1
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Chen WK, Fang WH, Cui G. Extending multi-layer energy-based fragment method for excited-state calculations of large covalently bonded fragment systems. J Chem Phys 2023; 158:044110. [PMID: 36725521 DOI: 10.1063/5.0129458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recently, we developed a low-scaling Multi-Layer Energy-Based Fragment (MLEBF) method for accurate excited-state calculations and nonadiabatic dynamics simulations of nonbonded fragment systems. In this work, we extend the MLEBF method to treat covalently bonded fragment ones. The main idea is cutting a target system into many fragments according to chemical properties. Fragments with dangling bonds are first saturated by chemical groups; then, saturated fragments, together with the original fragments without dangling bonds, are grouped into different layers. The accurate total energy expression is formulated with the many-body energy expansion theory, in combination with the inclusion-exclusion principle that is used to delete the contribution of chemical groups introduced to saturate dangling bonds. Specifically, in a two-layer MLEBF model, the photochemically active and inert layers are calculated with high-level and efficient electronic structure methods, respectively. Intralayer and interlayer energies can be truncated at the two- or three-body interaction level. Subsequently, through several systems, including neutral and charged covalently bonded fragment systems, we demonstrate that MLEBF can provide accurate ground- and excited-state energies and gradients. Finally, we realize the structure, conical intersection, and path optimizations by combining our MLEBF program with commercial and free packages, e.g., ASE and SciPy. These developments make MLEBF a practical and reliable tool for studying complex photochemical and photophysical processes of large nonbonded and bonded fragment systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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2
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Du J, Liao K, Ma J, Li W, Li S. Generalized Energy-Based Fragmentation Approach for the Electronic Emission Spectra of Large Systems. J Chem Theory Comput 2022; 18:7630-7638. [PMID: 36399522 DOI: 10.1021/acs.jctc.2c00911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The excited-state (ES) geometry optimization and electronic emission (fluorescence and phosphorescence) spectra and the ES vibrational spectra of large systems are great challenges in quantum chemistry. In this work, we develop a generalized energy-based fragmentation (GEBF) approach to compute the localized ES structures and vibrational frequencies of large systems. In this approach, the ES energy derivatives (gradients or Hessians) for a localized ES of a large system can be obtained by combining the ES energy derivatives of the corresponding active subsystems (including local excitation center) and the ground-state energy derivatives of inactive subsystems. Two strategies are adopted to overcome two difficulties from state-classification and state-tracking for treating specific ESs. First, for state-classification, we develop an improved density-based spatial clustering applied with noise algorithm with a modified transition orbital projection (TOP) algorithm, which allow a certain ES energy and energy derivatives of the whole system to be calculated with different ES energies and energy derivatives of active subsystems. Furthermore, we also employ the TOP algorithm for tracking the ESs in their geometry optimizations at the time-dependent density functional theory (TDDFT) level. Then, the GEBF approach is applied to investigate the optimized ES geometries or ES vibrational frequencies for two typical systems. Our results show that the cost-effective GEBF approach can accurately reproduce the TDDFT fluorescence spectra of the cytosine derivative and the experimental phosphorescence spectra of the β-cyclodextrin derivative. The GEBF approach is expected to be routinely applied to investigate the electronic emission spectra of very large systems with local chromophores.
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Affiliation(s)
- Jiahui Du
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Kang Liao
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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3
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Liu J, He X. Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
- New York University‐East China Normal University Center for Computational Chemistry New York University Shanghai Shanghai China
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4
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Shen C, Wang X, He X. Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs. Front Chem 2022; 9:801062. [PMID: 35004616 PMCID: PMC8727457 DOI: 10.3389/fchem.2021.801062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Fluorescent RNA aptamers have been successfully applied to track and tag RNA in a biological system. However, it is still challenging to predict the excited-state properties of the RNA aptamer–fluorophore complex with the traditional electronic structure methods due to expensive computational costs. In this study, an accurate and efficient fragmentation quantum mechanical (QM) approach of the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) scheme was applied for calculations of excited-state properties of the RNA aptamer–fluorophore complex. In this method, the excited-state properties were first calculated with one-body fragment quantum mechanics/molecular mechanics (QM/MM) calculation (the excited-state properties of the fluorophore) and then corrected with a series of two-body fragment QM calculations for accounting for the QM effects from the RNA on the excited-state properties of the fluorophore. The performance of the EE-GMFCC on prediction of the absolute excitation energies, the corresponding transition electric dipole moment (TEDM), and atomic forces at both the TD-HF and TD-DFT levels was tested using the Mango-II RNA aptamer system as a model system. The results demonstrate that the calculated excited-state properties by EE-GMFCC are in excellent agreement with the traditional full-system time-dependent ab initio calculations. Moreover, the EE-GMFCC method is capable of providing an accurate prediction of the relative conformational excited-state energies for different configurations of the Mango-II RNA aptamer system extracted from the molecular dynamics (MD) simulations. The fragmentation method further provides a straightforward approach to decompose the excitation energy contribution per ribonucleotide around the fluorophore and then reveals the influence of the local chemical environment on the fluorophore. The applications of EE-GMFCC in calculations of excitation energies for other RNA aptamer–fluorophore complexes demonstrate that the EE-GMFCC method is a general approach for accurate and efficient calculations of excited-state properties of fluorescent RNAs.
