101
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Philips A, Marchenko A, Ducati LC, Autschbach J. Quadrupolar 14N NMR Relaxation from Force-Field and Ab Initio Molecular Dynamics in Different Solvents. J Chem Theory Comput 2018; 15:509-519. [PMID: 30462503 DOI: 10.1021/acs.jctc.8b00807] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quadrupolar NMR spin relaxation rates and corresponding line widths were computed for the quadrupolar nucleus 14N for neat acetonitrile as well as for 1-methyl-1,3-imidazole and 1-methyl-1,3,4-triazole in different solvents. Molecular dynamics (MD) was performed with forces from the Kohn-Sham (KS) theory (ab initio MD) and force-field molecular mechanics (classical MD), followed by KS electric field gradient (EFG) calculations. For acetonitrile the agreement of the 14N line width with experiment is very good. Relative line widths for the azole nitrogens are improved over simpler approximations used previously in conjunction with single-point calculations at the multiconfigurational self-consistent field level. Overall, the NMR line widths are computed within a factor of 2 of the experimental values, giving access to reasonable estimates both of the dynamic EFG variance in the solvated systems as well as the associated correlation times that determine the relaxation rates.
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Affiliation(s)
- Adam Philips
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Alex Marchenko
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Lucas C Ducati
- Department of Fundamental Chemistry Institute of Chemistry , University of São Paulo , Av. Prof. Lineu Prestes 748 , São Paulo , SP 05508-000 , Brazil
| | - Jochen Autschbach
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
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102
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Observation of the thermal influenced quantum behaviour of water near a solid interface. Sci Rep 2018; 8:7016. [PMID: 29725015 PMCID: PMC5934364 DOI: 10.1038/s41598-018-24886-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/11/2018] [Indexed: 11/25/2022] Open
Abstract
Water is essential for life. However, the structure and properties of water are still not well understood. It has been introduced that anomalies are in vicinal water near solid interfaces. We performed capillary flow experiments on water with a silica colloid sample using a high-performance liquid chromatography (HPLC) system by accurately varying the temperature and analysed the peak shape rigorously. We obtained a novel anomalous temperature spectrum from the peak-shape analysis. Here we report the observed distinct specific anomalous temperature (SAT) behaviour in vicinal water at silica interface. The anomaly appeared in the viscous force that was derived from a relationship between the shape of the HPLC peak and the velocity profile for the capillary flow. The observations were highly reproducible, and we conclude that the SAT is related to the quantum mechanical behaviour of water, in agreement of the characteristic acceptance of thermal displacement according to the Franck-Condon principle. We performed the same experiments using heavy water and water mixed with a small amount of methanol, and the results support the quantum phenomenological origin.
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103
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Liu J, Zhang JZH, He X. Probing the Ion-Specific Effects at the Water/Air Interface and Water-Mediated Ion Pairing in Sodium Halide Solution with Ab Initio Molecular Dynamics. J Phys Chem B 2018; 122:10202-10209. [PMID: 30351119 DOI: 10.1021/acs.jpcb.8b09513] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ion-specific effects at the water/air interface represent a fundamentally essential topic of research, and high-level ab initio simulations are still demanding to reveal the microscopic picture of the interactions between ions and water at the solvation interface. In this work, we present a fragment-based ab initio molecular dynamics (AIMD) simulation of sodium halide solution droplet (in a neutral mixture of Na+, F-, Cl-, and Br- ions) at the MP2/aug-cc-pVDZ level. We show that the studied halide ions exhibit surface preference in the order (F- < Cl- < Br-) which is in accordance with the experimental observation. The resulting potential of mean force (PMF) for Br- produces a distinct minimum at the water/air interface, while the minimum of the PMF for F- appears in the bulk region. The ion-pairing interactions between halide anions and Na+ cations are characterized, and it reveals that the specific solvent-separated ion pairs (SIPs) are more preferred than the direct contact ion pairs (CIPs). The transition between different types of SIPs is observed. Other structural and dynamical properties of ions and ion-hydration shells are investigated. These results provide broader and new physical insights for understanding the ion-specific behavior in interfacial solvation at the atomistic level.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Natural Medicines, Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing , 210009 , China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China.,Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China
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104
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König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules 2018; 23:E2695. [PMID: 30347691 PMCID: PMC6222909 DOI: 10.3390/molecules23102695] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/01/2022] Open
Abstract
Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
- School of Life Sciences, Westlake University, 18 Shilongshan Street, Hangzhou 310024, China.
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Alexander D MacKerell
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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105
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Mandal S, Debnath J, Meyer B, Nair NN. Enhanced sampling and free energy calculations with hybrid functionals and plane waves for chemical reactions. J Chem Phys 2018; 149:144113. [DOI: 10.1063/1.5049700] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sagarmoy Mandal
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jayashrita Debnath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Bernd Meyer
- Interdisciplinary Center of Molecular Materials (ICMM) and Computer-Chemistry-Center (CCC), Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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106
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Sun Z, Zheng L, Chen M, Klein ML, Paesani F, Wu X. Electron-Hole Theory of the Effect of Quantum Nuclei on the X-Ray Absorption Spectra of Liquid Water. PHYSICAL REVIEW LETTERS 2018; 121:137401. [PMID: 30312094 DOI: 10.1103/physrevlett.121.137401] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 06/08/2023]
Abstract
Electron-hole excitation theory is used to unveil the role of nuclear quantum effects on the x-ray absorption spectral signatures of water, whose structure is computed via path-integral molecular dynamics with the MB-pol intermolecular potential model. Compared to spectra generated from the classically modeled water, quantum nuclei introduce important effects on the spectra in terms of both the energies and line shapes. Fluctuations due to delocalized protons influence the short-range ordering of the hydrogen bond network via changes in the intramolecular covalence, which broaden the preedge spectra. For intermediate-range and long-range ordering, quantum nuclei approach the neighboring oxygen atoms more closely than classical protons, promoting an "icelike" spectral feature with the intensities shifted from the main edge to the postedge. Computed spectra are in nearly quantitative agreement with the available experimental data.
