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Zhang X, Li C, Ye HZ, Berkelbach TC, Chan GKL. Performant automatic differentiation of local coupled cluster theories: Response properties and ab initio molecular dynamics. J Chem Phys 2024; 161:014109. [PMID: 38949583 DOI: 10.1063/5.0212274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024] Open
Abstract
In this work, we introduce a differentiable implementation of the local natural orbital coupled cluster (LNO-CC) method within the automatic differentiation framework of the PySCFAD package. The implementation is comprehensively tuned for enhanced performance, which enables the calculation of first-order static response properties on medium-sized molecular systems using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. We evaluate the accuracy of our method by benchmarking it against the canonical CCSD(T) reference for nuclear gradients, dipole moments, and geometry optimizations. In addition, we demonstrate the possibility of property calculations for chemically interesting systems through the computation of bond orders and Mössbauer spectroscopy parameters for a [NiFe]-hydrogenase active site model, along with the simulation of infrared spectra via ab initio LNO-CC molecular dynamics for a protonated water hexamer.
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Affiliation(s)
- Xing Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Chenghan Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Hong-Zhou Ye
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | | | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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2
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Li W, Wang Y, Ni Z, Li S. Cluster-in-Molecule Local Correlation Method for Dispersion Interactions in Large Systems and Periodic Systems. Acc Chem Res 2023; 56:3462-3474. [PMID: 37991873 DOI: 10.1021/acs.accounts.3c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
ConspectusThe noncovalent interactions, including dispersion interactions, control the structures and stabilities of complex chemical systems, including host-guest complexes and the adsorption process of molecules on the solid surfaces. The density functional theory (DFT) with empirical dispersion correction is now the working horse in many areas of applications. Post-Hartree-Fock (post-HF) methods have been well recognized to provide more accurate descriptions in a systematic way. However, traditional post-HF methods are mainly limited to small- or medium-sized systems, and their applications to periodic condensed phase systems are still very limited due to their expensive computational costs.To extend post-HF calculations to large molecules, the cluster-in-molecule (CIM) local correlation approach has been established, allowing highly accurate electron correlation calculations that are routinely available for very large systems. In the CIM approach, the electron correlation energy of a large molecule could be obtained from electron correlation calculations on a series of clusters, each of which contains a subset of occupied and virtual localized molecular orbitals. The CIM method could be massively and efficiently parallelized on general computer clusters. The CIM method has been implemented at various electron correlation levels, including second-order Mo̷ller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), CCSD with perturbative triples correction [CCSD(T)], etc. The CIM-MP2 energy gradient algorithm was developed and applied to the geometry optimizations of large systems. The CIM method has also been extended to condensed-phase systems under periodic boundary conditions (PBC-CIM). For periodic systems, the correlation energy per unit cell could be evaluated with correlation energy contributions from a series of clusters that are built with localized Wannier functions.CIM-based electron correlation calculations have been employed to investigate a number of chemical problems in which the dispersion interaction is important. CIM-based post-HF methods including CIM domain-based local pair natural orbital (DLPNO) CCSD(T) are applied to compute the relative or binding energies of biological systems or supramolecular complexes, the reaction barrier in a relatively complex chemical reaction. The CIM-MP2 method is used to obtain the optimized geometry of large systems. CIM-based post-HF calculations have also been used to compute the cohesive energies of molecular crystals and adsorption energies of molecules on the solid surfaces. The CIM and its PBC variant are expected to become a powerful theoretical tool for accurate calculations of the energies and structures for a broad range of large systems and condensed-phase systems with significant dispersion interactions.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yuqi Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zhigang Ni
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, People's Republic of China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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3
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Szabó PB, Csóka J, Kállay M, Nagy PR. Linear-Scaling Local Natural Orbital CCSD(T) Approach for Open-Shell Systems: Algorithms, Benchmarks, and Large-Scale Applications. J Chem Theory Comput 2023; 19:8166-8188. [PMID: 37921429 PMCID: PMC10687875 DOI: 10.1021/acs.jctc.3c00881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The extension of the highly optimized local natural orbital (LNO) coupled cluster (CC) with single-, double-, and perturbative triple excitations [LNO-CCSD(T)] method is presented for high-spin open-shell molecules based on restricted open-shell references. The techniques enabling the outstanding efficiency of the closed-shell LNO-CCSD(T) variant are adopted, including the iteration- and redundancy-free second-order Møller-Plesset and (T) formulations as well as the integral-direct, memory- and disk use-economic, and OpenMP-parallel algorithms. For large molecules, the efficiency of our open-shell LNO-CCSD(T) method approaches that of its closed-shell parent method due to the application of restricted orbital sets for demanding integral transformations and a novel approximation for higher-order long-range spin-polarization effects. The accuracy of open-shell LNO-CCSD(T) is extensively tested for radicals and reactions thereof, ionization processes, as well as spin-state splittings, and transition-metal compounds. At the size range where the canonical CCSD(T) reference is accessible (up to 20-30 atoms), the average open-shell LNO-CCSD(T) correlation energies are found to be 99.9 to 99.95% accurate, which translates into average absolute deviations of a few tenths of kcal/mol in the investigated energy differences already with the default settings. For more extensive molecules, the local errors may grow, but they can be estimated and decreased via affordable systematic convergence studies. This enables the accurate modeling of large systems with complex electronic structures, as illustrated on open-shell organic radicals and transition-metal complexes of up to 179 atoms as well as on challenging biochemical systems, including up to 601 atoms and 11,000 basis functions. While the protein models involve difficulties for local approximations, such as the spin states of a bounded iron ion or an extremely delocalized singly occupied orbital, the corresponding single-node LNO-CCSD(T) computations were feasible in a matter of days with 10s to 100 GB of memory use. Therefore, the new LNO-CCSD(T) implementation enables highly accurate computations for open-shell systems of unprecedented size and complexity with widely accessible hardware.
