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Hillers-Bendtsen AE, Jensen F, Mikkelsen KV, Olsen J, Jørgensen P. Cluster perturbation theory IX: Perturbation series for the coupled cluster singles and doubles ground state energy. J Chem Phys 2024; 160:104108. [PMID: 38477336 DOI: 10.1063/5.0192388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
In this paper, we develop and analyze a number of perturbation series that target the coupled cluster singles and doubles (CCSD) ground state energy. We show how classical Møller-Plesset perturbation theory series can be restructured to target the CCSD energy based on a reference CCS calculation and how the corresponding cluster perturbation series differs from the classical Møller-Plesset perturbation series. Subsequently, we reformulate these series using the coupled cluster Lagrangian framework to obtain series, where fourth and fifth order energies are determined only using parameters through second order. To test the methods, we perform a series of test calculations on molecular photoswitches of both total energies and reaction energies. We find that the fifth order reaction energies are of CCSD quality and that they are of comparable accuracy to state-of-the-art approximations to the CCSD energy based on local pair natural orbitals. The advantage of the present approach over local correlation methods is the absence of user defined threshold parameters for neglecting or approximating contributions to the correlation energy. Fixed threshold parameters lead to discontinuous energy surfaces, although this effect is often small enough to be ignored, but the present approach has a differentiable energy that will facilitate derivation and implementation of gradients and higher derivatives. A further advantage is that the calculation of the perturbation correction is non-iterative and can, therefore, be calculated in parallel, leading to a short time-to-solution.
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Affiliation(s)
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK 8000 Aarhus C, Denmark
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen Ø, Denmark
| | - Jeppe Olsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK 8000 Aarhus C, Denmark
| | - Poul Jørgensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK 8000 Aarhus C, Denmark
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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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Wang Z, Aldossary A, Shi T, Liu Y, Li XS, Head-Gordon M. Local Second-Order Møller-Plesset Theory with a Single Threshold Using Orthogonal Virtual Orbitals: Theory, Implementation, and Assessment. J Chem Theory Comput 2023; 19:7577-7591. [PMID: 37877899 DOI: 10.1021/acs.jctc.3c00744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
It has long been clear that electron correlation methods exhibit unphysical compute scalings with molecular size, which has motivated the development of local correlation methods to discard effectively zero contributions in a controlled way to yield an approximate correlation energy. The ideal local correlation method should have a single numerical threshold that controls the dropping of terms with the ability to have that threshold set small enough so that the correlation energy is reproduced to enough significant figures such that the result is chemically identical. This work reports such a method for the second-order Møller-Plesset (MP2) theory. The theory, implementation, and testing of this local MP2 theory are reported. Thresholds ranging from 10-5 to 10-8 and basis sets ranging from split valence plus polarization through to quadruple-ζ are assessed for local MP2 calculations on a range of molecules, including linear chains and molecules with two- and three-dimensional character. The implementation is shared memory parallel via OpenMP and yields roughly 50% parallel efficiency with 16 cores for a large job. Considerable efforts were made to minimize memory demands, which increased as thresholds were tightened. A variety of relative energy calculations are presented as a function of threshold to provide some guidance to users on how to obtain adequate precision at a low compute cost. It is particularly clear that derivative properties require tighter thresholds in order to achieve an adequate precision.
