51
|
Orimoto Y, Aoki Y. Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA. J Chem Phys 2016; 145:024107. [PMID: 27421397 DOI: 10.1063/1.4956456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between "choose-maximum" (choose a base pair giving the maximum β for each step) and "choose-minimum" (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.
Collapse
Affiliation(s)
- Yuuichi Orimoto
- 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
| |
Collapse
|
52
|
Fang T, Jia J, Li S. Vibrational Spectra of Molecular Crystals with the Generalized Energy-Based Fragmentation Approach. J Phys Chem A 2016; 120:2700-11. [DOI: 10.1021/acs.jpca.5b10927] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Fang
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of
Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Junteng Jia
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of
Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of 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 210093, People’s Republic of China
| |
Collapse
|
53
|
Liu P, Li W, Kan Z, Sun H, Ma J. Factor Analysis of Conformations and NMR Signals of Rotaxanes: AIMD and Polarizable MD Simulations. J Phys Chem A 2016; 120:490-502. [PMID: 26756354 DOI: 10.1021/acs.jpca.5b10085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interlocked ⟨rod | ring⟩ structures of pseudorotaxanes and [2]rotaxanes are usually maintained by the complex hydrogen-bonding (H-bonding) network between the rod and ring. Ab initio molecular dynamics (AIMD) using generalized energy-based fragmentation approach and polarizable force field (polar FF)-based molecular dynamics (MD) simulations were performed to investigate the conformational changes of mechanically interlocked systems and to obtain the ensemble-averaged NMR chemical shifts. Factor analysis (FA) demonstrates that the ring H-donor (2,6 pyridinedicarboxamide group) plays an important role in the ring-rod recognition. In comparison to the conventional fixed-charge force field, the polarization effect is crucial to account for the H-bonding interactions in supramolecular systems. In the hybrid scheme, the polar FF-based MD simulations are used to generate different initial states for the AIMD simulations, which are able to give better prediction of ensemble-averaged NMR signals for chemically equivalent amide protons. The magnitude of the deshielding shift of NMR signal is correlated with the length of hydrogen bond. The polar FF model with variable charges shows that the dipole-dipole interactions between the flexible diethylene glycol chain of ring and polar solvents induce the upfield shifts of NMR signals of rod H-donors and the directional distribution of the neighboring CH3CN solvents.
Collapse
Affiliation(s)
- Pingying Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University , Nanjing 210093, People's Republic of China.,School of Materials Science and Engineering, Jingdezhen Ceramic Institute , Jingdezhen 333403, People's Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University , Nanjing 210093, People's Republic of China
| | - Zigui Kan
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University , Nanjing 210093, People's Republic of China
| | - Hui Sun
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University , Nanjing 210093, People's Republic of China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University , Nanjing 210093, People's Republic of China
| |
Collapse
|
54
|
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.
Collapse
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
| |
Collapse
|
55
|
Li W, Ni Z, Li S. Cluster-in-molecule local correlation method for post-Hartree–Fock calculations of large systems. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1139755] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
56
|
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]
|
57
|
Liu J, Herbert JM. Pair-Pair Approximation to the Generalized Many-Body Expansion: An Alternative to the Four-Body Expansion for ab Initio Prediction of Protein Energetics via Molecular Fragmentation. J Chem Theory Comput 2016; 12:572-84. [PMID: 26730608 DOI: 10.1021/acs.jctc.5b00955] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce a "pair-pair" approximation to the generalized many-body expansion (pp-GMBE) as an approximation to a traditional four-body expansion, the latter of which is accurate but quickly becomes numerically unstable and ultimately intractable as the number of "bodies" (fragments) increases. The pp-GMBE method achieves a good balance between accuracy and efficiency by defining significant fragment pairs and then fragment quartets. An efficient fragmentation scheme is introduced for proteins such that the largest subsystems contain about 60 atoms. Application of the pp-GMBE method to proteins with as many as 70 amino acids (1142 atoms) reveals that pp-GMBE energies are quite faithful to those obtained when the same level of density functional theory is applied to the entire macromolecule. When combined with embedding charges obtained from natural population analysis, the pp-GMBE approach affords absolute energies that differ by 1-3 kcal/mol from full supersystem results, but it yields conformational energy profiles that are practically indistinguishable from the supersystem calculation at the same level of theory.
