1
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O’Neill N, Shi BX, Fong K, Michaelides A, Schran C. To Pair or not to Pair? Machine-Learned Explicitly-Correlated Electronic Structure for NaCl in Water. J Phys Chem Lett 2024; 15:6081-6091. [PMID: 38820256 PMCID: PMC11181334 DOI: 10.1021/acs.jpclett.4c01030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
The extent of ion pairing in solution is an important phenomenon to rationalize transport and thermodynamic properties of electrolytes. A fundamental measure of this pairing is the potential of mean force (PMF) between solvated ions. The relative stabilities of the paired and solvent shared states in the PMF and the barrier between them are highly sensitive to the underlying potential energy surface. However, direct application of accurate electronic structure methods is challenging, since long simulations are required. We develop wave function based machine learning potentials with the random phase approximation (RPA) and second order Møller-Plesset (MP2) perturbation theory for the prototypical system of Na and Cl ions in water. We show both methods in agreement, predicting the paired and solvent shared states to have similar energies (within 0.2 kcal/mol). We also provide the same benchmarks for different DFT functionals as well as insight into the PMF based on simple analyses of the interactions in the system.
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Affiliation(s)
- Niamh O’Neill
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United
Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Benjamin X. Shi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Kara Fong
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Angelos Michaelides
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Christoph Schran
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United
Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
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2
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Weldon R, Wang F. Water Potential from Adaptive Force Matching for Ice and Liquid with Revised Dispersion Predicts Supercooled Liquid Anomalies in Good Agreement with Two Independent Experimental Fits. J Phys Chem B 2024; 128:3398-3407. [PMID: 38536126 PMCID: PMC11017247 DOI: 10.1021/acs.jpcb.3c06495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
A revised version of the Water potential from Adaptive force matching for Ice and Liquid (WAIL) was developed by using the previous data set for fitting the WAIL model but with a dispersion term calculated using symmetry adapted perturbation theory (SAPT). The model has no adjustable parameters and relies solely on fitting first-principles information. The new model, named revised WAIL (rWAIL), shows improved predictions of most properties of water when compared to the previously published WAIL model. The rWAIL model also compares favorably to other first-principles-derived water models, such as MB-Pol, at only a fraction of the computational cost. The rWAIL model is used to study the properties of supercooled water. The model shows evidence of a liquid-liquid phase transition (LLPT) in the supercooled regimes with the liquid-liquid critical point (LLCP) at 203 K and 90 MPa. This estimate is in good agreement with a recent polynomial fit to the experimental density of water. Also, the fit to the surface tension of supercooled water based on the rWAIL model shows excellent agreement with the corresponding fit to the experimental data. Consistent with previously published molecular dynamics and experimental data, the surface tension of water exhibits exponential growth in the supercooled regime, which is likely a result of the emergence of a low-density liquid form of water. The simulation thus unites two separate experimental fits with one first-principles-based model, lending strong evidence of an LLPT in real water.
