1
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Chen X, Liu M, Gao J. CARNOT: a Fragment-Based Direct Molecular Dynamics and Virtual-Reality Simulation Package for Reactive Systems. J Chem Theory Comput 2022; 18:1297-1313. [PMID: 35129348 DOI: 10.1021/acs.jctc.1c01032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Traditionally, the study of reaction mechanisms of complex reaction systems such as combustion has been performed on an individual basis by optimizations of transition structure and minimum energy path or by reaction dynamics trajectory calculations for one elementary reaction at a time. It is effective, but time-consuming, whereas important and unexpected processes could have been missed. In this article, we present a direct molecular dynamics (DMD) approach and a virtual-reality simulation program, CARNOT, in which plausible chemical reactions are simulated simultaneously at finite temperature and pressure conditions. A key concept of the present ab initio molecular dynamics method is to partition a large, chemically reactive system into molecular fragments that can be adjusted on the fly of a DMD simulation. The theory represents an extension of the explicit polarization method to reactive events, called ReX-Pol. We propose a highest-and-lowest adapted-spin approximation to define the local spins of individual fragments, rather than treating the entire system by a delocalized wave function. Consequently, the present ab initio DMD can be applied to reactive systems consisting of an arbitrarily varying number of closed and open-shell fragments such as free radicals, zwitterions, and separate ions found in combustion and other reactions. A graph-data structure algorithm was incorporated in CARNOT for the analysis of reaction networks, suitable for reaction mechanism reduction. Employing the PW91 density functional theory and the 6-31+G(d) basis set, the capabilities of the CARNOT program were illustrated by a combustion reaction, consisting of 28 650 atoms, and by reaction network analysis that revealed a range of mechanistic and dynamical events. The method may be useful for applications to other types of complex reactions.
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Affiliation(s)
- Xin Chen
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China
| | - Meiyi Liu
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China
| | - Jiali Gao
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Fink K, Höfener S. Combining wavefunction frozen-density embedding with one-dimensional periodicity. J Chem Phys 2021; 154:104114. [PMID: 33722017 DOI: 10.1063/5.0041501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present the combination of wavefunction frozen-density embedding (FDE) with a periodic repetition in one dimension (1D) for molecular systems in the KOALA program. In this periodic orbital-uncoupled FDE ansatz, no wavefunction overlap is taken into account, and only the electron density of the active subsystem is computed explicitly. This density is relaxed in the presence of the environment potential, which is obtained by translating the updated active subsystem density, yielding a fully self-consistent solution at convergence. Treating only one subsystem explicitly, the method allows for the calculation of local properties in condensed molecular systems, while no orbital band structure is obtained preventing the application, e.g., to systems with metallic bonding. In order to illustrate possible applications of the new implementation, selected case studies are presented, ranging from ground-state dipole moments using configuration interaction methods via excitation energies using time-dependent density-functional theory to ionization potentials obtained from equation-of-motion correlation methods. Different levels of approximations are assessed, revealing that an active subsystem consisting of two or three molecules leads to results that are converged with respect to the environment contributions.
