EXS127 V4 1 About this User Manual SMART X2S User Manual 1 1 1 The Ylid Crystal The
13. NOTE The SMART X2S has no known issues with any CD R media types 4 2 S DOC M86 EXS127 V4 SMART X2S User Manual Setting Up Data Collection Figure 4 3 Inserting a CD After the SMART X2S recognizes that an empty CD has been inserted a confirmation screen will appear Figure 4 4 Confirmation screen Please insert an empty CD Blank writable CD detected O 8 The SMART X2S automatically proceeds to the Please name your compound screen DOC M86 EXS127 V4 4 3 Setting Up Data Collection SMART X2S User Manual 4 4 Naming Your Sample After inserting a blank CD the Please enter the sample name screen appears Figure 4 5 Please enter the sample name Please enter the sample name 1 Use the keyboard on the touchscreen to name the compound This is the name that will be used in the report generated by the SMART X2S NOTE The compound name is limited to a maximum of 12 characters Figure 4 6 Please enter the sample name filled in Please enter the sample name Us es amp eT L1 29931 434553 094 79 595 9939 993 aR Clear wW a r t u wa y 14 411 Caps a 5 d f g h i k Enter LO TE FT UM o w Shift z x c v b n m Shift Space 0 oF 2 Press the Forward button or Enter on the touchscreen to proceed to the next screen i DOC M86 EXS127 V4 SMART X2S User Manual Setting Up Data Collect
14. SMART X2S System Serial ne A bn AJ u N css Pee Survey meter J 5 P poncmmer J d j J gj d jp j SURVEYED BY DATE 8 14 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 8 4 The SMART X2S Archival and Deletion Routine The data CD burned at the end of data collection is a copy of a folder on the SMART X2S internal hard drive An instrument administrator can easily retrieve any sample in the SMART X2S history of operation until the hard drive becomes nearly full Once the hard drive is nearly full the system automatically removes files each time a new sample is collected It goes through each sample folder oldest to newest and removes enough frame files to ensure that a new sample has enough space for data collection If the free space is still insufficient the system goes through each sample folder again oldest to newest to remove all remaining traces of the sample until there is enough space for the new sample s data Typically this means that when the SMART X2S hard drive is nearly full it removes the oldest sample to make room for the newest The number of samples that can be stored is dependent upon the hard drive s storage capacity and is subject to change without notice DOC M86 EXS127 V4 8 15 SMART X2S Administrator Information SMART X2S User Manual 8 5 NOTE 8 5 1 Remote Access to the SMART X2S Frames Direct
15. dimensional view of the diffraction pattern Greek and Roman Text This document uses scientific terminology that may be rendered in Greek text However this document follows a convention of using Roman text to the greatest extent possible Table 1 2 Greek and Roman Text 20 2theta W omega Q phi X chi 1 3 2 Notices Danger Caution and Note This document contains notices that must be observed to ensure personal safety as well as to protect the product and connected equipment These notices are highlighted as follows according to the level of danger The word DANGER alerts you to an immediate or potential hazard that can result in death severe personal injury or substantial property damage The word CAUTION alerts you to a potential practice or condition that could result in minor personal injury or damage to the product or property NOTE The word NOTE in bold capital letters draws your attention to particularly important information on the product or handling of the product or to a particular part of the product documentation DOC M86 EXS127 V4 1 3 About this User Manual SMART X2S User Manual 1 4 Safety Notices 1 4 1 General Safety Precautions of the SMART X2S X ray Radiation The SMART X2S is an analytical instrument with a strong X ray source Shielding and safety equipment guarantee that the emitted radiation does not exceed 1 0 uSv h during operation Shielding and
16. e Determine steps and conditions that recreate the problem if possible Failure to refer instrument servicing to qualified Bruker personnel may result in injury or property damage North American Service Center Contact Information Table 1 4 Bruker AXS North American Service Center contact information Bruker AXS North American Service Center Bruker AXS Inc Customer Support Address 5465 East Cheryl Parkway Madison WI 53711 5373 USA Toll free telephone 1 800 234 XRAY 9729 Direct line 1 608 276 3000 Fax 1 608 276 9162 E mail Customer Service bruker axs com Web http www bruker axs com DOC M86 EXS127 V4 1 13 About this User Manual SMART X2S User Manual Karlsruhe Service Center Contact Information Table 1 5 Bruker AXS Karlsruhe Service Center contact information Bruker AXS Karlsruhe Service Center Bruker AXS GmbH Customer Support Address stliche Rheinbr ckenstr 49 76187 Karlsruhe Germany Telephone 49 721 595 8403 XRD Hotline 49 721 50997 5208 E mail service bruker axs de Web http www bruker axs de 1 14 DOC M86 EXS127 V4 2 Introduction to the SMART X2S 2 1 SMART X2S Features The SMART X2S is designed specifically for walk up structure solution for the working chemist Features of the SMART X2S include Completely automated operation without user intervention from sample loading and alignment through data collect
17. radiation produced by the electrons that give up all their energy on the initial impact Thus for a particular supply voltage these electrons give rise to photons of maximum energy i e minimum wavelength With an increase in supply voltage the SWL as well as the point of maximum intensity of the continuous spectrum moves down the wavelength scale In other words an increase in operating potential produces a shift of the continuous spectrum in the direction of lower wavelengths and higher energy On the other hand the characteristic spectrum because it is characteristic of the anode metal merely undergoes an increase in intensity i e pulse count rate Figure 1 6 Spectrum of an X ray tube Spectral Intensity 0 02 04 06 08 1010 Wavelength 1 10 DOC M86 EXS127 V4 SMART X2S User Manual About this User Manual Biological Effects of X Rays Mechanisms of Damage Injury to living tissue results from the transfer of energy to atoms and molecules in the cellular structure lonizing radiation causes atoms and molecules to become ionized or excited These excitations and lonizations can e Produce free radicals Break chemical bonds Produce new chemical bonds and cross linkage between macromolecules Damage molecules that regulate vital cell processes e g DNA RNA proteins The cell can repair certain levels of cell damage At low doses such as that received every day from background radiation cellul
18. restored sample will overwrite the already existing sample in the Sample Database T Choose the appropriate group for the restored archive in the Put in Group drop down menu DOC M86 EXS127 V4 7 7 The Data CD SMART X2S User Manual 8 Click Restore Archive A progress bar and status data are shown as the software restores the archive Figure 7 8 Restore Archived Sample window From CD selected Restore Archived Sample 2l x From Zip File From CD Using CD Burner PLEXTOR DYDA PX 7164 using D Get Archive Information From CD Existing Samples Archive Name SingleS ample Restore As Singles ample2 Put In Group Users Total Progress Status Restoring archive SingleS ample from CD to database as SingleS ample2 Importing archived XML data into the database this may take a long time imported successfully Copying data files from CD copied successfully finished When the archive is restored it can be opened from the Sample gt Open Sample gt Open gt Sample dialog 9 Click Close to close the Restore Archived Sample window After restoring the sample you can work with it as you would any other sample in APEX2 For more information on working with APEX2 see M86 Exx078 APEX2 User Manual 7 8 DOC M86 EXS127 V4 8 SMART X2S Administrator Information 8 1 Access to the SMART X2S Interior 8 1 1 Administrator Ke
19. the Adhesive with Ultraviolet Light Ultraviolet curable adhesive leaves ample time for the crystal to be manipulated When the crystal is in the proper place it may be fixed within seconds by shining ultraviolet light on it The ultraviolet pen light radiates intense ultraviolet light when the button is pressed Do not look directly into the ultraviolet light during operation of the pen light Exposure to intense UV light even for a brief period can harm the eyes If viewing the UV light is necessary use UV filtered glasses to avoid eye damage Keep the ultraviolet pen light out of the reach of children Avoid direct exposure to ultraviolet light 1 When you have the desired crystal in the center of the micromount s aperture cure the adhesive by shining the ultraviolet pen light on the sample for about 20 seconds Figure 3 11 Adhesive illuminated by ultraviolet pen light 2 When the adhesive is cured place the Bruker Spine Pin in its protective cap The sample is now ready for use with the SMART X2S Figure 3 12 Successfully mounted crystal DOC M86 EXS127 V4 3 7 Sample Preparation and Mounting SMART X2S User Manual This page intentionally left blank 3 8 DOC M86 EXS127 V4 4 Setting Up Data Collection 4 1 The SMART X2S Touchscreen Interface The SMART X2S features an intuitive kiosk style interface with input through a touchscreen The interface guides the user through the experiment providing easy to unde