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Affiliation(s)
- Raymond Weldon
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Feng Wang
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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3
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Ricard TC, Zhu X, Iyengar SS. Capturing Weak Interactions in Surface Adsorbate Systems at Coupled Cluster Accuracy: A Graph-Theoretic Molecular Fragmentation Approach Improved through Machine Learning. J Chem Theory Comput 2023. [PMID: 38019639 DOI: 10.1021/acs.jctc.3c00955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The accurate and efficient study of the interactions of organic matter with the surface of water is critical to a wide range of applications. For example, environmental studies have found that acidic polyfluorinated alkyl substances, especially perfluorooctanoic acid (PFOA), have spread throughout the environment and bioaccumulate into human populations residing near contaminated watersheds, leading to many systemic maladies. Thus, the study of the interactions of PFOA with water surfaces became important for the mitigation of their activity as pollutants and threats to public health. However, theoretical study of the interactions of such organic adsorbates on the surface of water, and their bulk concerted properties, often necessitates the use of ab initio methods to properly incorporate the long-range electronic properties that govern these extended systems. Notable theoretical treatments of "on-water" reactions thus far have employed hybrid DFT and semilocal DFT, but the interactions involved are weak interactions that may be best described using post-Hartree-Fock theory. Here, we aim to demonstrate the utility of a graph-theoretic approach to molecular fragmentation that accurately captures the critical "weak" interactions while maintaining an efficient ab initio treatment of the long-range periodic interactions that underpin the physics of extended systems. We apply this graph-theoretical treatment to study PFOA on the surface of water as a model system for the study of weak interactions seen in the wide range of surface interactions and reactions. The approach divides a system into a set of vertices, that are then connected through edges, faces, and higher order graph theoretic objects known as simplexes, to represent a collection of locally interacting subsystems. These subsystems are then used to construct ab initio molecular dynamics simulations and for computing multidimensional potential energy surfaces. To further improve the computational efficiency of our graph theoretic fragmentation method, we use a recently developed transfer learning protocol to construct the full system potential energy from a family of neural networks each designed to accurately model the behavior of individual simplexes. We use a unique multidimensional clustering algorithm, based on the k-means clustering methodology, to define our training space for each separate simplex. These models are used to extrapolate the energies for molecular dynamics trajectories at PFOA water interfaces, at less than one-tenth the cost as compared to a regular molecular fragmentation-based dynamics calculation with excellent agreement with couple cluster level of full system potential energies.
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Affiliation(s)
- Timothy C Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Xiao Zhu
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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4
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Huo J, Chen J, Liu P, Hong B, Zhang J, Dong H, Li S. Microscopic Mechanism of Proton Transfer in Pure Water under Ambient Conditions. J Chem Theory Comput 2023. [PMID: 37365994 DOI: 10.1021/acs.jctc.3c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Water molecules and the associated proton transfer (PT) are prevalent in chemical and biological systems and have been a hot research topic. Spectroscopic characterization and ab initio molecular dynamics (AIMD) simulations have previously revealed insights into acidic and basic liquids. Presumably, the situation in the acidic/basic solution is not necessarily the same as in pure water; in addition, the autoionization constant for water is only 10-14 under ambient conditions, making the study of PT in pure water challenging. To overcome this issue, we modeled periodic water box systems containing 1000 molecules for tens of nanoseconds based on a neural network potential (NNP) with quantum mechanical accuracy. The NNP was generated by training a dataset containing the energies and atomic forces of 17 075 configurations of periodic water box systems, and these data points were calculated at the MP2 level that considers electron correlation effects. We found that the size of the system and the duration of the simulation have a significant impact on the convergence of the results. With these factors considered, our simulations showed that hydronium (H3O+) and hydroxide (OH-) ions in water have distinct hydration structures, thermodynamic and kinetic properties, e.g., the longer-lasting and more stable hydrated structure of OH- ions than that of H3O+, as well as a significantly higher free energy barrier for the OH--associated PT than that of H3O+, leading the two to exhibit completely different PT behaviors. Given these characteristics, we further found that PT via OH- ions tends not to occur multiple times or between many molecules. In contrast, PT via H3O+ can synergistically occur among multiple molecules and prefers to adopt a cyclic pattern among three water molecules, while it occurs mostly in a chain pattern when more water molecules are involved. Therefore, our studies provide a detailed and solid microscopic explanation for the PT process in pure water.
