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Yuan K, Zhou S, Li N, Li T, Ding B, Guo D, Ma Y. Fault-tolerant quantum chemical calculations with improved machine-learning models. J Comput Chem 2024. [PMID: 39072777 DOI: 10.1002/jcc.27459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/30/2024] [Accepted: 06/18/2024] [Indexed: 07/30/2024]
Abstract
Easy and effective usage of computational resources is crucial for scientific calculations. Following our recent work of machine-learning (ML) assisted scheduling optimization [J. Comput. Chem. 2023, 44, 1174], we further propose (1) the improved ML models for the better predictions of computational loads, and as such, more elaborate load-balancing calculations can be expected; (2) the idea of coded computation, that is, the integration of gradient coding, in order to introduce fault tolerance during the distributed calculations; and (3) their applications together with re-normalized exciton model with time-dependent density functional theory (REM-TDDFT) for calculating the excited states. Illustrated benchmark calculations include P38 protein, and solvent model with one or several excitable centers. The results show that the improved ML-assisted coded calculations can further improve the load-balancing and cluster utilization, owing primarily profit in fault tolerance that aims at the automated quantum chemical calculations for both ground and excited states.
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Affiliation(s)
- Kai Yuan
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhou
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Ning Li
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, China
| | - Tianyan Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Bowen Ding
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Danhuai Guo
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yingjin Ma
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
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2
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Wang Z, Wu C, Liu W. Toward the Rational Design of Organic Catalysts for Organocatalysed Atom Transfer Radical Polymerisation. Polymers (Basel) 2024; 16:323. [PMID: 38337212 DOI: 10.3390/polym16030323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Thanks to their diversity, organic photocatalysts (PCs) have been widely used in manufacturing polymeric products with well-defined molecular weights, block sequences, and architectures. Still, however, more universal property-performance relationships are needed to enable the rational design of such PCs. That is, a set of unique descriptors ought to be identified to represent key properties of the PCs relevant for polymerisation. Previously, the redox potentials of excited PCs (PC*) were used as a good descriptor for characterising very structurally similar PCs. However, it fails to elucidate PCs with diverse chromophore cores and ligands, among which those used for polymerisation are a good representative. As showcased by model systems of organocatalysed atom transfer radical polymerisation (O-ATRP), new universal descriptors accounting for additional factors, such as the binding and density overlap between the PC* and initiator, are proposed and proved to be successful in elucidating the experimental performances of PCs in polymerisation. While O-ATRP is exemplified here, the approach adopted is general for studying other photocatalytic systems.
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Affiliation(s)
- Zhilei Wang
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, China
| | - Chenyu Wu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, China
| | - Wenjian Liu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, China
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3
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Ma Y, Li Z, Chen X, Ding B, Li N, Lu T, Zhang B, Suo B, Jin Z. Machine-learning assisted scheduling optimization and its application in quantum chemical calculations. J Comput Chem 2023; 44:1174-1188. [PMID: 36648254 DOI: 10.1002/jcc.27075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023]
Abstract
Easy and effective usage of computational resources is crucial for scientific calculations, both from the perspectives of timeliness and economic efficiency. This work proposes a bi-level optimization framework to optimize the computational sequences. Machine-learning (ML) assisted static load-balancing, and different dynamic load-balancing algorithms can be integrated. Consequently, the computational and scheduling engine of the ParaEngine is developed to invoke optimized quantum chemical (QC) calculations. Illustrated benchmark calculations include high-throughput drug suit, solvent model, P38 protein, and SARS-CoV-2 systems. The results show that the usage rate of given computational resources for high throughput and large-scale fragmentation QC calculations can primarily profit, and faster accomplishing computational tasks can be expected when employing high-performance computing (HPC) clusters.
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Affiliation(s)
- Yingjin Ma
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - ZhiYing Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Xin Chen
- ShenZhen Bay Laboratory, Shenzhen, China
| | - Bowen Ding
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Ning Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- College of Chemistry and Materials Engineering, Wenzhou University, Wen Zhou, China
| | - Teng Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Baohua Zhang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - BingBing Suo
- Department of Physics, Northwest University, Xi'an, China
| | - Zhong Jin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
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4
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Zhou Z, Della Sala F, Parker SM. Minimal Auxiliary Basis Set Approach for the Electronic Excitation Spectra of Organic Molecules. J Phys Chem Lett 2023; 14:1968-1976. [PMID: 36787711 DOI: 10.1021/acs.jpclett.2c03698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report a minimal auxiliary basis model for time-dependent density functional theory (TDDFT) with hybrid density functionals that can accurately reproduce excitation energies and absorption spectra from TDDFT while reducing cost by about 2 orders of magnitude. Our method, dubbed TDDFT-ris, employs the resolution-of-the-identity technique with just one s-type auxiliary basis function per atom for the linear response operator, where the Gaussian exponents are parametrized across the periodic table using tabulated atomic radii with a single global scaling factor. By tuning on a small test set, we determine a single functional-independent scale factor that balances errors in excitation energies and absorption spectra. Benchmarked on organic molecules and compared to standard TDDFT, TDDFT-ris has an average energy error of only 0.06 eV and yields absorption spectra in close agreement with TDDFT. Thus, TDDFT-ris enables simulation of realistic absorption spectra in large molecules that would be inaccessible from standard TDDFT.