Collapse
Affiliation(s)
- Jie Liu
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| |
Collapse
|
58
|
Liu J, Zhang JZH, He X. Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins. Phys Chem Chem Phys 2016; 18:1864-75. [DOI: 10.1039/c5cp05693d] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Geometry optimization and vibrational spectra (infrared and Raman spectra) calculations of proteins are carried out by a quantum chemical approach using the EE-GMFCC (electrostatically embedded generalized molecular fractionation with conjugate caps) method (J. Phys. Chem. A, 2013, 117, 7149).
Collapse
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
| | - 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
| |
Collapse
|
59
|
Wen J, Li W, Chen S, Ma J. Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions. Phys Chem Chem Phys 2016; 18:22757-71. [DOI: 10.1039/c6cp01049k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Simulations using QM and MM methods guide the rational design of functionalized SAMs on surfaces.
Collapse
Affiliation(s)
- Jin Wen
- Institute of Theoretical and Computational Chemistry
- Key Laboratory of Mesoscopic Chemistry of MOE
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
| | - Wei Li
- Institute of Theoretical and Computational Chemistry
- Key Laboratory of Mesoscopic Chemistry of MOE
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
| | - Shuang Chen
- Kuang Yaming Honors School
- Nanjing University
- Nanjing
- P. R. China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry
- Key Laboratory of Mesoscopic Chemistry of MOE
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
| |
Collapse
|
60
|
Dahlke EE, Truhlar DG. Electrostatically Embedded Many-Body Correlation Energy, with Applications to the Calculation of Accurate Second-Order Møller-Plesset Perturbation Theory Energies for Large Water Clusters. J Chem Theory Comput 2015; 3:1342-8. [PMID: 26633207 DOI: 10.1021/ct700057x] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electrostatically embedded many-body expansion (EE-MB), previously applied to the total electronic energy, is here applied only to the electronic correlation energy (CE), combined with a Hartree-Fock calculation on the entire system. The separate treatment of the Hartree-Fock and correlation energies provides an efficient way to approximate correlation energy for extended systems. We illustrate this here by calculating accurate Møller-Plesset second-order perturbation theory (MP2) energies for a series of clusters ranging in size from 5 to 20 water molecules. In this new method, called EE-MB-CE, where MB is pairwise additive (PA) or three-body (3B), the full Hartree-Fock energy of a system of N monomers is calculated (i.e., the many-body expansion is carried out to the Nth order), while the EE-MB method is used to calculate the correlation energy of the system. We find that not only does this new method lead to better energetics than the original EE-MB method but also that one is able to obtain excellent agreement with full MP2 calculations by considering only a two-body expansion of the correlation energy, leading to a considerable savings in computational time as compared to the three-body expansion. Additionally, we propose the use of a cutoff to further reduce the number of two-body terms that must be calculated, and we show that if a cutoff of 6 Å is used, then one can eliminate up to 44% of the pairs and still calculate energies to within 0.1% of the net interaction energy of the full cluster.
Collapse
Affiliation(s)
- Erin E Dahlke
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| |
Collapse
|
61
|
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
| |
Collapse
|
62
|
Shrestha K, Jakubikova E. Ground-State Electronic Structure of RC-LH1 and LH2 Pigment Assemblies of Purple Bacteria via the EBF-MO Method. J Phys Chem A 2015. [DOI: 10.1021/acs.jpca.5b05644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kushal Shrestha
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Elena Jakubikova
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
63
|
Yuan X, Zhang W, Xie LH, Ma J, Huang W, Liu W. Role of Planar Conformations in Aggregation Induced Spectral Shifts of Supermolecular Oligofluorenols in Solutions and Films: A Combined Experimental and MD/TD-DFT Study. J Phys Chem B 2015; 119:10316-33. [DOI: 10.1021/acs.jpcb.5b04558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiangai Yuan
- Key Laboratory of Mesoscopic Chemistry of MOE School of Chemistry & Chemical Engineering, Nanjing University, 22 Hankou Road, Nanjing 210093, People’s Republic of China
| | - Wanwan Zhang
- Center for Molecular Systems & Organic Devices (CMSOD), Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Ling-Hai Xie
- Center for Molecular Systems & Organic Devices (CMSOD), Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of MOE School of Chemistry & Chemical Engineering, Nanjing University, 22 Hankou Road, Nanjing 210093, People’s Republic of China
| | - Wei Huang
- Center for Molecular Systems & Organic Devices (CMSOD), Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Wenjian Liu
- Beijing
National Laboratory for Molecular Sciences, Institute of Theoretical
and Computational Chemistry, State Key Laboratory of Rare Earth Materials
Chemistry and Applications, College of Chemistry and Molecular Engineering,
and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| |
Collapse
|
64
|
Collins MA. Molecular forces, geometries, and frequencies by systematic molecular fragmentation including embedded charges. J Chem Phys 2015; 141:094108. [PMID: 25194365 DOI: 10.1063/1.4894185] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The accuracy of energies, energy gradients, and hessians evaluated by systematic molecular fragmentation is examined for a wide range of neutral molecules, zwitterions, and ions. A protocol is established that may employ embedded charges in conjunction with fragmentation to provide accurate evaluation of minimum energy geometries and vibrational frequencies in an automated procedure.
