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Pavošević F, Culpitt T, Hammes-Schiffer S. Multicomponent Quantum Chemistry: Integrating Electronic and Nuclear Quantum Effects via the Nuclear–Electronic Orbital Method. Chem Rev 2020; 120:4222-4253. [DOI: 10.1021/acs.chemrev.9b00798] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabijan Pavošević
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Tanner Culpitt
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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The any particle molecular orbital/molecular mechanics approach. J Mol Model 2019; 25:316. [PMID: 31529219 DOI: 10.1007/s00894-019-4153-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
A computational scheme is proposed to broaden the range of applications of multicomponent methodologies for the study of local properties of big molecular systems existing in the gas phase and in solvated environments. This scheme extends the any particle molecular orbital (APMO) approach in the quantum mechanics/molecular mechanics (QM/MM) framework. As a first assessment of the performance of the proposed approach, we estimate the proton affinities (PAs) of seventy amines in the gas phase and the proton binding energies (PBEs) in the gas phase and in an explicitly solvated environment of the sixty-one protons present in the chignolin protein. These calculations are performed with the QM/MM versions of the APMO second-order proton propagator (APMO-PP2) and the APMO extended Koopmans' theorem (APMO-KT) approaches. Calculated PAs and PBEs show significant reductions in the computational effort with a reduced loss in accuracy. These results suggest that the APMO/MM scheme might be used as a low-cost multi-component alternative for studies of local properties in big molecular systems. Graphical Abstract QMMM regions and CPU times for the APMO/MM approach.
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Fedorov DG, Brekhov A, Mironov V, Alexeev Y. Molecular Electrostatic Potential and Electron Density of Large Systems in Solution Computed with the Fragment Molecular Orbital Method. J Phys Chem A 2019; 123:6281-6290. [DOI: 10.1021/acs.jpca.9b04936] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Anton Brekhov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Yuri Alexeev
- Argonne Leadership Computing Facility and Computational Science Division, Argonne National Laboratory, Argonne, Illinois, 60439, United States
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Rayka M, Goli M, Shahbazian S. Toward a muon-specific electronic structure theory: effective electronic Hartree-Fock equations for muonic molecules. Phys Chem Chem Phys 2018; 20:4466-4477. [PMID: 29372727 DOI: 10.1039/c7cp07599e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An effective set of Hartree-Fock (HF) equations are derived for electrons of muonic systems, i.e., molecules containing a positively charged muon, conceiving the muon as a quantum oscillator, which are completely equivalent to the usual two-component HF equations used to derive stationary states of the muonic molecules. In these effective equations, a non-Coulombic potential is added to the orthodox coulomb and exchange potential energy terms, which describes the interaction of the muon and the electrons effectively and is optimized during the self-consistent field cycles. While in the two-component HF equations a muon is treated as a quantum particle, in the effective HF equations it is absorbed into the effective potential and practically transformed into an effective potential field experienced by electrons. The explicit form of the effective potential depends on the nature of muon's vibrations and is derivable from the basis set used to expand the muonic spatial orbital. The resulting effective Hartree-Fock equations are implemented computationally and used successfully, as a proof of concept, in a series of muonic molecules containing all atoms from the second and third rows of the Periodic Table. To solve the algebraic version of the equations muon-specific Gaussian basis sets are designed for both muon and surrounding electrons and it is demonstrated that the optimized exponents are quite distinct from those derived for the hydrogen isotopes. The developed effective HF theory is quite general and in principle can be used for any muonic system while it is the starting point for a general effective electronic structure theory that incorporates various types of quantum correlations into the muonic systems beyond the HF equations.
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Affiliation(s)
- Milad Rayka
- Department of Physics and Department of Physical and Computational Chemistry, Shahid Beheshti University, G. C., Evin, P.O. Box 19395-4716, Tehran, 19839, Iran.
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Suzuki K, Tachikawa M, Shiga M. Temperature dependence on the structure of Zundel cation and its isotopomers. J Chem Phys 2013; 138:184307. [DOI: 10.1063/1.4803655] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Goli M, Shahbazian S. The two-component quantum theory of atoms in molecules (TC-QTAIM): foundations. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1208-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Efficient density functional theory calculations with weak hydrogen quantum effect: Electron density analysis. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.12.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Fedorov DG, Nagata T, Kitaura K. Exploring chemistry with the fragment molecular orbital method. Phys Chem Chem Phys 2012; 14:7562-77. [DOI: 10.1039/c2cp23784a] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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Ikabata Y, Imamura Y, Nakai H. Interpretation of intermolecular geometric isotope effect in hydrogen bonds: nuclear orbital plus molecular orbital study. J Phys Chem A 2011; 115:1433-9. [PMID: 21306139 DOI: 10.1021/jp111062n] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The intermolecular geometric isotope effect (GIE) in hydrogen bond A-X···B (X = H and D) is investigated theoretically using the nuclear orbital plus molecular orbital (NOMO) theory. To interpret the GIE in terms of physically meaningful energy components such as electrostatic and exchange-repulsion interactions, the reduced variational space self-consistent-field method is extended to the NOMO scheme. The intermolecular GIE is analyzed as a two-stage process: the intramolecular bond shrinkage and the intermolecular bond elongation. According to the isotopic shifts of energy components described by the NOMO/MP2 method, the intermolecular GIE is approximately interpreted as a process reducing the exchange-repulsion interaction after the decrease of electrostatic interaction.
