1
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Einsele R, Mitrić R. Nonadiabatic Exciton Dynamics and Energy Gradients in the Framework of FMO-LC-TDDFTB. J Chem Theory Comput 2024. [PMID: 39051619 DOI: 10.1021/acs.jctc.4c00539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
We introduce a novel methodology for simulating the excited-state dynamics of extensive molecular aggregates in the framework of the long-range corrected time-dependent density-functional tight-binding fragment molecular orbital method (FMO-LC-TDDFTB) combined with the mean-field Ehrenfest method. The electronic structure of the system is described in a quasi-diabatic basis composed of locally excited and charge-transfer states of all fragments. In order to carry out nonadiabatic molecular dynamics simulations, we derive and implement the excited-state gradients of the locally excited and charge-transfer states. Subsequently, the accuracy of the analytical excited-state gradients is evaluated. The applicability to the simulation of exciton transport in organic semiconductors is illustrated on a large cluster of anthracene molecules. Additionally, nonadiabatic molecular dynamics simulations of a model system of benzothieno-benzothiophene molecules highlight the method's utility in studying charge-transfer dynamics in organic materials. Our new methodology will facilitate the investigation of excitonic transfer in extensive biological systems, nanomaterials, and other 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 97074, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität, Würzburg 97074, Germany
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2
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Fedorov DG. Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method. J Comput Chem 2024; 45:1540-1551. [PMID: 38490813 DOI: 10.1002/jcc.27345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
An auxiliary polarization formulation of the fragment molecular orbital (FMO) method is developed, combining a basis set correction computed for capped isolated fragments with a polarization obtained from uncapped fragments. For a set of organic and inorganic test systems, it is shown that the total energy and atomic charges are accurately reproduced with respect to full unfragmented calculations. It is demonstrated that the method is accurate for computing electronic excited states. The developed approach is applied to rank the isomers of chignolin from experimental NMR data (PDB: 1UAO) according to their relative energy. Contributions of polarization and basis set effects to pair interactions between fragments are elucidated.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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3
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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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4
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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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5
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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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6
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Fedorov DG. Parametrized quantum-mechanical approaches combined with the fragment molecular orbital method. J Chem Phys 2022; 157:231001. [PMID: 36550057 DOI: 10.1063/5.0131256] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Fast parameterized methods such as density-functional tight-binding (DFTB) facilitate realistic calculations of large molecular systems, which can be accelerated by the fragment molecular orbital (FMO) method. Fragmentation facilitates interaction analyses between functional parts of molecular systems. In addition to DFTB, other parameterized methods combined with FMO are also described. Applications of FMO methods to biochemical and inorganic systems are reviewed.
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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
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7
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Fedorov DG. Polarization energies in the fragment molecular orbital method. J Comput Chem 2022; 43:1094-1103. [PMID: 35446441 DOI: 10.1002/jcc.26869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/25/2022] [Accepted: 04/05/2022] [Indexed: 12/23/2022]
Abstract
Using isolated and polarized states of fragments, a method for computing the polarization energies in density functional theory (DFT) and density-functional tight-binding (DFTB) is developed in the framework of the fragment molecular orbital method. For DFTB, the method is extended into the use of periodic boundary conditions (PBC), for which a new component, a periodic self-polarization energy, is derived. The couplings of the polarization to other components in the pair interaction energy analysis (PIEDA) are derived for DFT and DFTB, and compared to Hartree-Fock and second-order Møller-Plesset perturbation theory (MP2). The effect of the self-consistent (DFT) and perturbative (MP2) treatment of the electron correlation on the polarization is discussed. The difference in the polarization in the bulk (PBC) and micro (cluster) solvation is elucidated.
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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, Nakamura T. Free Energy Decomposition Analysis Based on the Fragment Molecular Orbital Method. J Phys Chem Lett 2022; 13:1596-1601. [PMID: 35142207 DOI: 10.1021/acs.jpclett.2c00040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A decomposition of the free energy is developed in the many-body expansion framework of the fragment molecular orbital (FMO) method combined with umbrella sampling molecular dynamics (MD). In FMO/MD simulations, performed with density-functional tight-binding and periodic boundary conditions, all atoms are treated quantum mechanically. The free energy is computed and decomposed for a series of SN2 Menshutkin reactions in water. The barrier lowering by the solvent is attributed to the competition between the solvent polarization and the solute-solvent interactions including charge transfer.
