Crystals User Guide

Chapter 7: Hydrogen Placing

7.1: EXAMPLE 1

A special case of regularisation is the computation of the position of hydrogen atoms in an organic structure. Unless there is likely to be some ambiguity over the nature of the bonding, there is generally little to be gained in searching for hydrogen atoms in difference Fourier maps. Instead, their coordinates can (and should) be computed geometrically. CRYSTALS has routines for placing sp1, sp2, sp3 and phenyl hydrogens, taking proper account of symmetry, bond lengths and angles.

Place the hydrogen atoms on carbons C(2) to C(6) of a phenyl group and the two hydrogens on C(31) of an aliphatic chain.

 \HYDROGEN
 \ note that the pivot atom C(1) must be given
 PHENYL C(1) UNTIL C(6)
 \ two H atoms on an sp3 C(31) atom
 H23 C(30) C(31) C(32)

Although the default bond length is suitable for placing hydrogen atoms as seen with X-rays, it can be changed to that suitable for neutrons, and \HYDROGENS can even be used to place non-hydrogen atoms, such as the oxygens in borate groups.