20. 1 22 6711 1808 R int 0 0235 99 9 Multiscan 0 8673 and 0 7941 Full matrix least squares on F 1808 0 129 1 046 R1 0 0289 wR2 0 0743 R1 0 0320 wR2 0 0765 0 01 7 0 140 and 0 205 w 1 o F aP bP where P is 2F Max F 0 3 SMART X2S User Manual DOC M86 EXS127 V4 SMART X2S User Manual The Data CD Atomic Coordinates and Isotropic Displacement Parameters Figure 7 4 Atomic coordinates and isotropic displacement parameters Table 2 Atomic coordinates x10 and equivalent isotropic displacement parameters x10 for ylid U eq is defined as one third of the trace of the orthogonalized U4 tensor x y z U eq S1 1903 1 6814 1 2596 1 39 1 O1 66422 8021 1 3230 1 50 1 02 1583 3 41091 3706 1 52 1 C1 1652 4 87682 2710 1 50 1 c2 36423 62452 3280 1 36 1 C3 5662 3 6946 2 3500 1 37 1 C4 64226 6143 2 4174 1 37 1 C5 82224 640102 462001 48 1 C6 8505 4 5491 3 5224 1 57 1 C7 3505 5 6760 3 1773 1 61 1 C8 6998 5 438763 5373 1 60 1 C9 5130 4 4127Q 4925 1 51 1 C10 49016 5018 2 432001 391 C11 3105 3 5015 2 3747 1 37 1 Bond Lengths and Angles Figure 7 5 Bond lengths and angles Table 3 Bond lengths A and angles for ylid S1 C2 1712718 S1 C1 1 787 2 S1 C7 1 792 2 01 C3 1 240 2 O2 C11 1 226 2 C2 C3 1 423 3 Chri 1 442 3 C3 C4 1 507 2 C4 C5 1 3720 C4 C10 1 3916 C5 C6 1 396 3 C6 C8 1 372
21. ES usare va ee oe toe E RN PUE ee DES 1 3 1 3 2 Notices Danger Caution and Note 00 0008 1 3 1 4 Safety Nollces sua tors rata dat Rica Wea ae eee eae aba 1 4 1 4 1 General Safety Precautions of the SMART X2S 1 4 1 4 2 Correct Usage of the SMART X2S 0 0 00 ce ee 1 4 1 4 3 Safety related Graphic Symbols 0 000 0 1 5 WA Keay Sally iu a Wut edo ue Ce oad or ee c vere GU eh Sake os 1 6 1 4 5 Beryllium SalGly 2 2 9 auci ER Gu EXS Mees E ERE EG am Eb 1 12 1 4 6 Perchlorate Safety 0 0 0 0 eens 1 12 1 5 Help and Technical Support 000 ccc es 1 13 1 5 1 Help within the Interface 0 0 0 0 cee 1 13 1 5 2 Technical Support from Bruker Service Centers 1 13 2 Introduction to the SMART X2S 0 0 ee 2 1 2 1 SMART X25 Features is ii bch anke na 2 1 2 2 DIAGlAMS rauen eee tee eee ee 2 2 2 3 Technical Specifications 0 00 es 2 3 2 3 1 Dimensions and Weight 0 0 00 eee ee 2 3 2 3 2 Power Requirements 0000 cece eee eee eee eee 2 3 2 3 3 Environment Requirements llle 2 4 2 3 4 Other Specifications a anaana aaa eee 2 4 2 4 Startup and Shutdown ee 2 5 2 4 1 Starting Up the SMART X2S llle 2 5 2 4 2 Shutting Down the SMART X2S 0 0 0 0 ee 2 8 DOC M86 EXS127 V4 Table of Contents SMART X2S User Manual Sample Prepa
22. Figure 2 5 Initializing serial ports Waiting for Serial Ports to initialize DOC M86 EXS127 V4 2 5 Introduction to the SMART X2S SMART X2S User Manual Then the instrument starts GIS the control software for the SMART X2S hardware Figure 2 6 Starting GIS Launching GIS Software j E i a Soe After the system finishes initializing it begins cooling the detector and desktop cooler if present As cooling proceeds the system displays the temperatures graphically Figure 2 7 Cooling displays Detector DTG 2 6 DOC M86 EXS127 V4 SMART X2S User Manual Introduction to the SMART X2S After cooling is complete the kiosk style interface appears Figure 2 8 Starting kiosk application Please wait while data is loaded Finally the system checks whether a sample is loaded If a sample is loaded the instrument will eject the sample and make it available at the sample port If no sample is loaded the instrument will display the Welcome screen Figure 2 9 Kiosk Welcome screen Welcome to the SMART X2S DOC M86 EXS127 V4 2 7 Introduction to the SMART X2S SMART X2S User Manual 2 4 2 Shutting Down the SMART X2S 1 Flip the power switch on the front of the SMART X25 to the Off position 0 2 If your SMART X2S unit has a safety key switch turn it to the Off position and remove it to prevent unauthorized access 2 8 DOC M86 EXS127 V4 3 Sample Prepa
23. G generating report Index 2 5 2 5 4 SMART X2S User Manual generator power GIS Greek and Roman text H heat dissipation help button humidity range inserting your sample integration parameters and results integration while collecting 1 2 2 6 1 3 2 4 4 1 4 11 1 2 5 3 International Union of Crystallography standards 5 4 ipconfig J Jmol K Karlsruhe service center kiosk application L Laue class check least squares lithium battery lower drawer low temperature device specifications mains power disconnection requirements malware MiTeGen MicroMount molecule viewer monochromatization method mounting 8 16 1 3 5 3 1 2 8 10 8 2 2 4 2 3 8 16 DOC M86 EXS127 V4 SMART X2S User Manual Moving the SMART X2S N naming your compound network configuration network drive North American service center Note defined O opening the SMART X2S chassis optics specifications organic compounds orientation matrix collection outriggers overvoltage design P pipes display button please insert a blank CD screen pollution degree power requirements power supply compartment process steps SUCCESS icons process steps overview Q Q peak visibility buttons question mark button color crystal shape size R Radiation Safety Officer radiation survey red X on Sample Formula screen DOC M86 EXS127 V4 8 4 4 4 8 16 8 17 1 13
24. and move mouse to orient structure Hold middle mouse button and move mouse left and right to rotate structure Hold middle mouse button and move mouse up and down to zoom in and out Jmol Press right mouse button for context menu ellen Vl VSD NEE DOC M86 EXS127 V4 7 3 The Data CD 7 1 3 Detailed Report Section Crystal Data and Structure Refinement Figure 7 3 Crystal data and structure refinement Table 1 Crystal data and structure refinement for ylid Identification code Empirical formula Formula weight Temperature Wavelength Crystal system Space group Unit cell dimensions Volume Z Density calculated Absorption coefficient F 000 Crystal size Theta range for data collection Index ranges Reflections collected Independent reflections Completeness to theta 25 35 Absorption correction Max and min transmission Refinement method Data restraints parameters Goodness of fit on F Final R indices I gt 2sigma T R indices all data Absolute structure parameter Largest diff peak and hole 2 2 2 Ru ZF r mean Y F R ZJF Full EF GOOF EWF F2 a p wR Iw FP xpo 2 ylid C11H1002S 206 25 300 2 K 0 71073 A Orthorhombic P 212121 a 597240 a 90 b 9 0512 2 A p 90 c 18 4171 8 y 2 907 995 58 7 A 4 1 376 Mg cm 0 293 mm 432 0 50 x 0 50 x 0 60 mn 2 51 to 25 35 T h 7 10 lt k lt 9 22 2
25. ar damage is rapidly repaired At higher levels cell death results At extremely high doses cells cannot be replaced quickly enough and tissues fail to function Tissue Sensitivity In general the radiation sensitivity of a tissue is e proportional to the rate of proliferation of its cells inversely proportional to the degree of cell differentiation For example the following tissues and organs are listed from most radiosensitive to least radiosensitive 1 Blood forming organs Reproductive organs okin Bone and teeth QE IE eS Muscle 6 Nervous system This also means that a developing embryo is most sensitive to radiation during the early stages of differentiation and an embryo fetus is more sensitive to radiation exposure in the first trimester than in later trimesters Prompt and Delayed Effects Radiation effects can be categorized by when they appear Prompt effects effects including radiation sickness and radiation burns seen immediately after large doses of radiation delivered over short periods of time Delayed effects effects such as cancer induction that may appear months or years after a radiation exposure Delayed Effects of Radiation Exposure Cancer Studies of people exposed to high doses of radiation have shown that there is a risk of cancer induction associated with high doses e The specific types of cancers associated with radiation exposure include leukemia multiple myeloma breast cance
26. cation will appear In the SMART X2S Control Panel application click the WebEx button Internet Explorer opens and contacts https bruker axs webex com sc to begin the WebEx session 8 6 1 Connecting to WebEx without a SMART X2S Service CD If the SMART X2S Service CD is not available contact Bruker AXS Service DOC M86 EXS127 V4 8 17 SMART X2S Administrator Information 8 7 Updating the SMART X2S Software 8 7 1 Preparing for the Software Update 1 Power down the SMART X2S by flipping the green power switch Figure 8 14 Power switch 2 Use the Administrator key to unlock the lower drawer Figure 8 15 Using the Administrator key 3 Pull out the lower drawer Figure 8 16 Lower drawer pulled out a ae t 90600e000 0cco eocccocen SMART X2S User Manual DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 4 Some SMART X2S models have the Compact Flash card slot on the inside of the computer compartment Look for the Compact Flash card slot on the computer compartment left hand side Figure 8 17 Computer compartment left hand side Compact Flash card slot present If the slot is visible proceed to Section 8 7 2 If the slot is not visible open the computer compartment 4 1 Locate the four hex bolts in the computer compartment s top cover Figure 8 18 Computer compartment top cover locations of hex bolts 4 2 Remove the four hex bolts usin
