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Burger S, Stopkowicz S, Gauss J. Cholesky Decomposition and the Second-Derivative Two-Electron Integrals Required for the Computation of Magnetizabilities Using Gauge-Including Atomic Orbitals. J Phys Chem A 2025; 129:623-632. [PMID: 39737870 DOI: 10.1021/acs.jpca.4c07421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2025]
Abstract
The computation of magnetizability tensors using gauge-including atomic orbitals is discussed in the context of Cholesky decomposition (CD) for the two-electron repulsion integrals with a focus on the involved doubly differentiated integrals. Three schemes for their handling are suggested: the first exploits the density fitting (DF) aspect of Cholesky decomposition, the second uses expressions obtained by differentiating the CD expression for the unperturbed two-electron integrals, while the third addresses the issue that the first two schemes are not able to represent the doubly differentiated integrals with arbitrary accuracy. This scheme uses a separate Cholesky decomposition for the cross terms in the doubly differentiated two-electron integrals. Test calculations reveal that all three schemes are able to represent the integrals with similar accuracy and yield indistinguishable results for the values of the computed magnetizability tensor elements. Thus, we recommend our first scheme which has the lowest computational cost for routine computations. The applicability of our CD schemes is further shown in large-scale Hartree-Fock calculations of the magnetizability tensor of coronene (C24H12) with a doubly polarized triple-ζ basis consisting of 684 basis functions.
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Affiliation(s)
- Sophia Burger
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Stella Stopkowicz
- Fachrichtung Chemie, Universität des Saarlandes, Campus B2.2, D-66123 Saarbrücken, Germany
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern N-0315, Oslo, Norway
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
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2
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Ahmadkhani S, Boguslawski K, Tecmer P. Linear Response pCCD-Based Methods: LR-pCCD and LR-pCCD+S Approaches for the Efficient and Reliable Modeling of Excited State Properties. J Chem Theory Comput 2024; 20:10443-10452. [PMID: 39564917 DOI: 10.1021/acs.jctc.4c01017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2024]
Abstract
In this work, we derive working equations for the linear response pair coupled cluster doubles (LR-pCCD) ansatz and its extension to singles (S), LR-pCCD+S. These methods allow us to compute electronic excitation energies and transition dipole moments based on a pCCD reference function. We benchmark the LR-pCCD+S model against the linear response coupled-cluster singles and doubles method for modeling electronic spectra (excitation energies and transition dipole moments) of the BH, H2O, H2CO, and furan molecules. We also analyze the effect of orbital optimization within pCCD on the resulting LR-pCCD+S transition dipole moments and oscillator strengths and perform a statistical error analysis. We show that the LR-pCCD+S method can correctly reproduce the transition dipole moments features, thus representing a reliable and cost-effective alternative to standard, more expensive electronic structure methods for modeling electronic spectra of simple molecules. Specifically, the proposed models require only mean-field-like computational cost, while excited-state properties may approach the CCSD level of accuracy. Moreover, we demonstrate the capability of our model to simulate electronic transitions with non-negligible contributions of double excitations and the electronic spectra of polyenes of various chain lengths, for which standard electronic structure methods perform purely.
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Affiliation(s)
- Somayeh Ahmadkhani
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Toruń, Grudziadzka 5, Toruń 87-100, Poland
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Toruń, Grudziadzka 5, Toruń 87-100, Poland
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Toruń, Grudziadzka 5, Toruń 87-100, Poland
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3
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Blaschke S, Kitsaras MP, Stopkowicz S. Finite-field Cholesky decomposed coupled-cluster techniques (ff-CD-CC): theory and application to pressure broadening of Mg by a He atmosphere and a strong magnetic field. Phys Chem Chem Phys 2024; 26:28828-28848. [PMID: 39540271 DOI: 10.1039/d4cp03103b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
For the interpretation of spectra of magnetic stellar objects such as magnetic white dwarfs (WDs), highly accurate quantum chemical predictions for atoms and molecules in finite magnetic field are required. Especially the accurate description of electronically excited states and their properties requires established methods such as those from coupled-cluster (CC) theory. However, respective calculations are computationally challenging even for medium-sized systems. Cholesky decomposition (CD) techniques may be used to alleviate memory bottlenecks. In finite magnetic field computations, the latter are increased due to the reduction of permutational symmetry within the electron-repulsion-integrals (ERIs) as well as the need for complex-valued data types. CD enables a memory-efficient, approximate description of the ERIs with rigorous error control and thus the treatment of larger systems at the CC level becomes feasible. In order to treat molecules in a finite magnetic field, we present in this work the working equations of the left and right-hand side equations for finite field (ff)-EOM-CD-CCSD for various EOM flavours as well as for the approximate ff-EOM-CD-CC2 method. The methods are applied to the study of the modification of the spectral lines of a magnesium transition by a helium atmosphere that can be found on magnetic WD stars.
