Decomposition Analysis for Visualization of Noncovalent Interactions Based on the Fragment Molecular Orbital Method.

IF 5.7 1区化学 Q2 CHEMISTRY, PHYSICAL

Journal of Chemical Theory and Computation Pub Date : 2025-02-19 DOI:10.1021/acs.jctc.4c01654

Dmitri G Fedorov, Diego Inostroza, Bastien Courbiere, Fréderic Guegan, Julia Contreras-García, Seiji Mori

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引用次数: 0

Abstract

Many-body expansions of the electron density and Fock matrix in the fragment molecular orbital method (FMO) are used to reveal the role of polarization and charge transfer on noncovalent interactions (NCI). In addition to the physicochemical insight gained from these analyses, the use of FMO permits a rapid evaluation of electron densities to study NCI. The developed method is applied to a solvated sodium cation and a small polypeptide, validating the accuracy of the approach with respect to full calculations and revealing the role of polarization and charge transfer in NCI. In order to show the full potential of the approach, the FMO/NCI method is applied to a complex of the Trp-cage (PDB: 1L2Y) protein with a ligand, delivering fruitful insights into binding from both density and energy perspectives. NCI is shown to provide a comprehensive visual picture of interactions that might be missed without it, in particular, interactions between functional groups in a fragment.

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来源期刊

Journal of Chemical Theory and Computation 化学-物理：原子、分子和化学物理

CiteScore

9.90

自引率

16.40%

发文量

568

审稿时长

1 months

期刊介绍： The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.