1
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Bhattacharya S, Li J, Yang W, Kanai Y. BSE@ GW Prediction of Charge Transfer Exciton in Molecular Complexes: Assessment of Self-Energy and Exchange-Correlation Dependence. J Phys Chem A 2024; 128:6072-6083. [PMID: 39011742 DOI: 10.1021/acs.jpca.4c02898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The Bethe-Salpeter equation using the GW approximation to the self-energy (BSE@GW) is a computationally attractive method for studying electronic excitation from first principles within the many-body Green's function theory framework. We examine its dependence on the underlying exchange-correlation (XC) approximation as well as on the GW approximation for predicting the charge transfer exciton formation at representative type-II interfaces between molecular systems of tetrachloro-1,2-benzoquinone (TCBQ) and acene derivatives. For the XC approximation, we consider several widely used generalized gradient approximation (GGA) and hybrid GGA functionals. For the GW self-energy approximation, we examine the recently proposed renormalized singles approach by Yang and coauthors [J. Phys. Chem. Lett. 2019, 10 (3), 447-452; J. Chem. Theory Comput. 2022, 18, 7570-7585] in addition to other commonly employed approximated GW schemes. We demonstrate a reliable prediction of the charge transfer exciton within the BSE@GW level of theory.
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Affiliation(s)
- Sampreeti Bhattacharya
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Jiachen Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
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2
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Jin Y, Yu VWZ, Govoni M, Xu AC, Galli G. Excited State Properties of Point Defects in Semiconductors and Insulators Investigated with Time-Dependent Density Functional Theory. J Chem Theory Comput 2023. [PMID: 38039161 DOI: 10.1021/acs.jctc.3c00986] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
We present a formulation of spin-conserving and spin-flip hybrid time-dependent density functional theory (TDDFT), including the calculation of analytical forces, which allows for efficient calculations of excited state properties of solid-state systems with hundreds to thousands of atoms. We discuss an implementation on both GPU- and CPU-based architectures along with several acceleration techniques. We then apply our formulation to the study of several point defects in semiconductors and insulators, specifically the negatively charged nitrogen-vacancy and neutral silicon-vacancy centers in diamond, the neutral divacancy center in 4H silicon carbide, and the neutral oxygen-vacancy center in magnesium oxide. Our results highlight the importance of taking into account structural relaxations in excited states in order to interpret and predict optical absorption and emission mechanisms in spin defects.
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Affiliation(s)
- Yu Jin
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Victor Wen-Zhe Yu
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Marco Govoni
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Department of Physics, Computer Science, and Mathematics, University of Modena and Reggio Emilia, Modena 41125, Italy
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Andrew C Xu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Giulia Galli
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, 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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Begušić T, Blake GA. Two-dimensional infrared-Raman spectroscopy as a probe of water's tetrahedrality. Nat Commun 2023; 14:1950. [PMID: 37029146 PMCID: PMC10082090 DOI: 10.1038/s41467-023-37667-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
Two-dimensional spectroscopic techniques combining terahertz (THz), infrared (IR), and visible pulses offer a wealth of information about coupling among vibrational modes in molecular liquids, thus providing a promising probe of their local structure. However, the capabilities of these spectroscopies are still largely unexplored due to experimental limitations and inherently weak nonlinear signals. Here, through a combination of equilibrium-nonequilibrium molecular dynamics (MD) and a tailored spectrum decomposition scheme, we identify a relationship between the tetrahedral order of liquid water and its two-dimensional IR-IR-Raman (IIR) spectrum. The structure-spectrum relationship can explain the temperature dependence of the spectral features corresponding to the anharmonic coupling between low-frequency intermolecular and high-frequency intramolecular vibrational modes of water. In light of these results, we propose new experiments and discuss the implications for the study of tetrahedrality of liquid water.
