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Einsele R, Hoche J, Mitrić R. Long-range corrected fragment molecular orbital density functional tight-binding method for excited states in large molecular systems. J Chem Phys 2023; 158:044121. [PMID: 36725509 DOI: 10.1063/5.0136844] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Herein, we present a new method to efficiently calculate electronically excited states in large molecular assemblies, consisting of hundreds of molecules. For this purpose, we combine the long-range corrected tight-binding density functional fragment molecular orbital method (FMO-LC-DFTB) with an excitonic Hamiltonian, which is constructed in the basis of locally excited and charge-transfer configuration state functions calculated for embedded monomers and dimers and accounts explicitly for the electronic coupling between all types of excitons. We first evaluate both the accuracy and efficiency of our fragmentation approach for molecular dimers and aggregates by comparing it with the full LC-TD-DFTB method. The comparison of the calculated spectra of an anthracene cluster shows a very good agreement between our method and the LC-TD-DFTB reference. The effective computational scaling of our method has been explored for anthracene clusters and for perylene bisimide aggregates. We demonstrate the applicability of our method by the calculation of the excited state properties of pentacene crystal models consisting of up to 319 molecules. Furthermore, the participation ratio of the monomer fragments to the excited states is analyzed by the calculation of natural transition orbital participation numbers, which are verified by the hole and particle density for a chosen pentacene cluster. The use of our FMO-LC-TDDFTB method will allow for future studies of excitonic dynamics and charge transport to be performed on complex molecular systems consisting of thousands of atoms.
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Affiliation(s)
- Richard Einsele
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
| | - Joscha Hoche
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
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2
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Nishimoto Y, Fedorov DG. Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding. J Chem Phys 2018; 148:064115. [DOI: 10.1063/1.5012935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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3
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Fedorov DG, Kitaura K. Pair Interaction Energy Decomposition Analysis for Density Functional Theory and Density-Functional Tight-Binding with an Evaluation of Energy Fluctuations in Molecular Dynamics. J Phys Chem A 2018; 122:1781-1795. [DOI: 10.1021/acs.jpca.7b12000] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - Kazuo Kitaura
- Advanced
Institute for Computational Science (AICS), RIKEN, 7-1-26 Minatojima-Minami-Machi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho
34-4, Sakyou-ku, Kyoto 606-8103, 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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Pruitt SR, Steinmann C. Mapping Interaction Energies in Chorismate Mutase with the Fragment Molecular Orbital Method. J Phys Chem A 2017; 121:1797-1807. [DOI: 10.1021/acs.jpca.6b12830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Spencer R. Pruitt
- Academic & Research Computing, Worcester Polytechnic Institute, Worcester, Massachusetts 01602, United States
| | - Casper Steinmann
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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6
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Genova A, Ceresoli D, Pavanello M. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical. J Chem Phys 2016; 144:234105. [DOI: 10.1063/1.4953363] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alessandro Genova
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
| | - Davide Ceresoli
- CNR-ISTM: Institute of Molecular Sciences and Technologies, Milano, Italy
| | - Michele Pavanello
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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7
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Fedorov DG, Kitaura K. Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in Solution. J Phys Chem A 2016; 120:2218-31. [PMID: 26949816 DOI: 10.1021/acs.jpca.6b00163] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A subsystem analysis is derived incorporating interfragment interactions into the fragment properties, such as energies or charges. The relative stabilities of three alanine isomers, the α-helix, the β-turn, and the extended form are studied and the differences in fragment properties are elucidated. The analysis is further elaborated for studies of binding energies. The binding of the Trp-cage protein (PDB: 1L2Y ) to two ligands is studied in detail. Binding energies defined for each fragment can be used as a convenient descriptor for analyzing contributions to binding in solution.