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Affiliation(s)
- Zehao Zhou
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Fabio Della Sala
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, 73010 Arnesano (LE), Italy
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
| | - Shane M Parker
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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5
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Sen S, Senjean B, Visscher L. Characterization of excited states in time-dependent density functional theory using localized molecular orbitals. J Chem Phys 2023; 158:054115. [PMID: 36754801 DOI: 10.1063/5.0137729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Localized molecular orbitals are often used for the analysis of chemical bonds, but they can also serve to efficiently and comprehensibly compute linear response properties. While conventional canonical molecular orbitals provide an adequate basis for the treatment of excited states, a chemically meaningful identification of the different excited-state processes is difficult within such a delocalized orbital basis. In this work, starting from an initial set of supermolecular canonical molecular orbitals, we provide a simple one-step top-down embedding procedure for generating a set of orbitals, which are localized in terms of the supermolecule but delocalized over each subsystem composing the supermolecule. Using an orbital partitioning scheme based on such sets of localized orbitals, we further present a procedure for the construction of local excitations and charge-transfer states within the linear response framework of time-dependent density functional theory (TDDFT). This procedure provides direct access to approximate diabatic excitation energies and, under the Tamm-Dancoff approximation, also their corresponding electronic couplings-quantities that are of primary importance in modeling energy transfer processes in complex biological systems. Our approach is compared with a recently developed diabatization procedure based on subsystem TDDFT using projection operators, which leads to a similar set of working equations. Although both of these methods differ in the general localization strategies adopted and the type of basis functions (Slaters vs Gaussians) employed, an overall decent agreement is obtained.
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Affiliation(s)
- Souloke Sen
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Bruno Senjean
- ICGM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Lucas Visscher
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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6
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Einsele R, Hoche J, Mitrić R. Long-range corrected fragment molecular orbital density functional tight-binding method for excited states in large molecular systems. J Chem Phys 2023; 158:044121. [PMID: 36725509 DOI: 10.1063/5.0136844] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Herein, we present a new method to efficiently calculate electronically excited states in large molecular assemblies, consisting of hundreds of molecules. For this purpose, we combine the long-range corrected tight-binding density functional fragment molecular orbital method (FMO-LC-DFTB) with an excitonic Hamiltonian, which is constructed in the basis of locally excited and charge-transfer configuration state functions calculated for embedded monomers and dimers and accounts explicitly for the electronic coupling between all types of excitons. We first evaluate both the accuracy and efficiency of our fragmentation approach for molecular dimers and aggregates by comparing it with the full LC-TD-DFTB method. The comparison of the calculated spectra of an anthracene cluster shows a very good agreement between our method and the LC-TD-DFTB reference. The effective computational scaling of our method has been explored for anthracene clusters and for perylene bisimide aggregates. We demonstrate the applicability of our method by the calculation of the excited state properties of pentacene crystal models consisting of up to 319 molecules. Furthermore, the participation ratio of the monomer fragments to the excited states is analyzed by the calculation of natural transition orbital participation numbers, which are verified by the hole and particle density for a chosen pentacene cluster. The use of our FMO-LC-TDDFTB method will allow for future studies of excitonic dynamics and charge transport to be performed on complex molecular systems consisting of thousands of atoms.
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Affiliation(s)
- Richard Einsele
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
| | - Joscha Hoche
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
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7
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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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8
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Liu W. Perspective: Simultaneous treatment of relativity, correlation, and
QED. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science Shandong University Qingdao Shandong China
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9
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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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10
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Liu J, Hu W, Yang J. Accelerating Linear-Response Time-Dependent Hybrid Density Functional Theory with Low-Rank Decomposition Techniques in the Plane-Wave Basis. J Chem Theory Comput 2022; 18:6713-6721. [PMID: 36242561 DOI: 10.1021/acs.jctc.2c00763] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present an efficient low-rank implementation of linear-response time-dependent density functional theory for hybrid functionals (hybrid-LR-TDDFT) within the plane-wave pseudopotential framework. The adaptively compressed exchange (ACE) operator and the natural transition orbitals (NTOs) are introduced to build the low-rank representation of the nonlocal exchange operator in the hybrid-LR-TDDFT Hamiltonian. Numerical tests demonstrate that the ACE approximation significantly reduces the computational cost of applying the nonlocal exchange operator without loss of accuracy, and the NTO approximation can further accelerate the hybrid-LR-TDDFT calculations by introducing an NTO cutoff parameter. This new method enables us to effectively study the excitonic properties of two-dimensional MoS2 consisting of 216 atoms and ∼1900 electrons with range-separated hybrid functionals on a single graphics processing unit.
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Affiliation(s)
- Jie Liu
- Hefei National Laboratory, University of Science and Technology of China, Hefei230088, China
| | - Wei Hu
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui230026, China
| | - Jinlong Yang
- Hefei National Laboratory, University of Science and Technology of China, Hefei230088, China.,Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui230026, China
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11
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Wang K, Ma J, Ma H. Characterizing the excited states of large photoactive systems by exciton models. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ke Wang
- School of Chemistry and Chemical Engineering Nanjing University Nanjing China
| | - Jing Ma
- School of Chemistry and Chemical Engineering Nanjing University Nanjing China
| | - Haibo Ma
- School of Chemistry and Chemical Engineering Nanjing University Nanjing China
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12
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Della Sala F. Orbital-Free Methods for Plasmonics: Linear Response. J Chem Phys 2022; 157:104101. [DOI: 10.1063/5.0100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Plasmonic systems, such as metal nanoparticles, are widely used in different application areas, going from biology to photovoltaics.The modeling of the optical response of such systems is of fundamental importance to analyze their behavior and to design new systems with required properties.When the characteristic sizes/distances reach a few nanometers, non-local and spill-out effects become relevant and conventional classical electrodynamics models are no more appropriate. Methods based on the Time-Dependent Density-Functional Theory (TD-DFT) represent the current reference for the description of quantum effects. However, TD-DFT is based on knowledge of all occupied orbitals whose calculation is computationally prohibitive to model large plasmonic systems of interest for applications.On the other hand, methods based on the Orbital-Free (OF) formulation of TD-DFT, can scale linearly with the system size.In this Review, OF methods ranging from semiclassical models to the quantum hydrodynamic theory, will be derived from the linear response TD-DFT, so that the key approximations and properties of each method can be clearly highlighted. The accuracy of the various approximations will be then validated for the linear optical properties of jellium nanoparticles, the most relevant model system in plasmonics. OF methods can describe the collective excitations in plasmonic systems with great accuracy andwithout system-tuned parameters. The accuracy on these methods depends only on the accuracy on the (universal) kinetic energy functional of the ground-state electronic density. Current approximations and future development directions will be indicated.