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Affiliation(s)
- Tomislav Begušić
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Geoffrey A Blake
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
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5
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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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6
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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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7
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Sundararaman R, Vigil-Fowler D, Schwarz K. Improving the Accuracy of Atomistic Simulations of the Electrochemical Interface. Chem Rev 2022; 122:10651-10674. [PMID: 35522135 PMCID: PMC10127457 DOI: 10.1021/acs.chemrev.1c00800] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Atomistic simulation of the electrochemical double layer is an ambitious undertaking, requiring quantum mechanical description of electrons, phase space sampling of liquid electrolytes, and equilibration of electrolytes over nanosecond time scales. All models of electrochemistry make different trade-offs in the approximation of electrons and atomic configurations, from the extremes of classical molecular dynamics of a complete interface with point-charge atoms to correlated electronic structure methods of a single electrode configuration with no dynamics or electrolyte. Here, we review the spectrum of simulation techniques suitable for electrochemistry, focusing on the key approximations and accuracy considerations for each technique. We discuss promising approaches, such as enhanced sampling techniques for atomic configurations and computationally efficient beyond density functional theory (DFT) electronic methods, that will push electrochemical simulations beyond the present frontier.
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Affiliation(s)
- Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Derek Vigil-Fowler
- Materials, Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Kathleen Schwarz
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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8
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2208-2232. [PMID: 35313106 DOI: 10.1021/acs.jctc.1c01128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- MALTA Consolider Team, Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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9
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Liu J, He X. Ab initio molecular dynamics simulation of liquid water with fragment-based quantum mechanical approach under periodic boundary conditions. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - 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
- New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai 200062, China
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10
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Ko HY, Santra B, DiStasio RA. Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory-Based Ab Initio Molecular Dynamics II: Extensions to the Isobaric-Isoenthalpic and Isobaric-Isothermal Ensembles. J Chem Theory Comput 2021; 17:7789-7813. [PMID: 34775753 DOI: 10.1021/acs.jctc.0c01194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the previous paper of this series [Ko, H.-Y. et al. J. Chem. Theory Comput. 2020, 16, 3757-3785], we presented a theoretical and algorithmic framework based on a localized representation of the occupied space that exploits the inherent sparsity in the real-space evaluation of the exact exchange (EXX) interaction in finite-gap systems. This was accompanied by a detailed description of exx, a massively parallel hybrid message-passing interface MPI/OpenMP implementation of this approach in Quantum ESPRESSO (QE) that enables linear scaling hybrid density functional theory (DFT)-based ab initio molecular dynamics (AIMD) in the microcanonical/canonical (NVE/NVT) ensembles of condensed-phase systems containing 500-1000 atoms (in fixed orthorhombic cells) with a wall time cost comparable to semi-local DFT. In this work, we extend the current capabilities of exx to enable hybrid DFT-based AIMD simulations of large-scale condensed-phase systems with general and fluctuating cells in the isobaric-isoenthalpic/isobaric-isothermal (NpH/NpT) ensembles. The theoretical extensions to this approach include an analytical derivation of the EXX contribution to the stress tensor for systems in general simulation cells with a computational complexity that scales linearly with system size. The corresponding algorithmic extensions to exx include optimized routines that (i) handle both static and fluctuating simulation cells with non-orthogonal lattice symmetries, (ii) solve Poisson's equation in general/non-orthogonal cells via an automated selection of the auxiliary grid directions in the Natan-Kronik representation of the discrete Laplacian operator, and (iii) evaluate the EXX contribution to the stress tensor. Using this approach, we perform a case study on a variety of condensed-phase systems (including liquid water, a benzene molecular crystal polymorph, and semi-conducting crystalline silicon) and demonstrate that the EXX contributions to the energy and stress tensor simultaneously converge with an appropriate choice of exx parameters. This is followed by a critical assessment of the computational performance of the extended exx module across several different high-performance computing architectures via case studies on (i) the computational complexity due to lattice symmetry during NpT simulations of three different ice polymorphs (i.e., ice Ih, II, and III) and (ii) the strong/weak parallel scaling during large-scale NpT simulations of liquid water. We demonstrate that the robust and highly scalable implementation of this approach in the extended exx module is capable of evaluating the EXX contribution to the stress tensor with negligible cost (<1%) as well as all other EXX-related quantities needed during NpT simulations of liquid water (with a very tight 150 Ry planewave cutoff) in ≈5.2 s ((H2O)128) and ≈6.8 s ((H2O)256) per AIMD step. As such, the extended exx module presented in this work brings us another step closer to routinely performing hybrid DFT-based AIMD simulations of sufficient duration for large-scale condensed-phase systems across a wide range of thermodynamic conditions.
