Structure Solution and Refinement with OLEX2

Transcription

1 Structure Solution and Refinement with OLEX2 By Carla Slebodnick Department of Chemistry, Virginia Tech This version: 29 July 2014 (software version Olex , Compilation Info: svn.r2960 MSC: on WIN64 for OlexSys) This document was originally written for the Virginia Tech Crystallography Lab. Any comments or suggestions regarding the document should be addressed to Dr. Carla Slebodnick, Depart of Chemistry, Virginia Tech, Blacksburg, VA. Phone: (office); (lab). The purpose of this manual is to guide new users through the process of solving and refining a crystal structure using OLEX2 by way of a worked example. It is not intended to be comprehensive it covers structure solution and refinement for a routine sample without significant problems. Contents 6.1 Structure Solution 6.2 Structure Refinement 6.3 Generating the Final Merged CIF 6.4 Structure Validation Using CheckCIF 6.5 Publication 6.6 Generating Figures OLEX2 Manual Page 1 of 10

2 CS905 SAMPLE BACKGROUND Reference: Rossini, A. J.; Hung, I.; Johnson, S. A.; Slebodnick, C.; Mensch, M.; Deck, P. A.; Schurko, R. W. J. Am. Chem. Soc. 2010, 132 (51), Formula: C 14 H 20 Br 2 OSi 2 Zr Data collection: Agilent Gemini Ultra S Diffractometer with Mo-radiation at 100 K OLEX2 is a graphical user interface (GUI) with underlying structure solution and refinement software for solving and refining crystal structures. The GUI has with 3 main components: Main GUI: This is the GUI control system. It is divided into 5 panels: Home, Work, View, Tools, and Info. Graphics Display Window: Graphically display of the structure model. Also scrolls text output. Command line: enter typed commands. Output from commands will be displayed in the Graphics Display Window. Graphics Display Window Main GUI Panel Command Line OLEX2 Manual Page 2 of 10

3 6.1: Structure Solution 1) Open OLEX2. Click File Open. Browse and open cs905.hkl. 2) Enter lines -1 in the command line to view output details. 3) In the main GUI panel, click Work. Click the down triangle next to the Solve to expand the Solve window. Set the Solution Program to ShelXS. Click Solve. After viewing the output that scrolls down the Graphics Display Window, type lines 10 to reduce the amount of text obstructing the graphics window. 4) The graphics window shows your structure solution, which should resemble the figure at right. 5) Expand the Toolbox Work subpanel to gain access to the most useful visual/refinement controls. 6) The gold spheres are Q-peaks. Click to toggle between showq/showq+bonds/hideq until Q+bonds shows. Use your mouse to rotate your structure solution on the screen and try to identify the molecule amid the other nonsense. NOTE: If the molecule appears to be fragmented, click to assemble the molecule. NOTE: If the structure has internal symmetry and only a fraction of your molecule appears (e.g. Z =½), type grow in the command line to see the entire molecule. 6.2: Structure Refinement 6.2.1: Locate atoms and perform the initial refinement cycles. 1) F3 to toggles between show/hide atoms labels. Show the atom labels. 2) Select atoms that you know are nonsense selected atoms will turn green. Delete these atoms by right clicking and selecting Delete in the menu that appears. To deselect an atom, just click on it again so that it is no longer highlighted green. 3) Develop a systematic naming scheme for your compound. For cs905, use the numbering scheme at right. To name the atoms: a) Expand the Work Naming subpanel. b) Set Start = 1 and Type = Br. Click Name and select the two Br atoms to rename them Br1 and Br2. Hit Esc. c) Set Start = 1 and Type = Si. Click Name and select the two Si atoms to rename them Si1 and Si2. Hit Esc. d) Continue this procedure for the O and C atoms O 14 Si 1 Si Zr Br Br 2 1 OLEX2 Manual Page 3 of 10

