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Solve a small-molecule structure: Difference between revisions
→assigning chemical types
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We tell SHELXL the chemical identity by putting a 1 for a C, a 2 for a N, a 3 for an O, and a 4 for a H - the number is just the order of the atom in the SFAC line. | We tell SHELXL the chemical identity by putting a 1 for a C, a 2 for a N, a 3 for an O, and a 4 for a H - the number is just the order of the atom in the SFAC line. | ||
The chemical identity of an atom can be found from geometric parameters, and its electron density. The electron density can be displayed e.g. in [[coot]], by loading the 56.fcf file written by SHELXL. Geometric parameters (in particular distances) are listed in the 56.lst file. Typical bond distances of C-C, C=C, C-O, C=O, C-N | The chemical identity of an atom can be found from geometric parameters, and its electron density. The electron density can be displayed e.g. in [[coot]], by loading the 56.fcf file written by SHELXL. Geometric parameters (in particular distances) are listed in the 56.lst file. Typical bond distances of C-C, C=C, C-O, C=O, C-N and X-H are about 1.54, 1.34, 1.43, 1.24, 1.47 and 1.0 A, respectively. | ||
As a proxy to electron density we can use the refined ADPs. Atoms initially called "C", but with very low U values after refinement, are most likely O or N atoms. | As a proxy to electron density we can use the refined ADPs. Atoms initially called "C", but with very low U values after refinement, are most likely O or N atoms. | ||