27. ch lock and use the system s removable carrying handles 8 4 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 8 2 2 Crating the SMART X2S for Shipping Moving the SMART X2S to its Staging Location 1 Move the SMART X2S from its installed location to a safe staging location where it can be attached to its shipping skid and dressed for shipment Attaching the Outriggers 1 Elevate the SMART X2S e g on a cart to allow access to the right and left sides of the bottom of the unit The sides have screw holes that will be used to attach the wooden outriggers that attach to the shipping skid Figure 8 4 Underside of SMART X2S holes for outrigger u 2 Attach the outriggers to the bottom of the SMART X2S with two M10x30 screws with washers Tighten them just to the point where they are secure but can be knocked into position Figure 8 5 Outrigger Mi Jv DOC M86 EXS127 V4 8 5 SMART X2S Administrator Information SMART X2S User Manual Moving the SMART X2S onto its Shipping Skid The SMART X2S wooden outriggers attach to the shipping skid with four 9 16 bolts 1 Position the skid so that the SMART X2S can be moved onto it as easily as possible the skid does not have a special front back orientation Figure 8 7 Shipping skid with four 9 16 bolts and wrench BRETT TN NES De 4 i 2 With a person on each side move the SMART X2S directly down
28. cify the crystal color screen appears the color will be used in the report generated by the SMART X2S Figure 4 10 Please specify the crystal color Please specify the crystal color Colorless Orange Yellow Violet ooe os 1 Simply press the appropriate button on the touchscreen to choose the color NOTE If desired the color input can be skipped by pressing the SKIP button Figure 4 11 Please specify the crystal color yellow Please specify the crystal color Colorless Orange Yellow 2 Press the Forward button to proceed to the next screen DOC M86 EXS127 V4 4 7 Setting Up Data Collection SMART X2S User Manual 4 7 Specifying the Crystal Shape After specifying the crystal color the Please specify the crystal shape screen appears Figure 4 12 Please specify the crystal shape Please specify the crystal shape 0 ih e 4 l D y 1 Choose the appropriate shape by pressing one of the shape buttons NOTE Ifthe shape is not necessary press the SKIP button at the bottom of the screen Figure 4 13 Please specify the crystal shape sphere Please specify the crystal shape 2 Press the Forward button to proceed to the next screen DB DOC M86 EXS127 V4 SMART X2S User Manual Setting Up Data Collection 4 8 Specifying the Crystal Size After specifying the crystal shape the Please specify the crystal
29. compound used was 2 dimethylsulfuranylidene 1 3 indanedione abbreviated ylid C11H1002S More information on the ylid crystal is available in the article Polymorphism and History of 2 Dimethylsufuranylidene 1 3 indanedione YLID Ilia A Guzei Galina A Bikzhanova Lara C Spencer Tatiana V Timofeeva Tiffany L Kinnibrugh and Charles F Campana Cryst Growth Des 2008 8 7 pp 2411 2418 DOI 10 1021 cg701260p Figure 1 1 Ylid crystal structure 1 2 Referenced Documentation The following Table contains a list of documentation referenced by this document It is necessary to have this additional documentation available as you work with this document In the documents part numbers a variable revision number is indicated by a letter X Always use the most current revisions available All of the documents shown in the Table may be found at Bruker AXS comprehensive support site www brukersupport com or on the Online Documentation CD ROM that accompanies the shipment 1 2 1 Referenced Documentation Table 1 1 Referenced documentation Documentation Part Number A86 Exx003 Fundamentals of Single Crystal X ray Diffraction M86 Exx078 APEX2 Software User Manual if applicable 1 2 DOC M86 EXS127 V4 SMART X2S User Manual About this User Manual 1 3 Terms and Conventions 1 3 1 Equivalent Terms Frame Image In 2 dimensional X ray diffraction the terms frame and image refer to the same 2
30. cture View screen e Press the W button to discard the contents of the report or e Press the m gt y button to accept the report s contents and burn them to the CD After pressing the i button to discard the contents of the report the system will prompt to confirm the decision Press to go back or W to delete the report and return to the previous screen Figure 6 3 Are you sure that you want to discard your results Discard Results 6 4 DOC M86 EXS127 V4 SMART X2S User Manual Structure View Report Display and CD Burning 6 3 CD Burning After accepting the contents of the report and pressing the ay button the SMART X2S will burn the report along with all data collected onto the CD Figure 6 4 Burning the CD Writing CD k es 6 4 Removing the CD and Sample When CD burning is complete the SMART X2S will eject the CD The sample will also appear at the sample port on the front of the SMART X2S A screen appears prompting to remove the CD and sample Figure 6 5 Please take your CD and sample Please take your crystal sample and CD 1 Remove the CD from the drive and label it 2 Remove the sample from the SMART X2S sample port 3 Press the C button to return to the Welcome screen DOC M86 EXS127 V4 6 5 Structure View Report Display and CD Burning SMART X2S User Manual This page intentionally left blank 6 6 DOC M86 EXS127 V4 7 The Data CD
31. d by the sphere s opacity Residual peak hidden Hide the strongest residual peak Snapshot Save the current view of the structure as a jpg file which will be written to the CD when it is burned DOC M86 EXS127 V4 6 3 Structure View Report Display and CD Burning SMART X2S User Manual 6 2 Report Display After the Structure View screen the SMART X2S displays the report that will be burned to the CD Figure 6 2 Report display Sample Report Structure determination of ylid with the Bruker SMART X23 benchtop crystallographic 1 system A yellow crystal of ylid with the dimensions of 0 50 mm x 0 50 mm x 0 60 mm mounted on a Mitegen Micromount was automatically centered on a Bruker SMART X25 benchtop crystallographic system Intensity measurements were performed using a monochromated Doubly Curved Silicon Crystal Mo K radiation 0 71073 A from a sealed MicroFocus tube Generator settings were 50 kV 1 mA Data collection temperature was 0 C Data were acquired using three sets of Omega scans at different Phi settings The frame width was 0 5 with an exposure tima of 5 0 s The detailed data collection strategy was as follows Detector distance 40 mm Detector swing angle fixed 2 Theta 20 Run Omega Omega Phi Frames start end 1 20 0 1520 00 344 2 20 0 100 0 120 0 240 E 2n n ns 2An 41 After examining the report Press the button to go back to the Stru
32. e and Inspections 8 3 1 Cleaning the SMART X2S The SMART X2S exterior panels may be cleaned with a damp cloth Do not use soap or aggressive cleansing agents In order to avoid damage to the touchscreen the use of sharp objects such as styluses should be avoided To clean the touchscreen avoid the use of abrasives or aggressive solvents only use a soft damp cloth with a mild detergent if necessary To ensure adequate airflow through the SMART X2S periodically check that the rear ventilation holes are clear of dust and debris 8 3 2 Replacing the Lithium Battery The SMART X2S goniostat interlock PCB uses a lithium battery To ensure that the battery does not fail replace it once every 2 years as part of a biannual preventative maintenance procedure The battery is available from Bruker AXS as part number 122 004600 To replace the battery 1 Use the Administrator key to open the SMART X2S and lift off the top cover 2 Locate the battery in socket J16 on the goniostat interlock PCB i e the lower of the two circuit boards immediately to the right hand side of the radiation shield enclosure Figure 8 13 Lithium battery location 3 Remove the battery from under the contact clip A capacitor will preserve the board s memory while there is no battery in the socket 4 Place the new battery into the socket positive side up under the contact clip 8 10 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Adm