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Affiliation(s)
- P. Bernát Szabó
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - József Csóka
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Péter R. Nagy
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
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4
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Wang Y, Guo Y, Neese F, Valeev EF, Li W, Li S. Cluster-in-Molecule Approach with Explicitly Correlated Methods for Large Molecules. J Chem Theory Comput 2023; 19:8076-8089. [PMID: 37920973 DOI: 10.1021/acs.jctc.3c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
In this article, we present a series of explicitly correlated local correlation methods developed under the cluster-in-molecule (CIM) framework, including explicitly correlated second-order Møller-Plesset perturbation (MP2), coupled-cluster singles and doubles (CCSD), domain-based local pair natural orbital CCSD (DLPNO-CCSD), and DLPNO-CCSD with perturbative triples (DLPNO-CCSD(T)). In these methods, F12 correction is decomposed into contributions from each occupied local molecular orbital and then evaluated independently in a given cluster, which consists of a subset of localized orbitals. These newly developed methods allow F12 calculations of large molecules (up to 145 atoms for quasi-one-dimensional systems) on a single node. We use these methods to investigate the relative stability between extended and folded alkane C30H62, the relative stability of four secondary structures of a polyglycine Ace(Gly)10NH2, and the binding energies of two host-guest complexes. The results demonstrate that the combination of CIM with F12 methods is a promising way to investigate large molecules with small basis set errors.
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Affiliation(s)
- Yuqi Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, New Cornerstone Science Laboratory, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, New Cornerstone Science Laboratory, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, New Cornerstone Science Laboratory, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
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5
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Carter-Fenk K, Head-Gordon M. Repartitioned Brillouin-Wigner perturbation theory with a size-consistent second-order correlation energy. J Chem Phys 2023; 158:234108. [PMID: 37338032 PMCID: PMC10284609 DOI: 10.1063/5.0150033] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Second-order Møller-Plesset perturbation theory (MP2) often breaks down catastrophically in small-gap systems, leaving much to be desired in its performance for myriad chemical applications such as noncovalent interactions, thermochemistry, and dative bonding in transition metal complexes. This divergence problem has reignited interest in Brillouin-Wigner perturbation theory (BWPT), which is regular at all orders but lacks size consistency and extensivity, severely limiting its application to chemistry. In this work, we propose an alternative partitioning of the Hamiltonian that leads to a regular BWPT perturbation series that, through the second order, is size-extensive, size-consistent (provided its Hartree-Fock reference is also), and orbital invariant. Our second-order size-consistent Brillouin-Wigner (BW-s2) approach can describe the exact dissociation limit of H2 in a minimal basis set, regardless of the spin polarization of the reference orbitals. More broadly, we find that BW-s2 offers improvements relative to MP2 for covalent bond breaking, noncovalent interaction energies, and metal/organic reaction energies, although rivaling coupled-cluster with single and double substitutions for thermochemical properties.
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Affiliation(s)
- Kevin Carter-Fenk
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
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6
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Photocatalytic nitrogen fixation under an ambient atmosphere using a porous coordination polymer with bridging dinitrogen anions. Nat Chem 2023; 15:286-293. [PMID: 36522581 DOI: 10.1038/s41557-022-01088-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/14/2022] [Indexed: 12/23/2022]
Abstract
The design of highly electron-active and stable heterogeneous catalysts for the ambient nitrogen reduction reaction is challenging due to the inertness of the N2 molecule. Here, we report the synthesis of a zinc-based coordination polymer that features bridging dinitrogen anionic ligands, {[Zn(L)(N2)0.5(TCNQ-TCNQ)0.5]·(TCNQ)0.5}n (L is tetra(isoquinolin-6-yl)tetrathiafulvalene and TCNQ is tetracyanoquinodimethane), and show that it is an efficient photocatalyst for nitrogen fixation under an ambient atmosphere. It exhibits an ammonia conversion rate of 140 μmol g-1 h-1 and functions well also with unpurified air as the feeding gas. Experimental and theoretical studies show that the active [Zn2+-(N≡N)--Zn2+] sites can promote the formation of NH3 and the detachment of the NH3 formed creates unsaturated [Zn2+···Zn+] intermediates, which in turn can be refilled by external N2 sequestration and fast intermolecular electron migration. The [Zn2+···Zn+] intermediates stabilized by the sandwiched cage-like donor-acceptor-donor framework can sustain continuous catalytic cycles. This work presents an example of a molecular active site embedded within a coordination polymer for nitrogen fixation under mild conditions.
