1
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Nishimura R, Yoshikawa T, Sakata K, Nakai H. Excitation configuration analysis for divide-and-conquer excited-state calculation method using dynamical polarizability. J Chem Phys 2024; 160:244103. [PMID: 38913842 DOI: 10.1063/5.0207935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/23/2024] [Indexed: 06/26/2024] Open
Abstract
The authors previously developed a divide-and-conquer (DC)-based non-local excited-state calculation method for large systems using dynamical polarizability [Nakai and Yoshikawa, J. Chem. Phys. 146, 124123 (2017)]. This method evaluates the excitation energies and oscillator strengths using information on the dynamical polarizability poles. This article proposes a novel analysis of the previously developed method to obtain further configuration information on excited states, including excitation and de-excitation coefficients of each excitation configuration. Numerical applications to simple molecules, such as ethylene, hydrogen molecule, ammonia, and pyridazine, confirmed that the proposed analysis could accurately reproduce the excitation and de-excitation coefficients. The combination with the DC scheme enables both the local and non-local excited states of large systems with an excited nature to be treated.
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Affiliation(s)
- Ryusei Nishimura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Ken Sakata
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
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2
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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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3
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Nakai H, Kobayashi M, Yoshikawa T, Seino J, Ikabata Y, Nishimura Y. Divide-and-Conquer Linear-Scaling Quantum Chemical Computations. J Phys Chem A 2023; 127:589-618. [PMID: 36630608 DOI: 10.1021/acs.jpca.2c06965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Phys. 1995, 103, 5674-5678). First, the theoretical aspects of the DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, followed by the two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and the introduction of three programs, including DC-based schemes. Illustrative applications confirmed the accuracy and feasibility of the DC-based schemes.
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Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Masato Kobayashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido001-0021, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba274-8510, Japan
| | - Junji Seino
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Yasuhiro Ikabata
- Information and Media Center, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan.,Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
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4
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Nakai H, Takemura T, Ono J, Nishimura Y. Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models. J Phys Chem B 2021; 125:10947-10963. [PMID: 34582194 DOI: 10.1021/acs.jpcb.1c06231] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacteriorhodopsin (BR) transports a proton from intracellular to extracellular (EC) sites through five proton transfers. The second proton transfer is the release of an excess proton stored in BR into the EC medium, and an atomistic understanding of this whole process has remained unexplored due to its ubiquitous environment. Here, fully quantum mechanical (QM) molecular dynamics (MD) and metadynamics (MTD) simulations for this process were performed at the divide-and-conquer density-functional tight-binding level using realistic models (∼50000 and ∼20000 atoms) based on the time-resolved photointermediate structures from an X-ray free electron laser. Regarding the proton storage process, the QM-MD/MTD simulations confirmed the Glu-shared mechanism, in which an excess proton is stored between Glu194 and Glu204, and clarified that the activation occurs by localizing the proton at Glu204 in the photocycle. Furthermore, the QM-MD/MTD simulations elucidated a release pathway from Glu204 through Ser193 to the EC water molecules and clarified that the proton release starts at ∼250 μs. In the ubiquitous proton diffusion in the EC medium, the transient proton receptors predicted experimentally were assigned to carboxylates in Glu9 and Glu74. Large-scale QM-MD/MTD simulations beyond the conventional sizes, which provided the above findings and confirmations, were possible by adopting our Dcdftbmd program.
