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A systematic study of minima in alanine dipeptide

Journal Article · · Journal of Computational Chemistry
DOI:https://doi.org/10.1002/jcc.25589· OSTI ID:1510055
 [1];  [2];  [3];  [4]
  1. Lomonosov Moscow State Univ., Moscow (Russian Federation). Dept. of Chemistry
  2. Argonne National Lab. (ANL), Argonne, IL (United States). Computational Science Division
  3. Univ. of Washington, Seattle, WA (United States). Dept. of Biochemistry
  4. National Inst. of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan)
+ Show Author Affiliations

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. (c) 2018 Wiley Periodicals, Inc.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
Russian Science Foundation
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1510055
Alternate ID(s):
OSTI ID: 1485691
Journal Information:
Journal of Computational Chemistry, Journal Name: Journal of Computational Chemistry Journal Issue: 2 Vol. 40; ISSN 0192-8651
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English

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