33. e ports Exhaust fans RS 232 port 2 2 DOC M86 EXS127 V4 SMART X2S User Manual Introduction to the SMART X2S 2 3 Technical Specifications 2 3 1 Dimensions and Weight Table 2 1 SMART X2S dimensions and weight 64 cm 25 2 97 cm 38 2 47 cm 18 5 150 kg 331 Ibs Figure 2 3 SMART X2S dimensions 64 cm 25 2 97 cm 38 2 2 3 2 Power Requirements Table 2 2 SMART X2S power requirements Power Requirements Power 110 220 VAC 10 50 60 Hz 1 phase 300W Fuse Type 3 15 Time Lag 250 V 5x20 mm It is important to be able to easily disconnect the SMART X2S from mains power in the event of an emergency or for service Do not position the SMART X2S such that it is difficult to disconnect from the mains power supply DOC M86 EXS127 V4 2 3 Introduction to the SMART X2S SMART X2S User Manual 2 3 3 Environment Requirements Table 2 3 SMART X2S environment requirements Environment Requirements Horizontal tabletop countertop or other stable vibration free surface rated for the Installation surface weight of the SMART X2S For additional stability the SMART X2S may be bolted to the installation surface Heat dissipation less than 300 W 1024 btu hr Clearance behind at least 3 7 6 cm for proper airflow and ventilation Clearance above at least 3 91 m for service access Altitude up to 6562 2000 m above
34. f the crate 8 8 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 8 2 3 Uncrating the SMART X2S Moving the Crate to a Staging Location 1 Begin by moving the crate to a staging location clear on all sides where the SMART X2S can be safely uncrated and moved Unscrewing the Crate 1 Use a screw gun to remove the top and sides of the crate Removing the Shipping Materials 1 Remove any miscellaneous items e g documentation accessory kit from the inside of the crate 2 Remove and unpack the four carrying handles that are included with the unit 3 Remove the plastic shipping cover Removing the Unit from the Skid 1 Four bolts attach the SMART X2S two wooden outriggers to the skid Remove them 2 Install the carrying handles by inserting them and rotating them to their locking positions 3 Raise the SMART X2S and turn it 90 so that the two outriggers are elevated off the ground Figure 8 12 Turning the SMART X2S 90 on its skid for removal of outriggers 4 Unscrew and remove the outriggers Moving the Unit to its Installed Location 1 Use the carrying handles to move the unit to its installed location NOTE Observe proper safety and lifting precautions when moving the unit 2 Retain all shipping materials in case the unit must be returned to Bruker DOC M86 EXS127 V4 8 9 SMART X2S Administrator Information SMART X2S User Manual 8 3 Preventive Maintenanc
35. g a 2 mm hex wrench Figure 8 19 Removing the hex bolts DOC M86 EXS127 V4 8 19 SMART X2S Administrator Information SMART X2S User Manual 4 3 Liftthe top cover off the computer compartment and set it aside Figure 8 20 Removing the top cover 4 4 Remove the 4 mm hex bolts in the top left hand and top right hand corners of the drawer Figure 8 21 Top left hand hex bolt 1 8 20 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 4 5 Separate the drawer from the computer chassis and set it aside Figure 8 23 Removing the drawer from the computer chassis 4 6 Remove the drawer panel from the computer compartment DOC M86 EXS127 V4 8 21 SMART X2S Administrator Information SMART X2S User Manual 8 7 2 Replacing the Compact Flash Card 1 Remove the Compact Flash card 1 1 Press the small black eject button next to the card 1 2 Pull the card out of the slot and set it aside Figure 8 25 Removing the Compact Flash card 2 Insert the new Compact Flash card 2 1 Locate the new Compact Flash card Figure 8 26 New Compact Flash card your version number may vary Transcend CompactFlash 8 22 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 2 2 Insert the Compact Flash card into its slot making sure that the card orientation is the same as shown Figure 8 27 Inserting the Compact Flash card or
36. generation of X rays high voltages of 20 60 kV are required Much of the energy supplied to the tube is transferred to heat while less than 1 of it is converted into X rays The anode consists of a metal for example Cu Mo or Cr that produces a characteristic wavelength A water cooling system prevents it from overheating X ray tubes usually have a thin beryllium window by which the X rays escape to the outside The tube is partly clad with a heavy absorbing material such as lead to prevent the X rays emitted in other directions from penetrating to the outside Figure 1 2 Schematic diagram of an X ray tube Electron beam x sU Cathode Cooling water for anode Beryllium window QU pt D Anode positive X ray beam X 7 1 6 DOC M86 EXS127 V4 SMART X2S User Manual About this User Manual Continuous Spectrum When accelerated electrons collide with atoms in the metal target they can be stopped on impact in which case all their energy is converted into radiant energy or they can be decelerated in steps in which case a part of their total energy is released in the form of X rays of greater wavelengths at each step until it is expended The incident electron enters the electric field between the electrons and the nucleus of an atom and is deflected and decelerated by it at the same time This process is repeated when the deflected electron enters the electric fields of other atoms Figure 1 3 Production of co
37. h ofthe left and right displays When the shutter is open an additional red radiation symbol appears on each of the left and right displays DOC M86 EXS127 V4 1 5 About this User Manual SMART X2S User Manual 1 4 4 X ray Safety X ray equipment produces potentially harmful radiation and can be dangerous to anyone in the equipment vicinity unless safety precautions are completely understood and implemented All persons designated to operate or perform maintenance on this instrument must be fully trained on the nature of radiation X ray generating equipment and radiation safety All users of the X ray equipment are required to accurately monitor their exposure to X rays by proper use of X ray dosimeters For safety issues related to operation and maintenance of your particular X ray generator diffractometer and shield enclosure please refer to the manufacturer s operation manuals or to your Radiation Safety Officer The user is responsible for compliance with local safety regulations General Physical Principles of X rays Production of X rays X rays are photons that are emitted when electrons strike a metal target and interact with the electrons orbiting the nuclei of the metal atoms The electromagnetic waves in the A range 0 1 2 are emitted in all directions In X ray tubes electrons are emitted by a heated cathode accelerated and strike an anode material The cathode consists of a tungsten filament For the
38. igure 6 1 Structure view Processing Finished R1 2 62 To view the report press the Forward button to proceed to the report screen DOC M86 EXS127 V4 6 1 Structure View Report Display and CD Burning SMART X2S User Manual 6 1 1 Structure View Button Functions Table 6 1 Structure View button functions left side Button Function Zoom in Zoom into display less of the structure Zoom out Zoom out to display more of the structure Translate up Move the structure up Translate left Move the structure left Translate right Move the structure right Translate down Move the structure down Reset view Undo all translations rotations and zooms Return the structure to the initial view est 6 2 DOC M86 EXS127 V4 SMART X2S User Manual Structure View Report Display and CD Burning Table 6 2 Structure View button functions right side Button Function Atom labels visible Turn atom labels on Atom labels hidden Turn atom labels off Pipes display Display the structure as pipes Ball and stick display Display the structure as a ball and stick model Thermal ellipsoid display Display the structure with ellipsoids representing atomic motion Residual peak visible Show the strongest residual electron density peak i e unassigned peak The strength of the Q peak is represente
39. ile collecting data the SMART X25 displays the current detector frame in the upper right hand corner of the screen Touch the frame to exchange the positions of the Detector Frame and Time Displays providing a larger view To return to the original view simply touch the Time Displays Figure 5 3 Detector frame display Processing ylid 59 0 m Checking Quality 2 E i Acquiring Data Finding Structure J Generating Report Harsobuli n Lima 7 Unat Cell 7 DOC M86 EXS127 V4 5 Data Collection and Structure Solution SMART X2S User Manual 5 1 4 Process Steps To the left of the Time Displays are the Process Steps e Checking Quality e Acquiring Data Finding Structure and e Generating Report As the SMART X2S proceeds through the experiment it moves sequentially through these steps Each step has a status icon Table 5 1 that shows the SMART X25 level of success in performing that step Table 5 1 Process steps status icons Description Successful Successful but there may be a problem with data Unsuccessful unable to perform step Step complete Step not attempted yet 5 2 DOC M86 EXS127 V4 SMART X2S User Manual Data Collection and Structure Solution Checking Quality The SMART X2S begins by collecting data to determine the orientation matrix and evaluating the mosaicity of the crystal Figure 5 4 Checking quality Processing ylid
