2024-04-21 (Sun)

雨で 18 度程度と気温が下がった。

Hydrogens and elements in MicroED maps

Hydrogen visibility in MicroED depends on the dataset. On some datasets they are very clear in 2Fo-Fc maps, while others need Fo-Fc maps. In some cases they are not visible at all. I don't know what causes the difference. Crystal thickness (dynamical effects)? XRD-178 is an example of MicroED datasets with good hydrogen densities.

X-ray scattering factors (F000) are linearly proportional to the number of electrons but electron scattering factors behave in a more complex way (even for neutral atoms). Sometimes I find it difficult to confidently assign elements when the molecule is nearly symmetric. Which is N and which is O in urea? Where is N in pyridine? The issue is about the accuracy/sensitivity, not visualization. You may assign wrong elements and R values and CC won't necessarily tell. Same for bond geometries. As in protein cases, the context (e.g. hydrogen bonding) is informative. In addition, other experimental evidences (e.g. MS, NMR, synthetic routes) are also useful. That being said, traditional chemical X-ray crystallography usually provides the final, definite structural evidence without any prior information and my clients (chemists) often expect this. I sometimes have to explain the situation is different with MicroED. In favorable cases MicroED provides a similar level of information as chemical X-ray crystallography. Sometimes MicroED provides only qualitative information (e.g. we can discuss packing arrangement in a crystal but not the bond lengths to 0.01 Å precision). In the most difficult cases even element assignments are ambiguous. My clients usually do not realize this so I explain this every time I start a new collaboration.

Which prior information is useful to what extent is a good question but I myself prefer methods that stand by their own. Of course integrative approaches are valid and useful when used well, but they are not what I want to pursue (one reason I left biology).


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