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Affiliation(s)
- Zhenling Wang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Abdulrahman Aldossary
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Tianyi Shi
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yang Liu
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xiaoye S Li
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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4
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Werner HJ, Hansen A. Accurate Calculation of Isomerization and Conformational Energies of Larger Molecules Using Explicitly Correlated Local Coupled Cluster Methods in Molpro and ORCA. J Chem Theory Comput 2023; 19:7007-7030. [PMID: 37486154 DOI: 10.1021/acs.jctc.3c00270] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
An overview of the approximations in the explicitly correlated local coupled cluster methods PNO-LCCSD(T)-F12 in Molpro and DLPNO-CCSD(T)F12 in ORCA is given. Options to select the domains of projected atomic orbitals (PAOs), pair natural orbitals (PNOs), and triples natural orbitals (TNOs) in both programs are described and compared in detail. The two programs are applied to compute isomerization and conformational energies of the ISOL24 and ACONFL test sets, where the former is part of the GMTKN55 benchmark suite. Thorough studies of basis set effects are presented for selected systems. These revealed large intramolecular basis set superposition effects that make it practically impossible to reliably determine the complete basis set (CBS) limits without including explicitly correlated terms. The latter strongly reduce the basis set dependence and at the same time also errors caused by the local domain approximations. On the basis of these studies, the PNO-LCCSD(T)-F12 method is applied to determine new reference energies for the above-mentioned benchmark sets. We are confident that our results should agree within a few tenths of a kcal mol-1 with the (unknown) CCSD(T)/CBS values, which therefore allowed us to define computational settings for accurate explicitly correlated local coupled cluster methods with moderate computational effort. With these protocols, especially PNO-LCCSD(T)-F12b/AVTZ', reliable reference values for comprehensive benchmark sets can be generated efficiently. This can significantly advance the development and evaluation of the performance of approximate electronic structure methods, especially improved density functional approximations or machine learning approaches.
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Affiliation(s)
- Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
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5
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Hohenstein EG, Fales BS, Parrish RM, Martínez TJ. Rank-reduced coupled-cluster. III. Tensor hypercontraction of the doubles amplitudes. J Chem Phys 2022; 156:054102. [DOI: 10.1063/5.0077770] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - B. Scott Fales
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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6
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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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7
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Hansen AS, Aurbakken E, Pedersen TB. Smooth potential-energy surfaces in fragmentation-based local correlation methods for periodic systems. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1896046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- A. S. Hansen
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - E. Aurbakken
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - T. B. Pedersen
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
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8
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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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9
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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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10
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Ma Q, Werner HJ. Scalable Electron Correlation Methods. 8. Explicitly Correlated Open-Shell Coupled-Cluster with Pair Natural Orbitals PNO-RCCSD(T)-F12 and PNO-UCCSD(T)-F12. J Chem Theory Comput 2021; 17:902-926. [PMID: 33405921 DOI: 10.1021/acs.jctc.0c01129] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present explicitly correlated open-shell pair natural orbital local coupled-cluster methods, PNO-RCCSD(T)-F12 and PNO-UCCSD(T)-F12. The methods are extensions of our previously reported PNO-R/UCCSD methods (J. Chem. Theory Comput., 2020, 16, 3135-3151, https://pubs.acs.org/doi/10.1021/acs.jctc.0c00192) with additions of explicit correlation and perturbative triples corrections. The explicit correlation treatment follows the spin-orbital CCSD-F12b theory using Ansatz 3*A, which is found to yield comparable or better basis set convergence than the more rigorous Ansatz 3C in computed ionization potentials and reaction energies using double- to quaduple-ζ basis sets. The perturbative triples correction is adapted from the spin-orbital (T) theory to use triples natural orbitals (TNOs). To address the coupling due to off-diagonal Fock matrix elements, the local triples amplitudes are iteratively solved using small domains of TNOs, and a semicanonical (T0) domain correction with larger domains is applied to reduce the domain errors. The performance of the methods is demonstrated through benchmark calculations on ionization potentials, radical stabilization energies, reaction energies of fragmentations and rearrangements in radical cations, and spin-state energy differences of iron complexes. For a few test sets where canonical calculations are feasible, PNO-RCCSD(T)-F12 results agree with the canonical ones to within 0.4 kcal mol-1, and this maximum error is reduced to below 0.2 kcal mol-1 when large local domains are used. For larger systems, results using different thresholds for the local approximations are compared to demonstrate that 1 kcal mol-1 level of accuracy can be achieved using our default settings. For a couple of difficult cases, it is demonstrated that the errors from individual approximations are only a fraction of 1 kcal mol-1, and the overall accuracy of the method does not rely on error compensations. In contrast to canonical calculations, the use of spin-orbitals does not lead to a significant increase of computational time and memory usage in the most expensive steps of PNO-R/UCCSD(T)-F12 calculations. The only exception is the iterative solution of the (T) amplitudes, which can be avoided without significant errors by using a perturbative treatment of the off-diagonal coupling, known as (T1) approximation. For most systems, even the semicanonical approximation (T0) leads only to small errors in relative energies. Our program is well parallelized and capable of computing accurate correlation energies for molecules with 100-200 atoms using augmented triple-ζ basis sets in less than a day of elapsed time on a small computer cluster.