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Affiliation(s)
- Fabio Della Sala
- CNR-IMM, IMM CNR Lecce, Italy
- Istituto Italiano di Tecnologia Center for Biomolecular Nanotechnologies
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13
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Abstract
We introduce the concept of fragment localized molecular orbitals (FLMOs), which are Hartree-Fock molecular orbitals localized in specific fragments constituting a molecular system. In physical terms, we minimize the local electronic energies of the different fragments, at the cost of maximizing the repulsion between them. To showcase the approach, we rationalize the main interactions occurring in large biological systems in terms of interactions between the fragments of the system. In particular, we study an anticancer drug intercalated within DNA and retinal in anabaena sensory rhodopsin as prototypes of molecular systems embedded in biological matrixes. Finally, the FLMOs are exploited to rationalize the formation of two oligomers, prototypes of amyloid diseases, such as Parkinson and Alzheimer.
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Affiliation(s)
| | - Henrik Koch
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.,Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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14
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Li J, Wu C, Lei Y, Liu W. Tuning Catalyst-Free Photocontrolled Polymerization by Substitution: A Quantitative and Qualitative Interpretation. J Phys Chem Lett 2022; 13:3290-3296. [PMID: 35389216 DOI: 10.1021/acs.jpclett.2c00830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Catalyst-free photocontrolled reversible addition-fragmentation chain transfer (RAFT) polymerization avoids the side effects of photocatalysts but has the accompanying slow kinetics, thereby warranting more efficient photolysis and faster chain transfer. To understand the underlying mechanisms, both quantitative and qualitative interpretations are needed. Such a goal can be achieved by the iCAS (imposed automatic selection and localization of complete active spaces) approach [J. Chem. Theory Comput. 2021, 17, 4846], which maintains the same CAS and meanwhile provides localized orbitals along the whole reaction. Taking dithiobenzoate as a representative of RAFT agents, it is found here that electron-donating substitution (by methoxy) clearly outperforms both electron-standing (by methyl) and electron-withdrawing (by cyano) substitutions in facilitating photo-RAFT polymerization, by narrowing the gap between the π* and σ* orbitals, so as to facilitate the π* → σ* charge transfer dominating both the photolysis and chain transfer processes. Such findings are of general values.
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Affiliation(s)
- Jun Li
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
| | - Chenyu Wu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
| | - Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Shaanxi key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an 710127, Shaanxi, P. R. China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
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15
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Wang K, Xie Z, Luo Z, Ma H. Low-Scaling Excited State Calculation Using the Block Interaction Product State. J Phys Chem Lett 2022; 13:462-470. [PMID: 35015548 DOI: 10.1021/acs.jpclett.1c03445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We develop an automatic and efficient scheme for the accurate construction of the bases for excitonic models, which can enable "black-box" excited state structure calculations for large molecular systems. These new and optimized bases, which are named the block interaction product state (BIPS), can be expressed as the direct products of the local states for each chromophore. Each chromophore's local states are selected by diagonalization of its reduced density matrix, which is obtained by quantum chemical calculation of the small subsystem composed of the chromophore and its nearest neighbors. We implemented the BIPS framework with fragment-based calculations considering two- and three-body interactions. Test calculations for eight different molecular aggregates demonstrate that this framework provides an accurate description of not only the excitation energies but also the first-order wave function properties (dipole moment and transition dipole moment) of the low-lying excited states at a low-scaling computational cost.
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Affiliation(s)
- Ke Wang
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Zhaoxuan Xie
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Zhen Luo
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Haibo Ma
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
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16
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Li W, Ma H, Li S, Ma J. Computational and data driven molecular material design assisted by low scaling quantum mechanics calculations and machine learning. Chem Sci 2021; 12:14987-15006. [PMID: 34909141 PMCID: PMC8612375 DOI: 10.1039/d1sc02574k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Electronic structure methods based on quantum mechanics (QM) are widely employed in the computational predictions of the molecular properties and optoelectronic properties of molecular materials. The computational costs of these QM methods, ranging from density functional theory (DFT) or time-dependent DFT (TDDFT) to wave-function theory (WFT), usually increase sharply with the system size, causing the curse of dimensionality and hindering the QM calculations for large sized systems such as long polymer oligomers and complex molecular aggregates. In such cases, in recent years low scaling QM methods and machine learning (ML) techniques have been adopted to reduce the computational costs and thus assist computational and data driven molecular material design. In this review, we illustrated low scaling ground-state and excited-state QM approaches and their applications to long oligomers, self-assembled supramolecular complexes, stimuli-responsive materials, mechanically interlocked molecules, and excited state processes in molecular aggregates. Variable electrostatic parameters were also introduced in the modified force fields with the polarization model. On the basis of QM computational or experimental datasets, several ML algorithms, including explainable models, deep learning, and on-line learning methods, have been employed to predict the molecular energies, forces, electronic structure properties, and optical or electrical properties of materials. It can be conceived that low scaling algorithms with periodic boundary conditions are expected to be further applicable to functional materials, perhaps in combination with machine learning to fast predict the lattice energy, crystal structures, and spectroscopic properties of periodic functional materials.