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7
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Seeber P, Seidenath S, Steinmetzer J, Gräfe S. Growing Spicy
ONIOMs
: Extending and generalizing concepts of
ONIOM
and many body expansions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Phillip Seeber
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
| | - Sebastian Seidenath
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
| | | | - Stefanie Gräfe
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
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8
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Wang Y, Ni Z, Neese F, Li W, Guo Y, Li S. Cluster-in-Molecule Method Combined with the Domain-Based Local Pair Natural Orbital Approach for Electron Correlation Calculations of Periodic Systems. J Chem Theory Comput 2022; 18:6510-6521. [PMID: 36240189 DOI: 10.1021/acs.jctc.2c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cluster-in-molecule (CIM) method was extended to systems with periodic boundary conditions (PBCs) in a previous work (PBC-CIM) [J. Chem. Theory Comput.2019, 15, 2933], which is able to compute the electronic structures of periodic systems at second-order Møller-Plesset perturbation theory (MP2) and coupled cluster singles and doubles (CCSD) levels. However, the high computational costs of CCSD with respect to the size of clusters limit the usage of PBC-CIM to crystals with small or medium unit cells. In this work, we further develop the PBC-CIM method by employing the domain-based local pair natural orbital (DLPNO) methods for the electron correlation calculations of clusters to reduce the computational costs. The combined approach allows CCSD with perturbative triples, denoted as CCSD(T), to be computationally available for accurate descriptions of periodic systems. The distant-pair correction is also implemented to improve the accuracy of PBC-CIM. As in the molecular cases, the distant pair correction significantly improves the accuracy of various PBC-CIM methods with few additional costs. The PBC-CIM-DLPNO-CCSD(T) approach has been applied to investigate the optimized lattice parameter of the cubic LiCl crystal and two adsorption problems (CO on the NaCl(100) surface and H2O on the h-BN surface). The results show that the CIM-DLPNO-CCSD(T) method offers accurate and efficient descriptions for the studied systems. Another application to the cohesive energy of the acetic acid crystal reveals that large basis sets are necessary for reliable calculations on the cohesive energies of molecular crystals.
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Affiliation(s)
- Yuqi Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing210023, P. R. China
| | - Zhigang Ni
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou311121, P. R. China
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der RuhrD-45470, Germany
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing210023, P. R. China
| | - Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong266237, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing210023, P. R. China
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9
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Demir Gİ, Demir S, Tekin A. 2D‐FFCASP—A New Approach for 2D Structure Prediction Applied to Self‐Assemblies of DNA Bases. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gözde İniş Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
| | - Samet Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
| | - Adem Tekin
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
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10
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Bintrim SJ, Berkelbach TC, Ye HZ. Integral-Direct Hartree-Fock and Møller-Plesset Perturbation Theory for Periodic Systems with Density Fitting: Application to the Benzene Crystal. J Chem Theory Comput 2022; 18:5374-5381. [PMID: 35969856 DOI: 10.1021/acs.jctc.2c00640] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an algorithm and implementation of integral-direct, density-fitted Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory (MP2) for periodic systems. The new code eliminates the formerly prohibitive storage requirements and allows us to study systems 1 order of magnitude larger than before at the periodic MP2 level. We demonstrate the significance of the development by studying the benzene crystal in both the thermodynamic limit and the complete basis set limit, for which we predict an MP2 cohesive energy of -72.8 kJ/mol, which is about 10-15 kJ/mol larger in magnitude than all previously reported MP2 calculations. Compared to the best theoretical estimate from literature, several modified MP2 models approach chemical accuracy in the predicted cohesive energy of the benzene crystal and hence may be promising cost-effective choices for future applications on molecular crystals.
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Affiliation(s)
- Sylvia J Bintrim
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Timothy C Berkelbach
- Department of Chemistry, Columbia University, New York, New York 10027, United States.,Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, United States
| | - Hong-Zhou Ye
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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11
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Villot C, Ballesteros F, Wang D, Lao KU. Coupled Cluster Benchmarking of Large Noncovalent Complexes in L7 and S12L as Well as the C 60 Dimer, DNA-Ellipticine, and HIV-Indinavir. J Phys Chem A 2022; 126:4326-4341. [PMID: 35766331 DOI: 10.1021/acs.jpca.2c01421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we report the benchmark binding energies of the seven complexes within the L7 data set, six host-guest complexes from the S12L data set, a C60 dimer, the DNA-ellipticine intercalation complex, and the largest system of the study, the HIV-indinavir system, which contained 343 atoms or 139 heavy atoms. The high-quality values reported were obtained via a focal point method that relies on the canonical form of second-order Møller-Plesset theory and the domain-based local pair natural orbital scheme for the coupled cluster with single double and perturbative triple excitations [DLPNO-CCSD(T)] extrapolated to the complete basis set (CBS) limit. The results in this work not only corroborate but also improve upon some previous benchmark values for large noncovalent complexes albeit at a relatively steep cost. Although local CCSD(T) and the largely successful fixed-node diffusion Monte Carlo (FN-DMC) have been shown to generally agree for small- to medium-size systems, a discrepancy in their reported binding energy values arises for large complexes, where the magnitude of the disagreement is a definite cause for concern. For example, the largest deviation in the L7 data set was 2.8 kcal/mol (∼10%) on the low end in C3GC. Such a deviation only grows worse in the S12L set, which showed a difference of up to 10.4 kcal/mol (∼25%) by a conservative estimation in buckycatcher-C60. The DNA-ellipticine complex also generated a disagreement of 4.4 kcal/mol (∼10%) between both state-of-the-art methods. The disagreement between local CCSD(T) and FN-DMC in large noncovalent complexes shows that it is urgently needed to have the canonical CCSD(T), the Monte Carlo CCSD(T), or the full configuration interaction quantum Monte Carlo approaches available to large systems on the hundred-atom scale to solve this dilemma. In addition, the performances of cheaper popular computational methods were assessed for the studied complexes with respect to DLPNO-CCSD(T)/CBS. r2SCAN-3c, B97M-V, and PBE0+D4 work well in large noncovalent complexes in this work, and GFN2-xTB performs well in π-π stacking complexes. B97M-V is the most reliable computationally efficient approach to predicting noncovalent interactions for large complexes, being the only one to have binding errors within the so-called 1 kcal/mol "chemical accuracy". The benchmark interaction energies of these host-guest complexes, molecular materials, and biological systems with electronic and medicinal implications provide crucial reference data for the improvement of current and future lower-cost methods.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Francisco Ballesteros