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Affiliation(s)
- Qianli Ma
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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11
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Mukherjee M, Tripathi D, Brehm M, Riplinger C, Dutta AK. Efficient EOM-CC-based Protocol for the Calculation of Electron Affinity of Solvated Nucleobases: Uracil as a Case Study. J Chem Theory Comput 2020; 17:105-116. [DOI: 10.1021/acs.jctc.0c00655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Divya Tripathi
- Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Martin Brehm
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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12
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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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13
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Csóka J, Kállay M. Speeding up density fitting Hartree–Fock calculations with multipole approximations. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1769213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- József Csóka
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
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14
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Espinasse A, Wen X, Goodpaster JD, Carlson EE. Mechanistic Studies of Bioorthogonal ATP Analogues for Assessment of Histidine Kinase Autophosphorylation. ACS Chem Biol 2020; 15:1252-1260. [PMID: 32043868 DOI: 10.1021/acschembio.9b01024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Phosphorylation is an essential protein modification and is most commonly associated with hydroxyl-containing amino acids via an adenosine triphosphate (ATP) substrate. The last decades have brought greater appreciation to the roles that phosphorylation of myriad amino acids plays in biological signaling, metabolism, and gene transcription. Histidine phosphorylation occurs in both eukaryotes and prokaryotes but has been shown to dominate signaling networks in the latter due to its role in microbial two-component systems. Methods to investigate histidine phosphorylation have lagged behind those to study serine, threonine, and tyrosine modifications due to its inherent instability and the historical view that this protein modification was rare. An important strategy to overcome the reactivity of phosphohistidine is the development of substrate-based probes with altered chemical properties that improve modification longevity but that do not suffer from poor recognition or transfer by the protein. Here, we present combined experimental and computational studies to better understand the molecular requirements for efficient histidine phosphorylation by comparison of the native kinase substrate, ATP, and alkylated ATP derivatives. While recognition of the substrates by the histidine kinases is an important parameter for the formation of phosphohistidine derivatives, reaction sterics also affect the outcome. In addition, we found that stability of the resulting phosphohistidine moieties correlates with the stability of their hydrolysis products, specifically with their free energy in solution. Interestingly, alkylation dramatically affects the stability of the phosphohistidine derivatives at very acidic pH values. These results provide critical mechanistic insights into histidine phosphorylation and will facilitate the design of future probes to study enzymatic histidine phosphorylation.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Xuelan Wen
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
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15
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Ma Q, Werner HJ. Scalable Electron Correlation Methods. 7. Local Open-Shell Coupled-Cluster Methods Using Pair Natural Orbitals: PNO-RCCSD and PNO-UCCSD. J Chem Theory Comput 2020; 16:3135-3151. [PMID: 32275428 DOI: 10.1021/acs.jctc.0c00192] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present well-parallelized local implementations of high-spin open-shell coupled cluster methods with single and double excitations (CCSD) using pair natural orbitals (PNOs). The methods are based on the spin-orbital coupled cluster theory using restricted open-shell Hartree-Fock (ROHF) reference functions. Two variants, namely, PNO-UCCSD and PNO-RCCSD are implemented and compared. In PNO-UCCSD, the coupled cluster amplitudes are spin-unrestricted, while in PNO-RCCSD the linear terms are spin-adapted by a spin-projection approach as described in J. Chem. Phys. 1993, 99, 5219-5227. Near linear scaling of the computational cost with the number of correlated electrons is achieved by applying domain and pair approximations. The PNOs are spin-independent and obtained using a semicanonical spin-restricted MP2 approximation with large domains of projected atomic orbitals (PAOs). The pair approximations of our previously described closed-shell PNO-LCCSD method are carefully revised so that they are compatible to the UCCSD theory, and PNO-UCCSD or PNO-RCCSD calculations for closed-shell molecules yield exactly the same results as corresponding spin-free closed-shell PNO-LCCSD calculations. The convergence of the results with respect to the thresholds and options that control the domain and pair approximations is demonstrated. It is found that large domains are required for the single excitations in open-shell calculations in order to obtain converged results. In general, the errors of relative energies caused by the local approximations can be reduced to below 1 kcal mol-1, even for difficult cases. Presently, PNO-RCCSD and PNO-UCCSD calculations for molecules with 100-200 atoms and augmented triple-ζ basis sets can be carried out in a few hours of elapsed time using ∼100 CPU cores. In addition, the program is also capable of performing distinguishable cluster (PNO-RDCSD and PNO-UDCSC) calculations. The present work is a critical step in developing fully local open-shell PNO-RCCSD(T)-F12 methods.
