1
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Nakata H, Kitoh-Nishioka H, Sakai W, Choi CH. Toward Accurate Prediction of Ion Mobility in Organic Semiconductors by Atomistic Simulation. J Chem Theory Comput 2023; 19:1517-1528. [PMID: 36757219 DOI: 10.1021/acs.jctc.2c01221] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
A multiscale scheme (MLMS: Multi-Level Multi-Scale) to predict the ion mobility (μ) of amorphous organic semiconductors is proposed, which was successfully applied to the hole mobility predictions of 14 organic systems. An inverse relationship between μ and reorganization energy is observed due to local polaronic distortions. Another moderate inverse correlation between μ and distribution of site energy change exists, representing the effects of geometric flexibility. The former and the latter represent the intramolecular and intermolecular geometric effects, respectively. In addition, a linear correlation between transfer coupling and μ is observed, showing the importance of orbital overlaps between monomers. Especially, the highest hole mobility of C6-2TTN is due to its large transfer coupling. On the other hand, another high hole mobility of CBP turned out to come from the high first neighbor density (ρFND) of its first self-solvation, emphasizing the proper description of amorphous structural configurations with a sufficiently large number of monomers. In general, systems with either unusually high transfer coupling or high first neighbor density can potentially have high μ regardless of geometric effects. Especially, the newly suggested design parameter, ρFND, is pointing to a new direction as opposed to the traditional π-conjugation strategy.
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Affiliation(s)
- Hiroya Nakata
- Research Institute for Advanced Materials and Devices, Kyocera Corporation, 3-5-3 Hikaridai Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
| | - Hirotaka Kitoh-Nishioka
- Department of Energy and Materials, Faculty of Science and Engineering, Kindai University, 3 Chome-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Wakana Sakai
- Research Institute for Advanced Materials and Devices, Kyocera Corporation, 3-5-3 Hikaridai Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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2
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Nakata H, Fedorov DG. Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2023; 19:1276-1285. [PMID: 36753486 DOI: 10.1021/acs.jctc.2c01177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of a polarizable embedding are derived. The obtained analytic FMO-TDDFT gradient is shown to be accurate in comparison to both numerical FMO-TDDFT and unfragmented TDDFT gradients, at the level of two- and three-body expansions. The gradients are used for geometry optimizations, molecular dynamics, vibrational calculations, and simulations of IR and Raman spectra of excited states. The developed method is used to optimize the geometry of the ground and excited electronic states of the photoactive yellow protein (PDB: 2PHY).
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Affiliation(s)
- Hiroya Nakata
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - 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
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3
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Chen WK, Fang WH, Cui G. Extending multi-layer energy-based fragment method for excited-state calculations of large covalently bonded fragment systems. J Chem Phys 2023; 158:044110. [PMID: 36725521 DOI: 10.1063/5.0129458] [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
Recently, we developed a low-scaling Multi-Layer Energy-Based Fragment (MLEBF) method for accurate excited-state calculations and nonadiabatic dynamics simulations of nonbonded fragment systems. In this work, we extend the MLEBF method to treat covalently bonded fragment ones. The main idea is cutting a target system into many fragments according to chemical properties. Fragments with dangling bonds are first saturated by chemical groups; then, saturated fragments, together with the original fragments without dangling bonds, are grouped into different layers. The accurate total energy expression is formulated with the many-body energy expansion theory, in combination with the inclusion-exclusion principle that is used to delete the contribution of chemical groups introduced to saturate dangling bonds. Specifically, in a two-layer MLEBF model, the photochemically active and inert layers are calculated with high-level and efficient electronic structure methods, respectively. Intralayer and interlayer energies can be truncated at the two- or three-body interaction level. Subsequently, through several systems, including neutral and charged covalently bonded fragment systems, we demonstrate that MLEBF can provide accurate ground- and excited-state energies and gradients. Finally, we realize the structure, conical intersection, and path optimizations by combining our MLEBF program with commercial and free packages, e.g., ASE and SciPy. These developments make MLEBF a practical and reliable tool for studying complex photochemical and photophysical processes of large nonbonded and bonded fragment systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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4
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Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method. Methods Mol Biol 2020. [PMID: 32016888 DOI: 10.1007/978-1-0716-0282-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recent development of the fragment molecular orbital (FMO) method related to energy gradients, geometry optimization, transition state search, and chemical reaction mapping is summarized. The frozen domain formulation of FMO is introduced in detail, and the structure of related GAMESS input files for FMO is described.