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Affiliation(s)
- Chenfei Shen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Xianwei Wang
- College of Science, Zhejiang University of Technology, Hangzhou, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China
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5
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Wang Z, Liu W. iOI: An Iterative Orbital Interaction Approach for Solving the Self-Consistent Field Problem. J Chem Theory Comput 2021; 17:4831-4845. [PMID: 34240856 DOI: 10.1021/acs.jctc.1c00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An iterative orbital interaction (iOI) approach is proposed to solve, in a bottom-up fashion, the self-consistent field problem in quantum chemistry. While it belongs grossly to the family of fragment-based quantum chemical methods, iOI is distinctive in that (1) it divides and conquers not only the energy but also the wave function and that (2) the subsystem sizes are automatically determined by successively merging neighboring small subsystems until they are just enough for converging the wave function to a given accuracy. Orthonormal occupied and virtual localized molecular orbitals are obtained in a natural manner, which can be used for all post-SCF purposes.
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Affiliation(s)
- Zikuan Wang
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, P. R. China
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6
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Abraham V, Mayhall NJ. Cluster many-body expansion: A many-body expansion of the electron correlation energy about a cluster mean field reference. J Chem Phys 2021; 155:054101. [PMID: 34364343 DOI: 10.1063/5.0057752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The many-body expansion (MBE) is an efficient tool that has a long history of use for calculating interaction energies, binding energies, lattice energies, and so on. In the past, applications of MBE to correlation energy have been unfeasible for large systems, but recent improvements to computing resources have sparked renewed interest in capturing the correlation energy using the generalized nth order Bethe-Goldstone equation. In this work, we extend this approach, originally proposed for a Slater determinant, to a tensor product state (TPS) based wavefunction. By partitioning the active space into smaller orbital clusters, our approach starts from a cluster mean field reference TPS configuration and includes the correlation contribution of the excited TPSs using the MBE. This method, named cluster MBE (cMBE), improves the convergence of MBE at lower orders compared to directly doing a block-based MBE from a RHF reference. We present numerical results for strongly correlated systems, such as the one- and two-dimensional Hubbard models and the chromium dimer. The performance of the cMBE method is also tested by partitioning the extended π space of several large π-conjugated systems, including a graphene nano-sheet with a very large active space of 114 electrons in 114 orbitals, which would require 1066 determinants for the exact FCI solution.
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Affiliation(s)
- Vibin Abraham
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, USA
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7
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Shen C, Jin X, Glover WJ, He X. Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method. Molecules 2021; 26:4486. [PMID: 34361639 PMCID: PMC8347797 DOI: 10.3390/molecules26154486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method to the prediction of excitation energies of PRs. Excitation energies of 10 variants of Blue Proteorhodopsin (BPR-PR105Q) in residue 105GLN were calculated with the EE-GMFCC method at the TD-B3LYP/6-31G* level. The calculated results show good correlation with the experimental values of absorption wavelengths, although the experimental wavelength range among these systems is less than 50 nm. The ensemble-averaged electric fields along the polyene chain of retinal correlated well with EE-GMFCC calculated excitation energies for these 10 PRs, suggesting that electrostatic interactions from nearby residues are responsible for the color tuning. We also utilized the GMFCC method to decompose the excitation energy contribution per residue surrounding the chromophore. Our results show that residues ASP97 and ASP227 have the largest contribution to the absorption spectral shift of PR among the nearby residues of retinal. This work demonstrates that the EE-GMFCC method can be applied to accurately predict the absorption spectral shifts for biomacromolecules.