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Affiliation(s)
- Simon Blaschke
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
- Fachrichtung Chemie, Universität des Saarlandes, Campus B2.2, D-66123 Saarbrücken, Germany.
| | - Marios-Petros Kitsaras
- Fachrichtung Chemie, Universität des Saarlandes, Campus B2.2, D-66123 Saarbrücken, Germany.
| | - Stella Stopkowicz
- Fachrichtung Chemie, Universität des Saarlandes, Campus B2.2, D-66123 Saarbrücken, Germany.
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, N-0315 Oslo, Norway
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4
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Zhao C, Ou Q, Lee J, Dou W. Stochastic Resolution of Identity to CC2 for Large Systems: Excited State Properties. J Chem Theory Comput 2024; 20:5188-5195. [PMID: 38842259 DOI: 10.1021/acs.jctc.4c00629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
We apply a stochastic resolution of identity approximation (sRI) to the CC2 method for the excitation energy calculations. A set of stochastic orbitals are employed to decouple the crucial 4-index electron repulsion integrals and optimize the contraction steps in CC2 response theory. The CC2 response for excitations builds upon sRI-CC2 ground-state calculations, which scales as O(N3), where N is a measure for the system size. Overall, the current algorithm for excited states also allows a sharp scaling reduction from original O(N5) to O(N3). We test the sRI-CC2 for different molecular systems and basis sets, and we show that our sRI-CC2 method can accurately reproduce the results of the deterministic CC2 approach. Our sRI-CC2 exhibits an experimental scaling of O(N2.59) for a series of olefin chains, allowing us to calculate systems with nearly thousands of electrons.
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Affiliation(s)
- Chongxiao Zhao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- Department of Chemistry, School of Science, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Qi Ou
- AI for Science Institute, Beijing 100080, China
| | - Joonho Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Wenjie Dou
- Department of Chemistry, School of Science, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
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5
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Alessio M, Paran GP, Utku C, Grüneis A, Jagau TC. Coupled-cluster treatment of complex open-shell systems: the case of single-molecule magnets. Phys Chem Chem Phys 2024; 26:17028-17041. [PMID: 38836327 PMCID: PMC11186456 DOI: 10.1039/d4cp01129e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024]
Abstract
We investigate the reliability of two cost-effective coupled-cluster methods for computing spin-state energetics and spin-related properties of a set of open-shell transition-metal complexes. Specifically, we employ the second-order approximate coupled-cluster singles and doubles (CC2) method and projection-based embedding that combines equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) with density functional theory (DFT). The performance of CC2 and EOM-CCSD-in-DFT is assessed against EOM-CCSD. The chosen test set includes two hexaaqua transition-metal complexes containing Fe(II) and Fe(III), and a large Co(II)-based single-molecule magnet with a non-aufbau ground state. We find that CC2 describes the excited states more accurately, reproducing EOM-CCSD excitation energies within 0.05 eV. However, EOM-CCSD-in-DFT excels in describing transition orbital angular momenta and spin-orbit couplings. Moreover, for the Co(II) molecular magnet, using EOM-CCSD-in-DFT eigenstates and spin-orbit couplings, we compute spin-reversal energy barriers, as well as temperature-dependent and field-dependent magnetizations and magnetic susceptibilities that closely match experimental values within spectroscopic accuracy. These results underscore the efficiency of CC2 in computing state energies of multi-configurational, open-shell systems and highlight the utility of the more cost-efficient EOM-CCSD-in-DFT for computing spin-orbit couplings and magnetic properties of complex and large molecular magnets.