40. in its User Manual or Specification Sheet and only in conjunction with devices or components from other manufacturers that have been approved or recommended by Bruker AXS This product can only function correctly and safely if it is transported stored set up and installed correctly and if it is operated and maintained as recommended by Bruker AXS If the SMART X2S is used in a manner not specified by Bruker AXS the system s safety features may be impaired 1 4 DOC M86 EXS127 V4 SMART X2S User Manual About this User Manual 1 4 3 Safety related Graphic Symbols The safety related graphic symbols on the SMART X2S chassis need to be fully understood before using the unit Table 1 3 Safety related graphic symbols Symbol Meaning The radiation warning label contains two internationally recognized warning symbols with descriptive text in English and French The power switch uses the two icons 0 and 1 to describe the state of the switch When the switch is off i e 0 is in the depressed position no power is being supplied to the SMART X2S When the switch is on i e 1 is in the depressed position power is being supplied to the SMART X2S and the switch is illuminated green The SMART X2S left and right radiation warning displays each contain two illuminated trefoil radiation symbols When the X ray generator is active but the shutter is closed an orange radiation symbol appears on eac
41. inistrator Information 8 3 3 Surveying the SMART X2S for Radiation Leakage The SMART X2S should be surveyed for radiation leakage and stray radiation as a closed beam X ray diffraction system in accordance with the following documents e Guide for submission of information on Analytical X ray Equipment required pursuant 21 CFR 1002 10 e National Bureau of Standards Handbook III Radiation Safety for X ray Diffraction and Fluorescence Analysis Equipment Radiation surveys should only be performed by or under the immediate supervision of qualified Bruker AXS personnel X ray Emission 1 Perform the X ray emission survey with the X ray tube to be supplied with the instrument operated at a power level of 50kV and 1 mA to produce the maximum X ray exposure Reduce the mA as necessary so as not to exceed the maximum rated power of the tube The test shall be conducted with the supplied optics Individuals performing the survey should wear leaded safety glasses as a precaution Dosage in excess of 2 5 mR hr may be hazardous to the eyes DOC M86 EXS127 V4 8 11 SMART X2S Administrator Information SMART X2S User Manual Radiation Leakage 1 Close the shutter 2 Survey the entire tube housing with the Geiger counter at a distance of 50 mm from the surface of the tube housing to determine areas of high intensity radiation emission 3 When a radiation emission area has been located measure the specific emission averaged over
42. ion 4 5 Entering the Sample Formula After naming the compound the Please enter the sample formula screen appears Figure 4 7 Please enter the sample formula Please enter the sample formula 1 Use the periodic table s element buttons to enter the sample formula NOTE The CHK button checks the formula for consistency and the SUM button sums up separate elements in the entry e g CAHACAHA becomes C8H8 after pressing SUM NOTE The number of atoms can be entered by repeatedly pressing the same key or by using the number pad Figure 4 8 Please enter the sample formula filled in Please enter the sample formula TENE 0 Zu DOC M86 EXS127 V4 4 5 Setting Up Data Collection SMART X2S User Manual NOTE The SMART X2S will learn the 8 most frequently used elements and display them in a bar along the top of the periodic table If the formula is present and valid a green check mark will appear in the lower right hand corner of the screen If the formula is not present or valid this area will display a red X Figure 4 9 Please enter the sample formula red X Please enter the sample formula lad E B bd bd Mj d sue H aa 2 Press the Forward button gt to proceed to the next screen Da DOC M86 EXS127 V4 SMART X2S User Manual Setting Up Data Collection 4 6 Specifying the Crystal Color After entering the sample formula the Please spe
43. ion and structure solution and refinement Designed for the non specialist The automation software combines expert knowledge of structural chemistry with the power of cutting edge data processing for structure solution and refinement at the level of research instrumentation at laboratories worldwide The SMART X2S software automatically determines the structure of most routine organic and coordination compounds Extremely compact lightweight and completely air cooled Requires only standard AC power to operate drawing one tenth the power of a standard diffractometer and Closed beam i e the sample is inserted through an external port and then loaded and aligned automatically users never need to put their hands into the enclosure For more information about the theory behind the SMART X2S refer to Bruker AXS Application Note A86 Exx003 Fundamentals of Single Crystal Diffraction Before using your SMART X2S check that it is properly installed and in proper working order e g that the touch screen interface appears when the system is powered up DOC M86 EXS127 V4 2 Introduction to the SMART X2S SMART X2S User Manual 2 2 Diagrams Figure 2 1 Front panel diagram Sample port Touchscreen Left X ray Right X ray warning lamp warning lamp shutter status shutter status lamp lamp Administrator T key lock Power switch CD drive Figure 2 2 Rear panel diagram Power socket Ethernet port Air intak
44. isotropic displacement parameters Table 5 Hydrogen coordinates x10 and isotropic displacement parameters x10 for ylid x y z U eq H1A 844 8973 3149 75 H1B 859 9179 2304 75 HIC 3117 9200 2738 75 H5 9224 7161 4521 58 H6 9727 5633 5529 68 H7A 4948 7196 1857 91 H7B 2736 7303 1402 91 H7C 3689 5753 1622 91 H8 7217 3796 5779 72 H9 4096 3389 5031 61 7 1 4 Alerts Section Below the Detailed Report section is a list of alerts generated by the SMART X2S 7 6 DOC M86 EXS127 V4 SMART X2S User Manual The Data CD 7 2 Using the Data CD with APEX2 The data CD is designed to work with APEX2 To use the SMART X2S data CD with APEX2 1 2 3 Insert the data CD into the computer s drive If you have a sample open in APEX2 close it Choose Sample gt Archive gt Restore Archive from the Menu Bar The Restore Archived Sample window opens Choose the From CD tab The Using CD Burner field should show the drive you wish to restore from Otherwise use the button to locate the drive Click Get Archive Information from CD and insert the archive CD The archive name appears so that you can check it for name conflicts with the existing samples in the Sample Database shown on the right hand side of the window If there is a conflict you can choose to change the name of the sample in the Restore As field NOTE Ifyou restore an archived sample using the same name as an already existing sample the
45. k drive to the SMART X2S D frames directory by following these steps 1 On the Desktop right click the My Computer icon and choose Map Network Drive The Map Network Drive window opens Set the network drive options 2 1 In the Drive menu choose an available drive letter 2 2 In the Folder menu enter the following smartx2s frames 2 3 Activate the Reconnect at Logon checkbox Set the connection options 3 1 Click the words different user name The Connect As window opens 3 2 Enter a user name smartx2s Administrator 3 3 Enter a password Bruker 3 4 Click OK to exit the Connect As window Click Finish to create the mapped network drive 8 6 Connecting to WebEx WebEx is a network technology that allows remote control of computer systems over the internet In the event of a problem with the SMART X2S Bruker AXS Service personnel can remotely control diagnose and even repair your SMART X2S unit using WebEx NOTE Before connecting the system to WebEx Contact Bruker AXS Service by phone and follow the Service Engineer s instructions Make sure that the system is connected to the internet via the rear Ethernet port To use WebEx with the SMART X2S 1 Insert the SMART X2S Service CD into the CD writer while the system is booting This CD should be present in the lower drawer s right hand compartment After the boot process the SMART X2S Control Panel appli
46. move them to a separate area on the microscope slide Compare the crystals and choose the best one Figure 3 5 Candidate crystals separated from bulk sample 3 3 3 Wetting the Micromount with Adhesive 1 Add a drop of adhesive to the microscope slide away from the chosen crystals We will use this drop to wet the aperture of the micromount Figure 3 6 Adhesive on the microscope slide 3 4 DOC M86 EXS127 V4 SMART X2S User Manual Sample Preparation and Mounting NOTE The adhesive can be used to wash crystallites from the surface of the candidate crystal Be careful that the flowing adhesive does not carry the crystal out of the microscopes s field of view 2 Dip the aperture of the MicroGripper into the adhesive to wet it Figure 3 7 MicroGripper Figure 3 8 MicroGripper aperture in adhesive x Neo DOC M86 EXS127 V4 3 5 Sample Preparation and Mounting SMART X2S User Manual 3 3 4 Attaching the Crystal to the MicroGripper 1 Scoop up the desired crystal so that it is in the center of the MicroGripper aperture NOTE Make sure that the crystal is in the aperture If the crystal is not in the aperture the SMART X2S may not be able to collect data Figure 3 9 MicroGripper near desired crystal a Y Figure 3 10 Crystal in MicroGripper aperture Y 3 6 DOC M86 EXS127 V4 SMART X2S User Manual Sample Preparation and Mounting 3 3 5 Curing