Collapse
Affiliation(s)
- Michael A Collins
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| |
Collapse
|
65
|
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
| |
Collapse
|
66
|
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
| |
Collapse
|
67
|
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
| |
Collapse
|
68
|
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
| |
Collapse
|
69
|
Fang T, Li W, Gu F, Li S. Accurate Prediction of Lattice Energies and Structures of Molecular Crystals with Molecular Quantum Chemistry Methods. J Chem Theory Comput 2014; 11:91-8. [DOI: 10.1021/ct500833k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Tao Fang
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of
Education, 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 Ministry of
Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, 210093, People’s Republic of China
| | - Fangwei Gu
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of
Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, 210093, People’s Republic of 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, 210093, People’s Republic of China
| |
Collapse
|
70
|
Timm MJ, Matta CF, Massa L, Huang L. The Localization–Delocalization Matrix and the Electron-Density-Weighted Connectivity Matrix of a Finite Graphene Nanoribbon Reconstructed from Kernel Fragments. J Phys Chem A 2014; 118:11304-16. [DOI: 10.1021/jp508490p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew J. Timm
- Department
of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M2J6, Canada
| | - Chérif F. Matta
- Department
of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M2J6, Canada
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H4J3, Canada
- Department
of Chemistry, Saint Mary’s University, Halifax, Nova Scotia B3H3C3, Canada
| | - Lou Massa
- Hunter
College and the Graduate School, City University of New York, New York, New York 10065, United States
| | - Lulu Huang
- Center
for Computational Materials Science, Naval Research Laboratory, Washington, D.C. 20375-5341, United States
| |
Collapse
|
71
|
Collins MA, Cvitkovic MW, Bettens RPA. The combined fragmentation and systematic molecular fragmentation methods. Acc Chem Res 2014; 47:2776-85. [PMID: 24972052 DOI: 10.1021/ar500088d] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Conspectus Chemistry, particularly organic chemistry, is mostly concerned with functional groups: amines, amides, alcohols, ketones, and so forth. This is because the reactivity of molecules can be categorized in terms of the reactions of these functional groups, and by the influence of other adjacent groups in the molecule. These simple truths ought to be reflected in the electronic structure and electronic energy of molecules, as reactivity is determined by electronic structure. However, sophisticated ab initio quantum calculations of the molecular electronic energy usually do not make these truths apparent. In recent years, several computational chemistry groups have discovered methods for estimating the electronic energy as a sum of the energies of small molecular fragments, or small sets of groups. By decomposing molecules into such fragments of adjacent functional groups, researchers can estimate the electronic energy to chemical accuracy; not just qualitative trends, but accurate enough to understand reactivity. In addition, this has the benefit of cutting down on both computational time and cost, as the necessary calculation time increases rapidly with an increasing number of electrons. Even with steady advances in computer technology, progress in the study of large molecules is slow. In this Account, we describe two related "fragmentation" methods for treating molecules, the combined fragmentation method (CFM) and systematic molecular fragmentation (SMF). In addition, we show how we can use the SMF approach to estimate the energy and properties of nonconducting crystals, by fragmenting the periodic crystal structure into relatively small pieces. A large part of this Account is devoted to simple overviews of how the methods work. We also discuss the application of these approaches to calculating reactivity and other useful properties, such as the NMR and vibrational spectra of molecules and crystals. These applications rely on the ability of these fragmentation methods to accurately estimate derivatives of the molecular and crystal energies. Finally, to provide some common applications of CFM and SMF, we present some specific examples of energy calculations for moderately large molecules. For computational chemists, this fragmentation approach represents an important practical advance. It reduces the computer time required to estimate the energies of molecules so dramatically, that accurate calculations of the energies and reactivity of very large organic and biological molecules become feasible.