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Affiliation(s)
- Jun Huo
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Jianghao Chen
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Pei Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
| | - Benkun Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
| | - Jian Zhang
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
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5
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Park SJ, Narvaez WA, Schwartz BJ. Ab Initio Studies of Hydrated Electron/Cation Contact Pairs: Hydrated Electrons Simulated with Density Functional Theory Are Too Kosmotropic. J Phys Chem Lett 2023; 14:559-566. [PMID: 36630724 DOI: 10.1021/acs.jpclett.2c03705] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We have performed the first DFT-based ab initio MD simulations of a hydrated electron (eaq-) in the presence of Na+, a system chosen because ion-pairing behavior in water depends sensitively on the local hydration structure. Experiments show that eaq-'s interact weakly with Na+; the eaq-'s spectrum blue shifts by only a few tens of meV upon ion pairing without changing shape. We find that the spectrum of the DFT-simulated eaq- red shifts and changes shape upon interaction with Na+, in contrast with experiment. We show that this is because the hydration structure of the DFT-simulated eaq- is too ordered or kosmotropic. Conversely, simulations that produce eaq-'s with a less ordered or chaotropic hydration structure form weaker ion pairs with Na+, yielding predicted spectral blue shifts in better agreement with experiment. Thus, ab initio simulations based on hybrid GGA DFT functionals fail to produce the correct solvation structure for the hydrated electron.
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Affiliation(s)
- Sanghyun J Park
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - Wilberth A Narvaez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - Benjamin J Schwartz
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
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6
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Liu J, He X. Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
- New York University‐East China Normal University Center for Computational Chemistry New York University Shanghai Shanghai China
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7
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Park SJ, Schwartz BJ. Understanding the Temperature Dependence and Finite Size Effects in Ab Initio MD Simulations of the Hydrated Electron. J Chem Theory Comput 2022; 18:4973-4982. [PMID: 35834750 DOI: 10.1021/acs.jctc.2c00335] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrated electron is of interest to both theorists and experimentalists as a paradigm solution-phase quantum system. Although the bulk of the theoretical work studying the hydrated electron is based on mixed quantum/classical (MQC) methods, recent advances in computer power have allowed several attempts to study this object using ab initio methods. The difficulty with employing ab initio methods for this system is that even with relatively inexpensive quantum chemistry methods such as density functional theory (DFT), such calculations are still limited to at most a few tens of water molecules and only a few picoseconds duration, leaving open the question as to whether the calculations are converged with respect to either system size or dynamical fluctuations. Moreover, the ab initio simulations of the hydrated electron that have been published to date have provided only limited analysis. Most works calculate the electron's vertical detachment energy, which can be compared to experiment, and occasionally the electronic absorption spectrum is also computed. Structural features, such as pair distribution functions, are rare in the literature, with the majority of the structural analysis being simple statements that the electron resides in a cavity, which are often based only on a small number of simulation snapshots. Importantly, there has been no ab initio work examining the temperature-dependent behavior of the hydrated electron, which has not been satisfactorily explained by MQC simulations. In this work, we attempt to remedy this situation by running DFT-based ab initio simulations of the hydrated electron as a function of both box size and temperature. We show that the calculated properties of the hydrated electron are not converged even with simulation sizes up to 128 water molecules and durations of several tens of picoseconds. The simulations show significant changes in the water coordination and solvation structure with box size. Our temperature-dependent simulations predict a red-shift of the absorption spectrum (computed using TD-DFT with an optimally tuned range-separated hybrid functional) with increasing temperature, but the magnitude of the predicted red-shift is larger than that observed experimentally, and the absolute position of the calculated spectra are off by over half an eV. The spectral red-shift at high temperatures is accompanied by both a partial loss of structure of the electron's central cavity and an increased radius of gyration that pushes electron density onto and beyond the first solvation shell. Overall, although ab initio simulations can provide some insights into the temperature-dependent behavior of the hydrated electron, the simulation sizes and level of quantum chemistry theory that are currently accessible are inadequate for correctly describing the experimental properties of this fascinating object.
