151
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Christensen A, Kubař T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev 2016; 116:5301-37. [PMID: 27074247 PMCID: PMC4867870 DOI: 10.1021/acs.chemrev.5b00584] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Indexed: 12/28/2022]
Abstract
Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.
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Affiliation(s)
- Anders
S. Christensen
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Tomáš Kubař
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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152
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Huang C. Patching the Exchange-Correlation Potential in Density Functional Theory. J Chem Theory Comput 2016; 12:2224-33. [DOI: 10.1021/acs.jctc.6b00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chen Huang
- Department
of Scientific
Computing, Florida State University, Tallahassee, Florida 32306-4120, United States
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153
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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154
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Fedorov DG, Kitaura K. Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in Solution. J Phys Chem A 2016; 120:2218-31. [PMID: 26949816 DOI: 10.1021/acs.jpca.6b00163] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A subsystem analysis is derived incorporating interfragment interactions into the fragment properties, such as energies or charges. The relative stabilities of three alanine isomers, the α-helix, the β-turn, and the extended form are studied and the differences in fragment properties are elucidated. The analysis is further elaborated for studies of binding energies. The binding of the Trp-cage protein (PDB: 1L2Y ) to two ligands is studied in detail. Binding energies defined for each fragment can be used as a convenient descriptor for analyzing contributions to binding in solution.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST) , Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Kazuo Kitaura
- Graduate School of System Informatics, Kobe University , 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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155
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Meyer B, Guillot B, Ruiz-Lopez MF, Genoni A. Libraries of Extremely Localized Molecular Orbitals. 1. Model Molecules Approximation and Molecular Orbitals Transferability. J Chem Theory Comput 2016; 12:1052-67. [PMID: 26799516 DOI: 10.1021/acs.jctc.5b01007] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite more and more remarkable computational ab initio results are nowadays continuously obtained for large macromolecular systems, the development of new linear-scaling techniques is still an open and stimulating field of research in theoretical chemistry. In this family of methods, an important role is occupied by those strategies based on the observation that molecules are generally constituted by recurrent functional units with well-defined intrinsic features. In this context, we propose to exploit the notion of extremely localized molecular orbitals (ELMOs) that, due to their strict localization on small molecular fragments (e.g., atoms, bonds, or functional groups), are in principle transferable from one molecule to another. Accordingly, the construction of orbital libraries to almost instantaneously build up approximate wave functions and electron densities of very large systems becomes conceivable. In this work, the ELMOs transferability is further investigated in detail and, furthermore, suitable rules to construct model molecules for the computation of ELMOs to be stored in future databanks are also defined. The obtained results confirm the reliable transferability of the ELMOs and show that electron densities obtained from the transfer of extremely localized molecular orbitals are very close to the corresponding Hartree-Fock ones. These observations prompt us to construct new ELMOs databases that could represent an alternative/complement to the already popular pseudoatoms databanks both for determining electron densities and for refining crystallographic structures of very large molecules.
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Affiliation(s)
- Benjamin Meyer
- CNRS , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France
| | - Benoît Guillot
- CNRS , Laboratoire CRM2, UMR 7036, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire CRM2, UMR 7036, Vandoeuvre-lès-Nancy F-54506, France
| | - Manuel F Ruiz-Lopez
- CNRS , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France
| | - Alessandro Genoni
- CNRS , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France
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156
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Meyer B, Guillot B, Ruiz-Lopez MF, Jelsch C, Genoni A. Libraries of Extremely Localized Molecular Orbitals. 2. Comparison with the Pseudoatoms Transferability. J Chem Theory Comput 2016; 12:1068-81. [PMID: 26799595 DOI: 10.1021/acs.jctc.5b01008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Due to both technical and methodological difficulties, determining and analyzing charge densities of very large molecular systems represents a serious challenge that, in the crystallographers community, has been mainly tackled by observing that the so-called pseudoatoms of the electron density multipole expansions are reliably transferable from molecule to molecule. This has led to the construction of pseudoatoms databanks that have allowed successful refinements of crystallographic structures of macromolecules, while taking into account their corresponding reconstructed electron distributions. A recent alternative/complement to the previous approach is represented by techniques based on extremely localized molecular orbitals (ELMOs) that, due to their strict localization on small molecular fragments (e.g., atoms, bonds, and functional groups), are also in principle exportable from system to system. The ELMOs transferability has been already tested in detail, and, in this work, it has been compared to the one of the pseudoatoms. To accomplish this task, electron distributions obtained both through the transfer of pseudoatoms and through the transfer of extremely localized molecular orbitals have been analyzed, especially taking into account topological properties and similarity indexes. The obtained results indicate that all the considered reconstruction methods give completely reasonable and similar charge densities, and, consequently, the new ELMOs libraries will probably represent new useful tools not only for refining crystal structures but also for computing approximate electronic properties of very large molecules.