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Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto 615-8245, Japan
| | - Toshiaki Takemura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Junichi Ono
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto 615-8245, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
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5
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Nakai H. Development of Linear-Scaling Relativistic Quantum Chemistry Covering the Periodic Table. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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6
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Uratani H, Yoshikawa T, Nakai H. Trajectory Surface Hopping Approach to Condensed-Phase Nonradiative Relaxation Dynamics Using Divide-and-Conquer Spin-Flip Time-Dependent Density-Functional Tight Binding. J Chem Theory Comput 2021; 17:1290-1300. [PMID: 33577323 DOI: 10.1021/acs.jctc.0c01155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonradiative relaxation of excited molecules is central to many crucial issues in photochemistry. Condensed phases are typical contexts in which such problems are considered, and the nonradiative relaxation dynamics are expected to be significantly affected by interactions with the environment, for example, a solvent. We developed a nonadiabatic molecular dynamics simulation technique that can treat the nonradiative relaxation and explicitly include the environment in the calculations without a heavy computational burden. Specifically, we combined trajectory surface hopping with Tully's fewest-switches algorithm, a tight-binding approximated version of spin-flip time-dependent density-functional theory, and divide-and-conquer (DC) spatial fragmentation scheme. Numerical results showed that this method can treat systems with thousands of atoms within reasonable computational resources, and the error arising from DC fragmentation is negligibly small. Using this method, we obtained molecular insights into the solvent dependence of the photoexcited-state dynamics of trans-azobenzene, which demonstrate the importance of the environment for condensed-phase nonradiative relaxation.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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7
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Uratani H, Nakai H. Non-adiabatic molecular dynamics with divide-and-conquer type large-scale excited-state calculations. J Chem Phys 2020; 152:224109. [DOI: 10.1063/5.0006831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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8
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Sakti AW, Nishimura Y, Nakai H. Recent advances in quantum‐mechanical molecular dynamics simulations of proton transfer mechanism in various water‐based environments. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aditya W. Sakti
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
| | - Hiromi Nakai
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering Waseda University Tokyo Japan
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9
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Uratani H, Chou CP, Nakai H. Quantum mechanical molecular dynamics simulations of polaron formation in methylammonium lead iodide perovskite. Phys Chem Chem Phys 2020; 22:97-106. [DOI: 10.1039/c9cp04739e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polaron formation in a halide perovskite is analyzed via nanometre-scale quantum mechanical molecular dynamics simulations.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry
- School of Advanced Science and Engineering
- Waseda University
- Shinjuku-ku
- Japan
| | - Chien-Pin Chou
- Waseda Research Institute for Science and Engineering (WISE)
- Tokyo 169-8555
- Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry
- School of Advanced Science and Engineering
- Waseda University
- Shinjuku-ku
- Japan
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10
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Yoshikawa T, Komoto N, Nishimura Y, Nakai H. GPU-Accelerated Large-Scale Excited-State Simulation Based on Divide-and-Conquer Time-Dependent Density-Functional Tight-Binding. J Comput Chem 2019; 40:2778-2786. [PMID: 31441083 DOI: 10.1002/jcc.26053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 01/09/2023]
Abstract
The present study implemented the divide-and-conquer time-dependent density-functional tight-binding (DC-TDDFTB) code on a graphical processing unit (GPU). The DC method, which is a linear-scaling scheme, divides a total system into several fragments. By separately solving local equations in individual fragments, the DC method could reduce slow central processing unit (CPU)-GPU memory access, as well as computational cost, and avoid shortfalls of GPU memory. Numerical applications confirmed that the present code on GPU significantly accelerated the TDDFTB calculations, while maintaining accuracy. Furthermore, the DC-TDDFTB simulation of 2-acetylindan-1,3-dione displays excited-state intramolecular proton transfer and provides reasonable absorption and fluorescence energies with the corresponding experimental values. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Takeshi Yoshikawa
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Nana Komoto
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto, 615-8520, Japan
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11
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Nishimura Y, Nakai H. D
cdftbmd
: Divide‐and‐Conquer Density Functional Tight‐Binding Program for Huge‐System Quantum Mechanical Molecular Dynamics Simulations. J Comput Chem 2019; 40:1538-1549. [DOI: 10.1002/jcc.25804] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
- Department of Chemistry and BiochemistrySchool of Advanced Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
- ESICB, Kyoto University Kyotodaigaku‐Katsura, Kyoto 615‐8520 Japan
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12