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Affiliation(s)
- Zhaoru Sun
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Lixin Zheng
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Mohan Chen
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Michael L Klein
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, Materials Science and Engineering, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
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107
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Ruiz Pestana L, Marsalek O, Markland TE, Head-Gordon T. The Quest for Accurate Liquid Water Properties from First Principles. J Phys Chem Lett 2018; 9:5009-5016. [PMID: 30118601 DOI: 10.1021/acs.jpclett.8b02400] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Developing accurate ab initio molecular dynamics (AIMD) models that capture both electronic reorganization and nuclear quantum effects associated with hydrogen bonding is key to quantitative understanding of bulk water and its anomalies as well as its role as a universal solvent. For condensed phase simulations, AIMD has typically relied on the generalized gradient approximation (GGA) of density functional theory (DFT) as the underlying model chemistry for the potential energy surface, with nuclear quantum effects (NQEs) sometimes modeled by performing classical molecular dynamics simulations at elevated temperatures. Here we show that the properties of liquid water obtained from the meta-GGA B97M-rV functional, when evaluated using accelerated path integral molecular dynamics simulations, display accuracy comparable to a computationally expensive dispersion-corrected hybrid functional, revPBE0-D3. We show that the meta-GGA DFT functional reproduces bulk water properties including radial distribution functions, self-diffusion coefficients, and infrared spectra with comparable accuracy of a much more expensive hybrid functional. This work demonstrates that the underlying quality of a good DFT functional requires evaluation with quantum nuclei and that high-temperature simulations are a poor proxy for properly treating NQEs.
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Affiliation(s)
| | - Ondrej Marsalek
- Charles University , Faculty of Mathematics and Physics , Ke Karlovu 3 , 121 16 Prague 2 , Czech Republic
| | - Thomas E Markland
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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108
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Tsimpanogiannis IN, Moultos OA, Franco LFM, Spera MBDM, Erdős M, Economou IG. Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1511903] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ioannis N. Tsimpanogiannis
- Environmental Research Laboratory, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Luís F. M. Franco
- School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | | | - Máté Erdős
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Ioannis G. Economou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
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109
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Zhang L, Han J, Wang H, Car R, E W. DeePCG: Constructing coarse-grained models via deep neural networks. J Chem Phys 2018; 149:034101. [PMID: 30037247 DOI: 10.1063/1.5027645] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called the Deep Coarse-Grained Potential (abbreviated DeePCG), exploits a carefully crafted neural network to construct a many-body coarse-grained potential. The network is trained with full atomistic data in a way that preserves the natural symmetries of the system. The resulting model is very accurate and can be used to sample the configurations of the coarse-grained variables in a much faster way than with the original atomistic model. As an application, we consider liquid water and use the oxygen coordinates as the coarse-grained variables, starting from a full atomistic simulation of this system at the ab initio molecular dynamics level. We find that the two-body, three-body, and higher-order oxygen correlation functions produced by the coarse-grained and full atomistic models agree very well with each other, illustrating the effectiveness of the DeePCG model on a rather challenging task.
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Affiliation(s)
- Linfeng Zhang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
| | - Jiequn Han
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
| | - Han Wang
- Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094, People's Republic of China and CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, Beijing 100088, People's Republic of China
| | - Roberto Car
- Department of Chemistry, Department of Physics, Program in Applied and Computational Mathematics, Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, USA
| | - Weinan E
- Department of Mathematics and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA and Beijing Institute of Big Data Research, Beijing 100871, People's Republic of China
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110
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Cuny J, Jolibois F, Gerber IC. Evaluation of Gas-to-Liquid 17O Chemical Shift of Water: A Test Case for Molecular and Periodic Approaches. J Chem Theory Comput 2018; 14:4041-4051. [DOI: 10.1021/acs.jctc.8b00243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC), Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Franck Jolibois
- LPCNO, Université Fédérale de Toulouse Midi-Pyrénées, INSA-CNRS-UPS, 135 avenue de Rangueil, 31077 Cedex 4 Toulouse, France
| | - Iann C. Gerber
- LPCNO, Université Fédérale de Toulouse Midi-Pyrénées, INSA-CNRS-UPS, 135 avenue de Rangueil, 31077 Cedex 4 Toulouse, France
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111
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Abstract
We developed a novel neural network-based force field for water based on training with high-level ab initio theory. The force field was built based on an electrostatically embedded many-body expansion method truncated at binary interactions. The many-body expansion method is a common strategy to partition the total Hamiltonian of large systems into a hierarchy of few-body terms. Neural networks were trained to represent electrostatically embedded one-body and two-body interactions, which require as input only one and two water molecule calculations at the level of ab initio electronic structure method CCSD/aug-cc-pVDZ embedded in the molecular mechanics water environment, making it efficient as a general force field construction approach. Structural and dynamic properties of liquid water calculated with our force field show good agreement with experimental results. We constructed two sets of neural network based force fields: nonpolarizable and polarizable force fields. Simulation results show that the nonpolarizable force field using fixed TIP3P charges has already behaved well, since polarization effects and many-body effects are implicitly included due to the electrostatic embedding scheme. Our results demonstrate that the electrostatically embedded many-body expansion combined with neural network provides a promising and systematic way to build next-generation force fields at high accuracy and low computational costs, especially for large systems.
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Affiliation(s)
- Hao Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Weitao Yang
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry and Environment, South China Normal University, Guangzhou 510006, China
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112
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Ulman K, Busch S, Hassanali AA. Quantum mechanical effects in zwitterionic amino acids: The case of proline, hydroxyproline, and alanine in water. J Chem Phys 2018; 148:222826. [DOI: 10.1063/1.5008665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kanchan Ulman
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht GmbH, Lichtenbergstr. 1, 85747 Garching bei München, Germany
| | - Ali A. Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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113
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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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114
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Dawson W, Gygi F. Equilibration and analysis of first-principles molecular dynamics simulations of water. J Chem Phys 2018; 148:124501. [PMID: 29604876 DOI: 10.1063/1.5018116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.
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Affiliation(s)
- William Dawson
- Department of Computer Science, University of California, Davis, Davis, California 95616, USA
| | - François Gygi
- Department of Computer Science, University of California, Davis, Davis, California 95616, USA
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115
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Gaiduk AP, Gustafson J, Gygi F, Galli G. First-Principles Simulations of Liquid Water Using a Dielectric-Dependent Hybrid Functional. J Phys Chem Lett 2018; 9:3068-3073. [PMID: 29768015 DOI: 10.1021/acs.jpclett.8b01017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We carried out first-principles simulations of liquid water under ambient conditions using a dielectric-dependent hybrid functional, where the fraction of exact exchange is set equal to the inverse of the high-frequency dielectric constant of the liquid. We found excellent agreement with experiment for the oxygen-oxygen partial correlation function at the experimental equilibrium density and 311 ± 3 K. Other structural and dynamical properties, such as the diffusion coefficient, molecular dipole moments, and vibrational spectra, are also in good agreement with experiment. Our results, together with previous findings on electronic properties of the liquid with the same functional, show that the dielectric-dependent hybrid functional accurately describes both the structural and electronic properties of liquid water.
