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Parameterization of the approximate valence bond (AVB) method to describe potential energy surface in the reaction catalyzed by HIV‐1 protease
Author(s) -
Trylska Joanna,
Grochowski Paweł,
Geller Maciej
Publication year - 2001
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(2001)82:2<86::aid-qua1024>3.0.co;2-e
Subject(s) - chemistry , valence bond theory , parameterized complexity , nucleophile , computational chemistry , bond cleavage , valence (chemistry) , potential energy surface , molecule , molecular dynamics , proton , generalized valence bond , cleavage (geology) , catalysis , peptide bond , peptide , quantum mechanics , organic chemistry , physics , molecular orbital , materials science , biochemistry , mathematics , combinatorics , fracture (geology) , composite material
The approximate valence bond (AVB) method was parameterized to obtain the potential energy surface for ongoing classical and further quantum classical molecular dynamics simulations describing the enzymatic reaction of the human immunodeficiency virus type 1 protease (HIV‐1 PR). The parameterized AVB method allows to describe the complete enzymatic reaction, including a proton transfer between a water molecule and an aspartic acid, nucleophilic attack of a hydroxy anion on the substrate peptide bond, conformational changes of an intermediate, two proton transfers between the intermediate and aspartic acids, and cleavage of the intermediate into reaction products. The AVB method was parameterized based on density functional theory (DFT) calculations performed for small molecular systems. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 86–103, 2001