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Affiliation(s)
- Sanghyun J Park
- Department of Chemistry and Biochemistry University of California,Los Angeles Los Angeles California 90095-1569, United States
| | - Benjamin J Schwartz
- Department of Chemistry and Biochemistry University of California,Los Angeles Los Angeles California 90095-1569, United States
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8
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Liu J, Lan J, He X. Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks. J Phys Chem A 2022; 126:3926-3936. [PMID: 35679610 DOI: 10.1021/acs.jpca.2c00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jinggang Lan
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
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9
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Yao Y, Kanai Y. Nuclear Quantum Effect and Its Temperature Dependence in Liquid Water from Random Phase Approximation via Artificial Neural Network. J Phys Chem Lett 2021; 12:6354-6362. [PMID: 34231366 DOI: 10.1021/acs.jpclett.1c01566] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report structural and dynamical properties of liquid water described by the random phase approximation (RPA) correlation together with the exact exchange energy (EXX) within density functional theory. By utilizing thermostated ring polymer molecular dynamics, we examine the nuclear quantum effects and their temperature dependence. We circumvent the computational limitation of performing direct first-principles molecular dynamics simulation at this high level of electronic structure theory by adapting an artificial neural network model. We show that the EXX+RPA level of theory accurately describes liquid water in terms of both dynamical and structural properties.
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Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
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10
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Willow SY, Xie B, Lawrence J, Eisenberg RS, Minh DDL. On the polarization of ligands by proteins. Phys Chem Chem Phys 2020; 22:12044-12057. [PMID: 32421120 DOI: 10.1039/d0cp00376j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we use a quantum mechanics/molecular mechanics (QM/MM) approach, in which the ligand is the QM region, to compute the ligand polarization energy of 286 protein-ligand complexes from the PDBBind Core Set (release 2016). Calculations were performed both with and without implicit solvent based on the domain decomposition Conductor-like Screening Model. We observe that the ligand polarization energy is linearly correlated with the magnitude of the electric field acting on the ligand, the magnitude of the induced dipole moment, and the classical polarization energy. The influence of protein and cation charges on the ligand polarization diminishes with the distance and is below 2 kcal mol-1 at 9 Å and 1 kcal mol-1 at 12 Å. Compared to these embedding field charges, implicit solvent has a relatively minor effect on ligand polarization. Considering both polarization and solvation appears essential to computing negative binding energies in some crystallographic complexes. Solvation, but not polarization, is essential for achieving moderate correlation with experimental binding free energies.
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Affiliation(s)
- Soohaeng Yoo Willow
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA.
| | - Bing Xie
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA.
| | - Jason Lawrence
- Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - Robert S Eisenberg
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA.
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11
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Biswas S, Mallik BS. Probing the vibrational dynamics of amide bands of N-methylformamide, N, N-dimethylacetamide, and N-methylacetamide in water. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Yao Y, Kanai Y. Temperature dependence of nuclear quantum effects on liquid water via artificial neural network model based on SCAN meta-GGA functional. J Chem Phys 2020; 153:044114. [DOI: 10.1063/5.0012815] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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13
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Ninomiya M, Doi H, Matsumoto Y, Mochizuki Y, Komeiji Y. Ab Initio Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations of (NH 3) 32 Cluster: Effects of Electron Correlation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Moeko Ninomiya
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Hideo Doi
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology, AIST, Tsukuba Central 2, Tsukuba, Ibaraki 305-8568, Japan
| | - Yoshiteru Matsumoto
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Yuto Komeiji
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST, Tsukuba Central 6, Tsukuba, Ibaraki 305-8566, Japan
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14
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Hughes ZE, Ren E, Thacker JCR, Symons BCB, Silva AF, Popelier PLA. A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics. J Comput Chem 2020; 41:619-628. [PMID: 31747059 PMCID: PMC7004022 DOI: 10.1002/jcc.26111] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/21/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022]
Abstract
