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Scivetti I, Sen K, Elena AM, Todorov I. Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble. J Phys Chem A 2020; 124:7585-7597. [PMID: 32820921 DOI: 10.1021/acs.jpca.0c05461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.
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Affiliation(s)
- Ivan Scivetti
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K.,Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - Kakali Sen
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
| | - Alin M Elena
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
| | - Ilian Todorov
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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Kubař T, Welke K, Groenhof G. New QM/MM implementation of the DFTB3 method in the gromacs package. J Comput Chem 2015; 36:1978-89. [PMID: 26238364 DOI: 10.1002/jcc.24029] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/09/2015] [Indexed: 01/07/2023]
Abstract
The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle-mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) electron-induced repair of a DNA lesion. Also discussed is the further development of the framework, regarding mostly the options for parallelization.
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Affiliation(s)
- Tomáš Kubař
- Institute of Physical Chemistry and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| | - Kai Welke
- Department of Chemistry, Nagoya University, Nagoya, 464-8602, Japan
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, 40014, Finland
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Kojima H, Yamada A, Okazaki S. Free energy surface for rotamers ofcis-enol malonaldehyde in aqueous solution studied by molecular dynamics calculations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.945081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yamada A, Kojima H, Okazaki S. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water. J Chem Phys 2014; 141:084509. [DOI: 10.1063/1.4893933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bernstein N, Várnai C, Solt I, Winfield SA, Payne MC, Simon I, Fuxreiter M, Csányi G. QM/MM simulation of liquid water with an adaptive quantum region. Phys Chem Chem Phys 2011; 14:646-56. [PMID: 22089416 DOI: 10.1039/c1cp22600b] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.
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Affiliation(s)
- Noam Bernstein
- Center for Computational Materials Science, Naval Research Laboratory, Washington, DC 20375, USA.
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Yang Y, Meuwly M. A generalized reactive force field for nonlinear hydrogen bonds: hydrogen dynamics and transfer in malonaldehyde. J Chem Phys 2010; 133:064503. [PMID: 20707571 DOI: 10.1063/1.3447701] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using molecular dynamics (MD) simulations, the spectroscopy and dynamics of malonaldehyde is investigated. To this end, the recently proposed molecular mechanics with proton transfer (MMPT) potential is generalized to nonlinear hydrogen bonds. The calculated properties for malonaldehyde in both gas and condensed phases, including equilibrium geometries, infrared spectra, tunneling splittings, and hydrogen transfer rates, compare well with previous experimental and computational works. In particular, by using a harmonic bath averaged (HBA) Hamiltonian, which is based on a reaction path Hamiltonian, it is possible to estimate the tunneling splitting in an efficient manner. It is found that a zero point corrected barrier of 6.7 kcal/mol and effective masses of 1.234 (i.e., 23.4% larger than the mass of a physical H-atom) and 1.117 (for the physical D-atom) are consistent with the measured splittings of 21.6 and 2.9 cm(-1), respectively. The HBA Hamiltonian also yields a pair of hydrogen transfer fundamentals at 1573 and 1267 cm(-1), similar to results obtained with a reaction surface Hamiltonian on a MP2/6-31G(**) potential energy surface. This amounts to a substantial redshift of more than 1000 cm(-1) which can be rationalized by comparison with weakly (HCO(+): rare gas) and strongly (H(2)O-H(+)-OH(2)) proton-bound systems. Hydrogen transfer rates in vacuum and water were determined from the validated MMPT potential and it is found that the solvent enhances the rate by a factor of 5 at 300 K. The rates of 2.4/ns and 10/ns are commensurate with previous density functional tight binding ab initio MD studies.
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Affiliation(s)
- Yonggang Yang
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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Walewski Ł, Waluk J, Lesyng B. Car−Parrinello Molecular Dynamics Study of the Intramolecular Vibrational Mode-Sensitive Double Proton-Transfer Mechanisms in Porphycene. J Phys Chem A 2010; 114:2313-8. [DOI: 10.1021/jp907754r] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Łukasz Walewski
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland, Institute of Physical Chemistry, Department of Photochemistry and Spectroscopy, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Department of Biophysics and Centre of Excellence BioExploratorium, Faculty of Physics, University of Waraw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Jacek Waluk
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland, Institute of Physical Chemistry, Department of Photochemistry and Spectroscopy, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Department of Biophysics and Centre of Excellence BioExploratorium, Faculty of Physics, University of Waraw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Bogdan Lesyng
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland, Institute of Physical Chemistry, Department of Photochemistry and Spectroscopy, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Department of Biophysics and Centre of Excellence BioExploratorium, Faculty of Physics, University of Waraw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
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Poully JC, Grégoire G, Schermann JP. Evaluation of the ONIOM Method for Interpretation of Infrared Spectra of Gas-Phase Molecules of Biological Interest. J Phys Chem A 2009; 113:8020-6. [DOI: 10.1021/jp901696d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jean-Christophe Poully
- Laboratoire de Physique des Lasers, UMR 7538 CNRS, Université Paris 13, 93430 Villetaneuse, France
| | - Gilles Grégoire
- Laboratoire de Physique des Lasers, UMR 7538 CNRS, Université Paris 13, 93430 Villetaneuse, France
| | - Jean-Pierre Schermann
- Laboratoire de Physique des Lasers, UMR 7538 CNRS, Université Paris 13, 93430 Villetaneuse, France
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Pu J, Gao J, Truhlar DG. Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals. Chemphyschem 2005; 6:1853-65. [PMID: 16086343 PMCID: PMC4481131 DOI: 10.1002/cphc.200400602] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Indexed: 11/06/2022]
Abstract
The generalized hybrid orbital (GHO) method has previously been formulated for combining molecular mechanics with various levels of quantum mechanics, in particular semiempirical neglect of diatomic differential overlap theory, ab initio Hartree-Fock theory, and self-consistent charge density functional tight-binding theory. To include electron-correlation effects accurately and efficiently in GHO calculations, we extend the GHO method to density functional theory in the generalized-gradient approximation and hybrid density functional theory (denoted by GHO-DFT and GHO-HDFT, respectively) using Gaussian-type orbitals as basis functions. In the proposed GHO-(H)DFT formalism, charge densities in auxiliary hybrid orbitals are included to calculate the total electron density. The orthonormality constraints involving the auxiliary Kohn-Sham orbitals are satisfied by carrying out the hybridization in terms of a set of Löwdin symmetrically orthogonalized atomic basis functions. Analytical gradients are formulated for GHO-(H)DFT by incorporating additional forces associated with GHO basis transformations. Scaling parameters are introduced for some of the one-electron integrals and are optimized to obtain the correct charges and geometry near the QM/MM boundary region. The GHO-(H)DFT method based on the generalized gradient approach (GGA) (BLYP and mPWPW91) and HDFT methods (B3 LYP, mPW1PW91, and MPW1 K) is tested-for geometries and atomic charges-against a set of small molecules. The following quantities are tested: 1) the C--C stretch potential in ethane, 2) the torsional barrier for internal rotation around the central C--C bond in n-butane, 3) proton affinities for a set of alcohols, amines, thiols, and acids, 4) the conformational energies of alanine dipeptide, and 5) the barrier height of the hydrogen-atom transfer between n-C4H10 and n-C4H9, where the reaction center is described at the MPW1 K/6-31G(d) level of theory.
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Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
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