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Affiliation(s)
- Hsin-Yu Ko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Biswajit Santra
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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11
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Zhang C, Tang F, Chen M, Xu J, Zhang L, Qiu DY, Perdew JP, Klein ML, Wu X. Modeling Liquid Water by Climbing up Jacob's Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials. J Phys Chem B 2021; 125:11444-11456. [PMID: 34533960 DOI: 10.1021/acs.jpcb.1c03884] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Within the framework of Kohn-Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob's ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric-isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.
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Affiliation(s)
- Chunyi Zhang
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Fujie Tang
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Mohan Chen
- HEDPS, Center for Applied Physics and Technology, College of Engineering, Peking University, Beijing 100871, China
| | - Jianhang Xu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Linfeng Zhang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, United States
| | - Diana Y Qiu
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520, United States
| | - John P Perdew
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States.,Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Michael L Klein
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States.,Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
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12
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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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13
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de Almeida JM, Nguyen NL, Colonna N, Chen W, Rodrigues Miranda C, Pasquarello A, Marzari N. Electronic Structure of Water from Koopmans-Compliant Functionals. J Chem Theory Comput 2021; 17:3923-3930. [PMID: 34137253 DOI: 10.1021/acs.jctc.1c00063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Obtaining a precise theoretical description of the spectral properties of liquid water poses challenges for both molecular dynamics (MD) and electronic structure methods. The lower computational cost of the Koopmans-compliant functionals with respect to Green's function methods allows the simulations of many MD trajectories, with a description close to the state-of-art quasi-particle self-consistent GW plus vertex corrections method (QSGW + fxc). Thus, we explore water spectral properties when different MD approaches are used, ranging from classical MD to first-principles MD, and including nuclear quantum effects. We have observed that different MD approaches lead to up to 1 eV change in the average band gap; thus, we focused on the band gap dependence with the geometrical properties of a system to explain such spread. We have evaluated the changes in the band gap due to variations in the intramolecular O-H bond distance and HOH angle, as well as the intermolecular hydrogen bond O···O distance and the OHO angles. We have observed that the dominant contribution comes from the O-H bond length; the O···O distance plays a secondary role, and the other geometrical properties do not significantly influence the gap. Furthermore, we analyze the electronic density of states (DOS), where the KIPZ functional shows good agreement with the DOS obtained with state-of-art approaches employing quasi-particle self-consistent GW plus vertex corrections. The O-H bond length also significantly influences the DOS. When nuclear quantum effects are considered, broadening of the peaks driven by the broader distribution of the O-H bond lengths is observed, leading to a closer agreement with the experimental photoemission spectra.
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Affiliation(s)
- James Moraes de Almeida
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Santo André, 09210-580 SP, Brazil.,Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ngoc Linh Nguyen
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nicola Colonna
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, CH-5232 Villigen-PSI, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Wei Chen
- Institute of Condensed Matter and Nanoscience, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | | | - Alfredo Pasquarello
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nicola Marzari
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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14
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Rozsa VF, Galli G. Molecular Polarizabilities in Aqueous Systems from First-Principles. J Phys Chem B 2021; 125:2183-2192. [DOI: 10.1021/acs.jpcb.0c10732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Viktor F. Rozsa
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Giulia Galli
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Materials Science Division, Argonne National Laboratory, Chicago, Illinois 60439, United States
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15
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Apostolidou C. Vibrational Spectra of the OH Radical in Water: Ab Initio Molecular Dynamics Simulations and Quantum Chemical Calculations Using Hybrid Functionals. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Christina Apostolidou
- Mulliken Center for Theoretical Chemistry Institute of Physical and Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Beringstraße 4 Bonn 53115 Germany
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16
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Calio PB, Hocky GM, Voth GA. Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water. J Chem Theory Comput 2020; 16:5675-5684. [DOI: 10.1021/acs.jctc.0c00558] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul B. Calio
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Glen M. Hocky
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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17
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Bernardi M. Physical origin of the one-quarter exact exchange in density functional theory. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:385501. [PMID: 32422620 DOI: 10.1088/1361-648x/ab9409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Exchange interactions are a manifestation of the quantum mechanical nature of the electrons and play a key role in predicting the properties of materials from first principles. In density functional theory (DFT), a widely used approximation to the exchange energy combines fractions of density-based and Hartree-Fock (exact) exchange. This so-called hybrid DFT scheme is accurate in many materials, for reasons that are not fully understood. Here we show that a 1/4 fraction of exact exchange plus a 3/4 fraction of density-based exchange is compatible with a correct quantum mechanical treatment of the exchange energy of an electron pair in the unpolarized electron gas. We also show that the 1/4 exact-exchange fraction mimics a correlation interaction between doubly-excited electronic configurations. The relation between our results and trends observed in hybrid DFT calculations is discussed, along with other implications.