Collapse
Affiliation(s)
- Michael A. Collins
- Research
School of Chemistry, Australian National University, Canberra ACT 0200, Australia
| | - Milan W. Cvitkovic
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| |
Collapse
|
72
|
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.
Collapse
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
| |
Collapse
|
73
|
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.
Collapse
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
| |
Collapse
|
74
|
Guo Y, Li W, Yuan D, Li S. The relative energies of polypeptide conformers predicted by linear scaling second-order Møller-Plesset perturbation theory. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5181-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
75
|
Liu P, Li W, Liu L, Wang L, Ma J. Theoretical Study on Conformation Dynamics of Three-Station Molecular Shuttle in Different Environments and its Influence on NMR Chemical Shifts and Binding Interactions. J Phys Chem A 2014; 118:9032-44. [DOI: 10.1021/jp5020516] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pingying Liu
- School of Chemistry
and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of
MOE, Nanjing University, Nanjing 210093, People’s Republic of China
- School of Materials
Science and Engineering, Jingdezhen Ceramic Institute, Jingdezhen 333403, China
| | - Wei Li
- School of Chemistry
and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of
MOE, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Li Liu
- School of Chemistry
and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of
MOE, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Leyong Wang
- School of Chemistry
and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of
MOE, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry
and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of
MOE, Nanjing University, Nanjing 210093, People’s Republic of China
| |
Collapse
|
76
|
Wang K, Li W, Li S. Generalized Energy-Based Fragmentation CCSD(T)-F12a Method and Application to the Relative Energies of Water Clusters (H2O)20. J Chem Theory Comput 2014; 10:1546-53. [DOI: 10.1021/ct401060m] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kedong Wang
- School
of Physics and Electronical Engineering, Henan Normal University, Xinxiang, 453007, People’s Repubic of China
| | | | | |
Collapse
|
77
|
Brinkmann L, Heifets E, Kantorovich L. Density functional calculations of extended, periodic systems using Coulomb corrected molecular fractionation with conjugated caps method (CC-MFCC). Phys Chem Chem Phys 2014; 16:21252-70. [DOI: 10.1039/c3cp55119a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A consistent DFT based formulation of the order-N molecular fractionation with conjugated caps method in which a molecular system is calculated considering a set of finite fragments, is proposed. Here we apply the method and test its performance on a periodic metal–organic framework system.
Collapse
Affiliation(s)
| | - Eugene Heifets
- Max Planck Institute for Solid State Research
- D-70569 Stuttgart, Germany
| | | |
Collapse
|
78
|
Jia X, Wang X, Liu J, Zhang JZH, Mei Y, He X. An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins. J Chem Phys 2013; 139:214104. [DOI: 10.1063/1.4833678] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
79
|
Reid DM, Collins MA. Molecular electrostatic potentials by systematic molecular fragmentation. J Chem Phys 2013; 139:184117. [DOI: 10.1063/1.4827020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
80
|
|
81
|
Liu W, Ma J. Theoretical study of low-lying excited states of molecular aggregates. I. Development of linear-scaling TD-DFT. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4908-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
82
|
Kurbanov EK, Leverentz HR, Truhlar DG, Amin EA. Analysis of the Errors in the Electrostatically Embedded Many-Body Expansion of the Energy and the Correlation Energy for Zn and Cd Coordination Complexes with Five and Six Ligands and Use of the Analysis to Develop a Generally Successful Fragmentation Strategy. J Chem Theory Comput 2013; 9:2617-2628. [PMID: 23814509 DOI: 10.1021/ct4001872] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present paper, we apply the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE) to the calculation of zinc-ligand and cadmium-ligand bond dissociation energies, and we analyze the errors due to various fragmentation schemes in a variety of neutral, positively charged, and negatively charged Zn2+ and Cd2+ coordination complexes. As a result of the analysis, we are able to present a new, simple, and unambiguous fragmentation strategy. Following this strategy, we show that both methods perform well for zinc-ligand and cadmium-ligand bond dissociation energies for all systems studied in the paper, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor (LF), which has garnered substantial attention as a target for drug development. To draw general conclusions we consider ten pentacoordinate and hexacoordinate zinc and cadmium containing coordination complexes, each with 10 or 15 different fragmentation schemes. By analyzing errors, we developed a prescription for the optimal fragmentation strategy. With this scheme, and using MP2 correlation energies as a test, we find that the electrostatically embedded three-body expansion of the correlation energy (EE-3B-CE) method is able to reproduce all 53 conventionally calculated bond energies with an average absolute error of only 0.59 kcal/mol. The paper also presents EE-MB-CE calculations using the CCSD(T) level of theory on an LF model system. With CCSD(T), EE-3B-CE has an average error of 0.30 kcal/mol.