Key to progress in molecular simulation is the development of advanced models that go beyond the limitations of traditional force fields that employ a fixed, point charge-based description of electrostatics. Taking water as an example system, the FFLUX framework is shown capable of producing models that are flexible, polarizable and have a multipolar description of the electrostatics. The kriging machine-learning methods used in FFLUX are able to reproduce the intramolecular potential energy surface and multipole moments of a single water molecule with chemical accuracy using as few as 50 training configurations. Molecular dynamics simulations of water clusters (25-216 molecules) using the new FFLUX model reveal that incorporating charge-quadrupole, dipole-dipole, and quadrupole-charge interactions into the description of the electrostatics results in significant changes to the intermolecular structuring of the water molecules. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Zak E. Hughes
- Manchester Institute of Biotechnology, The University of ManchesterManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterManchesterM13 9PLUnited Kingdom
- School of Chemistry and Biosciences, University of BradfordBradfordBD7 1DPUnited Kingdom
| | - Emmanuel Ren
- Manchester Institute of Biotechnology, The University of ManchesterManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterManchesterM13 9PLUnited Kingdom
| | - Joseph C. R. Thacker
- Manchester Institute of Biotechnology, The University of ManchesterManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterManchesterM13 9PLUnited Kingdom
| | - Benjamin C. B. Symons
- Manchester Institute of Biotechnology, The University of ManchesterManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterManchesterM13 9PLUnited Kingdom
| | - Arnaldo F. Silva
- Manchester Institute of Biotechnology, The University of ManchesterManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterManchesterM13 9PLUnited Kingdom
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology, The University of ManchesterManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterManchesterM13 9PLUnited Kingdom
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15
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Fischer KC, Sherman SL, Garand E. Competition between Solvation and Intramolecular Hydrogen-Bonding in Microsolvated Protonated Glycine and β-Alanine. J Phys Chem A 2020; 124:1593-1602. [DOI: 10.1021/acs.jpca.9b11977] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kaitlyn C. Fischer
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Summer L. Sherman
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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16
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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17
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Fischer KC, Sherman SL, Voss JM, Zhou J, Garand E. Microsolvation Structures of Protonated Glycine and l-Alanine. J Phys Chem A 2019; 123:3355-3366. [DOI: 10.1021/acs.jpca.9b01578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kaitlyn C. Fischer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Summer L. Sherman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jonathan M. Voss
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jia Zhou
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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18
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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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19
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Lao KU, Jia J, Maitra R, DiStasio RA. On the geometric dependence of the molecular dipole polarizability in water: A benchmark study of higher-order electron correlation, basis set incompleteness error, core electron effects, and zero-point vibrational contributions. J Chem Phys 2018; 149:204303. [PMID: 30501247 DOI: 10.1063/1.5051458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we investigate how geometric changes influence the static dipole polarizability (α) of a water molecule by explicitly computing the corresponding dipole polarizability surface (DPS) across 3125 total (1625 symmetry-unique) geometries using linear response coupled cluster theory including single, double, and triple excitations (LR-CCSDT) and the doubly augmented triple-ζ basis set (d-aug-cc-pVTZ). Analytical formulae based on power series expansions of this ab initio surface are generated using linear least-squares analysis and provide highly accurate estimates of this quantity as a function of molecular geometry (i.e., bond and angle variations) in a computationally tractable manner. An additional database, which consists of 25 representative molecular geometries and incorporates a more thorough treatment of both basis sets and core electron effects, is provided as a current benchmark for this quantity and the corresponding leading-order C 6 dispersion coefficient. This database has been utilized to assess the importance of these effects as well as the relative accuracy that can be obtained using several quantum chemical methods and a library of density functional approximations. In addition to high-level electron correlation methods (like CCSD) and our analytical least-squares formulae, we find that the SCAN0, PBE0, MN15, and B97-2 hybrid functionals yield the most accurate descriptions of the molecular polarizability tensor in H2O. Using first-order perturbation theory, we compute the zero-point vibrational correction to α at the CCSDT/d-aug-cc-pVTZ level and find that this correction contributes approximately 3% to the isotropic (α iso) and nearly 50% to the anisotropic (α aniso) polarizability values. In doing so, we find that α iso = 9.8307 bohr3, which is in excellent agreement with the experimental value of 9.83 ± 0.02 bohr3 provided by Russell and Spackman. The DPS reported herein provides a benchmark-quality quantum mechanical estimate of this fundamental quantity of interest and should find extensive use in the development (and assessment) of next-generation force fields and machine-learning based approaches for modeling water in complex condensed-phase environments.