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Danyang Wang
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
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12
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Peng L, Peng D, Gu FL, Yang W. Regularized Localized Molecular Orbitals in a Divide-and-Conquer Approach for Linear Scaling Calculations. J Chem Theory Comput 2022; 18:2975-2982. [PMID: 35416665 PMCID: PMC9972215 DOI: 10.1021/acs.jctc.2c00142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Non-orthogonal localized molecular orbitals (NOLMOs) have been employed as building blocks for the divide-and-conquer (DC) linear scaling method. The NOLMOs are calculated from subsystems and used for constructing the density matrix (DM) of the entire system, instead of the subsystem DM in the original DC approach. Also, unlike the original DC method, the inverse electronic temperature parameter β is not needed anymore. Furthermore, a new regularized localization approach for NOLMOs has been developed, in which the localization cost function is a sum of the spatial spread function, as in the Boys method, and the kinetic energy, as a regularization measure to limit the oscillation of the NOLMOs. The optimal weight of the kinetic energy can be determined by optimization with analytical gradients. The resulting regularized NOLMOs have enhanced smoothness and better transferability because of reduced kinetic energies. Compared with the original DC, while NOLMO-DC has a similar computational linear scaling cost, the accuracy of NOLMO-DC is better by several orders of magnitude for large conjugated systems and by about 1 order of magnitude for other systems. The NOLMO-DC method is thus a promising development of the DC approach for linear scaling calculations.
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Affiliation(s)
- Liang Peng
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Environment, South China Normal University, Guangzhou 510006, People’s Republic of China
| | - Daoling Peng
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Environment, South China Normal University, Guangzhou 510006, People’s Republic of China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Environment, South China Normal University, Guangzhou 510006, People’s Republic of China
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708-0346, United States
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13
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Bensberg M, Neugebauer J. Direct orbital selection within the domain-based local pair natural orbital coupled-cluster method. J Chem Phys 2021; 155:224102. [PMID: 34911318 DOI: 10.1063/5.0071347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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 (DLPNO-CC) has become increasingly popular to calculate relative energies (e.g., reaction energies and reaction barriers). It can be applied within a multi-level DLPNO-CC-in-DLPNO-CC ansatz to reduce the computational cost and focus the available computational resources on a specific subset of the occupied orbitals. We demonstrate how this multi-level DLPNO-CC ansatz can be combined with our direct orbital selection (DOS) approach [M. Bensberg and J. Neugebauer, J. Chem. Phys. 150, 214106 (2019)] to automatically select orbital sets for any multi-level calculation. We find that the parameters for the DOS procedure can be chosen conservatively such that they are transferable between reactions. The resulting automatic multi-level DLPNO-CC method requires no user input and is extremely robust and accurate. The computational cost is easily reduced by a factor of 3 without sacrificing accuracy. We demonstrate the accuracy of the method for a total of 61 reactions containing up to 174 atoms and use it to predict the relative stability of conformers of a Ru-based catalyst.
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Affiliation(s)
- Moritz Bensberg
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
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14
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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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15
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Liang Q, Yang J. Third-Order Many-Body Expansion of OSV-MP2 Wave Function for Low-Order Scaling Analytical Gradient Computation. J Chem Theory Comput 2021; 17:6841-6860. [PMID: 34704757 DOI: 10.1021/acs.jctc.1c00581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present a many-body expansion (MBE) formulation and implementation for efficient computation of analytical energy gradients from the orbital-specific-virtual second-order Møllet-Plesset perturbation theory (OSV-MP2) based on our earlier work (Zhou et al. J. Chem. Theory Comput. 2020, 16, 196-210). The third-order MBE(3) expansion of OSV-MP2 amplitudes and density matrices was developed to adopt the orbital-specific clustering and long-range termination schemes, which avoids term-by-term differentiations of the MBE energy bodies. We achieve better efficiency by exploiting the algorithmic sparsity that allows us to prune out insignificant fitting integrals and OSV relaxations. With these approximations, the present implementation is benchmarked on a range of molecules that show an economic scaling in the linear and quadratic regimes for computing MBE(3)-OSV-MP2 amplitude and gradient equations, respectively, and yields normal accuracy comparable to the original OSV-MP2 results. The MPI-3-based parallelism through shared memory one-sided communication is further developed for improving parallel scalability and memory accessibility by sorting the MBE(3) orbital clusters into independent tasks that are distributed on multiple processes across many nodes, supporting both global and local data locations in which selected MBE(3)-OSV-MP2 intermediates of different sizes are distinguished and accordingly placed. The accuracy and efficiency level of our MBE(3)-OSV-MP2 analytical gradient implementation is finally illustrated in two applications: we show that the subtle coordination structure differences of mechanically interlocked Cu-catenane complexes can be distinguished when tuning ligand lengths; and the porphycene molecular dynamics reveals the emergence of the vibrational signature arising from softened N-H stretching associated with hydrogen transfer, using an MP2 level of electron correlation and classical nuclei for the first time.