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Affiliation(s)
- Maristella Alessio
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | | | - Cansu Utku
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Andreas Grüneis
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | - Thomas-C Jagau
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
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6
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Zhang C, Lipparini F, Stopkowicz S, Gauss J, Cheng L. Cholesky Decomposition-Based Implementation of Relativistic Two-Component Coupled-Cluster Methods for Medium-Sized Molecules. J Chem Theory Comput 2024; 20:787-798. [PMID: 38198515 DOI: 10.1021/acs.jctc.3c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
A Cholesky decomposition (CD)-based implementation of relativistic two-component coupled-cluster (CC) and equation-of-motion CC (EOM-CC) methods using an exact two-component Hamiltonian augmented with atomic-mean-field spin-orbit integrals (the X2CAMF scheme) is reported. The present CD-based implementation of X2CAMF-CC and EOM-CC methods employs atomic-orbital-based algorithms to avoid the construction of two-electron integrals and intermediates involving three and four virtual indices. Our CD-based implementation extends the applicability of X2CAMF-CC and EOM-CC methods to medium-sized molecules with the possibility to correlate around 1000 spinors. Benchmark calculations for uranium-containing small molecules were performed to assess the dependence of the CC results on the Cholesky threshold. A Cholesky threshold of 10-4 is shown to be sufficient to maintain chemical accuracy. Example calculations to illustrate the capability of the CD-based relativistic CC methods are reported for the bond-dissociation energy of the uranium hexafluoride molecule, UF6, with up to quadruple-ζ basis sets, and the lowest excitation energy in the solvated uranyl ion [UO22+(H2O)12].
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Affiliation(s)
- Chaoqun Zhang
- Department of Chemistry, the Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa I-56124, Italy
| | - Stella Stopkowicz
- Fachrichtung Chemie, Universität des Saarlandes, Saarbrücken D-66123, Germany
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, Oslo N-0315, Norway
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, Mainz D-55128, Germany
| | - Lan Cheng
- Department of Chemistry, the Johns Hopkins University, Baltimore, Maryland 21218, United States
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7
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Paran GP, Utku C, Jagau TC. On the performance of second-order approximate coupled-cluster singles and doubles methods for non-valence anions. Phys Chem Chem Phys 2024; 26:1809-1818. [PMID: 38168799 PMCID: PMC10793870 DOI: 10.1039/d3cp05923e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
We investigate the capability of several variants of the second-order approximate coupled-cluster singles and doubles (CC2) method to describe dipole-bound, quadrupole-bound, and correlation-bound molecular anions. The binding energy of anions formed by electron attachment to closed-shell molecules is computed using the electron attachment variant of CC2 (EA-CC2), whereas anions with a closed-shell ground state are treated with the standard CC2 method that preserves the number of particles. We find that EA-CC2 captures the binding energies of dipole-bound radical anions quite well, whereas results for other types of non-valence anions are less reliable. We also test the performance of semi-empirical spin-scaling factors for all types of non-valence anions and observe that the spin-scaled CC2 variants generally do not provide more accurate binding energies for dipole-bound anions, while the binding energies of quadrupole-bound and correlation-bound anions are improved. As exemplary applications of EA-CC2, we investigate the dipole-bound anions of the steroids cortisol, progesterone, and testosterone. In addition, we characterize electron attachment to sym-tetracyanonaphthalene, a molecule that supports five anionic states, two of which can be interpreted as hitherto unobserved π-type quadrupole-bound states.