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Affiliation(s)
- Benjamin Meyer
- CNRS , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France
| | - Benoît Guillot
- CNRS , Laboratoire CRM2, UMR 7036, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire CRM2, UMR 7036, Vandoeuvre-lès-Nancy F-54506, France
| | - Manuel F Ruiz-Lopez
- CNRS , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France
| | - Christian Jelsch
- CNRS , Laboratoire CRM2, UMR 7036, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire CRM2, UMR 7036, Vandoeuvre-lès-Nancy F-54506, France
| | - Alessandro Genoni
- CNRS , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine , Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France
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157
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Jin Y, Su NQ, Xu X, Hu H. Self-consistent field for fragmented quantum mechanical model of large molecular systems. J Comput Chem 2016; 37:321-6. [PMID: 26575414 DOI: 10.1002/jcc.24252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 10/15/2015] [Accepted: 10/19/2015] [Indexed: 11/12/2022]
Abstract
Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter-fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block-wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods.
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Affiliation(s)
- Yingdi Jin
- Hefei National Lab for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, China.,Department of Chemistry, University of Hong Kong, Hong Kong
| | - Neil Qiang Su
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Hao Hu
- Department of Chemistry, University of Hong Kong, Hong Kong.,The University of Hong Kong-Shenzhen Institute of Research and Innovation, Shenzhen, China
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158
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Zhang L, Li W, Fang T, Li S. Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides. Theor Chem Acc 2016. [DOI: 10.1007/s00214-015-1799-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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159
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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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160
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Li W, Kotsis K, Manzhos S. Comparative density functional theory and density functional tight binding study of arginine and arginine-rich cell penetrating peptide TAT adsorption on anatase TiO2. Phys Chem Chem Phys 2016; 18:19902-17. [DOI: 10.1039/c6cp02671k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparative DFT-DFTB study of geometries and electronic structures of arginine, arginine dipeptide, and arginine-rich cell penetrating peptide TAT on the surface of TiO2.
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Affiliation(s)
- Wenxuan Li
- Department of Mechanical Engineering
- National University of Singapore
- Singapore
| | - Konstantinos Kotsis
- Department of Mechanical Engineering
- National University of Singapore
- Singapore
| | - Sergei Manzhos
- Department of Mechanical Engineering
- National University of Singapore
- Singapore
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161
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NAKAJIMA Y, SEINO J, SCHMIDT MW, NAKAI H. Implementation of Efficient Two-component Relativistic Method Using Local Unitary Transformation to GAMESS Program. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2016. [DOI: 10.2477/jccj.2016-0029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yuya NAKAJIMA
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Junji SEINO
- Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Michael W. SCHMIDT
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011, United States
| | - 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, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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162
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Niklasson AMN, Cawkwell MJ, Rubensson EH, Rudberg E. Canonical density matrix perturbation theory. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:063301. [PMID: 26764847 DOI: 10.1103/physreve.92.063301] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Indexed: 06/05/2023]
Abstract
Density matrix perturbation theory [Niklasson and Challacombe, Phys. Rev. Lett. 92, 193001 (2004)] is generalized to canonical (NVT) free-energy ensembles in tight-binding, Hartree-Fock, or Kohn-Sham density-functional theory. The canonical density matrix perturbation theory can be used to calculate temperature-dependent response properties from the coupled perturbed self-consistent field equations as in density-functional perturbation theory. The method is well suited to take advantage of sparse matrix algebra to achieve linear scaling complexity in the computational cost as a function of system size for sufficiently large nonmetallic materials and metals at high temperatures.