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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) , Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Kazuo Kitaura
- Graduate School of System Informatics, Kobe University , 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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8
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Pruitt SR, Nakata H, Nagata T, Mayes M, Alexeev Y, Fletcher G, Fedorov DG, Kitaura K, Gordon MS. Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method. J Chem Theory Comput 2016; 12:1423-35. [DOI: 10.1021/acs.jctc.5b01208] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Spencer R. Pruitt
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Hiroya Nakata
- Department of Fundamental Technology Research, R&D Center Kagoshima, Kyocera Corporation, 1-4 Kokubu Yamashita-cho, Kirishima-shi, Kagoshima 899-4312, Japan
| | - Takeshi Nagata
- Nanosystem Research
Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umenzono, Tsukuba, Ibaraki 305-8568, Japan
| | - Maricris Mayes
- Department
of Chemistry and Biochemistry, University of Massachusetts Dartmouth, 285 Old Westport Road, Dartmouth, Massachusetts 02747-2300, United States
| | - Yuri Alexeev
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Graham Fletcher
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Dmitri G. Fedorov
- Nanosystem Research
Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umenzono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State University, 201 Spedding
Hall, Ames, Iowa 50011, United States
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9
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Simoncini D, Nakata H, Ogata K, Nakamura S, Zhang KY. Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method. Mol Inform 2015; 34:97-104. [PMID: 27490032 DOI: 10.1002/minf.201400108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/13/2014] [Indexed: 12/12/2022]
Abstract
Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.
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Affiliation(s)
- David Simoncini
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan phone: +81(0)45-503-9560/fax: +81(0)45-503-9559.,Present address: Mathématiques et Informatique Appliquées de Toulouse, Unité de Recherche 875, Institut National de la Recherche Agronomique, F-31320 Castanet-Tolosan, France
| | - Hiroya Nakata
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503.,Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Koji Ogata
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503
| | - Shinichiro Nakamura
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503.
| | - Kam Yj Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan phone: +81(0)45-503-9560/fax: +81(0)45-503-9559.
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10
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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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11
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Nishimoto Y, Fedorov DG, Irle S. Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:4801-12. [DOI: 10.1021/ct500489d] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan
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12
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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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13
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Fedorov DG, Asada N, Nakanishi I, Kitaura K. The use of many-body expansions and geometry optimizations in fragment-based methods. Acc Chem Res 2014; 47:2846-56. [PMID: 25144610 DOI: 10.1021/ar500224r] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conspectus Chemists routinely work with complex molecular systems: solutions, biochemical molecules, and amorphous and composite materials provide some typical examples. The questions one often asks are what are the driving forces for a chemical phenomenon? How reasonable are our views of chemical systems in terms of subunits, such as functional groups and individual molecules? How can one quantify the difference in physicochemical properties of functional units found in a different chemical environment? Are various effects on functional units in molecular systems additive? Can they be represented by pairwise potentials? Are there effects that cannot be represented in a simple picture of pairwise interactions? How can we obtain quantitative values for these effects? Many of these questions can be formulated in the language of many-body effects. They quantify the properties of subunits (fragments), referred to as one-body properties, pairwise interactions (two-body properties), couplings of two-body interactions described by three-body properties, and so on. By introducing the notion of fragments in the framework of quantum chemistry, one obtains two immense benefits: (a) chemists can finally relate to quantum chemistry, which now speaks their language, by discussing chemically interesting subunits and their interactions and (b) calculations become much faster due to a reduced computational scaling. For instance, the somewhat academic sounding question of the importance of three-body effects in water clusters is actually another way of asking how two hydrogen bonds affect each other, when they involve three water molecules. One aspect of this is the many-body charge transfer (CT), because the charge transfers in the two hydrogen bonds are coupled to each other (not independent). In this work, we provide a generalized view on the use of many-body expansions in fragment-based methods, focusing on the general aspects of the property expansion and a contraction of a many-body expansion in a formally two-body series, as exemplified in the development of the fragment molecular orbital (FMO) method. Fragment-based methods have been very successful in delivering the properties of fragments, as well as the fragment interactions, providing insights into complex chemical processes in large molecular systems. We briefly review geometry optimizations performed with fragment-based methods and present an efficient geometry optimization method based on the combination of FMO with molecular mechanics (MM), applied to the complex of a subunit of protein kinase 2 (CK2) with a ligand. FMO results are discussed in comparison with experimental and MM-optimized structures.
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Affiliation(s)
- Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Naoya Asada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kinki University, 3-4-1,
Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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