47. ntinuous white radiation e Ejected electron slowed down and changed direction Nucleus Fast incident electron e X ray Electrons Atom of the anode material The waves of X rays generated in this way are called continuous radiation because they form a continuous spectrum of wavelengths DOC M86 EXS127 V4 1 7 About this User Manual SMART X2S User Manual Characteristic Spectrum High energy electrons can also interact with the atoms of the metal target to produce another type of radiation called characteristic radiation because the wavelengths of the photons emitted are characteristic of the anode metal In this case the incident electron collides with an electron of the first innermost electron shell of an atom and knocks it out of its orbit To restore stability to the energy state of the atom the ejected electron is replaced by an electron from an outer shell Because the energy levels of shells increases with their distance from the nucleus of the atom the transition of a replacement electron from an outer to an inner shell is accompanied by a loss in energy which is released in the form of X rays Figure 1 4 Production of characteristic radiation simplified representation e Photoelectron Emission eo M Vv Ko Quant K EN It o o o Electron m Lo Quant Y K Quant Figure 1 4 is a simplified representation of the process by which characteristic radiation is produced
48. oduced in any way including but not limited to photocopy photography magnetic or other record without prior written permission of Bruker AXS Inc Address comments to Technical Publications Department Bruker AXS Inc 5465 East Cheryl Parkway Madison Wisconsin 537 11 5373 USA All trademarks and registered trademarks are the sole property of their respective owners Printed in the U S A Version History Version Changes 0 28 July 2008 Initial release 1 13 January 2009 Expanded and revised 2 27 February 2009 Expanded and revised for CE certification 3 17 September 2009 Expanded and revised 4 25 March 2011 Expanded and revised Bruker Corporation Bruker AXS Inc 40 Manning Road 5465 East Cheryl Parkway M C I A Billerica MA USA Madison WI 53711 5373 USA FO 9001 2008 Certified Phone 1 978 663 3660 Phone 1 800 234 XRAY 9729 er AMA Fax 1 978 667 5993 Fax 1 608 276 3006 E mail info bruker com E mail info brukeraxs com www bruker com www brukeraxs com Table of Contents 1 About this User Manual es 1 1 1 1 The Structure of this User Manual 0 0 0 cee nn 1 1 11 4 We NING Crystal x ut rx et behind the dt a emi Sue 1 2 1 2 Referenced Documentation nananana nnana ee 1 2 1 2 1 Referenced Documentation lll ernennen 1 2 1 3 Terms and Conventions 0 0000 cee eee 1 3 1 9 1 Equivalent F
49. one square cm with the Victoreen 440 RF C ionization detector at a distance of 50 mm from the surface of the tube housing 4 Record the location and measured intensity of leakage radiation on the diagram The leakage radiation shall not exceed 0 5 mR hr Tube Shield Radiation Leakage Survey Form Tube Shield Serial 3 a Ee ee Tel r Leon smywe TT T inchamber SURVEYED BY DATE 8 12 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information Stray Radiation 1 Use the SMART X2S Admin application on the SMART X2S Service CD to open the X ray shutter If you do not have the SMART X2S Service CD available contact Bruker AXS Do not attempt to open the X ray shutter in any other way unless specifically directed by Bruker AXS personnel 2 Survey the entire SMART X2S cabinet with the Geiger counter at a distance of 50 mm from the surface to determine areas of high intensity radiation emission 3 When a radiation emission area has been located measure the specific emission averaged over 100 square cm with the Victoreen RF C ionization detector at a distance of 50 mm from the surface of the goniometer cabinet 4 Record the location and measured intensity of stray radiation on the diagram The stray radiation shall not exceed 0 5 mR hr DOC M86 EXS127 V4 8 13 SMART X2S Administrator Information SMART X2S User Manual System Cabinet Radiation Survey Form
50. ong its edges pulling up slightly to make sure that the drawer does not bind against the surface the SMART X25 is sitting on and pulling outward Figure 8 2 Lower drawer open 8 2 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 3 If necessary the hinged upper portion of the system case can be raised for access to the generator detector goniostat sample loader et al Opening or closing the SMART X2S hinged upper cover creates a pinch hazard Be aware of this hazard whenever the upper cover is raised Figure 8 3 Hinged upper cover open 8 1 3 SMART X2S Compartments After opening the lower drawer with the Administrator key three compartments are visible e The leftmost compartment is a storage compartment and typically contains the system s USB keyboard and other miscellaneous items e The middle compartment contains a series of power supplies and distribution modules for the SMART X2S interior components and e The rightmost compartment contains the system computer DOC M86 EXS127 V4 8 3 SMART X2S Administrator Information SMART X2S User Manual 8 2 Moving the SMART X2S 8 2 1 Moving the SMART X2S over Short Distances When moving the SMART X2S over short distances Make sure that the system is powered down and unplugged Make sure that the system s path is clear from its current location to its destination e Use a suitable four wheeled cart or dolly and e Atta
51. onto the skid Figure 8 8 SMART X2S on shipping skid SMART X25 k 3 Attach the SMART X2S outriggers to the skid with the four 9 16 bolts It may be necessary to move the SMART X2S around on top of the skid to get the outriggers holes and the skid s holes to line up 8 6 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information Dressing the SMART X2S for Shipping After the SMART X2S is securely attached to the skid add the protective plastic cover and additional components 1 Slide the protective plastic cover over the SMART X2S Figure 8 9 Plastic cover 2 Wrap the carrying handles in bubble wrap and place them along the rear of the SMART X2S chassis Figure 8 10 Carrying handles along rear DOC M86 EXS127 V4 8 7 SMART X2S Administrator Information SMART X2S User Manual 3 Include any extra items to be shipped with the SMART X2S by bagging them and placing them along the top of the unit these may include the Accessory kit the USB keyboard and any documentation These items will be placed down along the sides of the unit when the crate is screwed together Figure 8 11 Extra items Screwing the Crate Together 1 Use a screw gun and wood screws to attach the sides of the crate 2 Move the additional materials from the top of the SMART X2S down into the bottom of the crate on one of the sides 3 Finally use the screw gun and wood screws to attach the top o
52. ory The SMART X2S does not have any intrinsic virus protection software installed and is therefore vulnerable to external network threats Protecting your SMART X2S from malware is your responsibility and Bruker AXS is not accountable for any inoperability or data loss as aresult of connectivity to a network Connect the Computer to the SMART X2S The preferred method of remote access to the data on your SMART X2S hard drive is to use an isolated private network configuration This consists of a computer with two separate network cards a router with DHCP and the SMART X28 The SMART X2S is set up to obtain an IP address automatically when connected to a DHCP enabled intranet connection 8 5 2 NOTE 1 Use a standard network cable to connect the computer s secondary network interface card to the router 2 Use a standard network cable to connect the Ethernet port on the SMART X2S rear to the router 3 Plug the router s power supply into a standard outlet Check that the SMART X2S Has a Dynamic IP Address Before checking be sure that the USB keyboard is connected Type Ctrl Alt Del Choose Task Manager Click the New Task button and type cmd a dq qe x At the command prompt type ipconfig to reveal the IP address assigned to the SMART X25 DOC M86 EXS127 V4 SMART X2S User Manual SMART X2S Administrator Information 8 5 3 Connect the SMART X2S to the Isolated Private Network Map a networ