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Affiliation(s)
- Alex P Gaiduk
- Institute for Molecular Engineering , The University of Chicago , Chicago , Illinois 60637 , United States
- Materials Science Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jeffrey Gustafson
- Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , United States
| | - François Gygi
- Department of Computer Science , University of California , Davis , California 95616 , United States
| | - Giulia Galli
- Institute for Molecular Engineering , The University of Chicago , Chicago , Illinois 60637 , United States
- Materials Science Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
- Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , United States
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116
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Zheng L, Chen M, Sun Z, Ko HY, Santra B, Dhuvad P, Wu X. Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble. J Chem Phys 2018; 148:164505. [DOI: 10.1063/1.5023611] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lixin Zheng
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Mohan Chen
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Zhaoru Sun
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Hsin-Yu Ko
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Biswajit Santra
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Pratikkumar Dhuvad
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
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117
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Śmiechowski M. Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water. J Phys Chem B 2018. [PMID: 29513989 DOI: 10.1021/acs.jpcb.7b11334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques can extract important information from the computed IR spectra of aqueous solutions of BF4- and PF6-, interesting weakly coordinating anions that have been known for a long time to alter the IR spectrum of water in an unusual manner. The distance-dependent spectra of both ions are analyzed using the spectral similarity method that provides a quantitative picture of both the spectrum of the solute-affected solvent and the number of solvent molecules thus altered. We find, in accordance with previous experiments, a considerable blue shift of the νOH stretching band of liquid water by 264 cm-1 for BF4- and 306 cm-1 for PF6-, with the affected numbers being 3.7 and 4.2, respectively. Considering also the additional information on solute-solvent dipolar couplings delivered by radially and spatially resolved IR spectra, the computational IR spectroscopy based on AIMD simulations is shown to be a viable predictive tool with strong interpretative power.
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Affiliation(s)
- Maciej Śmiechowski
- Department of Physical Chemistry, Chemical Faculty , Gdańsk University of Technology , Narutowicza 11/12 , 80-233 Gdańsk , Poland
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118
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Machida M, Kato K, Shiga M. Nuclear quantum effects of light and heavy water studied by all-electron first principles path integral simulations. J Chem Phys 2018; 148:102324. [DOI: 10.1063/1.5000091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Masahiko Machida
- CCSE, Japan Atomic Energy Agency (JAEA), 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Koichiro Kato
- Mizuho Information and Research Institute, Inc., 2-3, Kandanishiki-cho, Chiyoda-ku, Tokyo 101-8443, Japan
| | - Motoyuki Shiga
- CCSE, Japan Atomic Energy Agency (JAEA), 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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119
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Dong K, Hu W, Lin L. Interpolative Separable Density Fitting through Centroidal Voronoi Tessellation with Applications to Hybrid Functional Electronic Structure Calculations. J Chem Theory Comput 2018; 14:1311-1320. [PMID: 29370521 DOI: 10.1021/acs.jctc.7b01113] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recently developed interpolative separable density fitting (ISDF) decomposition is a powerful way for compressing the redundant information in the set of orbital pairs and has been used to accelerate quantum chemistry calculations in a number of contexts. The key ingredient of the ISDF decomposition is to select a set of nonuniform grid points, so that the values of the orbital pairs evaluated at such grid points can be used to accurately interpolate those evaluated at all grid points. The set of nonuniform grid points, called the interpolation points, can be automatically selected by a QR factorization with column pivoting (QRCP) procedure. This is the computationally most expensive step in the construction of the ISDF decomposition. In this work, we propose a new approach to find the interpolation points based on the centroidal Voronoi tessellation (CVT) method, which offers a much less expensive alternative to the QRCP procedure when ISDF is used in the context of hybrid functional electronic structure calculations. The CVT method only uses information from the electron density and can be efficiently implemented using a K-Means algorithm. We find that this new method achieves comparable accuracy to the ISDF-QRCP method, at a cost that is negligible in the overall hybrid functional calculations. For instance, for a system containing 1000 silicon atoms simulated using the HSE06 hybrid functional on 2000 computational cores, the cost of the QRCP-based method for finding the interpolation points is 38.1 s, while the CVT procedure only takes 0.7 s. We also find that the ISDF-CVT method enhances the smoothness of the potential energy surface in the context of ab initio molecular dynamics (AIMD) simulations with hybrid functionals.
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Affiliation(s)
- Kun Dong
- Center for Applied Mathematics , Cornell University , Ithaca , New York 14853 , United States
| | - Wei Hu
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Lin Lin
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Mathematics , University of California , Berkeley , California 94720 , United States
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120
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Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer. Nat Chem 2018. [DOI: 10.1038/s41557-018-0010-2] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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121
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Liu J, He X, Zhang JZH, Qi LW. Hydrogen-bond structure dynamics in bulk water: insights from ab initio simulations with coupled cluster theory. Chem Sci 2018; 9:2065-2073. [PMID: 29675248 PMCID: PMC5885775 DOI: 10.1039/c7sc04205a] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/04/2017] [Indexed: 02/04/2023] Open
Abstract
An accurate and efficient ab initio molecular dynamics (AIMD) simulation of liquid water was made possible using the fragment-based approach (J. F. Liu, X. He and J. Z. H. Zhang, Phys. Chem. Chem. Phys., 2017, 19, 11931-11936). In this study, we advance the AIMD simulations using the fragment-based coupled cluster (CC) theory, more accurately revealing the structural and dynamical properties of liquid water under ambient conditions. The results show that the double-donor hydrogen-bond configurations in liquid water are nearly in balance with the single-donor configurations, with a slight bias towards the former. Our observation is in contrast to the traditional tetrahedral water structure. The hydrogen-bond switching dynamics in liquid water are very fast, with a hydrogen-bond life time of around 0.78 picoseconds, determined using AIMD simulation at the CCD/aug-cc-pVDZ level. This time scale is remarkably shorter than the ∼3.0 picoseconds that is commonly obtained from traditional nonpolarized force fields and density functional theory (DFT) based first-principles simulations. Additionally, the obtained radial distribution functions, triplet oxygen angular distribution, diffusion coefficient, and the dipole moment of the water molecule are uniformly in good agreement with the experimental observations. The current high-level AIMD simulation sheds light on the understanding of the structural and dynamical properties of liquid water.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Natural Medicines , Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing , 210009 , China .
| | - Xiao He
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
- NYU-ECNU Center for Computational Chemistry , NYU Shanghai , Shanghai , 200062 , China
| | - John Z H Zhang
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
- NYU-ECNU Center for Computational Chemistry , NYU Shanghai , Shanghai , 200062 , China
- Department of Chemistry , New York University , New York , NY 10003 , USA
| | - Lian-Wen Qi
- State Key Laboratory of Natural Medicines , Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing , 210009 , China .