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Affiliation(s)
- Yasuhiro Ikabata
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan
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KANEKO M, UDAGAWA T, TACHIKAWA M. Geometric Isotope Effect on Low Barrier Hydrogen-Bonding Systems of Acetic Acid Dimer, Formic Acid Dimer, and Their Anionic Clusters by Using the Multi-Component Molecular Orbital Method. ACTA ACUST UNITED AC 2010. [DOI: 10.2477/jccj.h2124m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Shigeta Y. Molecular Theory Including Quantum Effects and Thermal Fluctuations. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.1323] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ishimoto T, Ishihara Y, Teramae H, Baba M, Nagashima U. H/D isotope effect in methyl torsional interaction of acetone as calculated by a multicomponent molecular orbital method. J Chem Phys 2008; 129:214116. [DOI: 10.1063/1.3028540] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Shigeta Y, Miyachi H, Matsui T, Hirao K. Dynamic Quantum Isotope Effects on Multiple Proton-Transfer Reactions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.1230] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kikuta Y, Ishimoto T, Nagashima U. Geometrical and Kinetic Isotope Effects on R–H(D)···R Type Intramolecular Hydrogen Bonds (R = CH2, NH, and O) Using a Multi-Component Molecular Orbital Method. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.820] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Ishimoto T, Tachikawa M, Nagashima U. Simultaneous analytical optimization of variational parameters in Gaussian-type functions with full configuration interaction of multicomponent molecular orbital method by elimination of translational and rotational motions: Application to isotopomers of the hydrogen molecule. J Chem Phys 2008; 128:164118. [DOI: 10.1063/1.2912939] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Fedorov DG, Kitaura K. Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method. J Phys Chem A 2007; 111:6904-14. [PMID: 17511437 DOI: 10.1021/jp0716740] [Citation(s) in RCA: 437] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following the brief review of the modern fragment-based methods and other approaches to perform quantum-mechanical calculations of large systems, the theoretical development of the fragment molecular orbital method (FMO) is covered in detail, with the emphasis on the physical properties, which can be computed with FMO. The FMO-based polarizable continuum model (PCM) for treating the solvent effects in large systems and the pair interaction energy decomposition analysis (PIEDA) are described in some detail, and a range of applications of FMO to biological studies is introduced. The factors determining the relative stability of polypeptide conformers (alpha-helix, beta-turn, and extended form) are elucidated using FMO/PCM and PIEDA, and the interactions in the Trp-cage miniprotein construct (PDB: 1L2Y) are analyzed using PIEDA.
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Affiliation(s)
- Dmitri G Fedorov
- Research Institute for Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, Japan 305-8568.
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Ishimoto T, Tachikawa M, Nagashima U. Electron-electron and electron-nucleus correlation effects on exponent values of Gaussian-type functions for quantum protons and deuterons. J Chem Phys 2006; 125:144103. [PMID: 17042575 DOI: 10.1063/1.2352753] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Electron-electron and electron-nucleus correlation effects on exponent (alpha) values of Gaussian-type functions (GTFs) for quantum protons and deuterons in BH3, CH4, NH3, H2O, and HF molecular systems and their deuterated counterparts were analyzed using the second-order Moller-Plesset (MP2) level of theory of the multicomponent molecular orbital (MCMO-MP2) method. This method can simultaneously determine both nuclear and electronic wave functions. Results showed that the average alpha value (alpha(ave)) of the optimized alpha in single s-type ([1s]) GTF for a proton and a deuteron is similar to that determined using the Hartree-Fock level of the MCMO (MCMO-HF) method. In contrast, due to the electron-nucleus correlation effect, the s- and p-type ([1s1p]) GTFs are delocalized compared with those determined using the MCMO-HF method. For the H-bonded complexes, differences in the interaction energy induced by the H/D isotope effect were clearly evident because the D...Y bond distance for D complex is longer than the H...Y for H complex. Also, the basis set superposition error for the interaction energy in every H complex was similar to that in every D complex. The results here clearly demonstrate that the protonic and deuteronic basis functions based on alpha(ave) values for correlation effects can be applied to the detailed analysis of the quantum effects of protons and the H/D isotope effect in widespread fields that involve H bonds and weak interactions, such as the function of biological molecules, chemical reaction processes, and the design of new materials.
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Affiliation(s)
- Takayoshi Ishimoto
- Research Institute for Computational Science, National Institute of Advanced Industrial Science and Technology, Umezono 1-1-1, Tsukuba, Ibaraki 305-8568, Japan.
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