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Affiliation(s)
- Anders M N Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M J Cawkwell
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Emanuel H Rubensson
- Division of Scientific Computing, Department of Information Technology, Uppsala University Box 337, SE-751 05 Uppsala, Sweden
| | - Elias Rudberg
- Division of Scientific Computing, Department of Information Technology, Uppsala University Box 337, SE-751 05 Uppsala, Sweden
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163
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Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding. J Comput Chem 2015; 37:448-59. [DOI: 10.1002/jcc.24254] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/15/2015] [Accepted: 10/25/2015] [Indexed: 01/12/2023]
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164
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Rao L, Chi B, Ren Y, Li Y, Xu X, Wan J. DOX: A new computational protocol for accurate prediction of the protein-ligand binding structures. J Comput Chem 2015; 37:336-44. [DOI: 10.1002/jcc.24217] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 08/20/2015] [Accepted: 09/02/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Li Rao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University; Wuhan 430079 People's Republic of China
| | - Bo Chi
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University; Wuhan 430079 People's Republic of China
| | - Yanliang Ren
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University; Wuhan 430079 People's Republic of China
| | - Yongjian Li
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University; Wuhan 430079 People's Republic of China
| | - Xin Xu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education (MOE) Laboratory for Computational Physical Science, Department of Chemistry, Fudan University; Shanghai 200433 People's Republic of China
| | - Jian Wan
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University; Wuhan 430079 People's Republic of China
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165
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Mitsuta Y, Yamanaka S, Saito T, Kawakami T, Yamaguchi K, Okumura M, Nakamura H. Nearsightedness-related indices of finite systems based on linear response function: one-dimensional cases. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1076581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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166
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Orimoto Y, Liu K, Aoki Y. Elongation method for electronic structure calculations of random DNA sequences. J Comput Chem 2015; 36:2103-13. [DOI: 10.1002/jcc.24047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/20/2015] [Accepted: 07/23/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences; Kyushu University; 6-1 Kasuga-Park Fukuoka 816-8580 Japan
| | - Kai Liu
- Department of Material Sciences, Faculty of Engineering Sciences; Kyushu University; 6-1 Kasuga-Park Fukuoka 816-8580 Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences; Kyushu University; 6-1 Kasuga-Park Fukuoka 816-8580 Japan
- Japan Science and Technology Agency, CREST; 4-1-8 Hon-Chou Kawaguchi Saitama 332-0012 Japan
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167
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Nishimoto Y, Fedorov DG, Irle S. Third-order density-functional tight-binding combined with the fragment molecular orbital method. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.07.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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168
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Second-order Møller–Plesset perturbation (MP2) theory at finite temperature: relation with Surján’s density matrix MP2 and its application to linear-scaling divide-and-conquer method. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1710-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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169
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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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170
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Hayami M, Seino J, Nakai H. Accompanying coordinate expansion and recurrence relation method using a transfer relation scheme for electron repulsion integrals with high angular momenta and long contractions. J Chem Phys 2015; 142:204110. [DOI: 10.1063/1.4921541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Masao Hayami
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Junji Seino
- Research Institute for 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
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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171
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Liu K, Korchowiec J, Aoki Y. Intermediate electrostatic field for the generalized elongation method. Chemphyschem 2015; 16:1551-6. [PMID: 25765254 DOI: 10.1002/cphc.201402901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 12/17/2022]
Abstract
An intermediate electrostatic field is introduced to improve the accuracy of fragment-based quantum-chemical computational methods by including long-range polarizations of biomolecules. The point charge distribution of the intermediate field is generated by a charge sensitivity analysis that is parameterized for five different population analyses, namely, atoms-in-molecules, Hirshfeld, Mulliken, natural orbital, and Voronoi population analysis. Two model systems are chosen to demonstrate the performance of the generalized elongation method (ELG) combined with the intermediate electrostatic field. The calculations are performed for the STO-3G, 6-31G, and 6-31G(d) basis sets and compared with reference Hartree-Fock calculations. It is shown that the error in the total energy is reduced by one order of magnitude, independently of the population analyses used. This demonstrates the importance of long-range polarization in electronic-structure calculations by fragmentation techniques.