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Affiliation(s)
- 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 China
| | - Haibo 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 China
- Jiangsu Key Laboratory of Advanced Organic Materials, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University Nanjing 210023 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 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 China
- Jiangsu Key Laboratory of Advanced Organic Materials, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University Nanjing 210023 China
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17
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Song Y, Guo Y, Lei Y, Zhang N, Liu W. The Static-Dynamic-Static Family of Methods for Strongly Correlated Electrons: Methodology and Benchmarking. Top Curr Chem (Cham) 2021; 379:43. [PMID: 34724123 DOI: 10.1007/s41061-021-00351-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022]
Abstract
A series of methods (SDSCI, SDSPT2, iCI, iCIPT2, iCISCF(2), iVI, and iCAS) is introduced to accurately describe strongly correlated systems of electrons. Born from the (restricted) static-dynamic-static (SDS) framework for designing many-electron wave functions, SDSCI is a minimal multireference (MR) configuration interaction (CI) approach that constructs and diagonalizes a [Formula: see text] matrix for [Formula: see text] states, regardless of the numbers of orbitals and electrons to be correlated. If the full molecular Hamiltonian H in the QHQ block (which describes couplings between functions of the first-order interaction space Q) of the SDSCI CI matrix is replaced with a zeroth-order Hamiltonian [Formula: see text] before the diagonalization is taken, we obtain SDSPT2, a CI-like second-order perturbation theory (PT2). Unlike most variants of MRPT2, SDSPT2 treats single and multiple states in the same way and is particularly advantageous in the presence of near degeneracy. On the other hand, if the SDSCI procedure is repeated until convergence, we will have iterative CI (iCI), which can converge quickly from the above to the exact solutions (full CI) even when starting with a poor guess. When further combined with the selection of important configurations followed by a PT2 treatment of dynamic correlation, iCI becomes iCIPT2, which is a near-exact theory for medium-sized systems. The microiterations of iCI for relaxing the coefficients of contracted many-electron functions can be generalized to an iterative vector interaction (iVI) approach for finding exterior or interior roots of a given matrix, in which the dimension of the search subspace is fixed by either the number of target roots or the user-specified energy window. Naturally, iCIPT2 can be employed as the active space solver of the complete active space (CAS) self-consistent field, leading to iCISCF(2), which can further be combined with iCAS for automated selection of active orbitals and assurance of the same CAS for all states and all geometries. The methods are calibrated by taking the Thiel set of benchmark systems as examples. Results for the corresponding cations, a new set of benchmark systems, are also reported.
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Affiliation(s)
- Yangyang Song
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, 266237, Shandong, China
| | - Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, 266237, Shandong, China
| | - Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Shaanxi key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an, 710127, Shaanxi, China
| | - Ning Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, 266237, Shandong, China.
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18
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Wang Z, Wu C, Liu W. NAC-TDDFT: Time-Dependent Density Functional Theory for Nonadiabatic Couplings. Acc Chem Res 2021; 54:3288-3297. [PMID: 34448566 DOI: 10.1021/acs.accounts.1c00312] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
First-order nonadiabatic coupling (NAC) matrix elements (fo-NACMEs) are the basic quantities in theoretical descriptions of electronically nonadiabatic processes that are ubiquitous in molecular physics and chemistry. Given the large size of systems of chemical interests, time-dependent density functional theory (TDDFT) is usually the first choice of methods. However, the lack of many-electron wave functions in TDDFT renders the formulation of NAC-TDDFT for fo-NACMEs conceptually difficult. Because of this, various variants of NAC-TDDFT have been proposed in the literature from different standing points, including the Hellmann-Feynman-like expression and auxiliary/pseudo-wave function (AWF)-, equation-of-motion (EOM)-, and time-dependent perturbation theory (TDPT)-based formulations. Based on critical analyses, the following conclusions are made here: (1) The Hellmann-Feynman-like expression, which is rooted in exact wave function theory, is hardly useful due to huge demand on basis sets. (2) Although most popular, the AWF variants of NAC-TDDFT are not theoretically founded and become ambiguous particularly for the fo-NACMEs between two excited states, although they do agree with the EOM and TDPT variants under the Tamm-Dancoff approximation. (3) The TDPT variant of NAC-TDDFT is theoretically most rigorous but suffers from numerical instabilities on the one hand and does not differ to a significant extent from the EOM variant on the other hand. (4) As such, the EOM variant of NAC-TDDFT for the fo-NACMEs between the ground and excited states and between two excited states is solely the right choice in practice. These formal analyses are fully supported by numerical experimentations, taking azulene as a showcase. The proper implementation of the EOM variant of NAC-TDDFT is also highlighted, showing that the fo-NACMEs between the ground and excited states and between two excited states are computationally very much the same as the analytic energy gradients of DFT and TDDFT, respectively. Possible future developments of the EOM variant of NAC-TDDFT are also highlighted. Its extensions to spin-adapted open-shell TDDFT and proper treatment of spin-orbit couplings (which are another source of force for electronically nonadiabatic processes) are particularly warranted in the near future.
