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Initial conformations of macrocyclic compounds with rotational symmetry generated from a molecular fragment
Author(s) -
Felder Clifford E.,
Shanzer Abraham,
Lifson Shneior
Publication year - 1984
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/jcc.540050207
Subject(s) - molecule , chemistry , cartesian coordinate system , symmetry (geometry) , homogeneous space , computational chemistry , field (mathematics) , rotation (mathematics) , crystallography , geometry , pure mathematics , mathematics , organic chemistry
An algorithm is described for generating atomic Cartesian coordinates of conformations of macrocyclic molecules possessing exact rotational or rotation‐reflection symmetries. A fragment representing the asymmetric unit of the molecule is suitably oriented in space, and then a symmetry operator is applied to generate the initial coordinates of the molecule. An empirical force field of interatomic interactions is used to generate equilibrium conformations. Results of calculations performed on two cyclic polylactones and one crown ether using this approach are given. They reveal that symmetric conformations of these molecules are often preferred. Since the latter conformations are probably responsible for the specialized properties of these molecules, this method should facilitate doing theoretical studies on these kinds of compounds.