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Theoretical studies on conformational preferences of model modified nucleic acid base N 6 ‐( N ‐alanylcarbonyl) adenine
Author(s) -
Tewari Ravindra
Publication year - 1988
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/qua.560340106
Subject(s) - chemistry , intramolecular force , hydrogen bond , dihedral angle , substituent , crystallography , nucleic acid , amino acid , stereochemistry , molecular orbital , transfer rna , crystal structure , molecule , rna , biochemistry , organic chemistry , gene
Conformational preferences of model modified nucleic acid base N 6 ‐( N ‐alanylcarbonyl) adenine, ac 6 Ade, have been investigated using the quantum chemical PCILO (perturbative configuration interaction using localized orbitals) method. The multidimensional conformational space has been searched using selected grid points formed by combining the various torsion angles that take favored values derived from energy variation with respect to each torsion angle individually. The preferred molecular structure is stabilized by an intramolecular hydrogen bond from N(11)H of the amino acid to N(1) of the adenine. The observed crystal structure conformations for the naturally occurring, anticodon adjacent, threonyl analogs, tc 6 Ade, correspond to the predicted most stable conformation for the model modified base ac 6 Ade. Three stable, low energy conformations differing in the orientations of the carboxyl group and the amino acid side chain are predicted within 1 kcal/mol of the most stable structure. The possible bifurcated hydrogen bonding of N(11)H with N(1) and either of the carboxyl oxygens is of minor significance. The indicated orientational flexibility for the carboxyl group and the amino acid side chain may enable convenient probing of the molecular environment, in the vicinity of the anticodon in t RNA, by the amino acid substituent, with only modest changes in energy stabilization.