MIT5_067F09_lec3 - Hydrogen Atoms It is electron density...

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It is electron density that we measure by X-ray diffraction. The heavier an atom is and the more electrons it has, the stronger is its effect on the diffraction pattern. This also means that, especially in the presence of heavy atoms, light atoms are somewhat more difficult to localize. The lightest atom of all is hydrogen: it has only one electron, localized away from the nucleus. Therefore, hydrogen atoms are notoriously difficult to detect with X-ray diffraction methods. Relatively high electron density between the atoms and libration effects make X—H bonds appear too short. <C—H> X-ray ca. 0.96 Å H • • C C • • H <C—H> neutron ca. 1.09 Å Courtesy of George Sheldrick. Used with permission. George M. Sheldrick Hydrogen Atoms Especially for hydrogen atoms bound to carbon it is frequently possible to calculate the hydrogen positions from the coordinates of the atoms the hydrogen atoms are attached to, as the standard bond lengths and angles are well known. Hydrogen atoms of water molecules must be detected in the experimental electron density or else they cannot be included into the model. Even more difficult to detect can be hydrogen atoms in heavy metal hydrides. The sometimes relatively strong Fourier truncation ripples close to heavy atom positions can overpower the rather weak electron density maxima representing the hydrogen atoms. Very accurate and especially complete high quality data and proper scaling are required to distinguish those hydrogen atoms from the background noise. 1
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This note was uploaded on 11/27/2011 for the course CHEMICAL E 20.410j taught by Professor Rogerd.kamm during the Spring '03 term at MIT.

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MIT5_067F09_lec3 - Hydrogen Atoms It is electron density...

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