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Affiliation(s)
- Qianli Ma
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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16
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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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17
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Werner HJ, Knowles PJ, Manby FR, Black JA, Doll K, Heßelmann A, Kats D, Köhn A, Korona T, Kreplin DA, Ma Q, Miller TF, Mitrushchenkov A, Peterson KA, Polyak I, Rauhut G, Sibaev M. The Molpro quantum chemistry package. J Chem Phys 2020; 152:144107. [PMID: 32295355 DOI: 10.1063/5.0005081] [Citation(s) in RCA: 475] [Impact Index Per Article: 118.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Molpro is a general purpose quantum chemistry software package with a long development history. It was originally focused on accurate wavefunction calculations for small molecules but now has many additional distinctive capabilities that include, inter alia, local correlation approximations combined with explicit correlation, highly efficient implementations of single-reference correlation methods, robust and efficient multireference methods for large molecules, projection embedding, and anharmonic vibrational spectra. In addition to conventional input-file specification of calculations, Molpro calculations can now be specified and analyzed via a new graphical user interface and through a Python framework.
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Affiliation(s)
- Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Peter J Knowles
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Frederick R Manby
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Joshua A Black
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Klaus Doll
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Andreas Heßelmann
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Daniel Kats
- Max-Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Andreas Köhn
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, L. Pasteura 1 St., 02-093 Warsaw, Poland
| | - David A Kreplin
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Qianli Ma
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Kirk A Peterson
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, USA
| | - Iakov Polyak
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Guntram Rauhut
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Marat Sibaev
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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18
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Saitow M, Yanai T. A multireference coupled-electron pair approximation combined with complete-active space perturbation theory in local pair-natural orbital framework. J Chem Phys 2020; 152:114111. [PMID: 32199413 DOI: 10.1063/1.5142622] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Complete-Active Space Second-order Perturbation Theory (CASPT2) has been one of the most widely-used methods for reliably calculating electronic structures of multireference systems. Because of its lowest level treatment of dynamic correlation, it has a high computational feasibility; however, its accuracy in some cases falls short of needs. Here, as a simple yet higher-order alternative, we introduce a hybrid theory of the CASPT2 and a multireference variant of the Coupled-Electron Pair Approximation (CEPA), which is a class of high level correlation theory. A central feature of our theory (CEPT2) is to use the two underlying theories for describing different divisions of correlation components based on the full internal contraction framework. The external components, which usually give a major contribution to the dynamic correlation, are intensively described using the CEPA Ansatz, while the rests are treated at the CASPT2 level. Furthermore, to drastically reduce the computational demands, we have incorporated the pair-natural orbital (PNO) method into our multireference implementations. This development, thus, requires highly complex derivations and coding, while it has been largely facilitated with an automatic expression and code generation technique. To highlight the accuracy of the CEPT2 approach and to assess the errors caused by the PNO truncation, benchmark calculations are shown on small- to medium-size molecules, illustrating the high accuracy of the present CEPT2 model. By tightening the truncation thresholds, the PNO-CEPT2 energy converges toward the canonical counterpart and is more accurate than that of PNO-CASPT2 as long as the same truncation thresholds are used.
