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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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Mattsson S, Paulus B. First principle calculations including ab initio molecular dynamics studies for the activation of hydrogen fluoride on Ni(111). Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Saito K, Torii H. Hidden Halogen-Bonding Ability of Fluorine Manifesting in the Hydrogen-Bond Configurations of Hydrogen Fluoride. J Phys Chem B 2021; 125:11742-11750. [PMID: 34662140 DOI: 10.1021/acs.jpcb.1c07211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Elucidating how the intermolecular interactions of a covalently bonded fluorine atom are similar to and different from those of the other halogen atoms will be helpful for a better unified understanding of them. In the present study, the case of hydrogen fluoride is theoretically studied from this viewpoint by using the techniques of electron density analysis, molecular dynamics of liquid, and others. It is shown that the extra-point model, which locates an additional charge site on the line extended from (not within) the covalent bond and has been adopted for halogen-bonding systems as a key to the generation of proper stability and directionality, works well also in this case. A significantly bent hydrogen-bond configuration, which is characteristic of the intermolecular interactions of hydrogen fluoride, is reasonably well reproduced, meaning that it is a manifestation of the latent halogen-bonding ability, which is hidden by the strongly electronegative nature.
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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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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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Experimental and theoretical assessment of the interactions of ionic liquids (ILs) with fluoridated compounds (HF, R-F) in organic medium. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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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: 13] [Impact Index Per Article: 1.9] [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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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: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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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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