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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
| | - Taiji Nakamura
- 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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9
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Abstract
Vibrational energies are partitioned into the contributions of molecular parts called segments, for instance, residues in proteins. The fragment molecular orbital method is used to facilitate vibrational calculations of large systems at the DFTB and HF-3c levels. The vibrational analysis is combined with the partitioning of the electronic energy, yielding free-energy contributions of segments to the binding energy, pinpointing hot spots for drug discovery and other studies. The analysis is illustrated on two protein-ligand complexes 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
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10
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Nishimoto Y, Fedorov DG. The fragment molecular orbital method combined with density-functional tight-binding and periodic boundary conditions. J Chem Phys 2021; 154:111102. [PMID: 33752370 DOI: 10.1063/5.0039520] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The density-functional tight-binding (DFTB) formulation of the fragment molecular orbital method is combined with periodic boundary conditions. Long-range electrostatics and dispersion are evaluated with the Ewald summation technique. The first analytic derivatives of the energy with respect to atomic coordinates and lattice parameters are formulated. The accuracy of the method is established in comparison to numerical gradients and DFTB without fragmentation. The largest elementary cell in this work has 1631 atoms. The method is applied to elucidate the polarization, charge transfer, and interactions in the solution.
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Affiliation(s)
- Yoshio Nishimoto
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwakecho, Sakyoku, Kyoto 606-8502, 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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11
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Abstract
High-order charge transfer is incorporated into the fragment molecular orbital (FMO) method using a charge transfer state with fractional charges. This state is used for a partition analysis of properties based on segments that may be different from fragments in FMO. The partition analysis is also formulated for calculations without fragmentation. All development in this work is limited to density-functional tight-binding. The analysis is applied to a water cluster, crambin (PDB: 1CBN), and two complexes of Trp-cage (1L2Y) with ligands. The contributions of functional groups in ligands are obtained, providing useful information for drug discovery.
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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
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12
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Kitoh-Nishioka H, Shigeta Y, Ando K. Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method. J Chem Phys 2020; 153:104104. [PMID: 32933280 DOI: 10.1063/5.0018423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.
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Affiliation(s)
- Hirotaka Kitoh-Nishioka
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Koji Ando
- Department of Information and Sciences, Tokyo Woman's Christian University, 2-6-1 Zenpukuji, Suginami-ku, Tokyo 167-8585, Japan
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13
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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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14
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Fedorov DG. Three-Body Energy Decomposition Analysis Based on the Fragment Molecular Orbital Method. J Phys Chem A 2020; 124:4956-4971. [DOI: 10.1021/acs.jpca.0c03085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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15
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Nishimura Y, Nakai H. Hierarchical parallelization of divide‐and‐conquer density functional tight‐binding molecular dynamics and metadynamics simulations. J Comput Chem 2020; 41:1759-1772. [DOI: 10.1002/jcc.26217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering Waseda University Tokyo Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering Waseda University Tokyo Japan
- Department of Chemistry and Biochemistry School of Advanced Science and Engineering, Waseda University Tokyo Japan
- Elements Strategy Initiative for Catalysts and Batteries Kyoto University Kyoto Japan
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16
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Barca GMJ, Bertoni C, Carrington L, Datta D, De Silva N, Deustua JE, Fedorov DG, Gour JR, Gunina AO, Guidez E, Harville T, Irle S, Ivanic J, Kowalski K, Leang SS, Li H, Li W, Lutz JJ, Magoulas I, Mato J, Mironov V, Nakata H, Pham BQ, Piecuch P, Poole D, Pruitt SR, Rendell AP, Roskop LB, Ruedenberg K, Sattasathuchana T, Schmidt MW, Shen J, Slipchenko L, Sosonkina M, Sundriyal V, Tiwari A, Galvez Vallejo JL, Westheimer B, Włoch M, Xu P, Zahariev F, Gordon MS. Recent developments in the general atomic and molecular electronic structure system. J Chem Phys 2020; 152:154102. [PMID: 32321259 DOI: 10.1063/5.0005188] [Citation(s) in RCA: 518] [Impact Index Per Article: 129.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.