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Affiliation(s)
- Masaaki Saitow
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa Ward, Nagoya, Aichi 464-8601, Japan
| | - Takeshi Yanai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa Ward, Nagoya, Aichi 464-8601, Japan
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19
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Hansen AS, Baardsen G, Rebolini E, Maschio L, Pedersen TB. Representation of the virtual space in extended systems – a correlation energy convergence study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1733118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- A. S. Hansen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
| | - G. Baardsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
| | - E. Rebolini
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
- Institut Laue Langevin, Grenoble, France
| | - L. Maschio
- Dipartimento di Chimica, Universitá di Torino, Torino, Italy
| | - T. B. Pedersen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
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20
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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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21
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Izsák R. Single‐reference coupled cluster methods for computing excitation energies in large molecules: The efficiency and accuracy of approximations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1445] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Róbert Izsák
- Max‐Planck‐Institut für Kohlenforschung Mülheim an der Ruhr Germany
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22
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Kats D, Werner HJ. Multi-state local complete active space second-order perturbation theory using pair natural orbitals (PNO-MS-CASPT2). J Chem Phys 2019; 150:214107. [DOI: 10.1063/1.5097644] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel Kats
- Max-Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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23
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Dutta AK, Saitow M, Demoulin B, Neese F, Izsák R. A domain-based local pair natural orbital implementation of the equation of motion coupled cluster method for electron attached states. J Chem Phys 2019; 150:164123. [DOI: 10.1063/1.5089637] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | - Masaaki Saitow
- Department of Chemistry, Graduate School of Science, Nagoya University, 1-5 Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Baptiste Demoulin
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
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24
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Krause C, Werner HJ. Scalable Electron Correlation Methods. 6. Local Spin-Restricted Open-Shell Second-Order Møller-Plesset Perturbation Theory Using Pair Natural Orbitals: PNO-RMP2. J Chem Theory Comput 2019; 15:987-1005. [PMID: 30571916 DOI: 10.1021/acs.jctc.8b01012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a (near) linear scaling implementation of high-spin open-shell Møller-Plesset perturbation theory using pair natural orbitals (PNO-RMP2). The theory is based on a new variant of open-shell MP2 which is fully spin-adapted and uses a single set of spin-free amplitudes, as in closed-shell MP2. This method, denoted SROMP2, is invariant to unitary orbital transformations within the closed, open, and virtual orbital subspaces. Accordingly, only a single set of PNOs per spatial orbital pair is needed, and the efficiency is similar to closed-shell calculations. The PNOs are obtained using a semicanonical approximation with large domains of projected atomic orbitals (PAOs). Linear scaling is achieved provided that the open-shell orbitals are local, and distant pairs are treated by multipole approximations. The method is efficiently parallelized. The convergence of ionization and reaction energies as a function of the PAO and PNO domain sizes is demonstrated and found to be very similar as for closed-shell calculations. The suitability of the PNOs for explicitly correlated PNO-RCCSD-F12 calculations is also tested. So far, this method is only simulated using a conventional program with appropriate projections to the PAO and PNO subspaces. It is demonstrated for radical stabilization energies as well as ionization potentials that the errors caused by the local domain approximations with our default thresholds are negligible.
