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Graphical approach for defining natural internal coordinates
Author(s) -
Pye Cory C.,
Poirier Raymond A.
Publication year - 1998
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(19980415)19:5<504::aid-jcc3>3.0.co;2-q
Subject(s) - ring (chemistry) , computer science , simple (philosophy) , graph , action angle coordinates , algorithm , mathematics , orthogonal coordinates , theoretical computer science , geometry , chemistry , philosophy , organic chemistry , epistemology
A simple, customizable connectivity scheme is rigorously defined in which pairs of atoms are classified into three categories. The tools of graph theory are used to analyze the molecular graph and to efficiently find rings and ring assemblies through a combination of pruning and homeomorphic reduction. The definition of natural internal coordinates is extended in a nonredundant fashion for the various cases of weakly interacting components and for fused ring systems. The ring system coordinates were tested and found to be superior to Z ‐matrix coordinates. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 504–511, 1998