Literature DB >> 28817382

Quantum mechanical force fields for condensed phase molecular simulations.

Timothy J Giese1, Darrin M York.   

Abstract

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

Entities:  

Year:  2017        PMID: 28817382      PMCID: PMC5821073          DOI: 10.1088/1361-648X/aa7c5c

Source DB:  PubMed          Journal:  J Phys Condens Matter        ISSN: 0953-8984            Impact factor:   2.333


  164 in total

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Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2005-10-22       Impact factor: 3.488

2.  Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

Authors:  Jan Gerit Brandenburg; Stefan Grimme
Journal:  Top Curr Chem       Date:  2014

3.  Energy-Based Molecular Fragmentation Methods.

Authors:  Michael A Collins; Ryan P A Bettens
Journal:  Chem Rev       Date:  2015-04-06       Impact factor: 60.622

4.  Subsystem density-functional theory as an effective tool for modeling ground and excited states, their dynamics and many-body interactions.

Authors:  Alisa Krishtal; Debalina Sinha; Alessandro Genova; Michele Pavanello
Journal:  J Phys Condens Matter       Date:  2015-04-16       Impact factor: 2.333

5.  Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations.

Authors:  Eric G Kratz; Robert E Duke; G Andrés Cisneros
Journal:  Theor Chem Acc       Date:  2016-06-17       Impact factor: 1.702

6.  Improved electronic properties from third-order SCC-DFTB with cost efficient post-SCF extensions.

Authors:  Steve Kaminski; Michael Gaus; Marcus Elstner
Journal:  J Phys Chem A       Date:  2012-11-20       Impact factor: 2.781

7.  pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

Authors:  Demian Riccardi; Patricia Schaefer; Qiang Cui
Journal:  J Phys Chem B       Date:  2005-09-22       Impact factor: 2.991

8.  Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms.

Authors:  Kwangho Nam; Qiang Cui; Jiali Gao; Darrin M York
Journal:  J Chem Theory Comput       Date:  2007-03       Impact factor: 6.006

9.  An SCC-DFTB Repulsive Potential for Various ZnO Polymorphs and the ZnO-Water System.

Authors:  Matti Hellström; Kjell Jorner; Maria Bryngelsson; Stefan E Huber; Jolla Kullgren; Thomas Frauenheim; Peter Broqvist
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2013-07-23       Impact factor: 4.126

10.  Multipolar Ewald methods, 2: applications using a quantum mechanical force field.

Authors:  Timothy J Giese; Maria T Panteva; Haoyuan Chen; Darrin M York
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

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  3 in total

1.  Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Authors:  Tai-Sung Lee; Bryce K Allen; Timothy J Giese; Zhenyu Guo; Pengfei Li; Charles Lin; T Dwight McGee; David A Pearlman; Brian K Radak; Yujun Tao; Hsu-Chun Tsai; Huafeng Xu; Woody Sherman; Darrin M York
Journal:  J Chem Inf Model       Date:  2020-09-16       Impact factor: 4.956

2.  A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2018-02-07       Impact factor: 6.006

3.  Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.

Authors:  Jorge Nochebuena; Sehr Naseem-Khan; G Andrés Cisneros
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2021-01-12
  3 in total

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