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Affiliation(s)
- Kai Liu
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga Park, Fukuoka 816-8580 (Japan)
| | - Jacek Korchowiec
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland)
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga Park, Fukuoka 816-8580 (Japan). .,Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama, 332-0012 (Japan).
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172
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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173
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Wesolowski TA, Shedge S, Zhou X. Frozen-Density Embedding Strategy for Multilevel Simulations of Electronic Structure. Chem Rev 2015; 115:5891-928. [DOI: 10.1021/cr500502v] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Sapana Shedge
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Xiuwen Zhou
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
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174
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175
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 758] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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176
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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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177
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Raghavachari K, Saha A. Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules. Chem Rev 2015; 115:5643-77. [PMID: 25849163 DOI: 10.1021/cr500606e] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Krishnan Raghavachari
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Arjun Saha
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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178
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Affiliation(s)
- Michael A Collins
- †Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Ryan P A Bettens
- ‡Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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179
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Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method. J Chem Phys 2015; 142:124101. [DOI: 10.1063/1.4915068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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180
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Vogiatzis KD, Klopper W, Friedrich J. Non-covalent Interactions of CO2 with Functional Groups of Metal–Organic Frameworks from a CCSD(T) Scheme Applicable to Large Systems. J Chem Theory Comput 2015; 11:1574-84. [DOI: 10.1021/ct5011888] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Konstantinos D. Vogiatzis
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
2, D-76131 Karlsruhe, Germany
| | - Wim Klopper
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
2, D-76131 Karlsruhe, Germany
| | - Joachim Friedrich
- Institute
of Chemistry, Chemnitz University of Technology, Strasse der Nationen 62, D-09111 Chemnitz, Germany
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181
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Orimoto Y, Yamamoto R, Xie P, Liu K, Imamura A, Aoki Y. Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems. J Chem Phys 2015; 142:104111. [DOI: 10.1063/1.4913931] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Ryohei Yamamoto
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Peng Xie
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Kai Liu
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Akira Imamura
- Hiroshima Kokusai Gakuin University, 6-20-1 Nakano, Aki-ku, Hiroshima 739-0321, Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012, Japan
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182
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Technical advances in molecular simulation since the 1980s. Arch Biochem Biophys 2015; 582:3-9. [PMID: 25772387 DOI: 10.1016/j.abb.2015.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 12/14/2022]
Abstract
This review describes how the theory and practice of molecular simulation have evolved since the beginning of the 1980s when the author started his career in this field. The account is of necessity brief and subjective and highlights the changes that the author considers have had significant impact on his research and mode of working.
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183
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Li S, Hu L, Peng L, Yang W, Gu FL. Coupled-Perturbed SCF Approach for Calculating Static Polarizabilities and Hyperpolarizabilities with Nonorthogonal Localized Molecular Orbitals. J Chem Theory Comput 2015; 11:923-31. [PMID: 26579746 DOI: 10.1021/ct500889k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coupled-perturbed self-consistent-field (CPSCF) approach has been broadly used for polarizabilities and hyperpolarizabilities computation. To extend this application to large systems, we have reformulated the CPSCF equations with nonorthogonal localized molecular orbitals (NOLMOs). NOLMOs are the most localized representation of electronic degrees of freedom. Methods based on NOLMOs are potentially ideal for investigating large systems. In atomic orbital representation, with a static external electric field added, the wave function and SCF operator of unperturbed NOLMO-SCF wave function/orbitals are expanded to different orders of perturbations. We have derived the corresponding equations up to the third order, which are significantly different from those of a conventional CPSCF method because of the release of the orthogonal restrictions on MOs. The solution to these equations has been implemented. Several chemical systems are used to verify our method. This work represents the first step toward efficient calculations of molecular response and excitation properties with NOLMOs.