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Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Junteng Jia
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Rahul Maitra
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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20
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Ohto T, Dodia M, Imoto S, Nagata Y. Structure and Dynamics of Water at the Water–Air Interface Using First-Principles Molecular Dynamics Simulations within Generalized Gradient Approximation. J Chem Theory Comput 2018; 15:595-602. [DOI: 10.1021/acs.jctc.8b00567] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatsuhiko Ohto
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mayank Dodia
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sho Imoto
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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21
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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22
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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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23
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Fischer SA, Dunlap BI, Gunlycke D. Correlated dynamics in aqueous proton diffusion. Chem Sci 2018; 9:7126-7132. [PMID: 30310634 PMCID: PMC6137442 DOI: 10.1039/c8sc01253a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 07/27/2018] [Indexed: 11/24/2022] Open
Abstract
The aqueous proton displays an anomalously large diffusion coefficient that is up to 7 times that of similarly sized cations. There is general consensus that the proton achieves its high diffusion through the Grotthuss mechanism, whereby protons hop from one molecule to the next. A main assumption concerning the extraction of the timescale of the Grotthuss mechanism from experimental results has been that, on average, there is an equal probability for the proton to hop to any of its neighboring water molecules. Herein, we present ab initio simulations that show this assumption is not generally valid. Specifically, we observe that there is an increased probability for the proton to revert back to its previous location. These correlations indicate that the interpretation of the experimental results need to be re-examined and suggest that the timescale of the Grotthuss mechanism is significantly shorter than was previously thought.
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Affiliation(s)
- Sean A Fischer
- Chemistry Division , U. S. Naval Research Laboratory , Washington , DC 20375 , USA .
| | - Brett I Dunlap
- Chemistry Division , U. S. Naval Research Laboratory , Washington , DC 20375 , USA .
| | - Daniel Gunlycke
- Chemistry Division , U. S. Naval Research Laboratory , Washington , DC 20375 , USA .
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24
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Liu J, Pantelides ST. Electrowetting on 2D dielectrics: a quantum molecular dynamics investigation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:375001. [PMID: 30079895 DOI: 10.1088/1361-648x/aad838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Electrowetting on dielectrics (EWOD) is widely used to manipulate the spreading of a conductive liquid on a dielectric surface by applying an electric field. 2D hydrophobic dielectrics are promising candidates for EWOD applications. In this study, extensive quantum molecular dynamics (MD) simulations are performed to investigate the electrowetting behavior of salty water on hexagonal boron nitride (h-BN) monolayer. The proximal adsorption of salt ions and the associated realignment of the dipole moments of interfacial water with the applied electric field are found to be the physical origin of the electrowetting behavior. At low salt concentration and low electric fields, the proximal adsorption and the realignment follow the applied electric field, and the cosine of the water contact angle (WCA) follows a quadratic dependence on the applied electric field. At high salt concentration and high electric fields, the proximal adsorption saturates, which restricts further realignment and causes a saturation of the WCA. This case study provides physical insights into the much debated mechanism that underlies the contact angle saturation (CAS) found in macroscopic electrowetting phenomena and also provides an avenue for further studies of electrowetting at the atomic scale.
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Affiliation(s)
- Jian Liu
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235, United States of America
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25
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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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26
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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27
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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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28
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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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29
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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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30
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Liu J, Lai CY, Zhang YY, Chiesa M, Pantelides ST. Water wettability of graphene: interplay between the interfacial water structure and the electronic structure. RSC Adv 2018; 8:16918-16926. [PMID: 35540542 PMCID: PMC9080294 DOI: 10.1039/c8ra03509a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 04/28/2018] [Indexed: 12/14/2022] Open
Abstract
Wettability of graphene is characterized from first principles.
