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Structural nonrigidity of nucleic acid bases. Post–Hartree–Fock ab initio study
Author(s) -
Shishkin Oleg V.,
Gorb Leonid,
Hobza Pavel,
Leszczynski Jerzy
Publication year - 2000
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/1097-461x(2000)80:4/5<1116::aid-qua61>3.0.co;2-o
Subject(s) - chemistry , ab initio , thymine , pyrimidine , nucleobase , ring (chemistry) , computational chemistry , uracil , molecule , ab initio quantum chemistry methods , molecular physics , atomic physics , stereochemistry , physics , dna , biochemistry , organic chemistry
Pyrimidine ring deformation modes in uracil, thymine, cytosine, isocytosine, guanine, and adenine were analyzed using normal vibrations calculated at the MP2/6‐31G(d,p) levels of theory. We have introduced the theoretical approach based on the combined analysis of the shape of the relaxed potential surface, normal out‐of‐plane frequencies, and the amplitudes of the corresponding vibrations. We have shown that the absolute value of the frequency is not the unique characteristic to determine the lowest modes of the molecular deformation. We have revealed the applications involved in the analysis of the amplitudes to locate the internal coordinates (torsional angels), which correspond to the set of lowest energy deformations. It was demonstrated that the pyrimidine ring possesses high structural nonrigidity. Two very soft modes of ring deformation were found for every molecule except adenine. An estimation of population of excited vibrational levels for the lowest out‐of‐plane ring vibrations reveals that in every moment of time about 50% of all considered molecules possess a nonplanar configuration in the pyrimidine ring with a relevant torsion angle up to 25° © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 1116–1124, 2000