Chemical Forums
Chemistry Forums for Students => Physical Chemistry Forum => Topic started by: f77126 on March 03, 2009, 02:28:03 AM
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Why is it that most structures determined by X-ray diffraction lack hydrogen atoms but
structures determined by neutron diffraction have coordinates for hydrogen atoms?
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X-ray scattering factors for hydrogen are very low, contrary deuterium (but not protium) show very large neutron scattering factors, ie X-ray practically does not see hydrogen atoms whereas neutrons see deuterium "without need of glasses"
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The difference between X-ray diffraction and neutron diffraction is that X-rays are scattered at the electrons, whereas neutrons are scattered at the cores. Since H atoms contain only one electron, their contribution to is low for X-ray diffraction.
Why is it that most structures determined by X-ray diffraction lack hydrogen atoms
In general, they don't lack hydrogen atoms, since these are placed at geometrically calculated positions. This is of course not possible in all cases (e.g. water molecules) but in these cases they can often be localized from the difference map. That depends on the data quality and whether the structure contains heavy atoms. However, their bond length are systematically determined too short from X-ray data. Therefore, for systematic analyses they should be neutron normalized.
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Sometimes, while studying the polymers in solutions, x-ray diffraction do not happen. It is because the x-ray will diffract only (at small angles) when there will be electron density difference. In such cases (specifically in polymers), samples are synthesized with deutriums instead of hydrogens.