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Affiliation(s)
- Qiujiang Liang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Jun Yang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
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16
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Ballesteros F, Dunivan S, Lao KU. Coupled cluster benchmarks of large noncovalent complexes: The L7 dataset as well as DNA-ellipticine and buckycatcher-fullerene. J Chem Phys 2021; 154:154104. [PMID: 33887937 DOI: 10.1063/5.0042906] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In this work, benchmark binding energies for dispersion-bound complexes in the L7 dataset, the DNA-ellipticine intercalation complex, and the buckycatcher-C60 complex with 120 heavy atoms using a focal-point method based on the canonical form of second-order Møller-Plesset theory (MP2) and the domain based local pair natural orbital scheme for the coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] extrapolated to the complete basis set (CBS) limit are reported. This work allows for increased confidence given the agreement with respect to values recently obtained using the local natural orbital CCSD(T) for L7 and the canonical CCSD(T)/CBS result for the coronene dimer (C2C2PD). Therefore, these results can be considered pushing the CCSD(T)/CBS binding benchmark to the hundred-atom scale. The disagreements between the two state-of-the-art methods, CCSD(T) and fixed-node diffusion Monte Carlo, are substantial with at least 2.0 (∼10%), 1.9 (∼5%), and 10.3 kcal/mol (∼25%) differences for C2C2PD in L7, DNA-ellipticine, and buckycatcher-C60, respectively. Such sizable discrepancy above "chemical accuracy" for large noncovalent complexes indicates how challenging it is to obtain benchmark binding interactions for systems beyond small molecules, although the three up-to-date density functionals, PBE0+D4, ωB97M-V, and B97M-V, agree better with CCSD(T) for these large systems. In addition to reporting these values, different basis sets and various CBS extrapolation parameters for Hartree-Fock and MP2 correlation energies were tested for the first time in large noncovalent complexes with the goal of providing some indications toward optimal cost effective routes to approach the CBS limit without substantial loss in quality.
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Affiliation(s)
- Francisco Ballesteros
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Shelbie Dunivan
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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17
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Haldar S, Dutta AK. An efficient Fock space multi-reference coupled cluster method based on natural orbitals: Theory, implementation, and benchmark. J Chem Phys 2021; 155:014105. [PMID: 34241374 DOI: 10.1063/5.0054171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a natural orbital-based implementation of the intermediate Hamiltonian Fock space coupled-cluster method for the (1, 1) sector of Fock space. The use of natural orbitals significantly reduces the computational cost and can automatically choose an appropriate set of active orbitals. The new method retains the charge transfer separability of the original intermediate Hamiltonian Fock space coupled-cluster method and gives excellent performance for valence, Rydberg, and charge-transfer excited states. It offers significant computational advantages over the popular equation of motion coupled cluster method for excited states dominated by single excitations.
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Affiliation(s)
- Soumi Haldar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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18
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Ghosh S, Neese F, Izsák R, Bistoni G. Fragment-Based Local Coupled Cluster Embedding Approach for the Quantification and Analysis of Noncovalent Interactions: Exploring the Many-Body Expansion of the Local Coupled Cluster Energy. J Chem Theory Comput 2021; 17:3348-3359. [PMID: 34037397 PMCID: PMC8190956 DOI: 10.1021/acs.jctc.1c00005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Indexed: 11/30/2022]
Abstract
Herein, we introduce a fragment-based local coupled cluster embedding approach for the accurate quantification and analysis of noncovalent interactions in molecular aggregates. Our scheme combines two different expansions of the domain-based local pair natural orbital coupled cluster (DLPNO-CCSD(T)) energy: the many-body expansion (MBE) and the local energy decomposition (LED). The low-order terms in the MBE are initially computed in the presence of an environment that is treated at a low level of theory. Then, LED is used to decompose the energy of each term in the embedded MBE into additive fragment and fragment-pairwise contributions. This information is used to quantify the total energy of the system while providing at the same time in-depth insights into the nature and cooperativity of noncovalent interactions. Two different approaches are introduced and tested, in which the environment is treated at different levels of theory: the local coupled cluster in the Hartree-Fock (LCC-in-HF) method, in which the environment is treated at the HF level; and the electrostatically embedded local coupled cluster method (LCC-in-EE), in which the environment is replaced by point charges. Both schemes are designed to preserve as much as possible the accuracy of the parent local coupled cluster method for total energies, while being embarrassingly parallel and less memory intensive. These schemes appear to be particularly promising for the study of large and complex molecular aggregates at the coupled cluster level, such as condensed phase systems and protein-ligand interactions.
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Affiliation(s)
- Soumen Ghosh
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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19
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Stoychev GL, Auer AA, Gauss J, Neese F. DLPNO-MP2 second derivatives for the computation of polarizabilities and NMR shieldings. J Chem Phys 2021; 154:164110. [PMID: 33940835 DOI: 10.1063/5.0047125] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a derivation and efficient implementation of the formally complete analytic second derivatives for the domain-based local pair natural orbital second order Møller-Plesset perturbation theory (MP2) method, applicable to electric or magnetic field-response properties but not yet to harmonic frequencies. We also discuss the occurrence and avoidance of numerical instability issues related to singular linear equation systems and near linear dependences in the projected atomic orbital domains. A series of benchmark calculations on medium-sized systems is performed to assess the effect of the local approximation on calculated nuclear magnetic resonance shieldings and the static dipole polarizabilities. Relative deviations from the resolution of the identity-based MP2 (RI-MP2) reference for both properties are below 0.5% with the default truncation thresholds. For large systems, our implementation achieves quadratic effective scaling, is more efficient than RI-MP2 starting at 280 correlated electrons, and is never more than 5-20 times slower than the equivalent Hartree-Fock property calculation. The largest calculation performed here was on the vancomycin molecule with 176 atoms, 542 correlated electrons, and 4700 basis functions and took 3.3 days on 12 central processing unit cores.