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Affiliation(s)
- Jian Liu
- Department of Physics and Astronomy
- Vanderbilt University
- Tennessee 37235
- USA
| | - Chia-Yun Lai
- Laboratory for Energy and Nano-Sciences
- Khalifa University of Science and Technology
- Abu Dhabi
- United Arab Emirates
| | - Yu-Yang Zhang
- Department of Physics and Astronomy
- Vanderbilt University
- Tennessee 37235
- USA
| | - Matteo Chiesa
- Laboratory for Energy and Nano-Sciences
- Khalifa University of Science and Technology
- Abu Dhabi
- United Arab Emirates
| | - Sokrates T. Pantelides
- Department of Physics and Astronomy
- Vanderbilt University
- Tennessee 37235
- USA
- Department of Electrical Engineering and Computer Science
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31
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Manna D, Kesharwani MK, Sylvetsky N, Martin JML. Conventional and Explicitly Correlated ab Initio Benchmark Study on Water Clusters: Revision of the BEGDB and WATER27 Data Sets. J Chem Theory Comput 2017; 13:3136-3152. [DOI: 10.1021/acs.jctc.6b01046] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Debashree Manna
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rechovot, Israel
| | - Manoj K. Kesharwani
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rechovot, Israel
| | - Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rechovot, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rechovot, Israel
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32
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Bai C, Kale S, Herzfeld J. Chemistry with semi-classical electrons: reaction trajectories auto-generated by sub-atomistic force fields. Chem Sci 2017; 8:4203-4210. [PMID: 28626563 PMCID: PMC5468998 DOI: 10.1039/c7sc01181d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/09/2017] [Indexed: 11/21/2022] Open
Abstract
For a century now, "Lewis dots" have been a mainstay of chemical thinking, teaching and communication. However, chemists have assumed that this semi-classical picture of electrons needs to be abandoned for quantitative work, and the recourse in computational simulations has been to the extremes of first principles treatments of electrons on the one hand and force fields that avoid explicit electrons on the other hand. Given both the successes and limitations of these highly divergent approaches, it seems worth considering whether the Lewis dot picture might be made quantitative after all. Here we review progress to that end, including variations that have been implemented and examples of applications, specifically the acid-base behavior of water, several organic reactions, and electron dynamics in silicon fracture. In each case, the semi-classical approach is highly efficient and generates reasonable and readily interpreted reaction trajectories in turnkey fashion (i.e., without any input about products). Avenues for further progress are also discussed.
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Affiliation(s)
- Chen Bai
- Department of Chemistry , Brandeis University , Waltham , MA 02454 , USA .
| | - Seyit Kale
- Department of Chemistry , Brandeis University , Waltham , MA 02454 , USA .
| | - Judith Herzfeld
- Department of Chemistry , Brandeis University , Waltham , MA 02454 , USA .
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Bai C, Herzfeld J. Special Pairs Are Decisive in the Autoionization and Recombination of Water. J Phys Chem B 2017; 121:4213-4219. [PMID: 28381087 DOI: 10.1021/acs.jpcb.7b02110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although water's chemical properties are no less important than its exceptional physical properties, its acid-base behavior is relatively poorly understood. In fact, the Grotthus trajectories for ion recombination predicted by density functional theory do not comport well with the almost 100-fold slower diffusive trajectories observed in time-resolved spectroscopy. And, in the reverse reaction, the barrier to autoionization is not well characterized. Here we develop a self-consistent picture of both processes based on the occurrence and role of ultrashort hydrogen bonds. The predicted populations of these special pairs in bulk water are consistent with the high frequency electrodynamics of water and its pressure dependence. The rate-limiting role of the special pairs manifests in autoionization as a two-stage barrier, first to form a contact ion pair and then to separate it by one water molecule. From this configuration, similar frequencies are observed for further separation vs recombination. The requirement of ultrashort hydrogen bonds for proton transfer in autoionization is consistent with the rise in Kw with increasing pressure and points to a role for density fluctuations in autoionization events. In neutralization, the manifestation of the role of special pairs is the prolonged diffusional process observed in time-resolved spectroscopy experiments. The requirement of special pairs as transition states for proton transfer is less obvious for neutralization in isolated water chains than in the bulk liquid only because an unbroken sequence of ultrashort H-bonds is more easily formed in a 1D H-bonded chain than in a 3D H-bonded network.