Collapse
Affiliation(s)
- Elbek K Kurbanov
- Department of Medicinal Chemistry, Department of Chemistry, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55414
| | | | | | | |
Collapse
|
83
|
Kiewisch K, Jacob CR, Visscher L. Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory. J Chem Theory Comput 2013; 9:2425-40. [DOI: 10.1021/ct3008759] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karin Kiewisch
- Amsterdam Center for Multiscale
Modeling, VU University Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - Christoph R. Jacob
- Center for Functional Nanostructures
and Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe,
Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale
Modeling, VU University Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
84
|
Song GL, Li ZH, Fan KN. Extended Energy Divide-and-Conquer Method Based on Charge Conservation. J Chem Theory Comput 2013; 9:1992-9. [DOI: 10.1021/ct300850q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guo-Liang Song
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Zhen Hua Li
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Kang-Nian Fan
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| |
Collapse
|
85
|
Wang X, Liu J, Zhang JZH, He X. Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy. J Phys Chem A 2013; 117:7149-61. [PMID: 23452268 DOI: 10.1021/jp400779t] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is developed for efficient linear-scaling quantum mechanical (QM) calculation of protein energy. This approach is based on our previously proposed GMFCC/MM method (He; et al. J. Chem. Phys. 2006, 124, 184703), In this EE-GMFCC scheme, the total energy of protein is calculated by taking a linear combination of the QM energy of the neighboring residues and the two-body QM interaction energy between non-neighboring residues that are spatially in close contact. All the fragment calculations are embedded in a field of point charges representing the remaining protein environment, which is the major improvement over our previous GMFCC/MM approach. Numerical studies are carried out to calculate the total energies of 18 real three-dimensional proteins of up to 1142 atoms using the EE-GMFCC approach at the HF/6-31G* level. The overall mean unsigned error of EE-GMFCC for the 18 proteins is 2.39 kcal/mol with reference to the full system HF/6-31G* energies. The EE-GMFCC approach is also applied for proteins at the levels of the density functional theory (DFT) and second-order many-body perturbation theory (MP2), also showing only a few kcal/mol deviation from the corresponding full system result. The EE-GMFCC method is linear-scaling with a low prefactor, trivially parallel, and can be readily applied to routinely perform structural optimization of proteins and molecular dynamics simulation with high level ab initio electronic structure theories.
Collapse
Affiliation(s)
- Xianwei Wang
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | | | | | | |
Collapse
|
86
|
Kobayashi M, Nakai H. An effective energy gradient expression for divide-and-conquer second-order Møller–Plesset perturbation theory. J Chem Phys 2013; 138:044102. [DOI: 10.1063/1.4776228] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
87
|
Li W. Linear scaling explicitly correlated MP2-F12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions. J Chem Phys 2013; 138:014106. [DOI: 10.1063/1.4773011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
88
|
Martins ACV, de Lima-Neto P, Barroso-Neto IL, Cavada BS, Freire VN, Caetano EWS. An ab initio explanation of the activation and antagonism strength of an AMPA-sensitive glutamate receptor. RSC Adv 2013. [DOI: 10.1039/c3ra42149j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
89
|
Tan HJ, Bettens RPA. Ab initio NMR chemical-shift calculations based on the combined fragmentation method. Phys Chem Chem Phys 2013; 15:7541-7. [DOI: 10.1039/c3cp50406a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
90
|
Hua S, Li W, Li S. The Generalized Energy-Based Fragmentation Approach with an Improved Fragmentation Scheme: Benchmark Results and Illustrative Applications. Chemphyschem 2012; 14:108-15. [DOI: 10.1002/cphc.201200867] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 11/09/2022]
|
91
|
Habgood M. Intermolecular electrostatics via molecular fragmentation: an application to crystal structure prediction. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.696110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
92
|
Chen S, Ma J. Substituent effects on packing entropy and film morphologies in the nucleation of functionalized pentacenes on SiO2 substrate: Molecular dynamics simulations. J Chem Phys 2012; 137:074708. [DOI: 10.1063/1.4745899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
93
|
Richard RM, Herbert JM. A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory. J Chem Phys 2012; 137:064113. [DOI: 10.1063/1.4742816] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
94
|
