Literature DB >> 22267958

Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development.

Zhenyu Lu1, Nengjie Zhou, Qin Wu, Yingkai Zhang.   

Abstract

One well-known shortcoming of widely-used biomolecular force fields is the description of the directional dependence of hydrogen bonding (HB). Here we aim to better understand the origin of this difficulty and thus provide some guidance for further force field development. Our theoretical approaches center on a novel density-based energy decomposition analysis (DEDA) method [J. Chem. Phys., 131, 164112 (2009)], in which the frozen density energy is variationally determined through constrained search. This unique and most significant feature of DEDA enables us to find that the frozen density interaction term is the key factor in determining the HB orientation, while the sum of polarization and charge-transfer components shows very little HB directional dependence. This new insight suggests that the difficulty for current non-polarizable force fields to describe the HB directional dependence is not due to the lack of explicit polarization or charge-transfer terms. Using the DEDA results as reference, we further demonstrate that the main failure coming from the atomic point charge model can be overcome largely by introducing extra charge sites or higher order multipole moments. Among all the electrostatic models explored, the smeared charge distributed multipole model (up to quadrupole), which also takes account of charge penetration effects, gives the best agreement with the corresponding DEDA results. Meanwhile, our results indicate that the van der Waals interaction term needs to be further improved to better model directional hydrogen bonding.

Entities:  

Year:  2011        PMID: 22267958      PMCID: PMC3259744          DOI: 10.1021/ct2003226

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  57 in total

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Review 2.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
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3.  Distributed Multipole Analysis:  Stability for Large Basis Sets.

Authors:  Anthony J Stone
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

4.  Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations.

Authors:  Petr Jurecka; Jirí Cerný; Pavel Hobza; Dennis R Salahub
Journal:  J Comput Chem       Date:  2007-01-30       Impact factor: 3.376

5.  Oscillations in meta-generalized-gradient approximation potential energy surfaces for dispersion-bound complexes.

Authors:  Erin R Johnson; Axel D Becke; C David Sherrill; Gino A DiLabio
Journal:  J Chem Phys       Date:  2009-07-21       Impact factor: 3.488

6.  Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding.

Authors:  G A Cisneros; S Na-Im Tholander; O Parisel; T A Darden; D Elking; L Perera; J-P Piquemal
Journal:  Int J Quantum Chem       Date:  2008       Impact factor: 2.444

7.  Extended Morse function model for angle-dependent hydrogen bond in protein-protein interactions.

Authors:  Hwanho Choi; Hongsuk Kang; Hwangseo Park
Journal:  J Phys Chem B       Date:  2010-03-04       Impact factor: 2.991

8.  Electrostatic energy in the effective fragment potential method: theory and application to benzene dimer.

Authors:  Lyudmila V Slipchenko; Mark S Gordon
Journal:  J Comput Chem       Date:  2007-01-15       Impact factor: 3.376

9.  Dispersion-corrected energy decomposition analysis for intermolecular interactions based on the BLW and dDXDM methods.

Authors:  Stephan N Steinmann; Clemence Corminboeuf; Wei Wu; Yirong Mo
Journal:  J Phys Chem A       Date:  2011-05-10       Impact factor: 2.781

10.  New angle-dependent potential energy function for backbone-backbone hydrogen bond in protein-protein interactions.

Authors:  Hwanho Choi; Hongsuk Kang; Hwangseo Park
Journal:  J Comput Chem       Date:  2010-04-15       Impact factor: 3.376

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  8 in total

1.  Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis.

Authors:  Nengjie Zhou; Zhenyu Lu; Qin Wu; Yingkai Zhang
Journal:  J Chem Phys       Date:  2014-06-07       Impact factor: 3.488

2.  Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization.

Authors:  Xin Cindy Yan; Michael J Robertson; Julian Tirado-Rives; William L Jorgensen
Journal:  J Phys Chem B       Date:  2017-06-29       Impact factor: 2.991

3.  Charting Hydrogen Bond Anisotropy.

Authors:  Diogo Santos-Martins; Stefano Forli
Journal:  J Chem Theory Comput       Date:  2020-03-10       Impact factor: 6.006

4.  Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM.

Authors:  Robert E Duke; G Andrés Cisneros
Journal:  J Mol Model       Date:  2019-09-09       Impact factor: 1.810

5.  GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations.

Authors:  Robert E Duke; Oleg N Starovoytov; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2014-03-03       Impact factor: 6.006

6.  Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models.

Authors:  Puja Goyal; Hu-Jun Qian; Stephan Irle; Xiya Lu; Daniel Roston; Toshifumi Mori; Marcus Elstner; Qiang Cui
Journal:  J Phys Chem B       Date:  2014-09-16       Impact factor: 2.991

7.  Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acid side chains in molecular dynamics simulation.

Authors:  Tomotaka Oroguchi; Masayoshi Nakasako
Journal:  Sci Rep       Date:  2017-11-20       Impact factor: 4.379

Review 8.  Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

Authors:  Gerardo Andrés Cisneros; Kjartan Thor Wikfeldt; Lars Ojamäe; Jibao Lu; Yao Xu; Hedieh Torabifard; Albert P Bartók; Gábor Csányi; Valeria Molinero; Francesco Paesani
Journal:  Chem Rev       Date:  2016-05-17       Impact factor: 60.622

  8 in total

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