X-ray crystallography: A powerful method used to determine the structure of crystalline solids. It is now used very broadly throughout the chemistry and biochemistry communities. In this stream, students are taught how to grow crystals and determine structure by single crystal X-ray diffraction. Students learn the basic principles of X-ray crystallography and use multiple single-crystal X-ray diffractometer to collect data under close supervision.
X-ray lab’s website at the University of Texas: http://sites.utexas.edu/chem-x-ray
While there are many ways to solve and refine or work up the data collected by the instruments, we will use the program called Olex2. Applicable to Mac and Linux platforms as well as Windows PC’s. Olex2 has a nice graphics interface.
To download and use Olex2, follow the notes produced by Ilia A. Guzei.
You will need to register for OlexSys before downloading: http://www.olexsys.org/Software
You will also need programs SHELXS and SHELXL (written by George Sheldrick) available free upon request (you will also need to register for these) from: http://shelx.uni-ac.gwdg.de/SHELX/
Northwestern University has a stellar guide for Structure Solution and Refinement with Olex2: http://imserc.facilities.northwestern.edu/files/2013/11/Olex2atNUv1.1.pdf
Introduction and Explanation of Space Groups: http://pd.chem.ucl.ac.uk/pdnn/symm3/sgintro.htm
CheckCIF:
http://checkcif.iucr.org
The Basics for Solving and Refining:
- Place the X.hkl and X.res files in an empty (or new) folder by themselves.
- In Olex, open the X.res file.
- Under Work, click the Solve arrow (not the word, the arrow). Under the Solution Program – choose ShelXT, click Solve. Olex will attempt to solve the structure for you.
- Colors of atoms:
- C = gray
- N = blue
- O = red
- Ln = green
- Br = dark red
- Click the Refine arrow. Under the Refinement Program – choose ShelXL, click Refine.
- Look at structure and correct any atoms that are not correct. To do this, right click on the atom and choose the correct atom under Type. Compare the ligand to the known structure, if you are missing an atom and a Q-peak is nearby you can right click on it and identify the atom as the missing one. Refine each time you make changes to save your changes.
- You can also delete atoms that don’t make sense. Either they are floating out in space, are solvent, or just extremely large on the screen. Choose the atom by clicking on it and hitting the delete key. Refine to save your changes.
- Once you have the correct structure, make the atoms anisotropic by clicking on the blue ellipsoid in the toolbox, Refine.
- Name the atoms (F3). Work your way around from left to right and top to bottom selecting all of the same atoms (such as all the C’s. Once finished choosing them all (they will be highlighted inn green), type “name 1”, enter). Refine.
- Sort atoms by moiety, type “sort”, enter, refine.
- Add H’s, refine.
- If the numbers after Weight: are in red, click on them and Olex will make suggested changes. Click Refine to see if your R1 value improves. You may need to do this several times.
- Make sure the dropdown menu box has ACTA showing and refine again. Go to the folder where you have the res and hkl files saved and you should see several new files there created by Olex. Look for the cif file.
- If the cif file is not present, type edit res and return to open the res text file. You will need to add the ACTA card. Somewhere after the LIST card but before the WGHT card add a new line and type “ACTA”. Save the changes in the res text file. Back in Olex, refine again. You will see the cif file present in the folder.
Notes:
- Control+Q = add/remove Q-peaks and show bonds between them
- Control+H = add/remove H’s
- Control+T = add/remove text in the background or the structure
- F3 = show atom labels
- F2 and F4 = changes the background color.
- To delete a bond: select the bond(s) and type “delbond” and return. Refine to save changes.
- Too many bonds to the Ln? That’s a connectivity issue.
Type “conn 8 2.7 $Ln” (the Ln = to your lanthanide…) Makes all Ln atoms have a max of 8 bonds with a max bond radius of 2.7
- Too look at the text in the res file, type “edit res” and return will open the file. Make sure to close it before moving on.