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122
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Sharma B, Chandra A. Born-Oppenheimer Molecular Dynamics Simulations of a Bromate Ion in Water Reveal Its Dual Kosmotropic and Chaotropic Behavior. J Phys Chem B 2018; 122:2090-2101. [PMID: 29376361 DOI: 10.1021/acs.jpcb.7b09300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solvation structure and dynamics of a bromate (BrO3-) ion in water are studied by means of Born-Oppenheimer molecular dynamics simulations at two different temperatures using the Becke-Lee-Yang-Parr functional with Grimme D3 dispersion corrections. The bromate ion possesses a pyramidal structure, and it has two types of solvation sites, namely, the bromine and oxygen atoms. We have looked at different radial and orientational distributions of water molecules around the bromate ion and also investigated their hydrogen bonding properties. The solvation structure of the bromate ion is also compared with that of the iodate (IO3-) ion, which is structurally rather similar to the bromate ion and was found to have some unusual solvation properties in water. It is found that the bromate ion follows a similar trend as that followed by the iodate ion as far as the solvation structure is concerned. However, the effect of the former on surrounding water is found to be much weaker than that of the latter. On the dynamical side, we have looked at diffusion, residence dynamics, and also the orientational and hydrogen bond relaxation of water molecules around the BrO3- ion and compared them with those of the bulk. Dynamical results are presented for both H2O and D2O around the BrO3- ion. Interpretation of the dynamical results in terms of structure-making (kosmotropic)/-breaking (chaotropic) properties of the BrO3- ion reveals that the bromine atom of this ion acts as a water structure breaker, whereas the three oxygens act as water structure makers. Thus, in spite of being a single ion, the bromate ion has dual characteristics and the experimentally observed kosmotropic ability of this ion is actually a trade-off between a chaotropic site (the bromine atom) and three kosmotropic sites (three oxygen atoms) that are present in the ion.
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Affiliation(s)
- Bikramjit Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
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123
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Liu J, He X, Zhang JZH. Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures. Phys Chem Chem Phys 2018; 19:11931-11936. [PMID: 28440370 DOI: 10.1039/c7cp00667e] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The nature of the dynamical hydrogen-bond network of liquid water under ambient conditions has challenged both experimental and theoretical researchers for decades and remains a topic of intense debate. In this work, we addressed the structural issue of the hydrogen-bond network of liquid water based on an accurate ab initio molecular dynamics simulation. The present work showed clearly that liquid water is neither accurately described by a static picture of mostly tetrahedral water molecules nor dominated by "ring-and-chain" like structures. Instead, the structure of water is a dynamical mixture of tetrahedral and 'ring-and-chain' like structures with a slight bias toward the former. On average, each water molecule forms about three hydrogen bonds with the surrounding water molecules. The present accurate ab initio molecular dynamics simulation of liquid water was made possible by using a fragment-based second-order Møller-Plesset perturbation theory (MP2) with a large basis set to treat a large body of water molecules. This level of ab initio theory is sufficiently accurate for describing water interactions, and the simulated structural and dynamical properties of liquid water, including radial distribution functions, diffusion coefficient, dipole moment, etc., are uniformly in excellent agreement with experimental observations.
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Affiliation(s)
- Jinfeng Liu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
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124
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Yadav S, Chandra A. Structural and Dynamical Nature of Hydration Shells of the Carbonate Ion in Water: An Ab Initio Molecular Dynamics Study. J Phys Chem B 2018; 122:1495-1504. [DOI: 10.1021/acs.jpcb.7b11636] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sushma Yadav
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
- Department
of Theoretical and Computational Molecular Science, Institute of Molecular Science, Myodaiji, Okazaki 444-8585, Aichi, Japan
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125
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Demichelis R, Garcia NA, Raiteri P, Innocenti Malini R, Freeman CL, Harding JH, Gale JD. Simulation of Calcium Phosphate Species in Aqueous Solution: Force Field Derivation. J Phys Chem B 2018; 122:1471-1483. [DOI: 10.1021/acs.jpcb.7b10697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raffaella Demichelis
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR)
and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Natalya A. Garcia
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR)
and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Paolo Raiteri
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR)
and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Riccardo Innocenti Malini
- Department
of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
- Laboratory
for Biomimetic Membranes and Textiles, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen 9014, Switzerland
| | - Colin L. Freeman
- Department
of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - John H. Harding
- Department
of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Julian D. Gale
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR)
and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
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126
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Yao Y, Kanai Y. Free Energy Profile of NaCl in Water: First-Principles Molecular Dynamics with SCAN and ωB97X-V Exchange–Correlation Functionals. J Chem Theory Comput 2018; 14:884-893. [DOI: 10.1021/acs.jctc.7b00846] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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127
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Suchan J, Hollas D, Curchod BFE, Slavíček P. On the importance of initial conditions for excited-state dynamics. Faraday Discuss 2018; 212:307-330. [DOI: 10.1039/c8fd00088c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The vast majority of ab initio excited-state simulations are performed within semiclassical, trajectory-based approaches. Apart from the underlying electronic-structure theory, the reliability of the simulations is controlled by a selection of initial conditions for the classical trajectories. We discuss appropriate choices of initial conditions for simulations of different experimental arrangements: dynamics initiated by continuum-wave (CW) laser fields or triggered by ultrashort laser pulses.