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Affiliation(s)
- Marco Bernardi
- Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA 91125, United States of America
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18
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Zhang C, Giberti F, Sevgen E, de Pablo JJ, Gygi F, Galli G. Dissociation of salts in water under pressure. Nat Commun 2020; 11:3037. [PMID: 32546791 PMCID: PMC7298052 DOI: 10.1038/s41467-020-16704-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 05/15/2020] [Indexed: 11/09/2022] Open
Abstract
The investigation of salts in water at extreme conditions is crucial to understanding the properties of aqueous fluids in the Earth. We report first principles (FP) and classical molecular dynamics simulations of NaCl in the dilute limit, at temperatures and pressures relevant to the Earth’s upper mantle. Similar to ambient conditions, we observe two metastable states of the salt: the contact (CIP) and the solvent-shared ion-pair (SIP), which are entropically and enthalpically favored, respectively. We find that the free energy barrier between the CIP and SIP minima increases at extreme conditions, and that the stability of the CIP is enhanced in FP simulations, consistent with the decrease of the dielectric constant of water. The minimum free energy path between the CIP and SIP becomes smoother at high pressure, and the relative stability of the two configurations is affected by water self-dissociation, which can only be described properly by FP simulations. Salts in water at extreme conditions play a fundamental role in determining the properties of the Earthʼs mantle constituents. Here the authors shed light on ion-water and ion-ion interactions for NaCl dissolved in water at conditions relevant to the Earthʼs upper mantle by molecular dynamics simulations.
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Affiliation(s)
- Cunzhi Zhang
- Department of Materials Science and Engineering, COE, Peking University, 100871, Beijing, China
| | - Federico Giberti
- University of Chicago, 5640 S. Ellis Ave., Chicago, IL, 60637, USA
| | - Emre Sevgen
- University of Chicago, 5640 S. Ellis Ave., Chicago, IL, 60637, USA
| | - Juan J de Pablo
- University of Chicago, 5640 S. Ellis Ave., Chicago, IL, 60637, USA.,Materials Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Francois Gygi
- University of California Davis, Davis, CA, 95616, USA
| | - Giulia Galli
- University of Chicago, 5640 S. Ellis Ave., Chicago, IL, 60637, USA. .,Materials Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
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19
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Ko HY, Jia J, Santra B, Wu X, Car R, DiStasio RA. Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance. J Chem Theory Comput 2020; 16:3757-3785. [PMID: 32045232 DOI: 10.1021/acs.jctc.9b01167] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car-Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson's equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. This is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500-1000 atoms (e.g., (H2O)256) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.
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Affiliation(s)
- Hsin-Yu Ko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Junteng Jia
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Biswajit Santra
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Physics, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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20
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Aydin F, Zhan C, Ritt C, Epsztein R, Elimelech M, Schwegler E, Pham TA. Similarities and differences between potassium and ammonium ions in liquid water: a first-principles study. Phys Chem Chem Phys 2020; 22:2540-2548. [DOI: 10.1039/c9cp06163k] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding ion solvation in liquid water is critical in optimizing materials for a wide variety of emerging technologies, including water desalination and purification.
