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Journal of Computational Chemistry, volume 40, issue 2, pages 297-309

A systematic study of minima in alanine dipeptide

Mironov Vladimir ¹

Alexeev Yuri ²

Mulligan Vikram Khipple ³

Fedorov D. V. ⁴

Hide authors affiliations Show authors affiliations: 4 affiliations

Department of Chemistry Lomonosov Moscow State University Leninskie Gory 1/3, Moscow 119991 Russia |

Argonne National Laboratory Computational Science Division Argonne Illinois 60439 |

Department of Biochemistry University of Washington, Institute for Protein Design Seattle Washington 98195 |

⁴

CD‐FMat National Institute of Advanced Industrial Science and Technology Central 2, Umezono 1‐1‐1, Tsukuba 305‐8568 Japan |

Publication type: Journal Article

Publication date: 2018-10-23

Wiley

Journal: Journal of Computational Chemistry

Quartile SCImago

Quartile WOS

Impact factor: 3

ISSN: 01928651, 1096987X

DOI: 10.1002/jcc.25589

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General Chemistry

Computational Mathematics

Abstract

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.

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Citations by publishers

	1 2 3 4 5 6 7 8 9
American Chemical Society (ACS)	American Chemical Society (ACS), 9, 37.5% American Chemical Society (ACS) 9 publications, 37.5%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 4, 16.67% Royal Society of Chemistry (RSC) 4 publications, 16.67%
Springer Nature	Springer Nature, 3, 12.5% Springer Nature 3 publications, 12.5%
Wiley	Wiley, 2, 8.33% Wiley 2 publications, 8.33%
Elsevier	Elsevier, 1, 4.17% Elsevier 1 publication, 4.17%
IOP Publishing	IOP Publishing, 1, 4.17% IOP Publishing 1 publication, 4.17%
Taylor & Francis	Taylor & Francis, 1, 4.17% Taylor & Francis 1 publication, 4.17%
American Institute of Physics (AIP)	American Institute of Physics (AIP), 1, 4.17% American Institute of Physics (AIP) 1 publication, 4.17%
Society for Industrial and Applied Mathematics (SIAM)	Society for Industrial and Applied Mathematics (SIAM), 1, 4.17% Society for Industrial and Applied Mathematics (SIAM) 1 publication, 4.17%
	1 2 3 4 5 6 7 8 9

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Mironov V. et al. A systematic study of minima in alanine dipeptide // Journal of Computational Chemistry. 2018. Vol. 40. No. 2. pp. 297-309.

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Mironov V., Alexeev Y., Mulligan V. K., Fedorov D. V. A systematic study of minima in alanine dipeptide // Journal of Computational Chemistry. 2018. Vol. 40. No. 2. pp. 297-309.

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RIS Copy

TY - JOUR

DO - 10.1002/jcc.25589

UR - https://doi.org/10.1002%2Fjcc.25589

TI - A systematic study of minima in alanine dipeptide

T2 - Journal of Computational Chemistry

AU - Mironov, Vladimir

AU - Fedorov, D. V.

AU - Alexeev, Yuri

AU - Mulligan, Vikram Khipple

PY - 2018

DA - 2018/10/23 00:00:00

PB - Wiley

SP - 297-309

IS - 2

VL - 40

SN - 0192-8651

SN - 1096-987X

ER -

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@article{2018_Mironov,

author = {Vladimir Mironov and D. V. Fedorov and Yuri Alexeev and Vikram Khipple Mulligan},

title = {A systematic study of minima in alanine dipeptide},

journal = {Journal of Computational Chemistry},

year = {2018},

volume = {40},

publisher = {Wiley},

month = {oct},

url = {https://doi.org/10.1002%2Fjcc.25589},

number = {2},

pages = {297--309},

doi = {10.1002/jcc.25589}

}

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Mironov, Vladimir, et al. “A systematic study of minima in alanine dipeptide.” Journal of Computational Chemistry, vol. 40, no. 2, Oct. 2018, pp. 297-309. https://doi.org/10.1002%2Fjcc.25589.

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Publisher

Wiley

Journal

Journal of Computational Chemistry

Quartile SCImago

Quartile WOS

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ISSN

01928651 (Print)
1096987X (Electronic)

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