4 NOTE: To name individual atoms, type name [current atom name] [new atom name] in the command line. For example, to rename Br3 to Br1, type name Br3 Br1. NOTE: If you make a mistake and want to start over again, type edit res to open cs905.res in a text editor. Save and close the file. The graphic display will return to the original model. My initial model is show at below. The methyl groups on Si2 are still missing. They will appear after the next refinement cycle. 4) In the Work panel, click the down arrow next to the Refine button to expand the Refine window. Expand the Refinement Settings Extra subpanel and check/set the following parameters. a) Refinement Program = ShelXL b) Refinement Method = Least Squares c) Weight: Check Auto update when R1 < 15.0% d) TEMP: Check the TEMP box. Enter the data collection temperature in C. (For cs905, entere -173.) e) ACTA: Check the ACTA box. Enter the 2thetafull cutoff value (For cs905, use 60.) 5) Click Refine. When the refinement is finished, a new structure model will appear on the display screen and refinement statistics will be displayed. Type lines -1 to text output. To view more statistics, expand the Info Refinement Indicators subpanel. 6) In the structure model displayed, label any new non-h atoms (e.g. C13 and C14). Delete all remaining Q-peaks by typing kill $q. OLEX2 Manual Page 4 of 10

5 7) Repeat the refinement step until all non-hydrogen atoms have been located/labeled and maximum shift < ) Sort the atoms in your instruction file. Scroll to the bottom of the Work panel and expand Sorting. The various pull-down menus allow you to set sorting priorities. Use the defaults and click Sort. In the command line, type edit ins to view the latest cs905.ins file to view your sorted list. Close the file : Anisotropic Refinement of non-hydrogen atoms. 1) In the Work Toolbox Work subpanel, click the anisotropic displacement ellipsoid. This will automatically set all non-hydrogen atoms anisotropic and run a cycle of refinement. 2) View your drawing in ellipsoid form. Select the View subpanel, expand the Quick Drawing Styles, and click Ellipsoids H. Your drawing should resemble the drawing at right (Q-peaks are hidden). 3) Look for 'non-positive definite' atoms and unreasonable displacement parameters. 4) Repeat the refinement until maximum shift < : Add Hydrogen Atoms 1) Hide all Q peaks by toggling. 2) In the Work Toolbox Work subpanel, click. Look over your molecule carefully software doesn t always assign H-atom positions correctly! NOTE: To assign H-atom positions manually (not necessary for cs905), use the Tools Hydrogen Atoms subpanel. NOTE: OLEX2 automatically assigns the H-atom names. If you prefer a custom naming scheme, in the Work Naming subpanel, UNcheck Automatic Hydrogen Naming. Then proceed with renaming the H-atoms. NOTE: If you want to refine an H-atom position (e.g. for H-bonding), but constrain U iso, right click on the H-atom, select Uiso, and chose your preferred constraint : Completing the Refinement 1) Center your molecule in the unit cell. Expand the View Symmetry Generation Symmetry Tools subpanel and click Center on Cell. 2) Return to the Work panel. Continue cycling through refinements until the data converges. Set the Maximum Refinement Cycles = 10 to help reach convergence. OLEX2 Manual Page 5 of 10

