Efficient algorithm for quantitative assessment of similarities among atoms in
molecules
J. Cioslowski, B. B. Stefanov, and P. Constans. Efficient algorithm for
quantitative assessment of similarities among atoms in molecules. Journal of
Computational Chemistry, 17, 1352-1358 (1996).
Abstract
A new algorithm for quantitative assessment of similarity between two atoms in
molecules is presented. Both the atomic similarity index and its derivatives with
respect to the three Euler angles that describe the mutual orientation of the atoms
under comparison are computed efficiently by taking advantage of the recently
developed analytical representations for atomic zero-flux surfaces. The use of such
representations makes it possible to substantially enhance the accuracy of the
computed similarity indices without increasing the cost of their evaluation.
Numerical tests involving oxygen atoms in several carbonyl compounds demonstrate the
ability of the new algorithm to discern small changes in atomic similarity that are
brought about by second-neighbor effects. Comparisons among hydrogen atoms in the
acrolein molecule reveal the usefulness of the similarity index in detection and
quantification of the effects of steric interactions on atomic shapes.
Keywords
Transferability.
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 Similarities among atoms in molecules
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