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Affiliation(s)
- Chenfei Shen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
| | - William J. Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China;
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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8
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Paz ASP, Glover WJ. Diabatic Many-Body Expansion: Development and Application to Charge-Transfer Reactions. J Chem Theory Comput 2021; 17:1497-1511. [DOI: 10.1021/acs.jctc.0c01231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amiel S. P. Paz
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshang Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - William J. Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshang Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
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9
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Servan SA, Ünal A, Hamarat B, Bozkaya U. Assessment of the Density-Fitted Second-Order Quasidegenerate Perturbation Theory for Transition Energies: Accurate Computations of Singlet-Triplet Gaps for Charge-Transfer Compounds. J Phys Chem A 2020; 124:6889-6898. [PMID: 32786988 DOI: 10.1021/acs.jpca.0c04555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Organic light-emitting diodes (OLEDs) have been of significant interest because of their superior performance and low cost of production. Thermally activated delayed fluorescence (TADF) has attracted significant interest in the OLED technology because it improves the efficiency of OLEDs by harvesting triplet excitons. Therefore, the accurate computation of singlet-triplet transition energies (ΔES1-T1) of charge-transfer molecules is very important. However, the accurate computation of the ΔES1-T1 values is a challenging problem for single-reference methods because of the multireference character of excited states. In this research, an assessment of density-fitted second-order quasidegenerate perturbation theory (DF-QDPT2) [Bozkaya, U.; J. Chem. Theory Comput. 2019, 15, 4415-4429] for singlet-triplet transition energies (ΔES1-T1) of charge-transfer compounds is presented. The performance of the DF-QDPT2 method has been compared with those of several density-functional theory functionals, such as B3LYP, PBE0, M06-2X, ωB97X-D, and MN15; density-fitted state-averaged CASSCF (DF-SA-CASSCF); and single-state single-reference second-order perturbation theory (SS-SR-CASPT2) methods. For the TADF molecules considered, the DF-QDPT2 method provides a mean absolute error (MAE) of 0.13 eV, while the MAE values of DF-SA-CASSCF and SS-SR-CASPT2 are 0.65 and 0.74 eV, respectively. The performances of B3LYP and PBE0 are slightly better than that of DF-QDPT2, while M06-2X and ωB97X-D provide noticeably higher errors compared with DF-QDPT2. Furthermore, the standard CASSCF without state-averaging yields dramatic errors with an MAE value of 3.0 eV. Our results demonstrate that eigenvalues of the DF-QDPT2-effective Hamiltonian can be reliably used for the prediction of singlet-triplet transition energies, while eigenvalues of DF-CASSCF/DF-SA-CASSCF fail to provide accurate predictions. Overall, we conclude that the DF-QDPT2 method emerges as a very useful tool for the computation of excited-state properties.
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Affiliation(s)
| | - Aslı Ünal
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Büşra Hamarat
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
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10
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Jin X, Glover WJ, He X. Fragment Quantum Mechanical Method for Excited States of Proteins: Development and Application to the Green Fluorescent Protein. J Chem Theory Comput 2020; 16:5174-5188. [PMID: 32551640 DOI: 10.1021/acs.jctc.9b00980] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Understanding the excited-state properties of luminescent biomolecules is of central importance to their biophysical applications. In this study, we develop the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method for quantitatively characterizing properties of covalently bonded systems with localized excitations (i.e., involving a single chromophore), such as fluorescent proteins. The excitation energy, transition dipole moment, and oscillator strength of wild-type Green Fluorescent Protein (wt-GFP) calculated by EE-GMFCC are found to be in excellent agreement with full system time-dependent density functional theory results. We also applied the Polarized Protein-Specific Charge model to wt-GFP, and found that electronic polarization of the protein is critical in stabilizing hydrogen bonding interactions in wt-GFP, which influences its absorption spectrum. The predicted absorption spectra of wt-GFP in the A and B states qualitatively agree with experiment. The fragmentation approach further allows a straightforward per residue decomposition of the excitation which reveals the influence of the protein environment on the absorption spectra of wt-GFP A and B states. Our results demonstrate that the EE-GMFCC method is both accurate and efficient for excited-state property calculations on proteins.
