Atom type assignment

The correct assignment of element types to electron-density maxima can be a serious pitfall (see Chapter 4 and Muller, 2001). Nitrogen and oxygen are often 

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Assign atom types Assign connectivity Assign partial atomic charges -------Assigninitiai-parameters. "... 

Todorov, N. P., Dean, P. M. (1998) A branch-and-bound method for optimal atom-type assignment in de novo ligand design. J Comput Aided Mol Des 12, 335-349. 

A smaller set of atom-centered fragments was later proposed to avoid ambiguity sometimes occurring in atom-type assignment. It is comprehensive for the common elements in organic molecules, and also includes metals and noble gases [Wildman and Crippen, 1999]. 

The task of atom type assignment would be easy if the electron density obtained from the experimental intensities and initial phases were somehow colour-coded and electron density for carbon was, say, black, for nitrogen blue, for sulfur yellow, for oxygen red and so forth, but unfortunately all electrons are blue, at least on the computer screen. ... 

Fig. 4.1 A Cartoon of a tetrahydrofuran molecule. The dashed circles in grey represent the atoms, the white rimmed black circles the volume increment corresponding to three electrons. B Isotropic displacement parameter (50% representation) of a tetrahydrofuran molecule, where aU atoms were refined as carbon the sphere representing the true oxygen is much smaller than the other four spheres. C The same molecule with correct atom type assignment aU five spheres are approximately equal in size.

With the intention to provide simpler molecular descriptors for use in 3D-QSAR, Manchester and Czerminski presented their so-called SAMFA descriptors. These are in principle atom-types assigned to each atom of the investigated molecules. They contain some pharmacophoric features such as aromaticity, hydrogen-bonding capability, and electron-withdrawing properties on top of the element information. These are contracted to... 

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