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A systematic study of minima in alanine dipeptide
Author(s) -
Mironov Vladimir,
Alexeev Yuri,
Mulligan Vikram Khipple,
Fedorov Dmitri G.
Publication year - 2019
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.25589
Subject(s) - ramachandran plot , maxima and minima , dihedral angle , dipeptide , conformational isomerism , computational chemistry , voronoi diagram , crystallography , chemistry , geometry , protein structure , mathematics , molecule , amino acid , mathematical analysis , biochemistry , hydrogen bond , organic chemistry
The alanine dipeptide is a standard system to model dihedral angles in proteins. It is shown that obtaining the Ramachandran plot accurately is a hard problem because of many local minima; depending on the details of geometry optimizations, different Ramachandran plots can be obtained. To locate all energy minima, starting from geometries from MD simulations, 250,000 geometry optimizations were performed at the level of RHF/6‐31G*, followed by re‐optimizations of the located 827 minima at the level of MP2/6–311++G**, yielding 30 unique minima, most of which were not previously reported in literature. Both in vacuo and solvated structures are discussed. The minima are systematically categorized based on four backbone dihedral angles. The Gibbs energies are evaluated and the structural factors determining the relative stabilities of conformers are discussed. © 2018 Wiley Periodicals, Inc.