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Affiliation(s)
- Shaopeng Li
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment, South China Normal University , Guangzhou 510006, China
| | - Linping Hu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment, South China Normal University , Guangzhou 510006, China
| | - Liang Peng
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment, South China Normal University , Guangzhou 510006, China
| | - Weitao Yang
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment, South China Normal University , Guangzhou 510006, China.,Department of Chemistry and Physics, Duke University , Box 90346, Durham, North Carolina 27708-0346, United States
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment, South China Normal University , Guangzhou 510006, China
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184
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Li Z. Density functional theory for field emission from carbon nano-structures. Ultramicroscopy 2015; 159 Pt 2:162-72. [PMID: 25747284 DOI: 10.1016/j.ultramic.2015.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 02/06/2015] [Accepted: 02/20/2015] [Indexed: 11/20/2022]
Abstract
Electron field emission is understood as a quantum mechanical many-body problem in which an electronic quasi-particle of the emitter is converted into an electron in vacuum. Fundamental concepts of field emission, such as the field enhancement factor, work-function, edge barrier and emission current density, will be investigated, using carbon nanotubes and graphene as examples. A multi-scale algorithm basing on density functional theory is introduced. We will argue that such a first principle approach is necessary and appropriate for field emission of nano-structures, not only for a more accurate quantitative description, but, more importantly, for deeper insight into field emission.
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Affiliation(s)
- Zhibing Li
- The State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.
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185
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Simoncini D, Nakata H, Ogata K, Nakamura S, Zhang KY. Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method. Mol Inform 2015; 34:97-104. [PMID: 27490032 DOI: 10.1002/minf.201400108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/13/2014] [Indexed: 12/12/2022]
Abstract
Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.
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Affiliation(s)
- David Simoncini
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan phone: +81(0)45-503-9560/fax: +81(0)45-503-9559.,Present address: Mathématiques et Informatique Appliquées de Toulouse, Unité de Recherche 875, Institut National de la Recherche Agronomique, F-31320 Castanet-Tolosan, France
| | - Hiroya Nakata
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503.,Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Koji Ogata
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503
| | - Shinichiro Nakamura
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503.
| | - Kam Yj Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan phone: +81(0)45-503-9560/fax: +81(0)45-503-9559.
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186
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Shen H, Hao T, Wen J, Tan RR, Zhang FS. Properties of pure water and sodium chloride solutions at high temperatures and pressures: a simulation study. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2014.992019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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187
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Liu J, Wang X, Zhang JZH, He X. Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method. RSC Adv 2015. [DOI: 10.1039/c5ra20185c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
An efficient fragment-based quantum mechanical method has been successfully applied for reliable prediction of protein–ligand binding affinities.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy
- Institute of Theoretical and Computational Science
- College of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
| | - Xianwei Wang
- Center for Optics & Optoelectronics Research
- College of Science
- Zhejiang University of Technology
- Hangzhou
- China
| | - John Z. H. Zhang
- State Key Laboratory of Precision Spectroscopy
- Institute of Theoretical and Computational Science
- College of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy
- Institute of Theoretical and Computational Science
- College of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
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188
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Torras J, Roberts BP, Seabra GM, Trickey SB. PUPIL. COMBINED QUANTUM MECHANICAL AND MOLECULAR MECHANICAL MODELLING OF BIOMOLECULAR INTERACTIONS 2015; 100:1-31. [DOI: 10.1016/bs.apcsb.2015.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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189
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Friedrich J, McAlexander HR, Kumar A, Crawford TD. Incremental evaluation of coupled cluster dipole polarizabilities. Phys Chem Chem Phys 2015; 17:14284-96. [DOI: 10.1039/c4cp05076b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we present the first implementation of the incremental scheme for coupled cluster linear-response frequency-dependent dipole polarizabilities.
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Affiliation(s)
- Joachim Friedrich
- Institute for Chemistry
- Chemnitz University of Technology
- 09111 Chemnitz
- Germany
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190
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Wang LW. Divide-and-conquer quantum mechanical material simulations with exascale supercomputers. Natl Sci Rev 2014. [DOI: 10.1093/nsr/nwu060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Recent developments in large-scale materials science simulations, especially under the divide-and-conquer method, are reviewed. The pros and cons of the divide-and-conquer method are discussed. It is argued that the divide-and-conquer method, such as the linear-scaling 3D fragment method, is an ideal approach to take advantage of the heterogeneous architectures of modern-day supercomputers despite their relatively large prefactors among linear-scaling methods. Some developments in graphics processing unit (GPU) electronic structure calculations are also reviewed. The accelerators like GPU could be an essential part for the future exascale supercomputing.