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Affiliation(s)
- Fikret Aydin
- Lawrence Livermore National Laboratory
- Livermore
- USA
| | - Cheng Zhan
- Lawrence Livermore National Laboratory
- Livermore
- USA
| | - Cody Ritt
- Department of Chemical and Environmental Engineering
- Yale University
- New Haven
- USA
| | - Razi Epsztein
- Department of Chemical and Environmental Engineering
- Yale University
- New Haven
- USA
- Faculty of Civil and Environmental Engineering
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering
- Yale University
- New Haven
- USA
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21
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LaCount MD, Gygi F. Ensemble first-principles molecular dynamics simulations of water using the SCAN meta-GGA density functional. J Chem Phys 2019; 151:164101. [DOI: 10.1063/1.5124957] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Michael D. LaCount
- Department of Computer Science, University of California, Davis, California 95616, USA
| | - François Gygi
- Department of Computer Science, University of California, Davis, California 95616, USA
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22
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Pizzochero M, Ambrosio F, Pasquarello A. Picture of the wet electron: a localized transient state in liquid water. Chem Sci 2019; 10:7442-7448. [PMID: 32180919 PMCID: PMC7053762 DOI: 10.1039/c8sc05101a] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/18/2019] [Indexed: 11/21/2022] Open
Abstract
A transient state of the excess electron in liquid water preceding the development of the solvation shell, the so-called wet electron, has been invoked to explain spectroscopic observations, but its binding energy and atomic structure have remained highly elusive. Here, we carry out hybrid functional molecular dynamics to unveil the ultrafast solvation mechanism leading to the hydrated electron. In the pre-hydrated regime, the electron is found to repeatedly switch between a quasi-free electron state in the conduction band and a localized state with a binding energy of 0.26 eV, which we assign to the wet electron. This transient state self-traps in a region of the liquid which extends up to ∼4.5 Å and involves a severe disruption of the hydrogen-bond network. Our picture provides an unprecedented view on the nature of the wet electron, which is instrumental to understanding the properties of this fundamental species in liquid water.
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Affiliation(s)
- Michele Pizzochero
- Chaire de Physique Numérique de la Matière Condensée (C3MP) , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland .
| | - Francesco Ambrosio
- Chaire de Simulation à l'Echelle Atomique (CSEA) , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Alfredo Pasquarello
- Chaire de Simulation à l'Echelle Atomique (CSEA) , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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23
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Hestand NJ, Strong SE, Shi L, Skinner JL. Mid-IR spectroscopy of supercritical water: From dilute gas to dense fluid. J Chem Phys 2019; 150:054505. [DOI: 10.1063/1.5079232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nicholas J. Hestand
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Steven E. Strong
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Liang Shi
- School of Natural Sciences, University of California, Merced, California 95344, USA
| | - J. L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
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24
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Bouchafra Y, Shee A, Réal F, Vallet V, Severo Pereira Gomes A. Predictive Simulations of Ionization Energies of Solvated Halide Ions with Relativistic Embedded Equation of Motion Coupled Cluster Theory. PHYSICAL REVIEW LETTERS 2018; 121:266001. [PMID: 30636145 DOI: 10.1103/physrevlett.121.266001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Indexed: 06/09/2023]
Abstract
A subsystem approach for obtaining electron binding energies in the valence region is presented and applied to the case of halide ions (X^{-},X=F-At) in water. This approach is based on electronic structure calculations combining the relativistic equation-of-motion coupled cluster method for electron detachment and density functional theory via the frozen density embedding approach, using structures from classical molecular dynamics with polarizable force fields for discrete systems (in our study, droplets containing the anion and 50 water molecules). Our results indicate that one can accurately capture both the large solvent effect observed for the halides and the splitting of their ionization signals due to the increasingly large spin-orbit coupling of the p_{3/2}-p_{1/2} manifold across the series, at an affordable computational cost. Furthermore, owing to the quantum mechanical treatment of both solute and solvent electron binding energies of semiquantitative quality are also obtained for (bulk) water as by-products of the calculations for the halogens (in droplets).
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Affiliation(s)
- Yassine Bouchafra
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Avijit Shee
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Florent Réal
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Valérie Vallet
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - André Severo Pereira Gomes
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
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25
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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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