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5
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Kaliakin DS, Fedorov DG, Alexeev Y, Varganov SA. Locating Minimum Energy Crossings of Different Spin States Using the Fragment Molecular Orbital Method. J Chem Theory Comput 2019; 15:6074-6084. [DOI: 10.1021/acs.jctc.9b00641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Danil S. Kaliakin
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - 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
| | - Yuri Alexeev
- Computational Science Division and Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
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6
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Terai Y, Sato R, Yumiba T, Harada R, Shimizu K, Toga T, Ishikawa-Fujiwara T, Todo T, Iwai S, Shigeta Y, Yamamoto J. Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities. Nucleic Acids Res 2019; 46:6761-6772. [PMID: 29762762 PMCID: PMC6061865 DOI: 10.1093/nar/gky364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/24/2018] [Indexed: 12/28/2022] Open
Abstract
(6–4) Photolyases ((6–4)PLs) are flavoenzymes that repair the carcinogenic UV-induced DNA damage, pyrimidine(6–4)pyrimidone photoproducts ((6–4)PPs), in a light-dependent manner. Although the reaction mechanism of DNA photorepair by (6–4)PLs has been intensively investigated, the molecular mechanism of the lesion recognition remains obscure. We show that a well-conserved arginine residue in Xenopus laevis (6–4)PL (Xl64) participates in DNA binding, through Coulomb and CH–π interactions. Fragment molecular orbital calculations estimated attractive interaction energies of –80–100 kcal mol–1 for the Coulomb interaction and –6 kcal mol–1 for the CH–π interaction, and the loss of either of them significantly reduced the affinity for (6–4)PP-containing oligonucleotides, as well as the quantum yield of DNA photorepair. From experimental and theoretical observations, we formulated a DNA binding model of (6–4)PLs. Based on the binding model, we mutated this Arg in Xl64 to His, which is well conserved among the animal cryptochromes (CRYs), and found that the CRY-type mutant exhibited reduced affinity for the (6–4)PP-containing oligonucleotides, implying the possible molecular origin of the functional diversity of the photolyase/cryptochrome superfamily.
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Affiliation(s)
- Yuma Terai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Ryuma Sato
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takahiro Yumiba
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Kohei Shimizu
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Tatsuya Toga
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Tomoko Ishikawa-Fujiwara
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Todo
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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7
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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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8
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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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9
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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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10
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Nishimoto Y, Nakata H, Fedorov DG, Irle S. Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method. J Phys Chem Lett 2015; 6:5034-9. [PMID: 26623658 DOI: 10.1021/acs.jpclett.5b02490] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with the fragment molecular orbital (FMO) method (FMO-DFTB). The response terms arising from the coupling of the electronic state to the embedding potential are derived, and the gradient accuracy is demonstrated on water clusters and a polypeptide. The radial distribution functions (RDFs) obtained with FMO-DFTB are found to be similar to those from conventional DFTB, while the computational cost is greatly reduced; for 256 water molecules one molecular dynamics (MD) step takes 73.26 and 0.68 s with full DFTB and FMO-DFTB, respectively, showing a speed-up factor of 108. FMO-DFTB/MD is applied to 100 ps MD simulations of liquid hydrogen halides and is found to reproduce experimental RDFs reasonably well.
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Affiliation(s)
- Yoshio Nishimoto
- Department of Chemistry, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University , 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
| | - Hiroya Nakata
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midoriku, Yokohama 226-8501, Japan
- RIKEN, Research Cluster for Innovation , Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198, 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
| | - Stephan Irle
- Department of Chemistry, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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11
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Extension of the fragment molecular orbital method to treat large open-shell systems in solution. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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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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13
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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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14
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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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15
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Yoshikawa T, Nakai H. Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units. J Comput Chem 2014; 36:164-70. [DOI: 10.1002/jcc.23782] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 10/21/2014] [Accepted: 10/22/2014] [Indexed: 01/27/2023]
Affiliation(s)
- Takeshi Yoshikawa
- Department of Chemistry and Biochemistry; School of Advanced Science and Engineering, Waseda University; Tokyo 169-8555 Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry; School of Advanced Science and Engineering, Waseda University; Tokyo 169-8555 Japan
- Research Institute for Science and Engineering, Waseda University; Tokyo 169-8555 Japan
- CREST; Japan Science and Technology Agency; Saitama 332-0012 Japan
- ESICB; Kyoto University, Kyotodaigaku-Katsura; Kyoto 615-8520 Japan
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16
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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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17
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Alexeev Y, Fedorov DG, Shvartsburg AA. Effective Ion Mobility Calculations for Macromolecules by Scattering on Electron Clouds. J Phys Chem A 2014; 118:6763-72. [DOI: 10.1021/jp505012c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuri Alexeev
- Argonne
Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8568, Japan
| | - Alexandre A. Shvartsburg
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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18
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Nakata H, Fedorov DG, Yokojima S, Kitaura K, Nakamura S. Simulations of Raman Spectra Using the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:3689-98. [DOI: 10.1021/ct5003829] [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)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Nakamura
Lab, 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
| | - Satoshi Yokojima
- Nakamura
Lab, Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachiouji-shi, Tokyo 192-0392, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 Japan
| | - Shinichiro Nakamura
- Nakamura
Lab, Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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19
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Kuźniarowicz P, Liu K, Aoki Y, Gu FL, Stachowicz A, Korchowiec J. Intermediate electrostatic field for the elongation method. J Mol Model 2014; 20:2277. [PMID: 24878802 PMCID: PMC4072069 DOI: 10.1007/s00894-014-2277-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 04/25/2014] [Indexed: 11/25/2022]
Abstract
A simple way to improve the accuracy of the fragmentation methods is proposed. The formalism was applied to the elongation (ELG) method at restricted open-shell Hartree-Fock (ROHF) level of theory. The α-helix conformer of polyglycine was taken as a model system. The modified ELG method includes a simplified electrostatic field resulting from point-charge distribution of the system's environment. In this way the long-distance polarization is approximately taken into account. The field attenuates during the ELG process to eventually disappear when the final structure is reached. The point-charge distributions for each ELG step are obtained from charge sensitivity analysis (CSA) in force-field atoms resolution. The presence of the intermediate field improves the accuracy of ELG calculations. The errors in total energy and its kinetic and potential contributions are reduced by at least one-order of magnitude. In addition the SCF convergence of ROHF scheme is improved.