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Affiliation(s)
- Georgi L Stoychev
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Alexander A Auer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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20
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Fujimori T, Kobayashi M, Taketsugu T. Energy-based automatic determination of buffer region in the divide-and-conquer second-order Møller-Plesset perturbation theory. J Comput Chem 2021; 42:620-629. [PMID: 33534916 PMCID: PMC7986104 DOI: 10.1002/jcc.26486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/19/2020] [Accepted: 01/15/2021] [Indexed: 11/21/2022]
Abstract
In the linear‐scaling divide‐and‐conquer (DC) electronic structure method, each subsystem is calculated together with the neighboring buffer region, the size of which affects the energy error introduced by the fragmentation in the DC method. The DC self‐consistent field calculation utilizes a scheme to automatically determine the appropriate buffer region that is as compact as possible for reducing the computational time while maintaining acceptable accuracy (J. Comput. Chem. 2018, 39, 909). To extend the automatic determination scheme of the buffer region to the DC second‐order Møller–Plesset perturbation (MP2) calculation, a scheme for estimating the subsystem MP2 correlation energy contribution from each atom in the buffer region is proposed. The estimation is based on the atomic orbital Laplace MP2 formalism. Based on this, an automatic buffer determination scheme for the DC‐MP2 calculation is constructed and its performance for several types of systems is assessed.
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Affiliation(s)
- Toshikazu Fujimori
- Graduate School of Chemical Sciences and EngineeringHokkaido UniversitySapporoJapan
| | - Masato Kobayashi
- Department of Chemistry, Faculty of ScienceHokkaido UniversitySapporoJapan
- WPI‐ICReDDHokkaido UniversitySapporoJapan
- ESICB, Kyoto UniversityKyotoJapan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of ScienceHokkaido UniversitySapporoJapan
- WPI‐ICReDDHokkaido UniversitySapporoJapan
- ESICB, Kyoto UniversityKyotoJapan
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21
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Ni Z, Guo Y, Neese F, Li W, Li S. Cluster-in-Molecule Local Correlation Method with an Accurate Distant Pair Correction for Large Systems. J Chem Theory Comput 2021; 17:756-766. [PMID: 33410327 DOI: 10.1021/acs.jctc.0c00831] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cluster-in-molecule (CIM) local correlation approach with an accurate distant pair correlation energy correction is presented. For large systems, the inclusion of distant pair correlation energies is essential for the accurate prediction of absolute correlation energies and relative energies. Here, we propose a simple and efficient scheme for evaluating the distant pair correlation energy correction for the CIM approaches. The corrections can be readily extracted from electron correlation calculations of clusters with almost no additional effort. Benchmark calculations show that the improved CIM approach can recover more than 99.94% of the correlation energy calculated by the parent method. By combining the CIM approach with the domain-based local pair natural orbital (DLPNO) local correlation approach, we have provided accurate binding energies at the CIM-DLPNO-CCSD(T) level for a test set consisting of eight weakly bound complexes ranging in size from 200 to 1027 atoms. With these results as the reference data, the accuracy and applicability of other electron correlation methods and a few density functional methods for large systems have been assessed.
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Affiliation(s)
- Zhigang Ni
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China.,College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, China
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany.,FAccTs GmbH, Rolandstr. 67, 50677 Köln, Germany
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
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22
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Calvin JA, Peng C, Rishi V, Kumar A, Valeev EF. Many-Body Quantum Chemistry on Massively Parallel Computers. Chem Rev 2020; 121:1203-1231. [DOI: 10.1021/acs.chemrev.0c00006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Justus A. Calvin
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chong Peng
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Varun Rishi
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ashutosh Kumar
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Edward F. Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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23
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Mukherjee M, Tripathi D, Dutta AK. Water mediated electron attachment to nucleobases: Surface-bound vs bulk solvated electrons. J Chem Phys 2020; 153:044305. [DOI: 10.1063/5.0010509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Madhubani Mukherjee
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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24
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Aysin RR, Leites LA, Bukalov SS. Aromaticity of 1-Heterocyclopropenes Containing an Atom of Group 14 or 4. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- R. R. Aysin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciencies, ul. Vavilova 28, Moscow 119991, Russia
| | - L. A. Leites
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciencies, ul. Vavilova 28, Moscow 119991, Russia
| | - S. S. Bukalov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciencies, ul. Vavilova 28, Moscow 119991, Russia
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25
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Neese F, Wennmohs F, Becker U, Riplinger C. The ORCA quantum chemistry program package. J Chem Phys 2020; 152:224108. [DOI: 10.1063/5.0004608] [Citation(s) in RCA: 697] [Impact Index Per Article: 174.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
- FAccTs GmbH, Rolandstr. 67, 50677 Köln, Germany
| | - Frank Wennmohs
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
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26
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Artiukhin DG, Klinting EL, König C, Christiansen O. Adaptive density-guided approach to double incremental potential energy surface construction. J Chem Phys 2020; 152:194105. [PMID: 33687258 DOI: 10.1063/5.0004686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We present a combination of the recently developed double incremental expansion of potential energy surfaces with the well-established adaptive density-guided approach to grid construction. This unique methodology is based on the use of an incremental expansion for potential energy surfaces, known as n-mode expansion; an incremental many-body representation of the electronic energy; and an efficient vibrational density-guided approach to automated determination of grid dimensions and granularity. The reliability of the method is validated calculating potential energy surfaces and obtaining fundamental excitation energies for three moderate-size chain-like molecular systems. The use of our methodology leads to considerable computational savings for potential energy surface construction compared to standard approaches while maintaining a high level of accuracy in the resulting potential energy surfaces. Additional investigations indicate that our method can be applied to covalently bound and strongly interacting molecular systems, even though these cases are known to be very unfavorable for fragmentation schemes. We therefore conclude that the presented methodology is a robust and flexible approach to potential energy surface construction, which introduces considerable computational savings without compromising the accuracy of vibrational spectra calculations.