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Affiliation(s)
- Jiří Suchan
- Department of Physical Chemistry
- University of Chemistry and Technology, Prague
- 16628 Prague
- Czech Republic
| | - Daniel Hollas
- Department of Physical Chemistry
- University of Chemistry and Technology, Prague
- 16628 Prague
- Czech Republic
| | | | - Petr Slavíček
- Department of Physical Chemistry
- University of Chemistry and Technology, Prague
- 16628 Prague
- Czech Republic
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128
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Karmakar A, Chandra A. Dynamics of vibrational spectral diffusion in water: Effects of dispersion interactions, temperature, density, system size and fictitious orbital mass. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.11.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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129
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Barnes TA, Wan LF, Kent PRC, Prendergast D. Hybrid DFT investigation of the energetics of Mg ion diffusion in α-MoO3. Phys Chem Chem Phys 2018; 20:24877-24884. [DOI: 10.1039/c8cp05511d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mg ion diffusion barriers in α-MoO3 are simulated using the GGA, GGA+U, and hybrid DFT approaches.
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Affiliation(s)
| | - Liwen F. Wan
- Joint Center for Energy Storage Research
- The Molecular Foundry
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - Paul R. C. Kent
- Center for Nanophase Materials Science and Computational Sciences and Engineering Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - David Prendergast
- Joint Center for Energy Storage Research
- The Molecular Foundry
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
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130
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Giannozzi P, Andreussi O, Brumme T, Bunau O, Buongiorno Nardelli M, Calandra M, Car R, Cavazzoni C, Ceresoli D, Cococcioni M, Colonna N, Carnimeo I, Dal Corso A, de Gironcoli S, Delugas P, DiStasio RA, Ferretti A, Floris A, Fratesi G, Fugallo G, Gebauer R, Gerstmann U, Giustino F, Gorni T, Jia J, Kawamura M, Ko HY, Kokalj A, Küçükbenli E, Lazzeri M, Marsili M, Marzari N, Mauri F, Nguyen NL, Nguyen HV, Otero-de-la-Roza A, Paulatto L, Poncé S, Rocca D, Sabatini R, Santra B, Schlipf M, Seitsonen AP, Smogunov A, Timrov I, Thonhauser T, Umari P, Vast N, Wu X, Baroni S. Advanced capabilities for materials modelling with Quantum ESPRESSO. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:465901. [PMID: 29064822 DOI: 10.1088/1361-648x/aa8f79] [Citation(s) in RCA: 1478] [Impact Index Per Article: 211.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
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Affiliation(s)
- P Giannozzi
- Department of Mathematics, Computer Science, and Physics, University of Udine, via delle Scienze 206, I-33100 Udine, Italy
| | - O Andreussi
- Institute of Computational Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - T Brumme
- Wilhelm-Ostwald-Institute of Physical and Theoretical Chemistry, Leipzig University, Linnéstr. 2, D-04103 Leipzig, Germany
| | - O Bunau
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
| | - M Buongiorno Nardelli
- Department of Physics and Department of Chemistry, University of North Texas, Denton, TX, United States of America
| | - M Calandra
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
| | - R Car
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States of America
| | - C Cavazzoni
- CINECA-Via Magnanelli 6/3, I-40033 Casalecchio di Reno, Bologna, Italy
| | - D Ceresoli
- Institute of Molecular Science and Technologies (ISTM), National Research Council (CNR), I-20133 Milano, Italy
| | - M Cococcioni
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - N Colonna
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - I Carnimeo
- Department of Mathematics, Computer Science, and Physics, University of Udine, via delle Scienze 206, I-33100 Udine, Italy
| | - A Dal Corso
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
- CNR-IOM DEMOCRITOS, Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Italy
| | - S de Gironcoli
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
- CNR-IOM DEMOCRITOS, Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Italy
| | - P Delugas
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
| | - R A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States of America
| | - A Ferretti
- CNR Istituto Nanoscienze, I-42125 Modena, Italy
| | - A Floris
- School of Mathematics and Physics, College of Science, University of Lincoln, United Kingdom
| | - G Fratesi
- Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
| | - G Fugallo
- ETSF, Laboratoire des Solides Irradiés, Ecole Polytechnique, F-91128 Palaiseau cedex, France
| | - R Gebauer
- The Abdus Salam International Centre for Theoretical Physics (ICTP), Strada Costiera 11, I-34151 Trieste, Italy
| | - U Gerstmann
- Department Physik, Universität Paderborn, D-33098 Paderborn, Germany
| | - F Giustino
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - T Gorni
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
| | - J Jia
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States of America
| | - M Kawamura
- The Institute for Solid State Physics, Kashiwa, Japan
| | - H-Y Ko
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States of America
| | - A Kokalj
- Department of Physical and Organic Chemistry, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - E Küçükbenli
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
| | - M Lazzeri
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
| | - M Marsili
- Dipartimento di Fisica e Astronomia, Università di Padova, via Marzolo 8, I-35131 Padova, Italy
| | - N Marzari
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - F Mauri
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - N L Nguyen
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - H-V Nguyen
- Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Hanoi, Vietnam
| | - A Otero-de-la-Roza
- Department of Chemistry, University of British Columbia, Okanagan, Kelowna BC V1V 1V7, Canada
| | - L Paulatto
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
| | - S Poncé
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - D Rocca
- Université de Lorraine, CRM2, UMR 7036, F-54506 Vandoeuvre-lès-Nancy, France
- CNRS, CRM2, UMR 7036, F-54506 Vandoeuvre-lès-Nancy, France
| | - R Sabatini
- Orionis Biosciences, Newton, MA 02466, United States of America
| | - B Santra
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States of America
| | - M Schlipf
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - A P Seitsonen
- Institut für Chimie, Universität Zurich, CH-8057 Zürich, Switzerland
- Département de Chimie, École Normale Supérieure, F-75005 Paris, France
| | - A Smogunov
- SPEC, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - I Timrov
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - T Thonhauser
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, United States of America
| | - P Umari
- Dipartimento di Fisica e Astronomia, Università di Padova, via Marzolo 8, I-35131 Padova, Italy
- CNR-IOM DEMOCRITOS, Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Italy
| | - N Vast
- Laboratoire des Solides Irradiés, École Polytechnique, CEA-DRF-IRAMIS, CNRS UMR 7642, Université Paris-Saclay, F-91120 Palaiseau, France
| | - X Wu
- Department of Physics, Temple University, Philadelphia, PA 19122-1801, United States of America
| | - S Baroni
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
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131
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Hu W, Lin L, Yang C. Interpolative Separable Density Fitting Decomposition for Accelerating Hybrid Density Functional Calculations with Applications to Defects in Silicon. J Chem Theory Comput 2017; 13:5420-5431. [PMID: 28960982 DOI: 10.1021/acs.jctc.7b00807] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a new efficient way to perform hybrid density functional theory (DFT)-based electronic structure calculations. The new method uses an interpolative separable density fitting (ISDF) procedure to construct a set of numerical auxiliary basis vectors and a compact approximation of the matrix consisting of products of occupied orbitals represented in a large basis set such as the planewave basis. Such an approximation allows us to reduce the number of Poisson solves from [Formula: see text] to [Formula: see text] when we apply the exchange operator to occupied orbitals in an iterative method for solving the Kohn-Sham equations, where Ne is the number of electrons in the system to be studied. We show that the ISDF procedure can be carried out in [Formula: see text] operations, with a much smaller preconstant compared to methods used in existing approaches. When combined with the recently developed adaptively compressed exchange (ACE) operator formalism, which reduces the number of times the exchange operator needs to be updated, the resulting ACE-ISDF method significantly reduces the computational cost associated with the exchange operator by nearly 2 orders of magnitude compared to existing approaches for a large silicon system with 1000 atoms. We demonstrate that the ACE-ISDF method can produce accurate energies and forces for insulating and metallic systems and that it is possible to obtain converged hybrid functional calculation results for a 1000-atom bulk silicon within 10 min on 2000 computational cores. We also show that ACE-ISDF can scale to 8192 computational cores for a 4096-atom bulk silicon system. We use the ACE-ISDF method to geometrically optimize a 1000-atom silicon system with a vacancy defect using the HSE06 functional and computes its electronic structure. We find that that the computed energy gap from the HSE06 functional is much closer to the experimental value compared to that produced by semilocal functionals in the DFT calculations.