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Affiliation(s)
- Giuseppe M J Barca
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Laura Carrington
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Nuwan De Silva
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119, USA
| | - J Emiliano Deustua
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Jeffrey R Gour
- Microsoft, 15590 NE 31st St., Redmond, Washington 98052, USA
| | - Anastasia O Gunina
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Taylor Harville
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Stephan Irle
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Joe Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Karol Kowalski
- Physical Sciences Division, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Sarom S Leang
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Hui Li
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jesse J Lutz
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Ilias Magoulas
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Joani Mato
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Hiroya Nakata
- Kyocera Corporation, Research Institute for Advanced Materials and Devices, 3-5-3 Hikaridai Seika-cho, Souraku-gun, Kyoto 619-0237, Japan
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Spencer R Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Alistair P Rendell
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Luke B Roskop
- Cray Inc., a Hewlett Packard Enterprise Company, 2131 Lindau Ln #1000, Bloomington, Minnesota 55425, USA
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | - Michael W Schmidt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Lyudmila Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Masha Sosonkina
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Vaibhav Sundriyal
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Ananta Tiwari
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Jorge L Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Bryce Westheimer
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Marta Włoch
- 530 Charlesina Dr., Rochester, Michigan 48306, USA
| | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Federico Zahariev
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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17
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Inamori M, Yoshikawa T, Ikabata Y, Nishimura Y, Nakai H. Spin‐flip approach within time‐dependent density functional tight‐binding method: Theory and applications. J Comput Chem 2020; 41:1538-1548. [DOI: 10.1002/jcc.26197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Mayu Inamori
- Department of Chemistry and Biochemistry, School of Advanced Science and EngineeringWaseda University Tokyo Japan
| | - Takeshi Yoshikawa
- Waseda Research Institute for Science and EngineeringWaseda University Tokyo Japan
| | - Yasuhiro Ikabata
- Waseda Research Institute for Science and EngineeringWaseda University Tokyo Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and EngineeringWaseda University Tokyo Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and EngineeringWaseda University Tokyo Japan
- Waseda Research Institute for Science and EngineeringWaseda University Tokyo Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB)Kyoto University Kyoto Japan
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18
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Komoto N, Yoshikawa T, Nishimura Y, Nakai H. Large-Scale Molecular Dynamics Simulation for Ground and Excited States Based on Divide-and-Conquer Long-Range Corrected Density-Functional Tight-Binding Method. J Chem Theory Comput 2020; 16:2369-2378. [DOI: 10.1021/acs.jctc.9b01268] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- 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
| | - Takeshi Yoshikawa
- Waseda Research Institute for 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
- 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, 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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19
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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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20
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Morao I, Heifetz A, Fedorov DG. Accurate Scoring in Seconds with the Fragment Molecular Orbital and Density-Functional Tight-Binding Methods. Methods Mol Biol 2020; 2114:143-148. [PMID: 32016891 DOI: 10.1007/978-1-0716-0282-9_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The accurate evaluation of receptor-ligand interactions is an essential part of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been combined with the density-functional tight-binding (DFTB) method to compute energy calculations of biological systems in seconds. FMO-DFTB outperformed GBVI/WSA in identifying a set of 10 binders versus a background of 500 decoys applied to human k-opioid receptor. The significant increase in the speed and the high accuracy achieved with FMO-DFTB calculations allows FMO to be applied in areas of drug discovery that were not previously accessible to traditional QM methodologies. For the first time, it is now possible to perform FMO calculations in a high-throughput manner.
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Affiliation(s)
- Inaki Morao
- Evotec (UK) Ltd., Abingdon, Oxfordshire, UK.
| | | | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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21
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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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22
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Vuong VQ, Nishimoto Y, Fedorov DG, Sumpter BG, Niehaus TA, Irle S. The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding. J Chem Theory Comput 2019; 15:3008-3020. [PMID: 30998360 DOI: 10.1021/acs.jctc.9b00108] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O( N1.13-1.28), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y ) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clusters containing up to 2300 atoms.
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Affiliation(s)
- Van Quan Vuong
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry , Kyoto University , Kyoto 606-8501 , Japan
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat) , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568 , Japan
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences and Computational Sciences and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Thomas A Niehaus
- Univ Lyon, Université Claude Bernard Lyon 1 , CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - Stephan Irle
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Center for Nanophase Materials Sciences and Computational Sciences and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States.,Chemical Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
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23
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Heifetz A, James T, Southey M, Morao I, Aldeghi M, Sarrat L, Fedorov DG, Bodkin MJ, Townsend-Nicholson A. Characterising GPCR-ligand interactions using a fragment molecular orbital-based approach. Curr Opin Struct Biol 2019; 55:85-92. [PMID: 31022570 DOI: 10.1016/j.sbi.2019.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/19/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
Abstract
There has been fantastic progress in solving GPCR crystal structures. However, the ability of X-ray crystallography to guide the drug discovery process for GPCR targets is limited by the availability of accurate tools to explore receptor-ligand interactions. Visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum mechanical approaches (QM) are often too computationally expensive, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed and the ability to reveal key interactions that would otherwise be hard to detect. Integration of GPCR crystallography or homology modelling with FMO reveals atomistic details of the individual contributions of each residue and water molecule towards ligand binding, including an analysis of their chemical nature.
