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PAPQMD/AM1 Parametrization of the bonded term of aromatic biomolecules
Author(s) -
Alemán Carlos,
Orozco Modesto
Publication year - 1994
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360340712
Subject(s) - chemistry , force field (fiction) , parametrization (atmospheric modeling) , uracil , thymine , biomolecule , guanine , computational chemistry , nucleic acid , cytosine , nucleotide , quantum mechanics , physics , dna , biochemistry , gene , radiative transfer
Abstract The suitability of the PAPQMD/AM1 (Program for Approximate Parametrization from Quantum Mechanical Data/based on AM1 calculations) strategy to provide force‐field parameters for large heteroaromatic compounds was studied. For this purpose, PAPQMD/AMI stretching and bending parameters for adenine, cytosine, thymine, guanine, and uracil were computed and compared with experimentally derived force‐field parameters. Furthermore, equilibrium geometries and vibrational spectra for the five nucleic acid bases obtained from molecular mechanical calculations using both PAPQMD/AM1 and AMBER (Assisted Model Building with Energy Refinement) All Atoms force fields were compared with the available experimental data. © 1994 John Wiley & Sons, Inc.