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Affiliation(s)
- Wei Hu
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Lin Lin
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Mathematics, University of California , Berkeley, California 94720, United States
| | - Chao Yang
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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132
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Hu W, Lin L, Yang C. Projected Commutator DIIS Method for Accelerating Hybrid Functional Electronic Structure Calculations. J Chem Theory Comput 2017; 13:5458-5467. [PMID: 28937762 DOI: 10.1021/acs.jctc.7b00892] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The commutator direct inversion of the iterative subspace (commutator DIIS or C-DIIS) method developed by Pulay is an efficient and the most widely used scheme in quantum chemistry to accelerate the convergence of self-consistent field (SCF) iterations in Hartree-Fock theory and Kohn-Sham density functional theory. The C-DIIS method requires the explicit storage of the density matrix, the Fock matrix, and the commutator matrix. Hence, the method can only be used for systems with a relatively small basis set, such as the Gaussian basis set. We develop a new method that enables the C-DIIS method to be efficiently employed in electronic structure calculations with a large basis set such as planewaves for the first time. The key ingredient is the projection of both the density matrix and the commutator matrix to an auxiliary matrix called the gauge-fixing matrix. The resulting projected commutator-DIIS method (PC-DIIS) only operates on matrices of the same dimension as that consists of Kohn-Sham orbitals. The cost of the method is comparable to that of standard charge mixing schemes used in large basis set calculations. The PC-DIIS method is gauge-invariant, which guarantees that its performance is invariant with respect to any unitary transformation of the Kohn-Sham orbitals. We demonstrate that the PC-DIIS method can be viewed as an extension of an iterative eigensolver for nonlinear problems. We use the PC-DIIS method for accelerating Kohn-Sham density functional theory calculations with hybrid exchange-correlation functionals, and demonstrate its superior performance compared to the commonly used nested two-level SCF iteration procedure. Furthermore, we demonstrate that in the context of ab initio molecular dynamics (MD) simulation with hybrid functionals one can extrapolate the gauge-fixing matrix to achieve the goal of extrapolating the entire density matrix implicitly along the MD trajectory. Numerical results indicate that the new method significantly reduces the number of SCF iterations per MD step, compared to the commonly used strategy of extrapolating the electron density.
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Affiliation(s)
- Wei Hu
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Lin Lin
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Mathematics, University of California , Berkeley, California 94720, United States
| | - Chao Yang
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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133
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Yong X, Tse JS, English NJ. optPBE-vdW density functional theory study of liquid water and pressure-induced structural evolution in ice Ih. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The accuracy of several local and non-local van der Waals (vdW) corrected exchange correlation functionals on the description of the effect of pressure on ice has been investigated. In a preliminary survey, the non-local vdW correction used in conjunction with the optPBE functional was shown to provide the best overall agreement on the structural parameters of ice Ih with experiments. More importantly, this combination reproduced correctly the recently observed crystal → crystal transformation in ice Ih at 80 K prior to amorphisation. The predicted transition pressure of 1.9 GPa is somewhat higher, showing that the current generation of vdW functionals are still not sufficiently accurate for the ice system. The existence of an intermediate crystalline state with a shear-hexagonal structure confirms the earlier prediction that the collapse of crystalline structure under compression originates from the softening of phonon modes in ice Ih’s basal plane.
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Affiliation(s)
- Xue Yong
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - John S. Tse
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Niall J. English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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134
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P SK, Genova A, Pavanello M. Cooperation and Environment Characterize the Low-Lying Optical Spectrum of Liquid Water. J Phys Chem Lett 2017; 8:5077-5083. [PMID: 28968128 DOI: 10.1021/acs.jpclett.7b02212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The optical spectrum of liquid water is analyzed by subsystem time-dependent density functional theory. We provide simple explanations for several important (and so far elusive) features. Due to the disordered environment surrounding each water molecule, the joint density of states of the liquid is much broader than that of the vapor, thus explaining the red-shifted Urbach tail of the liquid compared to the gas phase. Confinement effects provided by the first solvation shell are responsible for the blue shift of the first absorption peak compared to the vapor. In addition, we also characterize many-body excitonic effects. These dramatically affect the spectral weights at low frequencies, contributing to the refractive index by a small but significant amount.
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Affiliation(s)
- Sudheer Kumar P
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
| | - Alessandro Genova
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
| | - Michele Pavanello
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
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135
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Abstract
Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.