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Affiliation(s)
| | - Cansu Utku
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
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8
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Lesiuk M. Quintic-scaling rank-reduced coupled cluster theory with single and double excitations. J Chem Phys 2022; 156:064103. [DOI: 10.1063/5.0071916] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Lesiuk M. Near-Exact CCSDT Energetics from Rank-Reduced Formalism Supplemented by Non-iterative Corrections. J Chem Theory Comput 2021; 17:7632-7647. [PMID: 34860018 DOI: 10.1021/acs.jctc.1c00933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce a non-iterative energy correction, added on top of the rank-reduced coupled-cluster method with single, double, and triple substitutions, that accounts for excitations excluded from the parent triple excitation subspace. The formula for the correction is derived by employing the coupled-cluster Lagrangian formalism, with an additional assumption that the parent excitation subspace is closed under the action of the Fock operator. Owing to the rank-reduced form of the triple excitation amplitudes tensor, the computational cost of evaluating the correction scales as N7, where N is the system size. The accuracy and computational efficiency of the proposed method is assessed for both total and relative correlation energies. We show that the non-iterative correction can fulfill two separate roles. If the accuracy level of a fraction of kJ/mol is sufficient for a given system, the correction significantly reduces the dimension of the parent triple excitation subspace needed in the iterative part of the calculations. Simultaneously, it enables reproducing the exact CCSDT results to an accuracy level below 0.1 kJ/mol, with a larger, yet still reasonable, dimension of the parent excitation subspace. This typically can be achieved at a computational cost only several times larger than required for the CCSD(T) method. The proposed method retains the black-box features of the single-reference coupled-cluster theory; the dimension of the parent excitation subspace remains the only additional parameter that has to be specified.
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Affiliation(s)
- Michał Lesiuk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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10
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Kowalski K, Bair R, Bauman NP, Boschen JS, Bylaska EJ, Daily J, de Jong WA, Dunning T, Govind N, Harrison RJ, Keçeli M, Keipert K, Krishnamoorthy S, Kumar S, Mutlu E, Palmer B, Panyala A, Peng B, Richard RM, Straatsma TP, Sushko P, Valeev EF, Valiev M, van Dam HJJ, Waldrop JM, Williams-Young DB, Yang C, Zalewski M, Windus TL. From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape. Chem Rev 2021; 121:4962-4998. [PMID: 33788546 DOI: 10.1021/acs.chemrev.0c00998] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.
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Affiliation(s)
- Karol Kowalski
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Raymond Bair
- Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Nicholas P Bauman
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | - Eric J Bylaska
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jeff Daily
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Wibe A de Jong
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Thom Dunning
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Niranjan Govind
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Robert J Harrison
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, United States
| | - Murat Keçeli
- Argonne National Laboratory, Lemont, Illinois 60439, United States
| | | | | | - Suraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erdal Mutlu
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bruce Palmer
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ajay Panyala
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bo Peng
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | - T P Straatsma
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6373, United States
| | - Peter Sushko
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Marat Valiev
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | | | | | - Chao Yang
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Marcin Zalewski
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Theresa L Windus
- Department of Chemistry, Iowa State University and Ames Laboratory, Ames, Iowa 50011, United States
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11
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Lao KU, Yang Y, DiStasio RA. Electron confinement meet electron delocalization: non-additivity and finite-size effects in the polarizabilities and dispersion coefficients of the fullerenes. Phys Chem Chem Phys 2021; 23:5773-5779. [PMID: 33666598 DOI: 10.1039/d0cp05638c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we used finite-field derivative techniques and density functional theory (DFT) to compute the static isotropic polarizability series (αl with l = 1, 2, 3) for the C60-C84 fullerenes and quantitatively assess the intrinsic non-additivity in these fundamental response properties. By comparing against classical models of the fullerenes as conducting spherical shells (or solid spheres) of uniform electron density, a detailed critical analysis of the derived effective scaling laws (α1 ∼ N1.2, α2 ∼ N2.0, α3 ∼ N2.7) demonstrates that the electronic structure of finite-sized fullerenes-a unique dichotomy of electron confinement and delocalization effects due to their quasi-spherical cage-like structures and encapsulated void spaces-simultaneously limits and enhances their quantum mechanical response to electric field perturbations. Corresponding frequency-dependent polarizabilities were obtained by inputting the αl series into the hollow sphere model (within the modified single frequency approximation), and used to compute the molecular dispersion coefficients (Cn with n = 6, 8, 9, 10) needed to describe the non-trivial van der Waals (vdW) interactions in fullerene-based systems. Using first-order perturbation theory in conjunction with >140 000 DFT calculations, we also computed the non-negligible zero-point vibrational contributions to α1 in C60 and C70, thereby enabling a more accurate and direct comparison between theory and experiment for these quintessential nanostructures.
