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Pattnaik P, Raghunathan S, Kalluri T, Bhimalapuram P, Jawahar CV, Priyakumar UD. Machine Learning for Accurate Force Calculations in Molecular Dynamics Simulations. J Phys Chem A 2020; 124:6954-6967. [DOI: 10.1021/acs.jpca.0c03926] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Punyaslok Pattnaik
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Tarun Kalluri
- Center for Visual Information Technology, KCIS, International Institute of Information Technology, Hyderabad 500 032, India
| | - Prabhakar Bhimalapuram
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - C. V. Jawahar
- Center for Visual Information Technology, KCIS, International Institute of Information Technology, Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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Priyadarsini A, Dasari S, Mallik BS. Thermophysical Properties and Angular Jump Dynamics of Water: A Comparative DFT and DFT-Dispersion-Based Molecular Dynamics Study. J Phys Chem A 2020; 124:6039-6049. [DOI: 10.1021/acs.jpca.0c02909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
| | - Sathish Dasari
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
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Goel H, Ling S, Ellis BN, Taconi A, Slater B, Rai N. Predicting vapor liquid equilibria using density functional theory: A case study of argon. J Chem Phys 2018; 148:224501. [PMID: 29907054 DOI: 10.1063/1.5025726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Predicting vapor liquid equilibria (VLE) of molecules governed by weak van der Waals (vdW) interactions using the first principles approach is a significant challenge. Due to the poor scaling of the post Hartree-Fock wave function theory with system size/basis functions, the Kohn-Sham density functional theory (DFT) is preferred for systems with a large number of molecules. However, traditional DFT cannot adequately account for medium to long range correlations which are necessary for modeling vdW interactions. Recent developments in DFT such as dispersion corrected models and nonlocal van der Waals functionals have attempted to address this weakness with a varying degree of success. In this work, we predict the VLE of argon and assess the performance of several density functionals and the second order Møller-Plesset perturbation theory (MP2) by determining critical and structural properties via first principles Monte Carlo simulations. PBE-D3, BLYP-D3, and rVV10 functionals were used to compute vapor liquid coexistence curves, while PBE0-D3, M06-2X-D3, and MP2 were used for computing liquid density at a single state point. The performance of the PBE-D3 functional for VLE is superior to other functionals (BLYP-D3 and rVV10). At T = 85 K and P = 1 bar, MP2 performs well for the density and structural features of the first solvation shell in the liquid phase.
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Affiliation(s)
- Himanshu Goel
- Dave C. Swalm School of Chemical Engineering, and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Sanliang Ling
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Breanna Nicole Ellis
- Dave C. Swalm School of Chemical Engineering, and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Anna Taconi
- Dave C. Swalm School of Chemical Engineering, and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Ben Slater
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Neeraj Rai
- Dave C. Swalm School of Chemical Engineering, and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
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Shirkov L, Makarewicz J. Does DFT-SAPT method provide spectroscopic accuracy? J Chem Phys 2015; 142:064102. [DOI: 10.1063/1.4907204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Karmakar A, Chandra A. Effects of dispersion interaction on vibrational spectral diffusion in aqueous NaBr solutions: An ab initio molecular dynamics study. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2014.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Schwörer M, Breitenfeld B, Tröster P, Bauer S, Lorenzen K, Tavan P, Mathias G. Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations. J Chem Phys 2014; 138:244103. [PMID: 23822223 DOI: 10.1063/1.4811292] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.