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Affiliation(s)
- Karin Fink
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), P.O. Box 3630, 76021 Karlsruhe, Germany
| | - Sebastian Höfener
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), P.O. Box 6980, 76049 Karlsruhe, Germany
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3
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Li W, Dong H, Ma J, Li S. Structures and Spectroscopic Properties of Large Molecules and Condensed-Phase Systems Predicted by Generalized Energy-Based Fragmentation Approach. Acc Chem Res 2021; 54:169-181. [PMID: 33350806 DOI: 10.1021/acs.accounts.0c00580] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
ConspectusThe structures and spectroscopic properties of molecules and condensed-phase systems are usually experimentally characterized by X-ray, infrared (IR), Raman, nuclear magnetic resonance (NMR), and electronic absorption/emission spectra. Quantum mechanics (QM) calculations are critical in quantitatively understanding the relationship between the structure and physicochemical properties of various chemical systems. However, it is very challenging to apply traditional QM methods to large molecules and condensed-phase systems with large unit cells due to their steep computational scaling with the system size. To overcome this difficulty, theoretical chemists have developed various linear (or low) scaling QM methods, among which energy-based fragmentation methods have achieved great success for large molecules or clusters. One of the most popular energy-based fragmentation methods is the generalized energy-based fragmentation (GEBF) approach developed by us.In this approach, the ground-state energy of a large molecule can be evaluated from the ground-state energies of a series of embedded subsystems. In this Account, we focus on the recent developments and applicability of the GEBF approach for the structures and spectroscopic properties of complicated large molecules and condensed-phase systems. With new fragmentation schemes, the GEBF approach can now describe ionic liquid clusters and metal-containing supramolecular systems accurately and can provide accurate binding energies for host-guest complexes. In addition, the GEBF approach is now available for describing the localized excited states of large systems including a chromophore. More importantly, the GEBF approach under periodic boundary conditions (PBC-GEBF) has been developed to deal with periodic molecular crystals and liquids. Then, the ground-state energy (or property) per unit cell of a periodic condensed phase system can be predicted with QM calculations on nonperiodic embedded subsystems. This feature enables accurate electron correlation calculations on molecular crystals and liquids to be feasible on ordinary workstations. The PBC-GEBF approach has been applied to predict the crystal structures, lattice energies, and spectroscopic properties of some typical molecular crystals and solutions. By combining the GEBF method and machine learning (ML) method, a GEBF-ML force field has been developed for long normal alkanes, and the IR spectra of long alkanes can be obtained from the GEBF-ML molecular dynamics (MD) simulations. The GEBF and its periodic variant are expected to play increasingly important roles in investigating real-life chemical systems of broad interests at the ab initio levels.
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Affiliation(s)
- Wei Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Hao Dong
- Kuang Yaming Honors School and Institute for Brain Sciences, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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4
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Chen X, Qu Z, Suo B, Gao J. A self-consistent coulomb bath model using density fitting. J Comput Chem 2020; 41:1698-1708. [PMID: 32369627 DOI: 10.1002/jcc.26211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/02/2020] [Accepted: 04/05/2020] [Indexed: 12/24/2022]
Abstract
A self-consistent Coulomb bath model is presented to provide an accurate and efficient way of performing calculations for interfragment electrostatic and polarization interactions. In this method, a condensed-phase system is partitioned into molecular fragment blocks. Each fragment is embedded in the Coulomb bath due to other fragments. Importantly, the present Coulomb bath is represented using a density fitting method in which the electron densities of molecular fragments are fitted using an atom-centered auxiliary basis set of Gaussian type. The Coulomb bath is incorporated into an effective Hamiltonian for each fragment, with which the electron density is optimized through an iterative double self-consistent field (DSCF) procedure to realize the mutual many-body polarization effects. In this work, the accuracy of interfragment interaction energies enumerated using the Coulomb bath is tested, showing a good agreement with the exact results from an energy decomposition analysis. The qualitative features of many-body polarization effects are visualized by electron density difference plots. It is also shown that the present DSCF method can yield fast and robust convergence with near-linear scaling in performance with increase in system size.
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Affiliation(s)
- Xin Chen
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Zexing Qu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Bingbing Suo
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Institute of Modern Physics, Northwest University, Xi'an, Shaanxi, China
| | - Jiali Gao
- Shenzhen Bay Laboratory, Shenzhen, China.,Laboratory of Computational Chemistry and Drug Design, Peking University Shenzhen Graduate School, Shenzhen, China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
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5
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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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6
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Kawashima Y, Ishimura K, Shiga M. Ab initio quantum mechanics/molecular mechanics method with periodic boundaries employing Ewald summation technique to electron-charge interaction: Treatment of the surface-dipole term. J Chem Phys 2019; 150:124103. [DOI: 10.1063/1.5048451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Y. Kawashima
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - K. Ishimura
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - M. Shiga
- CCSE, Japan Atomic Energy Agency (JAEA), 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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7
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Giese TJ, York DM. Quantum mechanical force fields for condensed phase molecular simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:383002. [PMID: 28817382 PMCID: PMC5821073 DOI: 10.1088/1361-648x/aa7c5c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.
