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Abstract
Basic concepts in the analysis of binding using the fragment molecular orbital method are discussed at length: polarization, desolvation, and interaction. The components in the pair interaction energy decomposition analysis are introduced, and the analysis is illustrated for a water dimer and a protein-ligand complex.
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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), Tsukuba, Japan.
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2
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Nakata H, Fedorov DG. Simulations of infrared and Raman spectra in solution using the fragment molecular orbital method. Phys Chem Chem Phys 2019; 21:13641-13652. [DOI: 10.1039/c9cp00940j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Calculation of IR and Raman spectra in solution for large molecular systems made possible with analytic FMO/PCM Hessians.
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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)
- Tsukuba
- Japan
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3
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Okiyama Y, Nakano T, Watanabe C, Fukuzawa K, Mochizuki Y, Tanaka S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study. J Phys Chem B 2018; 122:4457-4471. [DOI: 10.1021/acs.jpcb.8b01172] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Yoshio Okiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Tatsuya Nakano
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Chiduru Watanabe
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Faculty of Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yuji Mochizuki
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan
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4
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Fedorov DG. The fragment molecular orbital method: theoretical development, implementation in
GAMESS
, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1322] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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)TsukubaJapan
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5
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Nebgen B, Prezhdo OV. Fragment Molecular Orbital Nonadiabatic Molecular Dynamics for Condensed Phase Systems. J Phys Chem A 2016; 120:7205-12. [DOI: 10.1021/acs.jpca.6b05607] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ben Nebgen
- Department
of Chemistry, University of Southern California, Los Angeles, California 90037, United States
| | - Oleg V. Prezhdo
- Department
of Chemistry, University of Southern California, Los Angeles, California 90037, United States
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6
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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7
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Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method. J Chem Phys 2015; 142:124101. [DOI: 10.1063/1.4915068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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8
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Brorsen KR, Zahariev F, Nakata H, Fedorov DG, Gordon MS. Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:5297-307. [DOI: 10.1021/ct500808p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kurt R. Brorsen
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Federico Zahariev
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Kanagawa, Yokohama 226-8501, Japan
- Nakamura
Laboratory, RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Japan Society
for the Promotion of Science, Kojimachi
Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Dmitri G. Fedorov
- NRI, National
Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Mark S. Gordon
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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9
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Nakata H, Schmidt MW, Fedorov DG, Kitaura K, Nakamura S, Gordon MS. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method. J Phys Chem A 2014; 118:9762-71. [DOI: 10.1021/jp507726m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Research Cluster
for Innovation, Nakamura Lab, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Kojimachi Business
Center Building, Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Michael W. Schmidt
- Department
of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Shinichiro Nakamura
- Research Cluster
for Innovation, Nakamura Lab, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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10
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Pruitt SR, Bertoni C, Brorsen KR, Gordon MS. Efficient and accurate fragmentation methods. Acc Chem Res 2014; 47:2786-94. [PMID: 24810424 DOI: 10.1021/ar500097m] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment-fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method.
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Affiliation(s)
- Spencer R. Pruitt
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, United States
| | - Colleen Bertoni
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Kurt R. Brorsen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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Nakata H, Fedorov DG, Yokojima S, Kitaura K, Sakurai M, Nakamura S. Unrestricted density functional theory based on the fragment molecular orbital method for the ground and excited state calculations of large systems. J Chem Phys 2014; 140:144101. [DOI: 10.1063/1.4870261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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12
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Nakata H, Nagata T, Fedorov DG, Yokojima S, Kitaura K, Nakamura S. Analytic second derivatives of the energy in the fragment molecular orbital method. J Chem Phys 2013; 138:164103. [DOI: 10.1063/1.4800990] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Komeiji Y, Fujiwara T, Okiyama Y, Mochizuki Y. Dynamic fragmentation with static fragments (DF/SF) algorithm designed for <i>ab initio</i> fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of polypeptides. CHEM-BIO INFORMATICS JOURNAL 2013. [DOI: 10.1273/cbij.13.45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | - Yoshio Okiyama
- Institute of Industrial Science, The University of Tokyo
| | - Yuji Mochizuki
- Institute of Industrial Science, The University of Tokyo
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
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Nagata T, Fedorov DG, Sawada T, Kitaura K. Analysis of Solute–Solvent Interactions in the Fragment Molecular Orbital Method Interfaced with Effective Fragment Potentials: Theory and Application to a Solvated Griffithsin–Carbohydrate Complex. J Phys Chem A 2012; 116:9088-99. [DOI: 10.1021/jp304991a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Takeshi Nagata
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29 Yoshidashimo
Adachi, Sakyo-ku, Kyoto 606-8501, Japan
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Toshihiko Sawada
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012,
Japan
| | - Kazuo Kitaura
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29 Yoshidashimo
Adachi, Sakyo-ku, Kyoto 606-8501, Japan
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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15
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Nagata T, Fedorov DG, Kitaura K. Analytic gradient for the embedding potential with approximations in the fragment molecular orbital method. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Nakata H, Fedorov DG, Nagata T, Yokojima S, Ogata K, Kitaura K, Nakamura S. Unrestricted Hartree-Fock based on the fragment molecular orbital method: Energy and its analytic gradient. J Chem Phys 2012; 137:044110. [DOI: 10.1063/1.4737860] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Nagata T, Fedorov DG, Li H, Kitaura K. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method. J Chem Phys 2012; 136:204112. [DOI: 10.1063/1.4714601] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Tsukamoto T, Mochizuki Y, Watanabe N, Fukuzawa K, Nakano T. Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.03.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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