Literature DB >> 23814506

A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields.

Timothy J Giese1, Haoyuan Chen, Thakshila Dissanayake, George M Giambaşu, Hugh Heldenbrand, Ming Huang, Erich R Kuechler, Tai-Sung Lee, Maria T Panteva, Brian K Radak, Darrin M York.   

Abstract

We introduce a new hybrid molecular orbital/density-functional modified divide-and-conquer (mDC) approach that allows the linear-scaling calculation of very large quantum systems. The method provides a powerful framework from which linear-scaling force fields for molecular simulations can be developed. The method is variational in the energy, and has simple, analytic gradients and essentially no break-even point with respect to the corresponding full electronic structure calculation. Furthermore, the new approach allows intermolecular forces to be properly balanced such that non-bonded interactions can be treated, in some cases, to much higher accuracy than the full calculation. The approach is illustrated using the second-order self-consistent charge density-functional tight-binding model (DFTB2). Using this model as a base Hamiltonian, the new mDC approach is applied to a series of water systems, where results show that geometries and interaction energies between water molecules are greatly improved relative to full DFTB2. In order to achieve substantial improvement in the accuracy of intermolecular binding energies and hydrogen bonded cluster geometries, it was necessary to extend the DFTB2 model to higher-order atom-centered multipoles for the second-order self-consistent intermolecular electrostatic term. Using generalized, linear-scaling electrostatic methods, timings demonstrate that the method is able to calculate a water system of 3000 atoms in less than half of a second, and systems of up to one million atoms in only a few minutes using a conventional desktop workstation.

Entities:  

Year:  2013        PMID: 23814506      PMCID: PMC3694615          DOI: 10.1021/ct3010134

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


  56 in total

1.  Ionic liquids: structure and photochemical reactions.

Authors:  Edward W Castner; Claudio J Margulis; Mark Maroncelli; James F Wishart
Journal:  Annu Rev Phys Chem       Date:  2011       Impact factor: 12.703

2.  Open-Shell Formulation of the Fragment Molecular Orbital Method.

Authors:  Spencer R Pruitt; Dmitri G Fedorov; Kazuo Kitaura; Mark S Gordon
Journal:  J Chem Theory Comput       Date:  2010-01-12       Impact factor: 6.006

3.  Benchmark Assessment of the Accuracy of Several van der Waals Density Functionals.

Authors:  Oleg A Vydrov; Troy Van Voorhis
Journal:  J Chem Theory Comput       Date:  2012-05-16       Impact factor: 6.006

4.  Many-Overlapping-Body (MOB) Expansion: A Generalized Many Body Expansion for Nondisjoint Monomers in Molecular Fragmentation Calculations of Covalent Molecules.

Authors:  Nicholas J Mayhall; Krishnan Raghavachari
Journal:  J Chem Theory Comput       Date:  2012-07-06       Impact factor: 6.006

Review 5.  Advances in methods and algorithms in a modern quantum chemistry program package.

Authors:  Yihan Shao; Laszlo Fusti Molnar; Yousung Jung; Jörg Kussmann; Christian Ochsenfeld; Shawn T Brown; Andrew T B Gilbert; Lyudmila V Slipchenko; Sergey V Levchenko; Darragh P O'Neill; Robert A DiStasio; Rohini C Lochan; Tao Wang; Gregory J O Beran; Nicholas A Besley; John M Herbert; Ching Yeh Lin; Troy Van Voorhis; Siu Hung Chien; Alex Sodt; Ryan P Steele; Vitaly A Rassolov; Paul E Maslen; Prakashan P Korambath; Ross D Adamson; Brian Austin; Jon Baker; Edward F C Byrd; Holger Dachsel; Robert J Doerksen; Andreas Dreuw; Barry D Dunietz; Anthony D Dutoi; Thomas R Furlani; Steven R Gwaltney; Andreas Heyden; So Hirata; Chao-Ping Hsu; Gary Kedziora; Rustam Z Khalliulin; Phil Klunzinger; Aaron M Lee; Michael S Lee; Wanzhen Liang; Itay Lotan; Nikhil Nair; Baron Peters; Emil I Proynov; Piotr A Pieniazek; Young Min Rhee; Jim Ritchie; Edina Rosta; C David Sherrill; Andrew C Simmonett; Joseph E Subotnik; H Lee Woodcock; Weimin Zhang; Alexis T Bell; Arup K Chakraborty; Daniel M Chipman; Frerich J Keil; Arieh Warshel; Warren J Hehre; Henry F Schaefer; Jing Kong; Anna I Krylov; Peter M W Gill; Martin Head-Gordon
Journal:  Phys Chem Chem Phys       Date:  2006-06-12       Impact factor: 3.676

6.  Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach.

Authors:  G Monard; M I Bernal-Uruchurtu; A van der Vaart; K M Merz; M F Ruiz-López
Journal:  J Phys Chem A       Date:  2005-04-21       Impact factor: 2.781

7.  Extending the power of quantum chemistry to large systems with the fragment molecular orbital method.

Authors:  Dmitri G Fedorov; Kazuo Kitaura
Journal:  J Phys Chem A       Date:  2007-05-19       Impact factor: 2.781

8.  Spherical tensor gradient operator method for integral rotation: a simple, efficient, and extendable alternative to Slater-Koster tables.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2008-07-07       Impact factor: 3.488

9.  Density-functional expansion methods: generalization of the auxiliary basis.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2011-05-21       Impact factor: 3.488

10.  Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization.

Authors:  Yang Yang; Haibo Yu; Darrin York; Marcus Elstner; Qiang Cui
Journal:  J Chem Theory Comput       Date:  2008       Impact factor: 6.006

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  22 in total

1.  Quantum mechanical force field for water with explicit electronic polarization.

Authors:  Jaebeom Han; Michael J M Mazack; Peng Zhang; Donald G Truhlar; Jiali Gao
Journal:  J Chem Phys       Date:  2013-08-07       Impact factor: 3.488

2.  Density functional tight binding: values of semi-empirical methods in an ab initio era.

Authors:  Qiang Cui; Marcus Elstner
Journal:  Phys Chem Chem Phys       Date:  2014-07-28       Impact factor: 3.676

3.  Nucleic acid reactivity: challenges for next-generation semiempirical quantum models.

Authors:  Ming Huang; Timothy J Giese; Darrin M York
Journal:  J Comput Chem       Date:  2015-05-06       Impact factor: 3.376

4.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

Review 5.  Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation.

Authors:  Daniel L Kellerman; Darrin M York; Joseph A Piccirilli; Michael E Harris
Journal:  Curr Opin Chem Biol       Date:  2014-07-12       Impact factor: 8.822

6.  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

Review 7.  Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.

Authors:  Anders S Christensen; Tomáš Kubař; Qiang Cui; Marcus Elstner
Journal:  Chem Rev       Date:  2016-04-13       Impact factor: 60.622

8.  Multi-level free energy simulation with a staged transformation approach.

Authors:  Shingo Ito; Qiang Cui
Journal:  J Chem Phys       Date:  2020-07-28       Impact factor: 3.488

9.  Quantum mechanical force fields for condensed phase molecular simulations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Phys Condens Matter       Date:  2017-08-17       Impact factor: 2.333

10.  Analysis of Density Functional Tight Binding with Natural Bonding Orbitals.

Authors:  Xiya Lu; Juan Duchimaza-Heredia; Qiang Cui
Journal:  J Phys Chem A       Date:  2019-08-15       Impact factor: 2.781

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