6 6.3: Generating the Final Merged CIF We will merge two CIFs into one CIF called name.cif. The files that we will combine are: name.cif_od (e.g. cs905.cif_od): Contains instrument parameters and data collection details. This file is created by Agilent s CrysAlisPro software. name.cif (e.g. cs905.cif): Contains structure solution and refinement parameters and metrical parameters. This file is created by SHELXL or olex2.refine. NOTE: The *.cif_od file is specific to Agilent instruments. Other manufacturers have an equivalent file under a different name. 1) In the main GUI panel, click Work. Click the down triangle next to the Report button to expand the Report window. 2) A CIF Conflicts window will likely appear. This occurs for any entries that are not perfectly duplicated between name.cif and name.cif_od. For each conflict listed, click on your preferred value, or manually enter a user value. 3) Work through the different menus according to the instructions below: Collection: This is self-explanatory. Entries are optional. Crystal: Follow the specific directions below. Systematic Name: skip unless submitting to IUCr journal. Colour: Values should automatically upload from name.cif_od. Manually enter values if none are reported. (cs905 is colorless.) Size: Values should automatically upload from name.cif_od. Manually enter values if none are reported. Shape: Values should automatically upload from name.cif_od. Manually enter a value if none is reported. (cs905 is a prism.) Preparation Details: Optional. Crystallization Details: Optional. Crystal Mounting: Optional. Diffraction: Follow the specific directions below. Diffractometer: Leave as default. Definition File: Leave blank. Diffraction T and Cell Measurement T: Values should automatically upload from name.cif_od. Manually enter values if none are reported. Special Details and Refine Special Details: Enter experimental and refinement details such as twinning or disorder models. (Leave as default for cs905.) Absorption Correction: Details should automatically upload. Manually enter values if none are reported. OLEX2 Manual Page 6 of 10

7 Publication: If you are submitting the structure for publication, enter the submission information here. Reference: If the structure has been published, enter the publication information here. Source File: This should automatically link to name.cif_od (e.g. cs905.cif_od). 4) If your space group is acentric, select the absolute structure determination method from the pull-down menu: Anomalous dispersion: Absolution configuration determined from anomalous dispersion effects. Reference molecule: Absolute configuration established by co crystallizing with a chiral reference molecule of known absolute configuration. Reference molecule + AD: Absolute configuration established by by co crystallizing with a chiral reference molecule of known absolute configuration and confirmed by anomalous-dispersion effects. Synthesis: Absolute configuration has not been established by anomalous-dispersion effects. The enantiomer has been assigned by reference to an unchanging chiral centre in the synthetic procedure. Unknown: Absolute configuration is unknown, there being no firm chemical evidence for its assignment to hand and it having not been established by anomalousdispersion effects in diffraction measurements on the crystal. An arbitrary choice of enantiomer has been made. Not applicable. 5) Click. The software will combine any information entered manually with name.cif and name.cif_od. The merged cif will automatically open in a text editor. Browse the file and check that entries are correct. 6) Replace the data name _shelx_res_file with _iucr_refine_instructions_details. 7) File Save. Close the file. OLEX2 Manual Page 7 of 10

8 6.4: Structure Validation Using CheckCIF Run your CIF through CheckCIF, an automated structure checking program that checks for a variety of common and no-so-common errors in crystal structure determination. 1) On Olex2, click. Wait for a PDF report to appear and review carefully. The report is automatically saved to your Refinement folder as name_cifreport.pdf. NOTE: If the CheckCIF Alerts require additional refinement cycles, you must repeat Section 6.3, Steps 5-7 (i.e. merging CIFs) after completing the refinements. 2) Once you are satisfied with your CheckCIF analysis, reaname your CIF as name_final.cif. 6.5 Publication Congratulations! Your structure is ready for publications. Some final comments about publishing or presenting crystal structures: 1) The final CIF should be approved by the local crystallographer. 2) Deposit the final CIF with the CCDC and reference the CSD number in the manuscript. (Bonus not covered in the document OLEX2 has automated features for submitting the CIF to the CCDC). 3) A set of tables in HTML format can be generated quickly in OLEX2 by clicking. To generate tables for manuscripts in MSWord format, use ciftab. 4) A guide for generating figures is included below (Section 6.6). 5) An experimental section should be written and included in the main manuscript or Supporting Information. 6) The final draft of the manuscript should be reviewed by the crystallographer, specifically to check the crystallographic contributions for accuracy. 7) Send the crystallographer the final reference for papers and abstracts. Crystallographers need to justify our existence to various university departments, and state and federal agencies! OLEX2 Manual Page 8 of 10

