I am solving crystal structure with Olex2 (using ShelXL settings). The structure solves well to R value 2.95% but during the refinement one carbon atom in a thiophene ring in my structure shows 2 hydrogen atoms. Any suggestions how to model this disorder ?
Having Olex2 showing you two hydrogens does not mean there is disorder. Are you identifying two hydrogen atoms via Q peaks, or is the program adding two hydrogens with the hadd command? If the latter, that just means it thinks the C atom is sp3 and so adds two Hs. You can fix this by specifying that it is sp2 and only one H will be added. If it is through Q peaks then make sure they are of decent electron density. In general, even for simple structures, you are better off adding the H atoms via variants of the hadd command. If you are free to either share a .cif file here or send it to me, I will take a look at what is going on.
Thanks Dr Joseph for your reply. I am actually getting this by using hadd command. How can I specify carbon atom to be sp2 rather than sp3 in olex2 ?
Click on the "Tools" button in Olexs. One of the menus below that is "Hydrogen Atoms" At the top of that group, you can see buttons for adding 1 or two hydrogens to sp2 carbons or for adding 1,2 or 3 hydrogens to sp3 carbons.
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