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Affiliation(s)
- Christine Krause
- Institut für Theoretische Chemie , Universität Stuttgart , Pfaffenwaldring 55 , D-70569 Stuttgart , Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie , Universität Stuttgart , Pfaffenwaldring 55 , D-70569 Stuttgart , Germany
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25
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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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26
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Sen A, de Souza B, Huntington LMJ, Krupička M, Neese F, Izsák R. An efficient pair natural orbital based configuration interaction scheme for the calculation of open-shell ionization potentials. J Chem Phys 2018; 149:114108. [DOI: 10.1063/1.5048688] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Avijit Sen
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Bernardo de Souza
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
- Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Lee M. J. Huntington
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Martin Krupička
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
- University of Chemistry and Technology, Prague, Czech Republic
| | - 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
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27
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Hallmen PP, Rauhut G, Stoll H, Mitrushchenkov AO, van Slageren J. Crystal Field Splittings in Lanthanide Complexes: Inclusion of Correlation Effects beyond Second Order Perturbation Theory. J Chem Theory Comput 2018; 14:3998-4009. [PMID: 29906105 DOI: 10.1021/acs.jctc.8b00184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
State-averaged complete active space self-consistent field (CASSCF) calculations and a subsequent spin-orbit calculation mixing the CASSCF wave functions (CASSCF/state-interaction with spin-orbit coupling) is the conventional approach used for ab initio calculations of crystal-field splittings and magnetic properties of lanthanide complexes. However, this approach neglects dynamical correlation. Complete active space second-order perturbation theory (CASPT2) can be used to account for dynamical correlation but suffers from the well-known problems of multireference perturbation theory, e.g., intruder state problems. Variational multireference configuration interaction (MRCI) calculations do not show these problems but are usually not feasible due to the large size of real lanthanide complexes. Here, we present a quasi-local projected internally contracted MRCI approach which makes MRCI calculations of lanthanide complexes feasible and allows assessing the influence of dynamical correlation beyond second-order perturbation theory. We apply the method to two well-studied molecules, namely, [Er{N(SiMe3)2}3] and {C(NH2)3}5[Er(CO3)4]·11H2O.
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Affiliation(s)
- P P Hallmen
- Institute of Physical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany.,Institute of Theoretical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
| | - G Rauhut
- Institute of Theoretical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
| | - H Stoll
- Institute of Theoretical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
| | - A O Mitrushchenkov
- Laboratoire de Modélisation et Simulation Multi Echelle , Université Paris-Est , MSME UMR 8208, 5 bd Descartes , 77454 Marne-la-Vallée , France
| | - J van Slageren
- Institute of Physical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
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28
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Ma Q, Werner H. Explicitly correlated local coupled‐cluster methods using pair natural orbitals. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1371] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Qianli Ma
- Institute for Theoretical ChemistryUniversity of StuttgartStuttgartGermany
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29
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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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30
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Dutta AK, Saitow M, Riplinger C, Neese F, Izsák R. A near-linear scaling equation of motion coupled cluster method for ionized states. J Chem Phys 2018; 148:244101. [DOI: 10.1063/1.5029470] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Achintya Kumar Dutta
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Masaaki Saitow
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
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31
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Guo Y, Becker U, Neese F. Comparison and combination of “direct” and fragment based local correlation methods: Cluster in molecules and domain based local pair natural orbital perturbation and coupled cluster theories. J Chem Phys 2018; 148:124117. [DOI: 10.1063/1.5021898] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Yang Guo
- 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
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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32
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Dutta AK, Neese F, Izsák R. Accelerating the coupled-cluster singles and doubles method using the chain-of-sphere approximation. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1416201] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Achintya Kumar Dutta
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36., 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36., 45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36., 45470 Mülheim an der Ruhr, Germany
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33
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Ma Q, Werner HJ. Scalable Electron Correlation Methods. 5. Parallel Perturbative Triples Correction for Explicitly Correlated Local Coupled Cluster with Pair Natural Orbitals. J Chem Theory Comput 2017; 14:198-215. [DOI: 10.1021/acs.jctc.7b01141] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qianli Ma
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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34
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Gonthier JF, Head-Gordon M. Compressed representation of dispersion interactions and long-range electronic correlations. J Chem Phys 2017; 147:144110. [DOI: 10.1063/1.4997186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jérôme F. Gonthier
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division, 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 and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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35
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Schwilk M, Ma Q, Köppl C, Werner HJ. Scalable Electron Correlation Methods. 3. Efficient and Accurate Parallel Local Coupled Cluster with Pair Natural Orbitals (PNO-LCCSD). J Chem Theory Comput 2017; 13:3650-3675. [DOI: 10.1021/acs.jctc.7b00554] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Max Schwilk
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Qianli Ma
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Christoph Köppl
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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