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136
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Philips A, Marchenko A, Truflandier LA, Autschbach J. Quadrupolar NMR Relaxation from ab Initio Molecular Dynamics: Improved Sampling and Cluster Models versus Periodic Calculations. J Chem Theory Comput 2017; 13:4397-4409. [PMID: 28719202 DOI: 10.1021/acs.jctc.7b00584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quadrupolar NMR relaxation rates are computed for 17O and 2H nuclei of liquid water, and of 23Na+, and 35Cl- in aqueous solution via Kohn-Sham (KS) density functional theory ab initio molecular dynamics (aiMD) and subsequent KS electric field gradient (EFG) calculations along the trajectories. The calculated relaxation rates are within about a factor of 2 of experimental results and improved over previous aiMD simulations. The relaxation rates are assessed with regard to the lengths of the simulations as well as configurational sampling. The latter is found to be the more limiting factor in obtaining good statistical sampling and is improved by averaging over many equivalent nuclei of a system or over several independent trajectories. Further, full periodic plane-wave basis calculations of the EFGs are compared with molecular-cluster atomic-orbital basis calculations. The two methods deliver comparable results with nonhybrid functionals. With the molecular-cluster approach, a larger variety of electronic structure methods is available. For chloride, the EFG computations benefit from using a hybrid KS functional.
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Affiliation(s)
- Adam Philips
- Department of Chemistry University at Buffalo, State University of New York , Buffalo, New York 14260-3000, United States
| | - Alex Marchenko
- Department of Chemistry University at Buffalo, State University of New York , Buffalo, New York 14260-3000, United States
| | - Lionel A Truflandier
- CNRS UMR 5255, Institut des Sciences Moléculaires Université Bordeaux , 351 cours de la Libération, 33405 Talence cedex, France
| | - Jochen Autschbach
- Department of Chemistry University at Buffalo, State University of New York , Buffalo, New York 14260-3000, United States
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137
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Guillaud E, Joly L, de Ligny D, Merabia S. Assessment of elastic models in supercooled water: A molecular dynamics study with the TIP4P/2005f force field. J Chem Phys 2017; 147:014504. [DOI: 10.1063/1.4991372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Emmanuel Guillaud
- Institut Lumière Matière, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France
- Department of Materials Science, Institute of Glass and Ceramics, University of Erlangen-Nürnberg, Martensstrasse 5, 91058 Erlangen, Germany
| | - Laurent Joly
- Institut Lumière Matière, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France
| | - Dominique de Ligny
- Department of Materials Science, Institute of Glass and Ceramics, University of Erlangen-Nürnberg, Martensstrasse 5, 91058 Erlangen, Germany
| | - Samy Merabia
- Institut Lumière Matière, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France
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138
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Galib M, Duignan TT, Misteli Y, Baer MD, Schenter GK, Hutter J, Mundy CJ. Mass density fluctuations in quantum and classical descriptions of liquid water. J Chem Phys 2017; 146:244501. [DOI: 10.1063/1.4986284] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Mirza Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Timothy T. Duignan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Yannick Misteli
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Gregory K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Jürg Hutter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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139
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Marchenko A, Truflandier LA, Autschbach J. Uranyl Carbonate Complexes in Aqueous Solution and Their Ligand NMR Chemical Shifts and 17O Quadrupolar Relaxation Studied by ab Initio Molecular Dynamics. Inorg Chem 2017; 56:7384-7396. [PMID: 28598146 DOI: 10.1021/acs.inorgchem.7b00396] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic structural effects, NMR ligand chemical shifts, and 17O NMR quadrupolar relaxation rates are investigated in the series of complexes UO22+, UO2(CO3)34-, and (UO2)3(CO3)66-. Car-Parrinello molecular dynamics (CPMD) is used to simulate the dynamics of the complexes in water. NMR properties are computed on clusters extracted from the CPMD trajectories. In the UO22+ complex, coordination at the uranium center by water molecules causes a decrease of around 300 ppm for the uranyl 17O chemical shift. The final value of this chemical shift is within 40 ppm of the experimental range. The UO2(CO3)34- and (UO2)3(CO3)66- complexes show a solvent dependence of the terminal carbonate 17O and 13C chemical shifts that is less pronounced than that for the uranyl oxygen atom. Corrections to the chemical shift from hybrid functionals and spin-orbit coupling improve the accuracy of chemical shifts if the sensitivity of the uranyl chemical shift to the uranyl bond length (estimated at 140 ppm per 0.1 Å from trajectory data) is taken into consideration. The experimentally reported trend in the two unique 13C chemical shifts is correctly reproduced for (UO2)3(CO3)66-. NMR relaxation rate data support large 17O peak widths, but remain below those noted in the experimental literature. Comparison of relaxation data for solvent-including versus solvent-free models suggest that carbonate ligand motion overshadows explicit solvent effects.
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Affiliation(s)
- Alex Marchenko
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260-3000, United States
| | - Lionel A Truflandier
- Institut des Sciences Moleculaires, Universite Bordeaux , CNRS UMR 5255, 33405 Talence cedex, France
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260-3000, United States
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140
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Liu F, Kong J. Efficient Computation of Exchange Energy Density with Gaussian Basis Functions. J Chem Theory Comput 2017; 13:2571-2580. [DOI: 10.1021/acs.jctc.7b00055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fenglai Liu
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee 37130, United States
| | - Jing Kong
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee 37130, United States
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141
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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142
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Ruiz Pestana L, Mardirossian N, Head-Gordon M, Head-Gordon T. Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals. Chem Sci 2017; 8:3554-3565. [PMID: 30155200 PMCID: PMC6092720 DOI: 10.1039/c6sc04711d] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/24/2017] [Indexed: 01/23/2023] Open
Abstract
We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm-3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreement with experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.
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Affiliation(s)
- Luis Ruiz Pestana
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , USA .
| | - Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
| | - Teresa Head-Gordon
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , USA .
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
- Departments of Chemistry , Bioengineering , Chemical and Biomolecular Engineering , University of California , Berkeley , USA
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143
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Marsalek O, Markland TE. Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects. J Phys Chem Lett 2017; 8:1545-1551. [PMID: 28296422 DOI: 10.1021/acs.jpclett.7b00391] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the reactivity and spectroscopy of aqueous solutions at the atomistic level is crucial for the elucidation and design of chemical processes. However, the simulation of these systems requires addressing the formidable challenges of treating the quantum nature of both the electrons and nuclei. Exploiting our recently developed methods that provide acceleration by up to 2 orders of magnitude, we combine path integral simulations with on-the-fly evaluation of the electronic structure at the hybrid density functional theory level to capture the interplay between nuclear quantum effects and the electronic surface. Here we show that this combination provides accurate structure and dynamics, including the full infrared and Raman spectra of liquid water. This allows us to demonstrate and explain the failings of lower-level density functionals for dynamics and vibrational spectroscopy when the nuclei are treated quantum mechanically. These insights thus provide a foundation for the reliable investigation of spectroscopy and reactivity in aqueous environments.