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Affiliation(s)
- Alexander Heifetz
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom.
| | - Tim James
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Michelle Southey
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Inaki Morao
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Laurie Sarrat
- Evotec (France) SAS, 195 Route d' Espagne, 31036 Toulouse, France
| | - 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
| | - Mike J Bodkin
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London,WC1E 6BT, United Kingdom
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24
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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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25
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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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26
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Lee KH, Schnupf U, Sumpter BG, Irle S. Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution. ACS OMEGA 2018; 3:16899-16915. [PMID: 31458314 PMCID: PMC6643604 DOI: 10.1021/acsomega.8b02213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 05/12/2023]
Abstract
Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowest-energy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.
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Affiliation(s)
- Ka Hung Lee
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Bredesen
Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Udo Schnupf
- Department
of Chemistry and Biochemistry, Bradley University, Peoria, Illinois 61625, United States
- E-mail: (U.S.)
| | - Bobby G. Sumpter
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan Irle
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- E-mail: (S.I.)
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27
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Simon A, Rapacioli M, Michoulier E, Zheng L, Korchagina K, Cuny J. Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1554903] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- A. Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - M. Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - E. Michoulier
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - L. Zheng
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - K. Korchagina
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - J. Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
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28
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Nakata H, Fedorov DG. Analytic second derivatives for the efficient electrostatic embedding in the fragment molecular orbital method. J Comput Chem 2018; 39:2039-2050. [DOI: 10.1002/jcc.25360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/27/2018] [Accepted: 04/29/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Hiroya Nakata
- Department of Fundamental Technology Research; Research and Development Center Kagoshima, Kyocera, 1-4 Kokubu Yamashita-cho; Kirishima-shi Kagoshima, 899-4312 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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29
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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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30
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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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31
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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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32
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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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33
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Yuan D, Li Y, Ni Z, Pulay P, Li W, Li S. Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2017; 13:2696-2704. [DOI: 10.1021/acs.jctc.7b00284] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dandan Yuan
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Yunzhi Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Zhigang Ni
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Peter Pulay
- Department
of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Wei Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
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34
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Nishimoto Y, Fedorov DG. Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding. J Comput Chem 2017; 38:406-418. [DOI: 10.1002/jcc.24693] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/14/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022]
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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35
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Ratcliff LE, Mohr S, Huhs G, Deutsch T, Masella M, Genovese L. Challenges in large scale quantum mechanical calculations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1290] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura E. Ratcliff
- Argonne Leadership Computing Facility Argonne National Laboratory Lemon IL USA
| | - Stephan Mohr
- Department of Computer Applications in Science and Engineering Barcelona Supercomputing Center (BSC‐CNS) Barcelona Spain
| | - Georg Huhs
- Department of Computer Applications in Science and Engineering Barcelona Supercomputing Center (BSC‐CNS) Barcelona Spain
| | - Thierry Deutsch
- University Grenoble Alpes INAC‐MEM Grenoble France
- CEA, INAC‐MEM Grenoble France
| | - Michel Masella
- Laboratoire de Biologie Structurale et Radiologie, Service de Bioénergétique, Biologie Structurale et Mécanisme Institut de Biologie et de Technologie de Saclay, CEA Saclay Gif‐sur‐Yvette Cedex France
| | - Luigi Genovese
- University Grenoble Alpes INAC‐MEM Grenoble France
- CEA, INAC‐MEM Grenoble France
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36
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Nakata H, Nishimoto Y, Fedorov DG. Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method. J Chem Phys 2016; 145:044113. [DOI: 10.1063/1.4959231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Hiroya Nakata
- Department of Fundamental Technology Research, R and D Center Kagoshima, Kyocera, 1-4 Kokubu Yamashita-cho, Kirishima-shi, Kagoshima 899-4312, Japan
| | - 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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37
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Nishimoto Y, Fedorov DG. The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model. Phys Chem Chem Phys 2016; 18:22047-61. [DOI: 10.1039/c6cp02186g] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electronic gap in proteins is analyzed in detail, and it is shown that FMO-DFTB/PCM is efficient and accurate in describing the molecular structure of proteins in solution.
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Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry
- Kyoto University
- 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)
- Tsukuba
- Japan
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