53. r lung cancer and skin cancer e Radiation induced cancers may take 10 15 years or more to appear There may be a risk of cancer at low doses as well DOC M86 EXS127 V4 1 11 About this User Manual SMART X2S User Manual 1 4 5 Beryllium Safety This product contains beryllium a toxic metal used in the radiation outlet window of the X ray optics Fumes or dust from beryllium and its compounds can be hazardous if inhaled Beryllium must not be cut machined or handled under any circumstances Disposal of beryllium must comply with all applicable national state and local regulations 1 4 6 Perchlorate Safety The SMART X2S uses a lithium coin battery that contains perchlorate a hazardous material Disposal of perchlorate must comply with all applicable national state and local regulations 1 12 DOC M86 EXS127 V4 SMART X2S User Manual About this User Manual 1 5 Help and Technical Support 1 5 1 Help within the Interface Context sensitive help is available by simply pressing the Help button on the touchscreen Figure 1 7 Figure 1 7 Help button 1 5 2 Technical Support from Bruker Service Centers You are invited to contact Bruker AXS whenever there are problems or questions related to the system Before contacting Bruker AXS please Have the system s serial number available e Determine the system s software version if you suspect a software problem e Record any error messages that appear and
54. ration and Mounting Lese 3 1 3 1 Sample Preparation Overview es 3 1 3 2 The Bruker Spine PID lt 3 4 50 53 039 ee PS ea et ie ea 3 2 3 2 1 Reusing Bruker Spine Pins 0 0000 cece nenn 3 2 3 3 Sample Preparation Procedure eee lererns 3 3 3 3 1 Identifying Suitable Crystals llle 3 3 3 3 2 Separating the Crystals 2 222 llle 3 4 3 3 3 Wetting the Micromount with Adhesive 000 0 eee 3 4 3 3 4 Attaching the Crystal to the MicroGripper 3 6 3 3 5 Curing the Adhesive with Ultraviolet Light 3 7 Setting Up Data Collection 0 0 cee 4 1 4 1 The SMART X2S Touchscreen Interface 4 1 AAS Man IBUMONS s dob tet prn Seh Irre ey sc 4 1 4 2 Ihe welcome SCreen 244 534 sas ae einer 4 2 4 3 Inserting an Empty CD iuis bie sad oe ea se 4 2 4 4 Naming Your Sample 2232 9 Et ieee ee eta 4 4 4 5 Entering the Sample Formula 0 000 cee eee 4 5 4 6 Specifying the Crystal Color 0 0 ces 4 7 4 7 Specifying the Crystal Shape 0 0 cece es 4 8 4 8 Specifying the Crystal Size 1 es 4 9 4 9 Selecting the Redundancy Mode ees 4 10 4 10 Inserting the Sample ses a Siete wel eth ee ee Sa ne Su wk Be ae 4 11 Data Collection and Structure Solution 5 1 5 1 TNE Processing Screen u
55. ration and Mounting To study a sample with the SMART X2S the sample must be mounted on a Bruker Spine Pin 3 1 Sample Preparation Overview The process of sample mounting is simple from the many crystals within a bulk sample identify the best candidate for study and affix it to the Bruker Spine Pin with a special ultraviolet curable adhesive Once the adhesive is cured the sample is ready for use with the SMART X2S You will need Your bulk sample e A microscope for identifying suitable candidate crystals for study e A preparation needle or other tool for separating the candidate crystals e A Bruker Spine Pin micromount and cap Ultraviolet curable adhesive to fix the crystal on the Bruker Spine Pin and e An ultraviolet penlight for rapidly curing the adhesive DOC M86 EXS127 V4 3 Sample Preparation and Mounting SMART X2S User Manual 3 2 The Bruker Spine Pin The Bruker Spine Pin uses a MiTeGen MicroGripper precision manufactured to work properly within the SMART X2S The Pin has a magnetic cap that protects the sample The crystal needs to be attached across the crystal aperture at the tip of the MicroGripper Figure 3 1 Bruker Spine Pin with cap crystal aperture at tip of MicroGripper Crystal Aperture MiteGen MicroGripper NOTE When attaching the crystal be sure to attach it to the inner surface of the MicroGripper Figure 3 2 The inner surface will be readily visible under the
56. rstand graphical feedback about the status and quality of the structure determination process 4 1 1 Main Buttons Table 4 1 SMART X2S main buttons Button Function Forward Proceed to the next screen Back Ignore any data entered on the current screen and return to the previous screen Back to beginning Ignore all data entered and return to the Welcome Screen Forward to CD burning Proceed to the CD burning phase skipping all steps in between Help Press at any time for context sensitive help Stop Stop the instrument When pressed you are prompted to confirm When you confirm all internal movement stops and the experiment is aborted Discard report Throw away the report generated from the current dataset and return to the Welcome screen DOC M86 EXS127 V4 4 1 Setting Up Data Collection SMART X2S User Manual 4 2 The Welcome Screen The system displays a Welcome screen Touch the Welcome screen anywhere to begin Figure 4 1 Welcome to the SMART X2S Welcome to the SMART X2S 4 3 Inserting an Empty CD After touching the Welcome screen the Please insert an empty CD screen appears Figure 4 2 Please insert an empty CD Please insert an empty CD Checking for an empty writable CD m O e gt 1 Insert an empty CD label side up into the slot on the front of the SMART X2S
57. safety features designed into the equipment guarantee that the emitted radiation does not exceed 1 0 uSv h at 5 cm from any external surface of the device during operation This level is below the regulatory limit in all jurisdictions The ICRP dose limits in Publication 60 and 103 to the whole body for a radiation worker averaged over a 5 yr period is 20 mSv in a year and for a member of the public it is 1 mSv in a year It is highly unlikely that the radiation worker dose limits will be exceeded when trained and qualified personnel use such devices Read Section 1 4 4 X ray Safety before turning on the system Please observe local regulations for the operation of X ray systems If you suspect that the safety system does not work correctly or that radiation protection is impaired for any reason immediately switch off the system and contact your local Bruker AXS Service Representative Manipulations and modifications of the safety systems are strictly forbidden NOTE The X ray generator is controlled by a two position Keyed switch OFF ON similar to the ignition switch of a car The key can only be removed when the switch is in the OFF position The switch will remain in the OFF position until the key is inserted and turned Therefore the removal of the key will terminate production of X ray 1 4 2 Correct Usage of the SMART X2S The SMART X2S is intended for benchtop use only The SMART X2S may only be used for the applications specified
58. sea level Ambient temperature range 59 77 F 15 25 C Ambient humidity range 20 80 non condensing NOTE The SMART X2S is designed for indoor use only 2 3 4 Other Specifications Table 2 4 SMART X2S other specifications Specification Value SMART X2S Electronic Components Overvoltage l Category SMART X2S Pollution Degree 2 X ray Tube 50 W microfocus tube molybdenum anode air cooled l Toroidally curved Si crystals for three dimensionally focused X ray Optics l l monochromatic X rays with very high flux density CCD Detector Air cooled no spatial distortion Sample Mount Type Bruker Spine Pin Low temperature Device optional Supports DTC Desktop Cooler low temperature device Data Collection Resolution To IUCr standards 2 4 DOC M86 EXS127 V4 SMART X2S User Manual Introduction to the SMART X2S 2 4 Startup and Shutdown 2 4 1 Starting Up the SMART X2S 1 Some SMART X2S units have a safety key switch that must be unlocked before the system can be turned on If you have a safety key switch turn it to the On position 2 Press the power switch on the front panel to the On position The power switch illuminates Figure 2 4 Power switch The system beeps and the touchscreen displays the system BIOS during the CPU s self test After about one more minute the SMART X2S begins to initialize First the instrument initializes tts serial ports
59. size screen appears Figure 4 14 Please specify the crystal size Please specify the crystal size Minimum Size Medium Size Maximum Size 1 Use the touchscreen controls to set the dimensions of the crystal NOTE Ifthe size is not known or not necessary press the SKIP button at the bottom of the screen Figure 4 15 Please choose your crystal s size 0 50 mm x 0 50 mm x 0 60 mm chosen Please specify the crystal size Minimum Size 0 50 mm Medium Size Maximum Size M w D 2 Press the Forward button 7 to proceed to the next screen DOC M86 EXS127 V4 4 9 Setting Up Data Collection SMART X2S User Manual 4 9 Selecting the Redundancy Mode After specifying the crystal size the Please select the redundancy mode screen appears Figure 4 16 Please select the redundancy mode Please select the redundancy mode 1 Use the touchscreen controls to select the redundancy mode for the data collection The button on the left activated by default chooses standard redundancy mode 3 data collections The button on the right chooses extended redundancy mode 6 data collections NOTE When extended redundancy mode is used the data collection time will be approximately twice as long as in standard redundancy mode 2 Press the Forward button to proceed to the next screen B10 DOC M86 EXS127 V4 SMART X2S User Manual Setting Up Data Collec