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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, China
| | - Chenyu Wu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
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19
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Giannone G, Śmiga S, D'Agostino S, Fabiano E, Della Sala F. Plasmon Couplings from Subsystem Time-Dependent Density Functional Theory. J Phys Chem A 2021; 125:7246-7259. [PMID: 34403247 DOI: 10.1021/acs.jpca.1c05384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many applications in plasmonics are related to the coupling between metallic nanoparticles (MNPs) or between an emitter and a MNP. The theoretical analysis of such a coupling is thus of fundamental importance to analyze the plasmonic behavior and to design new systems. While classical methods neglect quantum and spill-out effects, time-dependent density functional theory (TD-DFT) considers all of them and with Kohn-Sham orbitals delocalized over the whole system. Thus, within TD-DFT, no definite separation of the subsystems (the single MNP or the emitter) and their couplings is directly available. This important feature is obtained here using the subsystem formulation of TD-DFT, which has been originally developed in the context of weakly interacting organic molecules. In subsystem TD-DFT, interacting MNPs are treated independently, thus allowing us to compute the plasmon couplings directly from the subsystem TD-DFT transition densities. We show that subsystem TD-DFT, as well as a simplified version of it in which kinetic contributions are neglected, can reproduce the reference TD-DFT calculations for gap distances greater than about 6 Å or even smaller in the case of hybrid plasmonic systems (i.e., molecules interacting with MNPs). We also show that the subsystem TD-DFT can be also used as a tool to analyze the impact of charge-transfer effects.
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Affiliation(s)
- Giulia Giannone
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, Arnesano (LE) 73010, Italy.,Department of Mathematics and Physics "E. De Giorgi", University of Salento, Via Arnesano, Lecce 73100, Italy
| | - Szymon Śmiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudzia̧dzka 5, Toruń 87-100, Poland
| | - Stefania D'Agostino
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, Arnesano (LE) 73010, Italy.,Department of Mathematics and Physics "E. De Giorgi", University of Salento, Via Arnesano, Lecce 73100, Italy.,Institute of Nanotechnology, National Research Council (CNR-NANOTEC), c/o Campus Ecotekne, via Monteroni, Lecce 73100, Italy
| | - Eduardo Fabiano
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, Arnesano (LE) 73010, Italy.,Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, Lecce 73100, Italy
| | - Fabio Della Sala
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, Arnesano (LE) 73010, Italy.,Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, Lecce 73100, Italy
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20
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Lei Y, Suo B, Liu W. iCAS: Imposed Automatic Selection and Localization of Complete Active Spaces. J Chem Theory Comput 2021; 17:4846-4859. [PMID: 34314180 DOI: 10.1021/acs.jctc.1c00456] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
It is shown that in the spirit of "from fragments to molecule" for localizing molecular orbitals [J. Chem. Theory Comput. 2011, 7, 3643], a prechosen set of occupied/virtual valence/core atomic/fragmental orbitals can be transformed to an equivalent set of localized occupied/virtual pre-localized molecular orbitals (pre-LMO), which can then be taken as probes to select the same number of maximally matching localized occupied/virtual Hartree-Fock (HF) or restricted open-shell HF (ROHF) molecular orbitals as the initial local orbitals spanning the desired complete active space (CAS). In each cycle of the self-consistent field (SCF) calculation, the CASSCF orbitals can be localized by means of the noniterative "top-down least-change" algorithm for localizing ROHF orbitals [J. Chem. Phys. 2017, 146, 104104] such that the maximum matching between the orbitals of two adjacent iterations can readily be monitored, leading finally to converged localized CASSCF orbitals that overlap most the guess orbitals. Such an approach is to be dubbed as "imposed CASSCF" (iCASSCF or simply iCAS in short) for good reasons: (1) it has been assumed that only those electronic states that have largest projections onto the active space defined by the prechosen atomic/fragmental orbitals are to be targeted. This is certainly an imposed constraint but has wide applications in organic and transition metal chemistry where valence (or core) atomic/fragmental orbitals can readily be identified. (2) The selection of both initial and optimized local active orbitals is imposed from the very beginning by the pre-LMOs (which span the same space as the prechosen atomic/fragmental orbitals). Apart from the (imposed) automation and localization, iCAS has two additional merits: (a) the guess orbitals are guaranteed to be the same for all geometries, for the pre-LMOs do not change in character with geometry and (b) the use of localized orbitals facilitates the SCF convergence, particularly for large active spaces. Both organic molecules and transition-metal complexes are taken as showcases to reveal the efficacy of iCAS.