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Affiliation(s)
- Magnus Schwörer
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
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Bankura A, Carnevale V, Klein ML. Hydration structure of salt solutions from ab initio molecular dynamics. J Chem Phys 2013; 138:014501. [PMID: 23298049 DOI: 10.1063/1.4772761] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
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Affiliation(s)
- Arindam Bankura
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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Tran F, Hutter J. Nonlocal van der Waals functionals: The case of rare-gas dimers and solids. J Chem Phys 2013; 138:204103. [DOI: 10.1063/1.4807332] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Otero-de-la-Roza A, Johnson ER. Many-body dispersion interactions from the exchange-hole dipole moment model. J Chem Phys 2013; 138:054103. [DOI: 10.1063/1.4789421] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bouchoux G, Rashad AM, Helal AI. Theoretical Investigation of Selenium Interferences in Inductively Coupled Plasma Mass Spectrometry. J Phys Chem A 2012; 116:9058-70. [DOI: 10.1021/jp304644u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Bouchoux
- Laboratoire des Mécanismes
Réactionnels, Département de Chimie, Ecole Polytechnique and CNRS, 91128 Palaiseau, France
| | - A. M. Rashad
- Central Laboratory for Elemental
and Isotopic Analysis, Nuclear Research Center, Atomic Energy Authority, Cairo 13759, Egypt
| | - A. I. Helal
- Central Laboratory for Elemental
and Isotopic Analysis, Nuclear Research Center, Atomic Energy Authority, Cairo 13759, Egypt
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Abstract
We discuss the source of errors in semiempirical density functional expansion (VE) methods. In particular, we show that VE methods are capable of well-reproducing their standard Kohn-Sham density functional method counterparts, but suffer from large errors upon using one or more of these approximations: the limited size of the atomic orbital basis, the Slater monopole auxiliary basis description of the response density, and the one- and two-body treatment of the core-Hamiltonian matrix elements. In the process of discussing these approximations and highlighting their symptoms, we introduce a new model that supplements the second-order density-functional tight-binding model with a self-consistent charge-dependent chemical potential equalization correction; we review our recently reported method for generalizing the auxiliary basis description of the atomic orbital response density; and we decompose the first-order potential into a summation of additive atomic components and many-body corrections, and from this examination, we provide new insights and preliminary results that motivate and inspire new approximate treatments of the core-Hamiltonian.
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Affiliation(s)
- Timothy J. Giese
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854-8087
| | - Darrin M. York
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854-8087
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Jonchiere R, Seitsonen AP, Ferlat G, Saitta AM, Vuilleumier R. Van der Waals effects inab initiowater at ambient and supercritical conditions. J Chem Phys 2011; 135:154503. [DOI: 10.1063/1.3651474] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Murdachaew G, Mundy CJ, Schenter GK, Laino T, Hutter J. Semiempirical self-consistent polarization description of bulk water, the liquid-vapor interface, and cubic ice. J Phys Chem A 2011; 115:6046-53. [PMID: 21370904 DOI: 10.1021/jp110481m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have applied an efficient electronic structure approach, the semiempirical self-consistent polarization neglect of diatomic differential overlap (SCP-NDDO) method, previously parametrized to reproduce properties of water clusters by Chang, Schenter, and Garrett [ J. Chem. Phys. 2008 , 128 , 164111 ] and now implemented in the CP2K package, to model ambient liquid water at 300 K (both the bulk and the liquid-vapor interface) and cubic ice at 15 and 250 K. The SCP-NDDO potential retains its transferability and good performance across the full range of conditions encountered in the clusters and the bulk phases of water. In particular, we obtain good results for the density, radial distribution functions, enthalpy of vaporization, self-diffusion coefficient, molecular dipole moment distribution, and hydrogen bond populations, in comparison to experimental measurements.
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Affiliation(s)
- Garold Murdachaew
- Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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Riley KE, Pitonák M, Jurecka P, Hobza P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 2010; 110:5023-63. [PMID: 20486691 DOI: 10.1021/cr1000173] [Citation(s) in RCA: 562] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
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Anatole von Lilienfeld O, Tkatchenko A. Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids. J Chem Phys 2010; 132:234109. [DOI: 10.1063/1.3432765] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Murdachaew G, Mundy CJ, Schenter GK. Improving the density functional theory description of water with self-consistent polarization. J Chem Phys 2010; 132:164102. [DOI: 10.1063/1.3385797] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Shamov GA, Budzelaar PHM, Schreckenbach G. Performance of the Empirical Dispersion Corrections to Density Functional Theory: Thermodynamics of Hydrocarbon Isomerizations and Olefin Monomer Insertion Reactions. J Chem Theory Comput 2010; 6:477-90. [DOI: 10.1021/ct9005135] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Grigory A. Shamov
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada, and Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Peter H. M. Budzelaar
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada, and Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada, and Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
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Hermann A, Schwerdtfeger P. Complete basis set limit second-order Møller–Plesset calculations for the fcc lattices of neon, argon, krypton, and xenon. J Chem Phys 2009; 131:244508. [DOI: 10.1063/1.3279303] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Maerzke KA, McGrath MJ, William Kuo IF, Tabacchi G, Siepmann JI, Mundy CJ. Vapor–liquid phase equilibria of water modelled by a Kim–Gordon potential. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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