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Affiliation(s)
- Ondrej Marsalek
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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144
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Pham TA, Ping Y, Galli G. Modelling heterogeneous interfaces for solar water splitting. NATURE MATERIALS 2017; 16:401-408. [PMID: 28068314 DOI: 10.1038/nmat4803] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 10/18/2016] [Indexed: 05/17/2023]
Abstract
The generation of hydrogen from water and sunlight offers a promising approach for producing scalable and sustainable carbon-free energy. The key of a successful solar-to-fuel technology is the design of efficient, long-lasting and low-cost photoelectrochemical cells, which are responsible for absorbing sunlight and driving water splitting reactions. To this end, a detailed understanding and control of heterogeneous interfaces between photoabsorbers, electrolytes and catalysts present in photoelectrochemical cells is essential. Here we review recent progress and open challenges in predicting physicochemical properties of heterogeneous interfaces for solar water splitting applications using first-principles-based approaches, and highlights the key role of these calculations in interpreting increasingly complex experiments.
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Affiliation(s)
- Tuan Anh Pham
- Quantum Simulations Group, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Yuan Ping
- Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Giulia Galli
- The Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
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145
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Vitale V, Dziedzic J, Albaugh A, Niklasson AMN, Head-Gordon T, Skylaris CK. Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory. J Chem Phys 2017; 146:124115. [DOI: 10.1063/1.4978684] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Valerio Vitale
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Alex Albaugh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | | | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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146
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Hu W, Lin L, Banerjee AS, Vecharynski E, Yang C. Adaptively Compressed Exchange Operator for Large-Scale Hybrid Density Functional Calculations with Applications to the Adsorption of Water on Silicene. J Chem Theory Comput 2017; 13:1188-1198. [PMID: 28177229 DOI: 10.1021/acs.jctc.6b01184] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory (DFT) calculations using hybrid exchange-correlation functionals have been shown to provide an accurate description of the electronic structures of nanosystems. However, such calculations are often limited to small system sizes due to the high computational cost associated with the construction and application of the Hartree-Fock (HF) exchange operator. In this paper, we demonstrate that the recently developed adaptively compressed exchange (ACE) operator formulation [J. Chem. Theory Comput. 2016, 12, 2242-2249] can enable hybrid functional DFT calculations for nanosystems with thousands of atoms. The cost of constructing the ACE operator is the same as that of applying the exchange operator to the occupied orbitals once, while the cost of applying the Hamiltonian operator with a hybrid functional (after construction of the ACE operator) is only marginally higher than that associated with applying a Hamiltonian constructed from local and semilocal exchange-correlation functionals. Therefore, this new development significantly lowers the computational barrier for using hybrid functionals in large-scale DFT calculations. We demonstrate that a parallel planewave implementation of this method can be used to compute the ground-state electronic structure of a 1000-atom bulk silicon system in less than 30 wall clock minutes and that this method scales beyond 8000 computational cores for a bulk silicon system containing about 4000 atoms. The efficiency of the present methodology in treating large systems enables us to investigate adsorption properties of water molecules on Ag-supported two-dimensional silicene. Our computational results show that water monomer, dimer, and trimer configurations exhibit distinct adsorption behaviors on silicene. In particular, the presence of additional water molecules in the dimer and trimer configurations induces a transition from physisorption to chemisorption, followed by dissociation on Ag-supported silicene. This is caused by the enhanced effect of hydrogen bonds on charge transfer and proton transfer processes. Such a hydrogen bond autocatalytic effect is expected to have broad applications for silicene as an efficient surface catalyst for oxygen reduction reactions and water dissociation.
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Affiliation(s)
- Wei Hu
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Lin Lin
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Mathematics, University of California , Berkeley, California 94720, United States
| | - Amartya S Banerjee
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Eugene Vecharynski
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Chao Yang
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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147
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Hermann J, DiStasio RA, Tkatchenko A. First-Principles Models for van der Waals Interactions in Molecules and Materials: Concepts, Theory, and Applications. Chem Rev 2017; 117:4714-4758. [PMID: 28272886 DOI: 10.1021/acs.chemrev.6b00446] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Noncovalent van der Waals (vdW) or dispersion forces are ubiquitous in nature and influence the structure, stability, dynamics, and function of molecules and materials throughout chemistry, biology, physics, and materials science. These forces are quantum mechanical in origin and arise from electrostatic interactions between fluctuations in the electronic charge density. Here, we explore the conceptual and mathematical ingredients required for an exact treatment of vdW interactions, and present a systematic and unified framework for classifying the current first-principles vdW methods based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem (namely the Rutgers-Chalmers vdW-DF, Vydrov-Van Voorhis (VV), exchange-hole dipole moment (XDM), Tkatchenko-Scheffler (TS), many-body dispersion (MBD), and random-phase approximation (RPA) approaches). Particular attention is paid to the intriguing nature of many-body vdW interactions, whose fundamental relevance has recently been highlighted in several landmark experiments. The performance of these models in predicting binding energetics as well as structural, electronic, and thermodynamic properties is connected with the theoretical concepts and provides a numerical summary of the state-of-the-art in the field. We conclude with a roadmap of the conceptual, methodological, practical, and numerical challenges that remain in obtaining a universally applicable and truly predictive vdW method for realistic molecular systems and materials.
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Affiliation(s)
- Jan Hermann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany.,Physics and Materials Science Research Unit, University of Luxembourg , L-1511 Luxembourg, Luxembourg
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148
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White AD, Knight C, Hocky GM, Voth GA. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data. J Chem Phys 2017; 146:041102. [DOI: 10.1063/1.4974837] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Andrew D. White
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, USA
| | - Chris Knight
- Leadership Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Glen M. Hocky
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
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149
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Awoonor-Williams E, Rowley CN. The hydration structure of carbon monoxide byab initiomethods. J Chem Phys 2017; 146:034503. [DOI: 10.1063/1.4974164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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150
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Ducati LC, Marchenko A, Autschbach J. NMR J-Coupling Constants of Tl–Pt Bonded Metal Complexes in Aqueous Solution: Ab Initio Molecular Dynamics and Localized Orbital Analysis. Inorg Chem 2016; 55:12011-12023. [DOI: 10.1021/acs.inorgchem.6b02180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lucas C. Ducati
- Department
of Fundamental Chemistry Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP 05508-000, Brazil
| | - Alex Marchenko
- Department of Chemistry University at Buffalo State, University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry University at Buffalo State, University of New York, Buffalo, New York 14260-3000, United States
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