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Affiliation(s)
- Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an 710127, Shaanxi, P. R. China
| | - Bingbing Suo
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi'an 710127, Shaanxi, P. R. China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
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21
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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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22
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Macetti G, Genoni A. Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Strategy for Excited States: Coupling to Time-Dependent Density Functional Theory and Equation-of-Motion Coupled Cluster. J Chem Theory Comput 2020; 16:7490-7506. [PMID: 33241930 DOI: 10.1021/acs.jctc.0c00956] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The QM/ELMO (quantum mechanics/extremely localized molecular orbital) method is a recently developed embedding technique in which the most important region of the system under examination is treated at fully quantum mechanical level, while the rest is described by means of transferred and frozen extremely localized molecular orbitals. In this paper, we propose the first application of the QM/ELMO approach to the investigation of excited states, and, in particular, we present the coupling of the QM/ELMO philosophy with Time-Dependent Density Functional Theory (TDDFT) and Equation-of-Motion Coupled Cluster with single and double substitutions (EOM-CCSD). The proposed TDDFT/ELMO and EOM-CCSD/ELMO strategies underwent a series of preliminary tests that were already considered for the validation of other embedding methods for excited states. The obtained results showed that the novel techniques allow the accurate description of localized excitations in large systems by only including a relatively small number of atoms in the region treated at fully quantum chemical level. Furthermore, for TDDFT/ELMO, it was also observed that (i) the method enables to avoid the presence of artificial low-lying charge-transfer states that may affect traditional TDDFT calculations, even using functionals that do not take into account long-range corrections, and (ii) the novel approach can be also successfully exploited to investigate local electronic transitions in quite large systems (e.g., reduced model of the Green Fluorescent Protein), and the accuracy of the results can be improved by including a sufficient number of chemically crucial fragments/residues in the quantum mechanical region. Finally, concerning EOM-CCSD/ELMO, it was also seen that, despite the quite crude approximation of an embedding potential given by frozen extremely localized molecular orbitals, the new strategy is able to satisfactorily account for the effects of the environment. This work paves the way to further extensions of the QM/ELMO philosophy for the study of local excitations in extended systems, suggesting the coupling of the QM/ELMO approach with other quantum chemical strategies for excited states, from the simplest ΔSCF techniques to the most advanced and computationally expensive multireferences methods.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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23
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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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24
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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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25
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Affiliation(s)
- Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
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26
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Zhang Y, Suo B, Wang Z, Zhang N, Li Z, Lei Y, Zou W, Gao J, Peng D, Pu Z, Xiao Y, Sun Q, Wang F, Ma Y, Wang X, Guo Y, Liu W. BDF: A relativistic electronic structure program package. J Chem Phys 2020; 152:064113. [DOI: 10.1063/1.5143173] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yong Zhang
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Bingbing Suo
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Institute of Modern Physics, Northwest University, Xi’an, Shaanxi 710127, People’s Republic of China
| | - Zikuan Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing 100871, People’s Republic of China
| | - Ning Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing 100871, People’s Republic of China
| | - Zhendong Li
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, College of Chemistry and Materials Science, Northwest University, Xi’an, Shaanxi 710127, People’s Republic of China
| | - Wenli Zou
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Institute of Modern Physics, Northwest University, Xi’an, Shaanxi 710127, People’s Republic of China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
| | - Daoling Peng
- College of Chemistry, South China Normal University, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Zhichen Pu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing 100871, People’s Republic of China
| | - Yunlong Xiao
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing 100871, People’s Republic of China
| | - Qiming Sun
- Tencent America LLC, Palo Alto, California 94306, USA
| | - Fan Wang
- Key Laboratory of High Energy Density Physics and Technology of Ministry of Education, Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, Sichuan 610065, People’s Republic of China
| | - Yongtao Ma
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Xiaopeng Wang
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
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27
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Yoshikawa T, Yoshihara J, Nakai H. Large-scale excited-state calculation using dynamical polarizability evaluated by divide-and-conquer based coupled cluster linear response method. J Chem Phys 2020; 152:024102. [PMID: 31941302 DOI: 10.1063/1.5124909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This study attempted to propose an efficient scheme at the coupled cluster linear response (CCLR) level to perform large-scale excited-state calculations of not only local excitations but also nonlocal ones such as charge transfers and transitions between delocalized orbitals. Although standard applications of fragmentation techniques to the excited-state calculations brought about the limitations that could only deal with local excitations, this study solved the problem by evaluating the excited states as the poles of dynamical polarizability. Because such an approach previously succeeded at the time-dependent density functional theory level [H. Nakai and T. Yoshikawa, J. Chem. Phys. 146, 124123 (2017)], this study was considered as an extension to the CCLR level. To evaluate the dynamical polarizability at the CCLR level, we revisited three equivalent formulas, namely, coupled-perturbed self-consistent field (CPSCF), random phase approximation (RPA), and Green's function (GF). We further extended these formulas to the linear-scaling methods based on the divide-and-conquer (DC) technique. We implemented the CCLR with singles and doubles (CCSDLR) program for the six schemes, i.e., the standard and DC-type CPSCF, RPA, and GF. Illustrative applications of the present methods demonstrated the accuracy and efficiency. Although the standard three treatments could exactly reproduced the conventional frequency-domain CCSDLR results, their computational costs were commonly higher than that of the conventional ones due to large amount of computations for individual frequencies of the external electric field. The DC-type treatments, which approximately reproduced the conventional results, could achieve quasilinear scaling computational costs. Among them, DC-GF was found to exhibit the best performance.
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Affiliation(s)
- Takeshi Yoshikawa
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Jyunya Yoshihara
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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28
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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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29
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Wen X, Graham DS, Chulhai DV, Goodpaster JD. Absolutely Localized Projection-Based Embedding for Excited States. J Chem Theory Comput 2019; 16:385-398. [DOI: 10.1021/acs.jctc.9b00959] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xuelan Wen
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Daniel S. Graham
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Dhabih V. Chulhai
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
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30
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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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31
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Yuan M, Zhang Y, Qu Z, Xiao Y, Liu W. Sublinear scaling quantum chemical methods for magnetic shieldings in large molecules. J Chem Phys 2019; 150:154113. [DOI: 10.1063/1.5083193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Minghong Yuan
- Beijing National Center for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yong Zhang
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, China
| | - Zhi Qu
- Beijing National Center for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yunlong Xiao
- Beijing National Center for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, China
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32
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Mester D, Kállay M. Reduced-Scaling Approach for Configuration Interaction Singles and Time-Dependent Density Functional Theory Calculations Using Hybrid Functionals. J Chem Theory Comput 2019; 15:1690-1704. [DOI: 10.1021/acs.jctc.8b01199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Dávid Mester
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box
91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box
91, H-1521 Budapest, Hungary
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33
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Thapa B, Beckett D, Jovan Jose KV, Raghavachari K. Assessment of Fragmentation Strategies for Large Proteins Using the Multilayer Molecules-in-Molecules Approach. J Chem Theory Comput 2018; 14:1383-1394. [DOI: 10.1021/acs.jctc.7b01198] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
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34
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Abstract
The foundations, formalisms, technicalities, and practicalities of relativistic time-dependent density functional theories (R-TD-DFT) for spinor excited states of molecular systems containing heavy elements are critically reviewed.