60. t R 2 89 for the observed data and wR 7 65 for all data The goodness of fit was 1 046 The largest peak on the final difference electron density synthesis was 0 14 e and the deepest hole was 0 20 e with an RMS deviation of 0 04 On the basis of the final model the calculated density is 1 376 g cm and F 000 432 APEX2 Version 2 2 Bruker AXS Inc 2007 SAINT Version 7 34a Bruker AXS Inc 2007 SADABS Version 2007 2 Sheldrick Bruker AXS Inc XPREP Version 2005 2 Sheldrick Bruker AXS Inc XS Version 2008 1 George M Sheldrick Acta Cryst 2008 A64 112 122 XL Version 2008 1 George M Sheldrick Acta Cryst 2008 A64 112 122 7 2 DOC M86 EXS127 V4 SMART X2S User Manual The Data CD 7 1 2 Molecule Viewer Section The molecule viewer allows for inspection of the structure The molecule can be rotated and displayed in various modes e g ball and stick space filling CPK model molecule surface and bond lengths angles and torsions can be measured The molecule viewer uses Jmol an open source Java viewer for chemical structures in 3D Full documentation for Jmol is available at http jmol sourceforge net Figure 7 2 Molecule viewer section ylid Windows Internet Explorer fel x a e le D reportireport html 4 X 7 Live Search p X File Edit View Favorites Tools Help w Favorites yia O a Pager Safety Tools e Reset Hold left mouse button
61. ta collection temperature was 27 C Data were acquired using three sets of Omega scans at different Phi settings The frame width was 0 5 with an exposure time of 5 0 s The detailed data collection strategy was as follows Detector distance 40 mm Detector swing angle fixed 2 Theta 20 Run Omega start Omega end Phi Frames 1 20 0 160 0 0 0 360 2 20 0 100 0 120 0 240 3 20 0 40 0 240 0 120 APEX2 software was used for preliminary determination of the unit cell Determination of integral intensities and unit cell refinement were performed using SAINT The integration of the data yielded a total of 6711 reflections to a maximum 0 angle of 25 35 0 83 A resolution The constants for the orthorhombic unit cell are a 5 9724 2 A b 9051202 c 18 4171 8 A V 995 58 7 A They are based upon the refinement of the XYZ centroids of 3191 reflections above 20 0 I o T with 2 21 0 25 25 Data were corrected for absorption effects with SADABS using the multiscan technique The ratio of minimum to maximum apparent transmission is 91 6 100 The average residual for symmetry equivalent reflections is R 2 35 and R 2 32 XPREP determined the space group to be P 21 21 21 with Z 4 for the formula unit C H O S The structure was solved with XS and subsequent structure refinements were performed with XL The final anisotropic full matrix least squares refinement on E with 129 variables converged a
62. the structure determination the SMART X2S generates the report that will appear on the CD The report can be previewed prior to burning the CD Figure 5 7 Generating report Processing ylid v Finding Structure a Generating Report Fartolution Limit 0 84 Amgstroms Unit Coll 475 96 b 9 05 c 18 36 a 90 0 pe s0 00 yon 00 Symmetry aP Rl 282 Overall Progress DOC M86 EXS127 V4 SMART X2S User Manual Data Collection and Structure Solution 9 2 Aborting Data Processing If you touch the us button while collecting or processing data the SMART X2S will stop After the system has stopped choose whether to delete the collected data or write it to the CD Figure 5 8 Data Processing Aborted screen Data Processing Aborted Save Data 5 s wy If you choose to delete the collected data the system deletes the data and returns to the Welcome screen FN To write the data to the CD press the m gt button The system then proceeds to the CD Writing screen DOC M86 EXS127 V4 5 5 Data Collection and Structure Solution SMART X2S User Manual This page intentionally left blank 5 6 DOC M86 EXS127 V4 6 Structure View Report Display and CD Burning 6 1 Structure View After refining the structure and generating the report the SMART X2S displays the structure in a 3D view that can be manipulated by simply touching the touchscreen The structure appears in standard CPK colors F
63. through the transition of electrons at the atomic level In this diagram the conventional notation for the electron shells and the photons produced by the transition of their respective electrons has been adopted Ka radiation is produced by an electron transfer from shell L to shell K K by a transfer from shell M to shell K and La by a transfer from M to L Note that the photons have different characteristic wavelengths 1 8 DOC M86 EXS127 V4 SMART X2S User Manual About this User Manual In fact on closer examination of the atom and its electron shells it can be seen that the shells are divided into subshells as shown in Figure 1 5 below For this reason Ka radiation can be divided into Ka and Ka radiation KB radiation into KB and KB radiation and so on The difference between the wavelengths of photons produced by the transfer of electrons of different subshells within the same shell is very small Figure 1 5 Subshells and their transferred electrons DOC M86 EXS127 V4 1 9 About this User Manual SMART X2S User Manual In Figure 1 6 below the wavelength distribution of both continuous and characteristic radiation is shown as a function of intensity or the number of pulse counts per second The characteristic peaks Ka Ka and K are clearly visible above the continuous spectrum The point on the wavelength scale at which the continuous spectrum begins is known as the short wavelength limit SWL and corresponds to the
64. tion 4 10 Inserting the Sample After specifying the crystal size the SMART X2S prompts for the sample Figure 4 17 Please insert your sample to begin processing Please insert the sample 1 Insert the sample vial into the sample port on the front of the SMART X2S NOTE Leavethe protective cap on the sample when inserting it Figure 4 18 Inserting the sample The sample loader mechanism automatically moves the sample into the SMART X28 After inserting the sample the SMART X2S automatically aligns it and begins collecting data DOC M86 EXS127 V4 4 11 Setting Up Data Collection SMART X2S User Manual This page intentionally left blank BaD DOC M86 EXS127 V4 5 Data Collection and Structure Solution 5 1 The Processing Screen 5 1 1 Time Displays The Time Displays give at a glance information about the data collection process Time Remaining and Elapsed Time are presented Figure 5 1 Time Displays H at CL Time Remaining no 02 5 wigs 5 1 2 Crystal Information Below the Process Steps and Time Displays are the Crystal Information area which gives at a glance information about the crystal Resolution Limit Unit Cell parameters Symmetry and R1 These readouts update as data is collected Figure 5 2 Crystal Information area Resolution Limit 0 84 Angstroms Unit Cell a 5 94 b 9 05 c 18 36 a 90 00 B 90 00 y 90 00 Symmetry oP R1 2 90 5 1 3 Detector Frame Display Wh
65. u aca qiero a aan 5 1 9 14 Time Displays ax codicis it EE RR LAU Edo res 5 1 5 1 2 Crystal Information tic 2 4 22 6 005 Geom enm Gok trea CURES ne rare 5 1 5 1 3 Detector Frame Display 0 0 0 0 nn 5 1 9 14 PROCESS Steps 4 254 orte Heed bee hte SERE Rat Be 308 reed do a BR he 5 2 9 2 Aborting Data Processing es 5 5 Structure View Report Display and CD Burning 6 1 6 1 Structure VIEW zu Sara RE aua du auda ebenen 6 1 6 1 1 Structure View Button Functions 0 0 0 0 00 cee eee 6 2 6 2 Report Display zu 2 dea M an ar deo Sea EX deg ee casada d Ge 6 4 6 3 CD BUNIN suicidio ee ese ae Sy Seat tale 6 5 DOC M86 EXS127 V4 SMART X2S User Manual Table of Contents 6 4 Removing the CD and Sample 0 02 ccc ee 6 5 7 The Data CDs ae RIPE e Nard ees abl d uk eae SS 7 1 7 1 The Crystallographic Report 0 00 ces 7 1 1 1 1 Report Summary Section 20 0000 ees 1 2 7 1 2 Molecule Viewer Section 0 0 0 cc ee eee 1 3 7 1 3 Detailed Report Section 0 0 0 0 cc eee 7 4 TVA Alens SOCOM asado a aac ur anne 7 6 7 2 Using the Data CD with APEX2 leeren 7 7 8 SMART X2S Administrator Information 8 1 8 1 Access to the SMART X2S Interior 222220 ne nn nun 8 1 8 1 1 Administrator Key and Accessories Kit Lun 8 1 8 1 2 Opening the SMART X2S Chassis 2 2 onen 8 2
66. y and Accessories Kit Administrator Key The Administrator key is shipped with the SMART X2S It allows access to the interior of the instrument including the storage compartment and computer drawer in the lower portion of the unit NOTE One individual should be designated as the SMART X2S instrument administrator and this individual should retain the key to prevent unauthorized access to the SMART X2S interior The upper portion of the SMART X2S which contains the X ray source contains no user serviceable parts and should only be opened by qualified Bruker AXS personnel Accessories Kit The SMART X2S Accessories Kit shipped with the SMART X2S unit and initially located in the internal accessory compartment contains the following items e Applicable documentation Bruker Spine Pins e Blank CD ROM media e Three standard crystals for performance verification YLID Aspirin Tartaric acid e A crystal preparation tool e Ultraviolet curing adhesive and e An ultraviolet penlight for curing the adhesive DOC M86 EXS127 V4 8 1 SMART X2S Administrator Information SMART X2S User Manual 8 1 2 Opening the SMART X2S Chassis 1 Insert the Administrator key and turn it to the 12 o clock position Figure 8 1 Administrator key at 12 o clock position The system s lower drawer will now open giving you access to the storage compartment power supplies and computer 2 Open the lower drawer by holding it al

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