Crystal structure analysis hydrogen atom positions

Scientists using crystal structure results need to be aware of several factors related to such data (4-71. Since x-rays interact with electrons in the crystal, x-ray diffraction does not give good experimental positions for hydrogen atoms which possess only one electron each. Also of major concern, is that crystal structure analysis measures the molecule in the conformation it assumes in the crystal, whereas for drug design, the chemist usually is interested in the the conformation at a receptor. 

Figure 20.5 Molecular structure of the linear compound 3, determined by single-crystal X-ray analysis. Hydrogen atoms have been calculated in idealized positions.

The above shows that 20-50% of the crystal structures stored in the database do not lend themselves to automatic renormalization of hydrogen atom positions and to immediate and unchecked use in crystal packing analysis studies. True, the checks... 

A preliminary knowledge of the crystal structure is important prior to a detailed charge density analysis. Direct methods are commonly used to solve structures in the spherical atom approximation. The most popular code is the Shelx from Sheldrick [26] which provides excellent graphical tools for visualization. The refinement of the atom positional parameters and anisotropic temperature factors are carried out by applying the full-matrix least-squares method on a data corrected if found necessary, for absorption and diffuse scattering. Hydrogen atoms are either fixed at idealized positions or located using the difference Fourier technique. 

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