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Affiliation(s)
- Wenjian Liu
- Beijing National Center for Molecular Sciences
- Institute of Theoretical and Computational Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
| | - Yunlong Xiao
- Beijing National Center for Molecular Sciences
- Institute of Theoretical and Computational Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
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35
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Yuan XA, Wen J, Zheng D, Ma J. Simulations of absorption spectra of conjugated oligomers: role of planar conformation and aggregation in condensed phase. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1402967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Xiang-Ai Yuan
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, P. R. China
| | - Jin Wen
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, P. R. China
| | - Dong Zheng
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, P. R. 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, P. R. China
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36
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Ding F, Tsuchiya T, Manby FR, Miller TF. Linear-Response Time-Dependent Embedded Mean-Field Theory. J Chem Theory Comput 2017; 13:4216-4227. [DOI: 10.1021/acs.jctc.7b00666] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Feizhi Ding
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Takashi Tsuchiya
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Frederick R. Manby
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Thomas F. Miller
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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37
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Huang C, Liu W, Xiao Y, Hoffmann MR. iVI: An iterative vector interaction method for large eigenvalue problems. J Comput Chem 2017; 38:2481-2499. [DOI: 10.1002/jcc.24907] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/07/2017] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Chao Huang
- Beijing National Laboratory for Molecular Sciences; Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University; Beijing 100871 People's Republic of China
| | - Wenjian Liu
- Beijing National Laboratory for Molecular Sciences; Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University; Beijing 100871 People's Republic of China
| | - Yunlong Xiao
- 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
| | - Mark R. Hoffmann
- Chemistry Department; University of North Dakota; Grand Forks ND 58202-9024
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38
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Mohr S, Masella M, Ratcliff LE, Genovese L. Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis. J Chem Theory Comput 2017; 13:4079-4088. [DOI: 10.1021/acs.jctc.7b00291] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Stephan Mohr
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Michel Masella
- Laboratoire
de
Biologie Structurale et Radiologie, Service de Bioénergétique,
Biologie Structurale et Mécanisme, Institut de Biologie et de Technologie de Saclay, CEA Saclay, F-91191 Gif-sur-Yvette Cedex, France
| | - Laura E. Ratcliff
- Argonne
Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Luigi Genovese
- Université Grenoble Alpes, INAC-MEM, L_Sim, F-38000 Grenoble, France
- CEA, INAC-MEM,
L_Sim, F-38000 Grenoble, France
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39
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Nakai H, Yoshikawa T. Development of an excited-state calculation method for large systems using dynamical polarizability: A divide-and-conquer approach at the time-dependent density functional level. J Chem Phys 2017; 146:124123. [DOI: 10.1063/1.4978952] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
| | - Takeshi Yoshikawa
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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40
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Li H, Liu W, Suo B. Localization of open-shell molecular orbitals via least change from fragments to molecule. J Chem Phys 2017; 146:104104. [DOI: 10.1063/1.4977929] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hongyang Li
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Wenjian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Bingbing Suo
- Institute of Modern Physics, Northwest University, Xi’an 710069, People’s Republic of China
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41
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Ge Q, Mao Y, White AF, Epifanovsky E, Closser KD, Head-Gordon M. Simulating the absorption spectra of helium clusters (N = 70, 150, 231, 300) using a charge transfer correction to superposition of fragment single excitations. J Chem Phys 2017; 146:044111. [DOI: 10.1063/1.4973611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qinghui Ge
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alec F. White
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Evgeny Epifanovsky
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Kristina D. Closser
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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42
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Tamukong PK, Khait YG, Hoffmann MR. Accurate Dissociation of Chemical Bonds Using DFT-in-DFT Embedding Theory with External Orbital Orthogonality. J Phys Chem A 2016; 121:256-264. [DOI: 10.1021/acs.jpca.6b09909] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick K. Tamukong
- Chemistry Department, University of North Dakota, Grand
Forks, North Dakota 58202, United States
| | - Yuriy G. Khait
- Chemistry Department, University of North Dakota, Grand
Forks, North Dakota 58202, United States
| | - Mark R. Hoffmann
- Chemistry Department, University of North Dakota, Grand
Forks, North Dakota 58202, United States
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43
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Li W, Li Y, Lin R, Li S. Generalized Energy-Based Fragmentation Approach for Localized Excited States of Large Systems. J Phys Chem A 2016; 120:9667-9677. [DOI: 10.1021/acs.jpca.6b11193] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- 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, People’s Repubic of China
| | - Yunzhi Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Repubic of China
| | - Ruochen Lin
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Repubic of China
| | - Shuhua Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Repubic of China
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44
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Riplinger C, Pinski P, Becker U, Valeev EF, Neese F. Sparse maps--A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory. J Chem Phys 2016; 144:024109. [PMID: 26772556 DOI: 10.1063/1.4939030] [Citation(s) in RCA: 646] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate previous implementation.