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8
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Fang T, Li Y, Li S. Generalized energy‐based fragmentation approach for modeling condensed phase systems. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1297] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tao Fang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational ChemistryNanjing University Nanjing P. R. China
| | - Yunzhi Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational ChemistryNanjing University Nanjing P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational ChemistryNanjing University Nanjing P. R. China
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9
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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: 278] [Impact Index Per Article: 34.8] [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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10
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Giese TJ, Panteva MT, Chen H, York DM. Multipolar Ewald methods, 2: applications using a quantum mechanical force field. J Chem Theory Comput 2016; 11:451-61. [PMID: 25691830 PMCID: PMC4325604 DOI: 10.1021/ct500799g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 01/08/2023]
Abstract
A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework.
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Affiliation(s)
- Timothy J Giese
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, United States
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11
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Giese TJ, York DM. Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation. J Chem Theory Comput 2016; 12:2611-32. [PMID: 27171914 DOI: 10.1021/acs.jctc.6b00198] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed.
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Affiliation(s)
- Timothy J Giese
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8087, United States
| | - Darrin M York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8087, United States
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12
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Fang T, Jia J, Li S. Vibrational Spectra of Molecular Crystals with the Generalized Energy-Based Fragmentation Approach. J Phys Chem A 2016; 120:2700-11. [DOI: 10.1021/acs.jpca.5b10927] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Fang
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of
Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Junteng Jia
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of
Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of 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 210093, People’s Republic of China
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13
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Fang D, Duke RE, Cisneros GA. A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations. J Chem Phys 2015; 143:044103. [PMID: 26233103 PMCID: PMC4514725 DOI: 10.1063/1.4926652] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/01/2015] [Indexed: 12/23/2022] Open
Abstract
A new method to account for long range electrostatic contributions is proposed and implemented for quantum mechanics/molecular mechanics long range electrostatic correction (QM/MM-LREC) calculations. This method involves the use of the minimum image convention under periodic boundary conditions and a new smoothing function for energies and forces at the cutoff boundary for the Coulomb interactions. Compared to conventional QM/MM calculations without long-range electrostatic corrections, the new method effectively includes effects on the MM environment in the primary image from its replicas in the neighborhood. QM/MM-LREC offers three useful features including the avoidance of calculations in reciprocal space (k-space), with the concomitant avoidance of having to reproduce (analytically or approximately) the QM charge density in k-space, and the straightforward availability of analytical Hessians. The new method is tested and compared with results from smooth particle mesh Ewald (PME) for three systems including a box of neat water, a double proton transfer reaction, and the geometry optimization of the critical point structures for the rate limiting step of the DNA dealkylase AlkB. As with other smoothing or shifting functions, relatively large cutoffs are necessary to achieve comparable accuracy with PME. For the double-proton transfer reaction, the use of a 22 Å cutoff shows a close reaction energy profile and geometries of stationary structures with QM/MM-LREC compared to conventional QM/MM with no truncation. Geometry optimization of stationary structures for the hydrogen abstraction step by AlkB shows some differences between QM/MM-LREC and the conventional QM/MM. These differences underscore the necessity of the inclusion of the long-range electrostatic contribution.
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Affiliation(s)
- Dong Fang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Robert E Duke
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - G Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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14
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Mazack MJM, Gao J. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization. J Chem Phys 2015; 140:204501. [PMID: 24880295 DOI: 10.1063/1.4875922] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.
