Chem242 - MIMT crystallography (S2007) Name: _______________________Structure solution and refinementEDIT FORMULA OF IMPORT.CIF FILEFile ImportLogin to one of the PC computers in the CRC. Go to the course web site and get the import.ciffile for the structure that you would like to investigate and place it in a new directory on your “J”drive (can be found through the MyComputer icon). If your web browser adds a .txt extension tothe file, be sure you manually remove that extension from the file name. Do not leave the file ina temporary workspace like the Desktop, or all of your work will be deleted when you log off. Itis recommended that you start working on the green complex, Co(MIMT)4(NO3)2, first.The import.cif file contains a concise summary of the single crystal diffraction experiment. Thisincludes the expected chemical formula of the compound, its unit cell (a,b,c,,,), and a list ofa few thousand diffraction peak intensities sorted by the three integer hkl (or Miller) indices ofthese peaks. It typically contains other experimental details which are useful for archivalpurposes (like an electronic lab notebook), but are not relevant to this class exercise. Start the program WinGX in the CRC by going to Start->Run… and typing C:\wingx\wingx.batat the prompt. Ignore any initial errors that occur from the program opening without a pre-existing experiment. At the “Start New Project” prompt, set the “Project working directory” todirectory your import.cif file is in (ie: J:\MIMT-Green) and choose a “Project ID” name based onyour last name (ie: KHAL-Green). If your project name is too long (>10 characters), certainsoftware programs you will need to use later will not work. Note that you will quickly go fromone file to many files in this directory, so each chemical compound must have its own directory.If the program does not automatically prompt you for the Project directory, go to “File->ChangeProject->Select New Project” menu. Ignore the error messages about the missing .INS file andmissing reflection files, as you have not generated these yet.Use the “Model->Prelim->Import KappaCCD” command to import the data from this file so thatyou can begin the process of structure solution and refinement. Note the three files that are beingcreated here (import_hkl.sortav, projectname.hkl, dreduc.cif). Of these, the .hkl file is the mostimportant for now as it contains the full list of hkl reflections and their measured intensities,which are used by the computer software to calculate the electron density within the unit cellthrough the formula below [x,y,z are fractional coordinates; h,k,l are the Miller indices of eachpeak; Fhkl is the “intensity” of a given hkl peak, with some phase information also included].There is a very high electron density near the center of every atom, and by looking for maxima(peaks) in the electron density, it will be possible to locate the positions of atoms within the unitcell.  h k llzkyhxihkleFVzyx)(21),,(Chem242 - MIMT crystallography (S2007) Name: _______________________Experiment initializationSelect “Model->Prelim->Initialize files”. Note that the program is now aware of most of thenecessary crystal information. Go to the second tab (“Crystal Data”). Enter the color of thecrystal (blue or green) and its dimensions (provided online). It is crucial that you click on thebutton “Estimate Z” in this panel to provide a reasonable estimate of the number of formula unitsin the full unit cell of the crystal. The chemical formula can be changed here if your proposedstructure proves to be incorrect. When you click on “OK”, you will get a message saying that.INS and STRUCT.CIF files have been written. (If you need to make additional changes, you canreturn to these panels through “Model->Edit STRUCT.CIF”) The .INS file will be used for thestructure solution step, while the struct.cif file will provide a record of crystal and proceduralinformation for publication. If later changes are necessary, go to “Model->Edit STRUCT.CIF”Space group determination.In order to progress further, we will need to determine which one of the 230 possible spacegroups most accurately describes the symmetry of the crystal. This is entirely analogous todetermining the point group of a molecule, although there two extra types of symmetryoperations (glide plane, screw axis) that are possible in 3D lattices but not in isolated molecules.The symmetry of a crystal is always the same as the symmetry of the diffraction spots itgenerates (remember how the optical diffraction spots from a rectangular lattice formed arectangular pattern, and the optical diffraction spots from a hexagonal lattice formed a hexagonalpattern) – the software will therefore search for patterns in the intensities of the 3D lattice ofdiffraction spots to determine the space group of our crystals. For the two MIMT structures, theautomated space group determination routines of the computer software will correctly assign thespace groups of the molecules. Go to “Model->Prelim->AssignSpaceGroup”, and accept thedefaults choices as the program runs. For one crystal, you will notice the software firstdetermining the crystal system to be monoclinic, and then assigns the space group as C2/c. Inthe other, the crystal system will be assigned as monoclinic and the space group as P-1.Structure solutionOnce we have a space group selected, we can try to obtain the atom positions within the unit cell.For this, you should use the “SIR97” software. Go to “Solve->Sir97->GUI Control” to start thestructure solution process. Click OK at all of the prompts, until the software stops doingcalculations, and shows a final structure picture. Then click on the “Exit” button, which willsave the data and terminate the program. The software will now have a good starting model ofyour chemical compound. [Hint: one complex will only show half of the expected number ofligands. This is due to the symmetry of the compound. The software only shows the minimumnumber of unique atoms. You can see the full structure later in the SXGRAPH utility using the“Model->Grow Fragments” command, or when you view the final refined structure in Mercury.Note that atoms which are in identical environments due to symmetry will be displayed with thesame name (ie C14) when atom labels are