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Affiliation(s)
- Chen Bai
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Judith Herzfeld
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
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Willow SY, Xantheas SS. Molecular-Level Insight of the Effect of Hofmeister Anions on the Interfacial Surface Tension of a Model Protein. J Phys Chem Lett 2017; 8:1574-1577. [PMID: 28325043 DOI: 10.1021/acs.jpclett.7b00069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The effect of the Hofmeister anions on the precipitation of proteins is often discussed using liquid-vapor coexisting systems with the assumption that the liquid-vapor interface mimics the liquid-protein interface. Solvated proteins, however, have both hydrophobic and hydrophilic regions on their surfaces rather than just a pure hydrophobic one. Using a solvated parallel β-sheet layer consisting of both hydrophobic and positively charged hydrophilic surfaces, we investigated the adsorption of kosmotropic (SO42-) and chaotropic (ClO4-) anions toward the protein's hydrophobic and hydrophilic surfaces via Born-Oppenheimer molecular dynamics simulations using the BLYP density functional theory. It was found that both anions prefer to reside on the hydrophilic surface. Furthermore, kosmotropic anions, like SO42-, enhance the interfacial surface tension of the protein and stabilize the protein, whereas, in contrast, chaotropic anions, like ClO4-, weaken the interfacial surface tension of the protein and allow water molecules to penetrate toward the peptide bonds to form water-peptide hydrogen bonds, thus destabilizing the protein.
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Affiliation(s)
- Soohaeng Yoo Willow
- Department of Micro/Nano-electronics, Shanghai Jiao Tong University , 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Sotiris S Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory , 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
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35
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Willow SY. Path integral molecular dynamics at zero thermal temperature. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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García de la Vega JM, Omar S, San Fabián J. Performance of wave function and density functional methods for water hydrogen bond spin–spin coupling constants. J Mol Model 2017; 23:134. [DOI: 10.1007/s00894-017-3303-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/27/2017] [Indexed: 11/29/2022]
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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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Cisneros G, Wikfeldt KT, Ojamäe L, Lu J, Xu Y, Torabifard H, Bartók AP, Csányi G, Molinero V, Paesani F. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chem Rev 2016; 116:7501-28. [PMID: 27186804 PMCID: PMC5450669 DOI: 10.1021/acs.chemrev.5b00644] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 12/17/2022]
Abstract
Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.
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Affiliation(s)
| | - Kjartan Thor Wikfeldt
- Science
Institute, University of Iceland, VR-III, 107, Reykjavik, Iceland
- Department
of Physics, Albanova, Stockholm University, S-106 91 Stockholm, Sweden
| | - Lars Ojamäe
- Department
of Chemistry, Linköping University, SE-581 83 Linköping, Sweden
| | - Jibao Lu
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Yao Xu
- Lehrstuhl
Physikalische Chemie II, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Hedieh Torabifard
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Albert P. Bartók
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Gábor Csányi
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Valeria Molinero
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Francesco Paesani
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
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Abstract
Hydrogen bond directionality in the water dimer is explained on the basis of symmetry-adapted intermolecular perturbation theory which directly separates the intermolecular interaction energy into four physically interpretable components: electrostatics, exchange-repulsion, dispersion, and induction. Analysis of these four main contributions to the binding energy allows a deeper understanding of the dominant factors ruling the mutual arrangement of the two monomers. A preference for the linear configuration is shown to be due to a subtle interplay of all four energy components. While the first-order terms, electrostatic and exchange-repulsion, almost perfectly cancel each other near the equilibrium geometry of the dimer, the importance of the second- and higher-order terms, induction and dispersion, becomes evident.
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Affiliation(s)
- Maxim Tafipolsky
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Campus Hubland Nord , Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
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Nagata Y, Ohto T, Backus EHG, Bonn M. Molecular Modeling of Water Interfaces: From Molecular Spectroscopy to Thermodynamics. J Phys Chem B 2016; 120:3785-96. [DOI: 10.1021/acs.jpcb.6b01012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tatsuhiko Ohto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Ellen H. G. Backus
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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