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Affiliation(s)
- Piotr Kuźniarowicz
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka, 816-8580 Japan
| | - Kai Liu
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, Kasuga, Fukuoka, 816-8580 Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, Kasuga, Fukuoka, 816-8580 Japan
| | - Feng Long Gu
- MOE Key Laboratory of Theoretical Chemistry of Environment; School of Chemistry and Environment, South China Normal University, Guangzhou, 510631 China
| | - Anna Stachowicz
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Jacek Korchowiec
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
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Nakata H, Fedorov DG, Yokojima S, Kitaura K, Nakamura S. Efficient vibrational analysis for unrestricted Hartree–Fock based on the fragment molecular orbital method. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.04.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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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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22
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Nakata H, Fedorov DG, Yokojima S, Kitaura K, Nakamura S. Derivatives of the approximated electrostatic potentials in unrestricted Hartree–Fock based on the fragment molecular orbital method and an application to polymer radicals. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1477-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Kato Y, Fujiwara T, Komeiji Y, Nakano T, Mori H, Okiyama Y, Mochizuki Y. Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion. CHEM-BIO INFORMATICS JOURNAL 2014. [DOI: 10.1273/cbij.14.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yuji Kato
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
| | - Takayuki Fujiwara
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
| | - Yuto Komeiji
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tatsuya Nakano
- Division of Medicinal Safety Science, National Institute of Health Sciences
| | - Hirotoshi Mori
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University
| | - Yoshio Okiyama
- Institute of Industrial Science, The University of Tokyo
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
- Institute of Industrial Science, The University of Tokyo
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24
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Yamamoto JI, Mochizuki Y. Optimal damping algorithm for unrestricted Hartree-Fock calculations. CHEM-BIO INFORMATICS JOURNAL 2014. [DOI: 10.1273/cbij.14.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
- Institute of Industrial Science, The University of Tokyo
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25
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Green MC, Fedorov DG, Kitaura K, Francisco JS, Slipchenko LV. Open-shell pair interaction energy decomposition analysis (PIEDA): formulation and application to the hydrogen abstraction in tripeptides. J Chem Phys 2013; 138:074111. [PMID: 23445001 DOI: 10.1063/1.4790616] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An open-shell extension of the pair interaction energy decomposition analysis (PIEDA) within the framework of the fragment molecular orbital (FMO) method is developed. The open-shell PIEDA method allows the analysis of inter- and intramolecular interactions in terms of electrostatic, exchange-repulsion, charge-transfer, dispersion, and optional polarization energies for molecular systems with a radical or high-spin fragment. Taking into account the low computational cost and scalability of the FMO and PIEDA methods, the new scheme provides a means to characterize the stabilization of radical and open-shell sites in biologically relevant species. The open-shell PIEDA is applied to the characterization of intramolecular interactions in capped trialanine upon hydrogen abstraction (HA) at various sites on the peptide. Hydrogen abstraction reaction is the first step in the oxidative pathway initiated by reactive oxygen or nitrogen species, associated with oxidative stress. It is found that HA results in significant geometrical reorganization of the trialanine peptide. Depending on the HA site, terminal interactions in the radical fold conformers may become weaker or stronger compared to the parent molecule, and often change the character of the non-covalent bonding from amide stacking to hydrogen bonding.
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Affiliation(s)
- Mandy C Green
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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26
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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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27
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Song GL, Li ZH, Fan KN. Extended Energy Divide-and-Conquer Method Based on Charge Conservation. J Chem Theory Comput 2013; 9:1992-9. [DOI: 10.1021/ct300850q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guo-Liang Song
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Zhen Hua Li
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Kang-Nian Fan
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
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