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Affiliation(s)
- Michael J M Mazack
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431, USA
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431, USA
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15
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Giese T, Panteva MT, Chen H, York DM. Multipolar Ewald methods, 1: theory, accuracy, and performance. J Chem Theory Comput 2015; 11:436-50. [PMID: 25691829 PMCID: PMC4325605 DOI: 10.1021/ct5007983] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 11/29/2022]
Abstract
The Ewald, Particle Mesh Ewald (PME), and Fast Fourier–Poisson (FFP) methods are developed for systems composed of spherical multipole moment expansions. A unified set of equations is derived that takes advantage of a spherical tensor gradient operator formalism in both real space and reciprocal space to allow extension to arbitrary multipole order. The implementation of these methods into a novel linear-scaling modified “divide-and-conquer” (mDC) quantum mechanical force field is discussed. The evaluation times and relative force errors are compared between the three methods, as a function of multipole expansion order. Timings and errors are also compared within the context of the quantum mechanical force field, which encounters primary errors related to the quality of reproducing electrostatic forces for a given density matrix and secondary errors resulting from the propagation of the approximate electrostatics into the self-consistent field procedure, which yields a converged, variational, but nonetheless approximate density matrix. Condensed-phase simulations of an mDC water model are performed with the multipolar PME method and compared to an electrostatic cutoff method, which is shown to artificially increase the density of water and heat of vaporization relative to full electrostatic treatment.
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Affiliation(s)
- Timothy
J. Giese
- Center for Integrative Proteomics
Research, BioMaPS Institute for Quantitative Biology and Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854-8087, United States
| | - Maria T. Panteva
- Center for Integrative Proteomics
Research, BioMaPS Institute for Quantitative Biology and Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854-8087, United States
| | - Haoyuan Chen
- Center for Integrative Proteomics
Research, BioMaPS Institute for Quantitative Biology and Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854-8087, United States
| | - Darrin M. York
- Center for Integrative Proteomics
Research, BioMaPS Institute for Quantitative Biology and Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854-8087, United States
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16
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Gao J, Truhlar DG, Wang Y, Mazack MJM, Löffler P, Provorse MR, Rehak P. Explicit polarization: a quantum mechanical framework for developing next generation force fields. Acc Chem Res 2014; 47:2837-45. [PMID: 25098651 PMCID: PMC4165456 DOI: 10.1021/ar5002186] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Molecular mechanical force fields have been successfully used to
model condensed-phase and biological systems for a half century. By
means of careful parametrization, such classical force fields can
be used to provide useful interpretations of experimental findings
and predictions of certain properties. Yet, there is a need to further
improve computational accuracy for the quantitative prediction of
biomolecular interactions and to model properties that depend on the
wave functions and not just the energy terms. A new strategy called
explicit polarization (X-Pol) has been developed to construct the
potential energy surface and wave functions for macromolecular and
liquid-phase simulations on the basis of quantum mechanics rather
than only using quantum mechanical results to fit analytic force fields.
In this spirit, this approach is called a quantum mechanical force
field (QMFF). X-Pol is a general fragment method for electronic
structure calculations
based on the partition of a condensed-phase or macromolecular system
into subsystems (“fragments”) to achieve computational
efficiency. Here, intrafragment energy and the mutual electronic polarization
of interfragment interactions are treated explicitly using quantum
mechanics. X-Pol can be used as a general, multilevel electronic structure
model for macromolecular systems, and it can also serve as a new-generation
force field. As a quantum chemical model, a variational many-body
(VMB) expansion approach is used to systematically improve interfragment
interactions, including exchange repulsion, charge delocalization,
dispersion, and other correlation energies. As a quantum mechanical
force field, these energy terms are approximated by empirical functions
in the spirit of conventional molecular mechanics. This Account first
reviews the formulation of X-Pol, in the full variationally correct
version, in the faster embedded version, and with systematic many-body
improvements. We discuss illustrative examples involving water clusters
(which show the power of two-body corrections), ethylmethylimidazolium
acetate ionic liquids (which reveal that the amount of charge transfer
between anion and cation is much smaller than what has been assumed
in some classical simulations), and a solvated protein in aqueous
solution (which shows that the average charge distribution of carbonyl
groups along the polypeptide chain depends strongly on their position
in the sequence, whereas they are fixed in most classical force fields).