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Kobayashi M, Fujimori T, Taketsugu T. Automated error control in divide-and-conquer self-consistent field calculations. J Comput Chem 2018; 39:909-916. [DOI: 10.1002/jcc.25174] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Masato Kobayashi
- Department of Chemistry, Faculty of Science, Hokkaido University; Sapporo 060-0810 Japan
- ESICB, Kyoto University; Kyoto 615-8520 Japan
- PRESTO, Japan Science and Technology Agency; Kawaguchi 332-0012 Japan
| | - Toshikazu Fujimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University; Sapporo 060-0810 Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University; Sapporo 060-0810 Japan
- ESICB, Kyoto University; Kyoto 615-8520 Japan
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13
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Nishimura Y, Nakai H. Parallel implementation of efficient charge-charge interaction evaluation scheme in periodic divide-and-conquer density-functional tight-binding calculations. J Comput Chem 2017; 39:105-116. [DOI: 10.1002/jcc.25086] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Yoshifumi Nishimura
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
| | - Hiromi Nakai
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering; Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho; Kawaguchi 332-0012 Japan
- ESICB, Kyoto University, Kyotodaigaku-Katsura; Kyoto 615-8520 Japan
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14
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Li H, Liu W, Suo B. Localization of open-shell molecular orbitals via least change from fragments to molecule. J Chem Phys 2017; 146:104104. [DOI: 10.1063/1.4977929] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hongyang Li
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Wenjian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Bingbing Suo
- Institute of Modern Physics, Northwest University, Xi’an 710069, People’s Republic of China
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15
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Nishizawa H, Nishimura Y, Kobayashi M, Irle S, Nakai H. Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation. J Comput Chem 2016; 37:1983-92. [DOI: 10.1002/jcc.24419] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Hiroaki Nishizawa
- Department of Theoretical and Computational Molecular Science; Institute for Molecular Science; Okazaki 444-8585 Japan
| | - Yoshifumi Nishimura
- Department of Theoretical and Computational Molecular Science; Institute for Molecular Science; Okazaki 444-8585 Japan
- Research Institute for Science and Engineering; Waseda University; Tokyo 169-8555 Japan
| | - Masato Kobayashi
- Department of Chemistry, Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
- ESICB, Kyoto University; Kyoto 615-8520 Japan
- PRESTO, Japan Science and Technology Agency; Kawaguchi 332-0012 Japan
| | - Stephan Irle
- Department of Chemistry; Graduate School of Science, and Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University; Nagoya 464-8602 Japan
| | - Hiromi Nakai
- Research Institute for Science and Engineering; Waseda University; Tokyo 169-8555 Japan
- ESICB, Kyoto University; Kyoto 615-8520 Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering; Waseda University; Tokyo 169-8555 Japan
- CREST, Japan Science and Technology Agency; Kawaguchi 332-0012 Japan
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16
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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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17
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Tsukamoto Y, Ikabata Y, Romero J, Reyes A, Nakai H. The divide-and-conquer second-order proton propagator method based on nuclear orbital plus molecular orbital theory for the efficient computation of proton binding energies. Phys Chem Chem Phys 2016; 18:27422-27431. [DOI: 10.1039/c6cp03786k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient computational method to evaluate the binding energies of many protons in large systems was developed.
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Affiliation(s)
- Yusuke Tsukamoto
- Department of Chemistry and Biochemistry
- School of Advanced Science and Engineering
- Waseda University
- Tokyo 169-8555
- Japan
| | - Yasuhiro Ikabata
- Department of Chemistry and Biochemistry
- School of Advanced Science and Engineering
- Waseda University
- Tokyo 169-8555
- Japan
| | - Jonathan Romero
- Department of Chemistry
- Universidad Nacional de Colombia
- Bogotá
- Colombia
| | - Andrés Reyes
- Department of Chemistry
- Universidad Nacional de Colombia
- Bogotá
- Colombia
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry
- School of Advanced Science and Engineering
- Waseda University
- Tokyo 169-8555
- Japan
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18
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Shoji M, Kayanuma M, Umeda H, Shigeta Y. Performance of the divide-and-conquer approach used as an initial guess. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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20
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Akimov AV, Prezhdo OV. Large-Scale Computations in Chemistry: A Bird’s Eye View of a Vibrant Field. Chem Rev 2015; 115:5797-890. [DOI: 10.1021/cr500524c] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexey V. Akimov
- Department
of Chemistry, University of South California, Los Angeles, California 90089, United States
| | - Oleg V. Prezhdo
- Department
of Chemistry, University of South California, Los Angeles, California 90089, United States
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21
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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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22
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Moreira RA, de Melo CP. On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes. J Chem Phys 2014; 141:124712. [PMID: 25273466 DOI: 10.1063/1.4894845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.