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Affiliation(s)
- Christoph Riplinger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Peter Pinski
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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45
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Li Z, Liu W. Critical Assessment of Time-Dependent Density Functional Theory for Excited States of Open-Shell Systems: II. Doublet-Quartet Transitions. J Chem Theory Comput 2016; 12:2517-27. [PMID: 27159167 DOI: 10.1021/acs.jctc.5b01219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Compared with closed-shell systems, open-shell systems place three additional challenges to time-dependent density functional theory (TD-DFT) for electronically excited states: (a) the spin-contamination problem is a serious issue; (b) the exchange-correlation (XC) kernel may be numerically instable; and (c) the single-determinant description of open-shell ground states readily becomes energetically instable. Confined to flip-up single excitations, the spin-contamination problem can largely be avoided by using the spin-flip TD-DFT (SF-TD-DFT) formalism, provided that a noncollinear XC kernel is employed. As for the numerical instabilities associated with such a kernel, only an ad hoc scheme has been proposed so far, viz., the ALDA0 kernel, which amounts to setting the divergent components (arising from density gradients and kinetic energy density) simply to zero. The ground-state instability problem can effectively be avoided by introducing the Tamm-Dancoff approximation (TDA) to TD-DFT. Therefore, on a general basis, the SF-TDA/ALDA0 Ansatz is so far the only promising means within the TD-DFT framework for flip-up single excitations of open-shell systems. To assess systematically the performance of SF-TDA/ALDA0, in total 61 low-lying quartet excited states of the benchmark set of 11 small radicals [J. Chem. Theory Comput. 2016, 12, 238] are investigated with various XC functionals. Taking the MRCISD+Q (multireference configuration interaction with singles and doubles plus the Davidson correction) results as benchmark, it is found that the mean absolute errors of SF-TDA/ALDA0 with the SAOP (statistical averaging of model orbital potentials), global hybrid, and range-separated hybrid functionals are in the range of 0.2-0.4 eV. This is in line not only with the typical accuracy of TD-DFT for singlet and triplet excited states of closed-shell systems but also with the gross accuracy of spin-adapted TD-DFT for spin-conserving excited states of open-shell systems.
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Affiliation(s)
- Zhendong Li
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University , Beijing 100871, People's Republic of China
| | - Wenjian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University , Beijing 100871, People's Republic of China
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46
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Høyvik IM, Jørgensen P. Characterization and Generation of Local Occupied and Virtual Hartree–Fock Orbitals. Chem Rev 2016; 116:3306-27. [DOI: 10.1021/acs.chemrev.5b00492] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ida-Marie Høyvik
- Department
of Chemistry, The Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Poul Jørgensen
- qLEAP
Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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47
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Zhao R, Zhang Y, Xiao Y, Liu W. Exact two-component relativistic energy band theory and application. J Chem Phys 2016; 144:044105. [DOI: 10.1063/1.4940140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rundong Zhao
- 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
| | - Yong Zhang
- 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
| | - Yunlong Xiao
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Wenjian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
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48
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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.
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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
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49
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Li Z, Liu W. Critical Assessment of TD-DFT for Excited States of Open-Shell Systems: I. Doublet–Doublet Transitions. J Chem Theory Comput 2015; 12:238-60. [DOI: 10.1021/acs.jctc.5b01158] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhendong Li
- Beijing National Laboratory
for Molecular Sciences, Institute of Theoretical and Computational
Chemistry, State Key Laboratory of Rare Earth Materials Chemistry
and Applications, College of Chemistry and Molecular Engineering,
and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Wenjian Liu
- Beijing National Laboratory
for Molecular Sciences, Institute of Theoretical and Computational
Chemistry, State Key Laboratory of Rare Earth Materials Chemistry
and Applications, College of Chemistry and Molecular Engineering,
and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
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50
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Abstract
Abstract
Any quantum mechanical calculation on electronic structure ought to choose first an appropriate Hamiltonian H and then an Ansatz for parameterizing the wave function Ψ, from which the desired energy/property E(λ) can finally be calculated. Therefore, the very first question is: what is the most accurate many-electron Hamiltonian H? It is shown that such a Hamiltonian i.e. effective quantum electrodynamics (eQED) Hamiltonian, can be obtained naturally by incorporating properly the charge conjugation symmetry when normal ordering the second quantized fermion operators. Taking this eQED Hamiltonian as the basis, various approximate relativistic many-electron Hamiltonians can be obtained based entirely on physical arguments. All these Hamiltonians together form a complete and continuous ‘Hamiltonian ladder’, from which one can pick up the right one according to the target physics and accuracy. As for the many-electron wave function Ψ, the most intriguing questions are as follows. (i) How to do relativistic explicit correlation? (ii) How to handle strong correlation? Both general principles and practical strategies are outlined here to handle these issues. Among the electronic properties E(λ) that sample the electronic wave function nearby the nuclear region, nuclear magnetic resonance (NMR) shielding and nuclear spin-rotation (NSR) coupling constant are especially challenging: they require body-fixed molecular Hamiltonians that treat both the electrons and nuclei as relativistic quantum particles. Nevertheless, they have been formulated rigorously. In particular, a very robust ‘relativistic mapping’ between the two properties has been established, which can translate experimentally measured NSR coupling constants to very accurate absolute NMR shielding scales that otherwise cannot be obtained experimentally. Since the most general and fundamental issues pertinent to all the three components of the quantum mechanical equation HΨ = EΨ (i.e. Hamiltonian H, wave function Ψ, and energy/property E(λ)) have fully been understood, the big picture of relativistic molecular quantum mechanics can now be regarded as established.
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Affiliation(s)
- 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, China
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