9 6.6: Generating Figures (See Appendix G for a sample figure) 1) Under, play with the graphics display options. Quick Drawing Style: Try the different drawing styles. Symmetry Generation: These tools allow you to show/hide unit cell, grow all or portions of your structure, display H-bonding, and generate packing diagrams. Play around. To return to your original model, in the Symmetry Tools submenu, click Fuse. Geometry: Calculate metrical parameters, including mean planes and π-π interactions. 2) Under, expand the Images subpanel to view your options. Figures can be generated as Bitmaps (bmp, jpg, png, tif), Postscript, or Povray formats. Use Image Series to generate a movie of the structure rotating. Label, change atom colors, and further adjust your image, according to the following guidelines: Adding Labels: Refer to the instructions directly under the Images bar (and elaborated upon below). 1. To prevent confusion, toggle the screen labels off (press F3). 2. On the graphics window, select the atoms you want to label and click Label selected atoms. Or just click non-h atoms. You can also use this feature to label specific bond lengths select the bond instead of the atom. NOTE: If you make a mistake and need to start over (i.e. delete all labels), select any one label (it will highlight in green), type Ctrl+A, and click Delete. 3. Move labels with left mouse button while holding down Shift. 4. Change the label color by clicking choose the label color. Double click the colour for Ambient Front and choose your preferred color from the pallet. Changing atom colors: Right click on an atom for which you want to change the color. In the menu that appears, choose Graphics and Draw style. A Material Parameters window opens the options available in this window are dependent on the drawing style of the selected atom (e.g. ball-and-stick vs. ellipsoid). The options described below appear if an ellipsoid is selected. 1. Primitive: Sphere = select to change atom color; Rim = select to change boundary and octant lines color. 2. Apply to: typically choose Atom Type (e.g. to change color of all Br atoms) or Individual Atom (to change color of only the selected atom). 3. Change colors by double clicking on Ambient Front and choosing from the color pallet. (I have no idea what the other colors do.) NOTE: bond and screen background colors can be changed in a similar manner (e.g. right click on a bond to access the corresponding Draw style window). Polyhedral drawing hints: 1. Right click on the atoms you want to represent as polyhedra (usually 4-, 5-, or 6- coordinate metals). OLEX2 Manual Page 9 of 10

10 2. Select bonds --> the expected number of bonds. (this deletes any M---M bonds that may have been drawn). 3. After you are happy with the number of bonds around the metals, select all the metals you want represented as polyhedra. Right click. Select polyhedron-->auto. 4. Use Grow and Pack options to generate extended structure. 3) Generating Bitmap Images (i.e. png, jpg, bmp, or tif): Less self-explanatory entries are described below. When you are happy with the settings, enter a Name and click Go. The file will automatically be written to your refinement folder. Transparent Background: Makes background transparent so that you can paste other images behind your structure. Press F4 until the screen background is white. (Note I ve only been successful getting a transparent background in PNG format). Trim: adds a frame to the figure. Padding and Border defines interior and exterior borders, respectively. Colour sets the color of the exterior border in hexadecimal color code. A quick web search will reveal the color codes. Atom Label Font and Bond Label Font, Type, and Size are self-explanatory. 4) Generating Postscript Images (i.e. ellipsoid drawings in eps format): Less self-explanatory entries are described below. When you are happy with the settings, enter a Name and click Go. EPS files can be converted to other formats with GSView (freeware) or Adobe Distiller. Coloured Atoms, Coloured Bonds, Filled Atoms: Olex2 defaults to black and white. Check the corresponding box to depict any of these in color. Bond thickness (default=1): type brad [value] in the cmd line to change the thickness. Ellipsoid probability (default=50%): type telp % in the cmd line (e.g. telp 99 ) NOTE: To generate a traditional black and white "ORTEP" style figure, make sure Coloured Atoms, Coloured Bonds, and Filled Atoms are NOT checked. OLEX2 Manual Page 10 of 10