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Affiliation(s)
- Rodrigo A Moreira
- Departamento de Física, Universidade Federal de Pernambuco, Recife-PE 50670-901, Brazil
| | - Celso P de Melo
- Departamento de Física, Universidade Federal de Pernambuco, Recife-PE 50670-901, Brazil
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23
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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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24
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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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Seino J, Nakai H. Local unitary transformation method toward practical electron correlation calculations with scalar relativistic effect in large-scale molecules. J Chem Phys 2013; 139:034109. [DOI: 10.1063/1.4813595] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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26
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Yoshikawa T, Kobayashi M, Fujii A, Nakai H. Novel Approach to Excited-State Calculations of Large Molecules Based on Divide-and-Conquer Method: Application to Photoactive Yellow Protein. J Phys Chem B 2013; 117:5565-73. [DOI: 10.1021/jp401819d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Masato Kobayashi
- Waseda Institute for Advanced Study, Waseda University, Tokyo 169-8050, Japan
| | | | - Hiromi Nakai
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama
332-0012, Japan
- ESICB, Kyoto University, Kyotodaigaku-Katsura, Nishigyoku,
Kyoto 615-8520, Japan
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Kobayashi M, Nakai H. An effective energy gradient expression for divide-and-conquer second-order Møller–Plesset perturbation theory. J Chem Phys 2013; 138:044102. [DOI: 10.1063/1.4776228] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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28
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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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Kobayashi M, Touma T, Nakai H. Dynamic hyperpolarizability calculations of large systems: The linear-scaling divide-and-conquer approach. J Chem Phys 2012; 136:084108. [DOI: 10.1063/1.3687341] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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30
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NAKAI H. Discovery of Chemical Principles:Symmetry Rules for Degenerate Excitations. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2012. [DOI: 10.2477/jccj.2012-0004] [Citation(s) in RCA: 3] [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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31
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Kobayashi M, Nakai H. How does it become possible to treat delocalized and/or open-shell systems in fragmentation-based linear-scaling electronic structure calculations? The case of the divide-and-conquer method. Phys Chem Chem Phys 2012; 14:7629-39. [DOI: 10.1039/c2cp40153c] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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32
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Aoki Y, Gu FL. An elongation method for large systems toward bio-systems. Phys Chem Chem Phys 2012; 14:7640-68. [DOI: 10.1039/c2cp24033e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Yoshikawa T, Kobayashi M, Nakai H. Linear-scaling divide-and-conquer second-order Møller–Plesset perturbation calculation for open-shell systems: implementation and application. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1008-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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34
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Katouda M, Kobayashi M, Nakai H, Nagase S. Two‐level hierarchical parallelization of second‐order Møller–plesset perturbation calculations in divide‐and‐conquer method. J Comput Chem 2011; 32:2756-64. [DOI: 10.1002/jcc.21855] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/30/2011] [Accepted: 05/13/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Michio Katouda
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan
| | - Masato Kobayashi
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169‐8555, Japan
| | - Hiromi Nakai
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan
- 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, Tokyo 102‐0075, Japan
| | - Shigeru Nagase
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan
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Touma T, Kobayashi M, Nakai H. Finite-field evaluation of static (hyper)polarizabilities based on the linear-scaling divide-and-conquer method. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0964-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Kobayashi M, Kunisada T, Akama T, Sakura D, Nakai H. Reconsidering an analytical gradient expression within a divide-and-conquer self-consistent field approach: Exact formula and its approximate treatment. J Chem Phys 2011; 134:034105. [DOI: 10.1063/1.3524337] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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Linear-scaling electronic structure calculation program based on divide-and-conquer method. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.procs.2011.04.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Divide-and-Conquer Approaches to Quantum Chemistry: Theory and Implementation. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2011. [DOI: 10.1007/978-90-481-2853-2_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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