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Affiliation(s)
- Denis G Artiukhin
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
| | | | - Carolin König
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Straße 1, D-24118 Kiel, Germany
| | - Ove Christiansen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
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27
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Haldar S, Dutta AK. A Multilayer Approach to the Equation of Motion Coupled-Cluster Method for the Electron Affinity. J Phys Chem A 2020; 124:3947-3962. [DOI: 10.1021/acs.jpca.0c01793] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Soumi Haldar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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28
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Ranga S, Mukherjee M, Dutta AK. Interactions of Solvated Electrons with Nucleobases: The Effect of Base Pairing. Chemphyschem 2020; 21:1019-1027. [DOI: 10.1002/cphc.202000133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/23/2020] [Indexed: 01/30/2023]
Affiliation(s)
- Santosh Ranga
- Department of ChemistryIndian Institute of Technology (IIT), Bombay Powai Maharastra 400076 India
| | - Madhubani Mukherjee
- Department of ChemistryIndian Institute of Technology (IIT), Bombay Powai Maharastra 400076 India
| | - Achintya Kumar Dutta
- Department of ChemistryIndian Institute of Technology (IIT), Bombay Powai Maharastra 400076 India
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29
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Guo Y, Riplinger C, Liakos DG, Becker U, Saitow M, Neese F. Linear scaling perturbative triples correction approximations for open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory [DLPNO-CCSD(T 0/T)]. J Chem Phys 2020; 152:024116. [PMID: 31941297 DOI: 10.1063/1.5127550] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The coupled cluster method with single-, double-, and perturbative triple excitations [CCSD(T)] is considered to be one of the most reliable quantum chemistry theories. However, the steep scaling of CCSD(T) has limited its application to small or medium-sized systems for a long time. In our previous work, the linear scaling domain based local pair natural orbital CCSD variant (DLPNO-CCSD) has been developed for closed-shell and open-shell. However, it is known from extensive benchmark studies that triple-excitation contributions are important to reach chemical accuracy. In the present work, two linear scaling (T) approximations for open-shell DLPNO-CCSD are implemented and compared: (a) an algorithm based on the semicanonical approximation, in which off-diagonal Fock matrix elements in the occupied space are neglected [referred to as DLPNO-(T0)]; and (b) an improved algorithm in which the triples amplitudes are computed iteratively [referred to as DLPNO-(T)]. This work is based on the previous open-shell DLPNO-CCSD algorithm [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)] as well as the iterative (T) correction for closed-shell systems [Y. Guo et al., J. Chem. Phys. 148, 011101 (2018)]. Our results show that the new open-shell perturbative corrections, DLPNO-(T0/T), can predict accurate absolute and relative correlation energies relative to the canonical reference calculations with the same basis set. The absolute energies from DLPNO-(T) are significantly more accurate than those of DLPNO-(T0). The additional computational effort of DLPNO-(T) relative to DLPNO-(T0) is a factor of 4 on average. We report calculations on systems with more than 4000 basis functions.
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Affiliation(s)
- Yang Guo
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | | | - Dimitrios G Liakos
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Masaaki Saitow
- Department of Chemistry, Graduate School of Science, Nagoya University, 1-5 Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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30
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Liakos DG, Guo Y, Neese F. Comprehensive Benchmark Results for the Domain Based Local Pair Natural Orbital Coupled Cluster Method (DLPNO-CCSD(T)) for Closed- and Open-Shell Systems. J Phys Chem A 2019; 124:90-100. [PMID: 31841627 DOI: 10.1021/acs.jpca.9b05734] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study we examine the accuracy of domain-based local pair natural orbital coupled cluster theory with single, double, and perturbative triple excitations (DLPNO-CCSD(T)) on a large benchmark data set. To this end, we use the recently published GMTKN55 superset of molecules that contains 1505 relative energies and 2462 single-point calculations. To our knowledge this is the most comprehensive benchmark evaluation of any highly correlated wave function based ab initio method to date. In the first part of the study, canonical CCSD(T) reference calculations were carried out on the entire test set in order to guarantee that the reference data are of uniform quality. Second, DLPNO-CCSD(T) calculations were carried out under identical conditions. The main finding is that with the exception of two data sets, all data sets have a MAD of 0.4 kcal/mol or less and the majority of sets have a MAD of less than 0.2 kcal/mol. For open shells, the accuracy of the DLPNO calculations was significantly improved through an iterative version of the triples correction.