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Affiliation(s)
- Lin-Wang Wang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mail Stop 66, Berkeley, CA 94720, USA
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191
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Affiliation(s)
- Francesco Ambrosio
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alessandro Troisi
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
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192
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Brorsen KR, Zahariev F, Nakata H, Fedorov DG, Gordon MS. Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:5297-307. [DOI: 10.1021/ct500808p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kurt R. Brorsen
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Federico Zahariev
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Kanagawa, Yokohama 226-8501, Japan
- Nakamura
Laboratory, RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Japan Society
for the Promotion of Science, Kojimachi
Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Dmitri G. Fedorov
- NRI, National
Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Mark S. Gordon
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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193
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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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194
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Fabiano E, Laricchia S, Della Sala F. Frozen density embedding with non-integer subsystems' particle numbers. J Chem Phys 2014; 140:114101. [PMID: 24655166 DOI: 10.1063/1.4868033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We extend the frozen density embedding theory to non-integer subsystems' particles numbers. Different features of this formulation are discussed, with special concern for approximate embedding calculations. In particular, we highlight the relation between the non-integer particle-number partition scheme and the resulting embedding errors. Finally, we provide a discussion of the implications of the present theory for the derivative discontinuity issue and the calculation of chemical reactivity descriptors.
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Affiliation(s)
- Eduardo Fabiano
- National Nanotechnology Laboratory (NNL), Istituto Nanoscienze-CNR, Via per Arnesano 16, I-73100 Lecce, Italy
| | - Savio Laricchia
- National Nanotechnology Laboratory (NNL), Istituto Nanoscienze-CNR, Via per Arnesano 16, I-73100 Lecce, Italy
| | - Fabio Della Sala
- National Nanotechnology Laboratory (NNL), Istituto Nanoscienze-CNR, Via per Arnesano 16, I-73100 Lecce, Italy
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195
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Nishimoto Y, Fedorov DG, Irle S. Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:4801-12. [DOI: 10.1021/ct500489d] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan
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196
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Nakata H, Schmidt MW, Fedorov DG, Kitaura K, Nakamura S, Gordon MS. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method. J Phys Chem A 2014; 118:9762-71. [DOI: 10.1021/jp507726m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Research Cluster
for Innovation, Nakamura Lab, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Kojimachi Business
Center Building, Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Michael W. Schmidt
- Department
of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Shinichiro Nakamura
- Research Cluster
for Innovation, Nakamura Lab, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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197
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He X, Zhu T, Wang X, Liu J, Zhang JZH. Fragment quantum mechanical calculation of proteins and its applications. Acc Chem Res 2014; 47:2748-57. [PMID: 24851673 DOI: 10.1021/ar500077t] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conspectus The desire to study molecular systems that are much larger than what the current state-of-the-art ab initio or density functional theory methods could handle has naturally led to the development of novel approximate methods, including semiempirical approaches, reduced-scaling methods, and fragmentation methods. The major computational limitation of ab initio methods is the scaling problem, because the cost of ab initio calculation scales nth power or worse with system size. In the past decade, the fragmentation approach based on chemical locality has opened a new door for developing linear-scaling quantum mechanical (QM) methods for large systems and for applications to large molecular systems such as biomolecules. The fragmentation approach is highly attractive from a computational standpoint. First, the ab initio calculation of individual fragments can be conducted almost independently, which makes it suitable for massively parallel computations. Second, the electron properties, such as density and energy, are typically combined in a linear fashion to reproduce those for the entire molecular system, which makes the overall computation scale linearly with the size of the system. In this Account, two fragmentation methods and their applications to macromolecules are described. They are the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method and the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. The EE-GMFCC method is developed from the MFCC approach, which was initially used to obtain accurate protein-ligand QM interaction energies. The main idea of the MFCC approach is that a pair of conjugate caps (concaps) is inserted at the location where the subsystem is divided by cutting the chemical bond. In addition, the pair of concaps is fused to form molecular species such that the overcounted effect from added concaps can be properly removed. By introducing the electrostatic embedding field in each fragment calculation and two-body interaction energy correction on top of the MFCC approach, the EE-GMFCC method is capable of accurately reproducing the QM molecular properties (such as the dipole moment, electron density, and electrostatic potential), the total energy, and the electrostatic solvation energy from full system calculations for proteins. On the other hand, the AF-QM/MM method was used for the efficient QM calculation of protein nuclear magnetic resonance (NMR) parameters, including the chemical shift, chemical shift anisotropy tensor, and spin-spin coupling constant. In the AF-QM/MM approach, each amino acid and all the residues in its vicinity are automatically assigned as the QM region through a distance cutoff for each residue-centric QM/MM calculation. Local chemical properties of the central residue can be obtained from individual QM/MM calculations. The AF-QM/MM approach precisely reproduces the NMR chemical shifts of proteins in the gas phase from full system QM calculations. Furthermore, via the incorporation of implicit and explicit solvent models, the protein NMR chemical shifts calculated by the AF-QM/MM method are in excellent agreement with experimental values. The applications of the AF-QM/MM method may also be extended to more general biological systems such as DNA/RNA and protein-ligand complexes.