Kang R, Lai W, Yao J, Shaik S, Chen H. How Accurate Can a Local Coupled Cluster Approach Be in Computing the Activation Energies of Late-Transition-Metal-Catalyzed Reactions with Au, Pt, and Ir? J Chem Theory Comput 2012; 8:3119-27. [PMID: 26605723 DOI: 10.1021/ct3003942] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To improve the accuracy of local coupled cluster (LCC) methods in computing activation energies, we propose herein a new computational scheme. Its applications to various types of late-transition-metal-catalyzed reactions involving Au, Pt, and Ir indicate that the new corrective approach for LCC methods can downsize the mean unsigned deviation and maximum deviation, from the CCSD(T)/CBS reference, to about 0.3 and 0.9 kcal/mol. Using this method, we also calibrated the performance of popular density functionals, with respect to the same test set of reactions. It is concluded that the best functional is the general-purpose double hybrid functional B2GP-PLYP. Other well-performing functionals include the "kinetic" functionals M06-2X and BMK, which have a large percentage of HF exchange, and general-purpose functionals like PBE0 and wB97X. Comparatively, general-purpose functionals like PBE0 and TPSSh perform much better than the tested "kinetic" functionals for Pt-/Ir-catalyzed reactions, while the opposite is true for Au-catalyzed reactions. In contrast, wB97X performs more uniformly in these two classes of reactions. These findings hint that even within the scope of late transition metals, different types of reactions may require different types of optimal DFT methods. Empirical dispersion correction of DFT was found to have a small or no effect on the studied reactions barriers.
Collapse
Affiliation(s)
- Runhua Kang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Jiannian Yao
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| |
Collapse
|
95
|
Mayhall NJ, Raghavachari K. Many-Overlapping-Body (MOB) Expansion: A Generalized Many Body Expansion for Nondisjoint Monomers in Molecular Fragmentation Calculations of Covalent Molecules. J Chem Theory Comput 2012; 8:2669-75. [DOI: 10.1021/ct300366e] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas J. Mayhall
- Department of Chemistry,
Indiana University, Bloomington,
Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry,
Indiana University, Bloomington,
Indiana 47405, United States
| |
Collapse
|
96
|
Assessment of density functionals on intramolecular dispersion interaction in large normal alkanes. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.05.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
97
|
Sandberg DJ, Rudnitskaya AN, Gascón JA. QM/MM Prediction of the Stark Shift in the Active Site of a Protein. J Chem Theory Comput 2012; 8:2817-23. [PMID: 26592122 DOI: 10.1021/ct300409t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent developments in the biophysical characterization of proteins have provided a means of directly measuring electrostatic fields by introducing a probe molecule to the system of interest and interpreting photon absorption in the context of the Stark effect. To fully account for this effect, the development of accurate atomistic models is of paramount importance. However, suitable computational protocols for evaluating Stark shifts in proteins are yet to be established. In this work, we present a comprehensive computational method to predict the change in absorption frequency of a probe functional group as a direct result of a perturbation in its surrounding electrostatic field created by a protein environment, i.e., the Stark shift. We apply the method to human aldose reductase, a key protein enzyme that catalyzes the reduction of monosaccharides. We develop a protocol based on a combination of molecular dynamics and moving-domain QM/MM methods, which achieves quantitative agreement with experiment. We outline the difficulties in predicting localized electrostatic field changes within a protein environment, and by extension the Stark shift, due to a protein site mutation. Furthermore, the combined use of Stark effect spectroscopy and computational modeling is used to predict the protonation state of ionizable residues in the vicinity of the electrostatic probe.
Collapse
Affiliation(s)
- Daniel J Sandberg
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | | | - José A Gascón
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| |
Collapse
|
98
|
Guo Y, Li W, Li S. An improved localized molecular-orbital assembler approach for Hartree–Fock calculations of general large molecules. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
99
|
Tsukamoto T, Mochizuki Y, Watanabe N, Fukuzawa K, Nakano T. Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.03.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
100
|
Wu A, Xu X. DCMB that combines divide-and-conquer and mixed-basis set methods for accurate geometry optimizations, total energies, and vibrational frequencies of large molecules. J Comput Chem 2012; 33:1421-32. [DOI: 10.1002/jcc.22973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 03/02/2012] [Indexed: 11/06/2022]
|