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Affiliation(s)
- Dimitrios G Liakos
- Department of Molecular Theory and Spectroscopy , Max Planck Institut für Kohlenforschung , Kaiser-Wilhelm Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Yang Guo
- Department of Molecular Theory and Spectroscopy , Max Planck Institut für Kohlenforschung , Kaiser-Wilhelm Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Frank Neese
- Department of Molecular Theory and Spectroscopy , Max Planck Institut für Kohlenforschung , Kaiser-Wilhelm Platz 1 , 45470 Mülheim an der Ruhr , Germany
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31
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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32
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Nagy PR, Kállay M. Approaching the Basis Set Limit of CCSD(T) Energies for Large Molecules with Local Natural Orbital Coupled-Cluster Methods. J Chem Theory Comput 2019; 15:5275-5298. [DOI: 10.1021/acs.jctc.9b00511] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Péter R. Nagy
- 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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Ni Z, Wang Y, Li W, Pulay P, Li S. Analytical Energy Gradients for the Cluster-in-Molecule MP2 Method and Its Application to Geometry Optimizations of Large Systems. J Chem Theory Comput 2019; 15:3623-3634. [PMID: 31091102 DOI: 10.1021/acs.jctc.9b00259] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient analytical energy gradient algorithm for the cluster-in-molecule (CIM) second order Møller-Plesset perturbation theory (MP2) method is presented. In our algorithm, the gradient contributions from the nonseparable term of the two-body density matrix on a given atom is extracted from calculations on a cluster constructed for this atom. The other terms in the CIM-MP2 energy gradient expression are evaluated by constructing the density matrices of the whole system with the contributions from all clusters constructed. For basis sets with diffuse functions, tight CIM parameters are necessary to obtain accurate gradients. Benchmark calculations show that the CIM-MP2 method can accurately reproduce the conventional MP2 gradients and geometries for larger systems. The optimized structure of a 174-atom oligopeptide using the CIM-MP2 method with the cc-pVDZ basis set is in good agreement with the corresponding crystal structure. The present CIM-MP2 gradient program can be used for optimizing the geometries of large systems with hundreds of atoms on ordinary workstations.
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Affiliation(s)
- Zhigang Ni
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , P. R. China.,Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Yuqi Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , P. R. China
| | - Peter Pulay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , P. R. China
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34
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Wang Y, Ni Z, Li W, Li S. Cluster-in-Molecule Local Correlation Approach for Periodic Systems. J Chem Theory Comput 2019; 15:2933-2943. [DOI: 10.1021/acs.jctc.8b01200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuqi Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Zhigang Ni
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
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35
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Altun A, Saitow M, Neese F, Bistoni G. Local Energy Decomposition of Open-Shell Molecular Systems in the Domain-Based Local Pair Natural Orbital Coupled Cluster Framework. J Chem Theory Comput 2019; 15:1616-1632. [PMID: 30702888 PMCID: PMC6728066 DOI: 10.1021/acs.jctc.8b01145] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Local
energy decomposition (LED) analysis decomposes the interaction
energy between two fragments calculated at the domain-based local
pair natural orbital CCSD(T) (DLPNO-CCSD(T)) level of theory into
a series of chemically meaningful contributions and has found widespread
applications in the study of noncovalent interactions. Herein, an
extension of this scheme that allows for the analysis of interaction
energies of open-shell molecular systems calculated at the UHF-DLPNO-CCSD(T)
level is presented. The new scheme is illustrated through applications
to the CH2···X (X = He, Ne, Ar, Kr, and
water) and heme···CO interactions in the low-lying
singlet and triplet spin states. The results are used to discuss the
mechanism that governs the change in the singlet–triplet energy
gap of methylene and heme upon adduct formation.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
| | - Masaaki Saitow
- Department of Chemistry, Graduate School of Science , Nagoya University , 1-5 Chikusa-ku , 464-8602 Nagoya , Japan
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
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36
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Saitow M, Dutta AK, Neese F. Accurate Ionization Potentials, Electron Affinities and Electronegativities of Single-Walled Carbon Nanotubes by State-of-the-Art Local Coupled-Cluster Theory. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Masaaki Saitow
- Department of Chemistry, Graduate School of Science, Nagoya University, 1-5 Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, 1 Kaiser-Wilhelm Platz, Mülheim an der Ruhr 45470, Germany
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37
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Harnessing desktop computers for ab initio calculation of vibrational IR/Raman spectra of large molecules. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1568-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Ni Z, Li W, Li S. Fully optimized implementation of the cluster-in-molecule local correlation approach for electron correlation calculations of large systems. J Comput Chem 2018; 40:1130-1140. [DOI: 10.1002/jcc.25730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/27/2018] [Accepted: 09/27/2018] [Indexed: 01/30/2023]
Affiliation(s)
- Zhigang Ni
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE; Institute of Theoretical and Computational Chemistry, Nanjing University; Nanjing 210023 People's Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE; Institute of Theoretical and Computational Chemistry, Nanjing University; Nanjing 210023 People's Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE; Institute of Theoretical and Computational Chemistry, Nanjing University; Nanjing 210023 People's Republic of China
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39
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Nagy PR, Samu G, Kállay M. Optimization of the Linear-Scaling Local Natural Orbital CCSD(T) Method: Improved Algorithm and Benchmark Applications. J Chem Theory Comput 2018; 14:4193-4215. [DOI: 10.1021/acs.jctc.8b00442] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Péter R. Nagy
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Gyula Samu
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, 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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