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Affiliation(s)
- Xiao He
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Tong Zhu
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
| | - Xianwei Wang
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
| | - Jinfeng Liu
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
| | - John Z. H. Zhang
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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198
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Li S, Li W, Ma J. Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates. Acc Chem Res 2014; 47:2712-20. [PMID: 24873495 DOI: 10.1021/ar500038z] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Conspectus The generalized energy-based fragmentation (GEBF) approach provides a very simple way of approximately evaluating the ground-state energy or properties of a large system in terms of ground-state energies of various small "electrostatically embedded" subsystems, which can be calculated with any traditional ab initio quantum chemistry (X) method (X = Hartree-Fock, density functional theory, and so on). Due to its excellent parallel efficiency, the GEBF approach at the X theory level (GEBF-X) allows full quantum mechanical (QM) calculations to be accessible for systems with hundreds and even thousands of atoms on ordinary workstations. The implementation of the GEBF approach at various theoretical levels can be easily done with existing quantum chemistry programs. This Account reviews the methodology, implementation, and applications of the GEBF-X approach. This method has been successfully applied to optimize the structures of various large systems including molecular clusters, polypeptides, proteins, and foldamers. Such investigations could allow us to elucidate the origin and nature of the cooperative interaction in secondary structures of long peptides or the driving force of the self-assembly processes of aromatic oligoamides. These GEBF-based QM calculations reveal that the structures and stability of various complex systems result from a subtle balance of many types of noncovalent interactions such as hydrogen bonding and van der Waals interactions. The GEBF-based ab initio molecular dynamics (AIMD) method also allows the investigation of dynamic behaviors of large systems on the order of tens of picoseconds. It was demonstrated that the conformational dynamics of two model peptides predicted by GEBF-based AIMD are noticeably different from those predicted by the classical force field MD method. With the target of extending QM calculations to molecular aggregates in the condensed phase, we have implemented the GEBF-based multilayer hybrid models, which could provide satisfactory descriptions of the binding energies between a solute molecule and its surrounding waters and the chain-length dependence of the conformational changes of oligomers in aqueous solutions. A coarse-grained polarizable molecular mechanics model, furnished with GEBF-X dipole moments of subsystems, exhibits some advantages of treating the electrostatic polarization with reduced computational costs. We anticipate that the GEBF approach will continue to develop with the ultimate goal of studying complicated phenomena at mesoscopic scales and serve as a practical tool to elucidate the structure and dynamics of chemical and biological systems.
