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Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database

Kim, Yongbin and Bui, Yen and Tazhigulov, Ruslan N. and Bravaya, Ksenia B. and Slipchenko, Lyudmila V. (2020) Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database. Journal of Chemical Theory and Computation, 16 (12). pp. 7735-7747. ISSN 1549-9618. https://resolver.caltech.edu/CaltechAUTHORS:20201125-103756620

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Abstract

An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is an ab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series of ab initio calculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function, etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as “flexible EFP”, is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1021/acs.jctc.0c00758DOIArticle
ORCID:
AuthorORCID
Tazhigulov, Ruslan N.0000-0002-0679-3078
Bravaya, Ksenia B.0000-0002-5033-8240
Slipchenko, Lyudmila V.0000-0002-0445-2990
Additional Information:© 2020 American Chemical Society. Received: July 21, 2020; Published: November 25, 2020. Y.K., Y.B. and L.V.S. acknowledge support of the National Science Foundation (Grants CHE-1450088, CHE-1800505, and IIP-1640646). The research reported in this publication was supported in part by the National Institute of General Medical Sciences of the National Institutes of Health under award R43GM126804. This research was supported in part through computational resources provided by Boston University Shared Computing Cluster and Information Technology at Purdue, West Lafayette, Indiana. The authors declare no competing financial interest.
Funders:
Funding AgencyGrant Number
NSFCHE-1450088
NSFCHE-1800505
NSFIIP-1640646
NIHR43GM126804
Issue or Number:12
Record Number:CaltechAUTHORS:20201125-103756620
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20201125-103756620
Official Citation:Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database. Yongbin Kim, Yen Bui, Ruslan N. Tazhigulov, Ksenia B. Bravaya, and Lyudmila V. Slipchenko. Journal of Chemical Theory and Computation 2020 16 (12), 7735-7747; DOI: 10.1021/acs.jctc.0c00758
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106826
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:25 Nov 2020 19:00
Last Modified:10 Dec 2020 23:06

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