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Affiliation(s)
- Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - William J Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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11
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Ricard TC, Iyengar SS. Efficient and Accurate Approach To Estimate Hybrid Functional and Large Basis-Set Contributions to Condensed-Phase Systems and Molecule–Surface Interactions. J Chem Theory Comput 2020; 16:4790-4812. [DOI: 10.1021/acs.jctc.9b01089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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12
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Chen WK, Zhang Y, Jiang B, Fang WH, Cui G. Efficient Construction of Excited-State Hessian Matrices with Machine Learning Accelerated Multilayer Energy-Based Fragment Method. J Phys Chem A 2020; 124:5684-5695. [DOI: 10.1021/acs.jpca.0c04117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yaolong Zhang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Jiang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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13
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Liu J, He X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Phys Chem Chem Phys 2020; 22:12341-12367. [PMID: 32459230 DOI: 10.1039/d0cp01095b] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To study large molecular systems beyond the system size that the current state-of-the-art ab initio electronic structure methods could handle, fragment-based quantum mechanical (QM) approaches have been developed over the past years, and proved to be efficient in dealing with large molecular systems at various ab initio levels. According to the fragmentation approach, a large molecular system can be divided into subsystems (fragments), and subsequently the property of the whole system can be approximately obtained by taking a proper combination of the corresponding terms of individual fragments. Therefore, the standard QM calculation of a large system could be circumvented by carrying out a series of calculations on small fragments, which significantly promotes computational efficiency. The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is one of the fragment-based QM approaches which has been developed by our research group in recent years. This Perspective presents the theoretical framework of this fragmentation method and its applications in biomolecules, molecular clusters, molecular crystals and liquids, including total energy calculation, protein-ligand/protein binding affinity prediction, geometry optimization, vibrational spectrum simulation, ab initio molecular dynamics simulation, and prediction of excited-state properties.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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14
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Zhang W, Liu J, Jin X, Gu X, Zeng XC, He X, Li H. Quantitative Prediction of Aggregation‐Induced Emission: A Full Quantum Mechanical Approach to the Optical Spectra. Angew Chem Int Ed Engl 2020; 59:11550-11555. [DOI: 10.1002/anie.202003326] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Wei Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
- Department of Chemistry University of Nebraska Lincoln NE 68588 USA
| | - Jinfeng Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing 210009 China
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
| | - Xinggui Gu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
| | - Xiao Cheng Zeng
- Department of Chemistry University of Nebraska Lincoln NE 68588 USA
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
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15
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Zhang W, Liu J, Jin X, Gu X, Zeng XC, He X, Li H. Quantitative Prediction of Aggregation‐Induced Emission: A Full Quantum Mechanical Approach to the Optical Spectra. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Wei Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
- Department of Chemistry University of Nebraska Lincoln NE 68588 USA
| | - Jinfeng Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing 210009 China
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
| | - Xinggui Gu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
| | - Xiao Cheng Zeng
- Department of Chemistry University of Nebraska Lincoln NE 68588 USA
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
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16
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Chen WK, Fang WH, Cui G. Integrating Machine Learning with the Multilayer Energy-Based Fragment Method for Excited States of Large Systems. J Phys Chem Lett 2019; 10:7836-7841. [PMID: 31786927 DOI: 10.1021/acs.jpclett.9b03113] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this work we have combined machine learning techniques with our recently developed multilayer energy-based fragment method for studying excited states of large systems. The photochemically active and inert regions are separately treated with the complete active space self-consistent field method and the trained models. This method is demonstrated to provide accurate energies and gradients leading to essentially the same excited-state potential energy surfaces and nonadiabatic dynamics compared with full ab initio results. Furthermore, in conjunction with the use of machine learning models, this method is highly parallel and exhibits low-scaling computational cost. Finally, the present work could encourage the marriage of machine learning with fragment-based electronic structure methods to explore photochemistry of large systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Chen WK, Fang WH, Cui G. A multi-layer energy-based fragment method for excited states and nonadiabatic dynamics. Phys Chem Chem Phys 2019; 21:22695-22699. [PMID: 31595910 DOI: 10.1039/c9cp04842a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a multi-layer energy-based fragment (MLEBF) method within the many-body energy expansion framework. It supplies accurate energies and gradients, and accurately reproduces excited-state topological structures. Moreover, MLEBF-based nonadiabatic dynamics simulations give nearly the same results compared with full ab initio ones. The present work could stimulate developing energy-based fragment methods for photochemistry of large systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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