The development of QMFFs also offers an opportunity to extend the
accuracy of biochemical simulations to areas where classical force
fields are often insufficient, especially in the areas of spectroscopy,
reactivity, and enzyme catalysis.
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Affiliation(s)
- Jiali Gao
- Theoretical
Chemistry Institute, State Key Laboratory of Theoretical and Computational
Chemistry, Jilin University, Changchun, Jilin Province 130028, People’s Republic of China
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Donald G. Truhlar
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yingjie Wang
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael J. M. Mazack
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Patrick Löffler
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Makenzie R. Provorse
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pavel Rehak
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
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17
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Giese T, Chen H, Huang M, York DM. Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions. J Chem Theory Comput 2014; 10:1086-1098. [PMID: 24803856 PMCID: PMC3985928 DOI: 10.1021/ct401035t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Indexed: 01/22/2023]
Abstract
We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein-ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O-O radial distribution functions similar to TIP4P-EW.
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Affiliation(s)
- Timothy
J. Giese
- BioMaPS
Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, United States
| | - Haoyuan Chen
- BioMaPS
Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, United States
| | - Ming Huang
- BioMaPS
Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, United States
- Scientific
Computation, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455−0431, United States
| | - Darrin M. York
- BioMaPS
Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, United States
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18
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Brinkmann L, Heifets E, Kantorovich L. Density functional calculations of extended, periodic systems using Coulomb corrected molecular fractionation with conjugated caps method (CC-MFCC). Phys Chem Chem Phys 2014; 16:21252-70. [DOI: 10.1039/c3cp55119a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A consistent DFT based formulation of the order-N molecular fractionation with conjugated caps method in which a molecular system is calculated considering a set of finite fragments, is proposed. Here we apply the method and test its performance on a periodic metal–organic framework system.
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Affiliation(s)
| | - Eugene Heifets
- Max Planck Institute for Solid State Research
- D-70569 Stuttgart, Germany
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20
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Han J, Mazack MJM, Zhang P, Truhlar DG, Gao J. Quantum mechanical force field for water with explicit electronic polarization. J Chem Phys 2013; 139:054503. [PMID: 23927266 PMCID: PMC3747793 DOI: 10.1063/1.4816280] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/08/2013] [Indexed: 11/14/2022] Open
Abstract
A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.
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Affiliation(s)
- Jaebeom Han
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431, USA
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21
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Giese TJ, Chen H, Dissanayake T, Giambaşu GM, Heldenbrand H, Huang M, Kuechler ER, Lee TS, Panteva MT, Radak BK, York DM. A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields. J Chem Theory Comput 2013; 9:1417-1427. [PMID: 23814506 DOI: 10.1021/ct3010134] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce a new hybrid molecular orbital/density-functional modified divide-and-conquer (mDC) approach that allows the linear-scaling calculation of very large quantum systems. The method provides a powerful framework from which linear-scaling force fields for molecular simulations can be developed. The method is variational in the energy, and has simple, analytic gradients and essentially no break-even point with respect to the corresponding full electronic structure calculation. Furthermore, the new approach allows intermolecular forces to be properly balanced such that non-bonded interactions can be treated, in some cases, to much higher accuracy than the full calculation. The approach is illustrated using the second-order self-consistent charge density-functional tight-binding model (DFTB2). Using this model as a base Hamiltonian, the new mDC approach is applied to a series of water systems, where results show that geometries and interaction energies between water molecules are greatly improved relative to full DFTB2. In order to achieve substantial improvement in the accuracy of intermolecular binding energies and hydrogen bonded cluster geometries, it was necessary to extend the DFTB2 model to higher-order atom-centered multipoles for the second-order self-consistent intermolecular electrostatic term. Using generalized, linear-scaling electrostatic methods, timings demonstrate that the method is able to calculate a water system of 3000 atoms in less than half of a second, and systems of up to one million atoms in only a few minutes using a conventional desktop workstation.
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Affiliation(s)
- Timothy J Giese
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087 USA
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