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Affiliation(s)
- Shuhua Li
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Wei Li
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
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199
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Abstract
Conspectus Quantum mechanics (QM) has revolutionized our understanding of the structure and reactivity of small molecular systems. Given the tremendous impact of QM in this research area, it is attractive to believe that this could also be brought into the biological realm where systems of a few thousand atoms and beyond are routine. Applying QM methods to biological problems brings an improved representation to these systems by the direct inclusion of inherently QM effects such as polarization and charge transfer. Because of the improved representation, novel insights can be gleaned from the application of QM tools to biomacromolecules in aqueous solution. To achieve this goal, the computational bottlenecks of QM methods had to be addressed. In semiempirical theory, matrix diagonalization is rate limiting, while in density functional theory or Hartree-Fock theory electron repulsion integral computation is rate-limiting. In this Account, we primarily focus on semiempirical models where the divide and conquer (D&C) approach linearizes the matrix diagonalization step with respect to the system size. Through the D&C approach, a number of applications to biological problems became tractable. Herein, we provide examples of QM studies on biological systems that focus on protein solvation as viewed by QM, QM enabled structure-based drug design, and NMR and X-ray biological structure refinement using QM derived restraints. Through the examples chosen, we show the power of QM to provide novel insights into biological systems, while also impacting practical applications such as structure refinement. While these methods can be more expensive than classical approaches, they make up for this deficiency by the more realistic modeling of the electronic nature of biological systems and in their ability to be broadly applied. Of the tools and applications discussed in this Account, X-ray structure refinement using QM models is now generally available to the community in the refinement package Phenix. While the power of this approach is manifest, challenges still remain. In particular, QM models are generally applied to static structures, so ways in which to include sampling is an ongoing challenge. Car-Parrinello or Born-Oppenheimer molecular dynamics approaches address the short time scale sampling issue, but how to effectively use QM to study phenomenon covering longer time scales will be the focus of future research. Finally, how to accurately and efficiently include electron correlation effects to facilitate the modeling of, for example, dispersive interactions, is also a major hurdle that a broad range of groups are addressing The use of QM models in biology is in its infancy, leading to the expectation that the most significant use of these tools to address biological problems will be seen in the coming years. It is hoped that while this Account summarizes where we have been, it will also help set the stage for future research directions at the interface of quantum mechanics and biology.
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Affiliation(s)
- Kenneth M Merz
- Department of Chemistry and the Department of Biochemistry and Molecular Biology, Michigan State University , 578 S. Shaw Lane, East Lansing Michigan 48824-1322, United States
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200
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Ji C, Mei Y. Some practical approaches to treating electrostatic polarization of proteins. Acc Chem Res 2014; 47:2795-803. [PMID: 24883956 DOI: 10.1021/ar500094n] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conspectus Electrostatic interaction plays a significant role in determining many properties of biomolecules, which exist and function in aqueous solution, a highly polar environment. For example, proteins are composed of amino acids with charged, polar, and nonpolar side chains and their specific electrostatic properties are fundamental to the structure and function of proteins. An important issue that arises in computational study of biomolecular interaction and dynamics based on classical force field is lack of polarization. Polarization is a phenomenon in which the charge distribution of an isolated molecule will be distorted when interacting with another molecule or presented in an external electric field. The distortion of charge distribution is intended to lower the overall energy of the molecular system, which is counter balanced by the increased internal energy of individual molecules due to the distorted charge distributions. The amount of the charge redistribution, which characterizes the polarizability of a molecule, is determined by the level of the charge distortion. Polarization is inherently quantum mechanical, and therefore classical force fields with fixed atomic charges are incapable of capturing this important effect. As a result, simulation studies based on popular force fields, AMBER, CHARMM, etc., lack the polarization effect, which is a widely known deficiency in most computational studies of biomolecules today. Many efforts have been devoted to remedy this deficiency, such as adding additional movable charge on the atom, allowing atomic charges to fluctuate, or including induced multipoles. Although various successes have been achieved and progress at various levels has been reported over the past decades, the issue of lacking polarization in force field based simulations is far from over. For example, some of these methods do not always give converged results, and other methods require huge computational cost. This Account reviews recent work on developing polarized and polarizable force fields based on fragment quantum mechanical calculations for proteins. The methods described here are based on quantum mechanical calculations of proteins in solution, but with a different level of rigor and different computational efficiency for the molecular dynamics applications. In the general approach, a fragment quantum mechanical calculation for protein with implicit solvation is carried out to derive a polarized protein-specific charge (PPC) for any given protein structure. The PPC correctly reflects the polarization state of the protein in a given conformation, and it can also be dynamically changed as the protein changes conformation in dynamics simulations. Another approach that is computationally more efficient is the effective polarizable bond method in which only polar bonds or groups can be polarized and their polarizabilities are predetermined from quantum mechanical calculations of these groups in external electric fields. Both methods can be employed for applications in various situations by taking advantage of their unique features.
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Affiliation(s)
- Changge Ji
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- Institute for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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