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Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Yan Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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12
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Sauer SPA, Sabin JR, Oddershede J. Calculation of mean excitation energies of 3d-elements and their cations. Mol Phys 2021. [DOI: 10.1080/00268976.2020.1823508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - John R. Sabin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- Departments of Physics and Chemistry, University of Florida, Gainesville, FL, USA
| | - Jens Oddershede
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- Departments of Physics and Chemistry, University of Florida, Gainesville, FL, USA
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13
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Jørgensen MW, Sauer SPA. Benchmarking doubles-corrected random-phase approximation methods for frequency dependent polarizabilities: Aromatic molecules calculated at the RPA, HRPA, RPA(D), HRPA(D), and SOPPA levels. J Chem Phys 2020; 152:234101. [DOI: 10.1063/5.0011195] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Maria W. Jørgensen
- Department of Chemistry, University of Copenhagen, Copenhagen Ø, Denmark
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14
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Aprà E, Bylaska EJ, de Jong WA, Govind N, Kowalski K, Straatsma TP, Valiev M, van Dam HJJ, Alexeev Y, Anchell J, Anisimov V, Aquino FW, Atta-Fynn R, Autschbach J, Bauman NP, Becca JC, Bernholdt DE, Bhaskaran-Nair K, Bogatko S, Borowski P, Boschen J, Brabec J, Bruner A, Cauët E, Chen Y, Chuev GN, Cramer CJ, Daily J, Deegan MJO, Dunning TH, Dupuis M, Dyall KG, Fann GI, Fischer SA, Fonari A, Früchtl H, Gagliardi L, Garza J, Gawande N, Ghosh S, Glaesemann K, Götz AW, Hammond J, Helms V, Hermes ED, Hirao K, Hirata S, Jacquelin M, Jensen L, Johnson BG, Jónsson H, Kendall RA, Klemm M, Kobayashi R, Konkov V, Krishnamoorthy S, Krishnan M, Lin Z, Lins RD, Littlefield RJ, Logsdail AJ, Lopata K, Ma W, Marenich AV, Martin Del Campo J, Mejia-Rodriguez D, Moore JE, Mullin JM, Nakajima T, Nascimento DR, Nichols JA, Nichols PJ, Nieplocha J, Otero-de-la-Roza A, Palmer B, Panyala A, Pirojsirikul T, Peng B, Peverati R, Pittner J, Pollack L, Richard RM, Sadayappan P, Schatz GC, Shelton WA, Silverstein DW, Smith DMA, Soares TA, Song D, Swart M, Taylor HL, Thomas GS, Tipparaju V, Truhlar DG, Tsemekhman K, Van Voorhis T, Vázquez-Mayagoitia Á, Verma P, Villa O, Vishnu A, Vogiatzis KD, Wang D, Weare JH, Williamson MJ, Windus TL, Woliński K, Wong AT, Wu Q, Yang C, Yu Q, Zacharias M, Zhang Z, Zhao Y, Harrison RJ. NWChem: Past, present, and future. J Chem Phys 2020; 152:184102. [PMID: 32414274 DOI: 10.1063/5.0004997] [Citation(s) in RCA: 337] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.
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Affiliation(s)
- E Aprà
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - E J Bylaska
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - W A de Jong
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - N Govind
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - K Kowalski
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - T P Straatsma
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Valiev
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - H J J van Dam
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Y Alexeev
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - J Anchell
- Intel Corporation, Santa Clara, California 95054, USA
| | - V Anisimov
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - F W Aquino
- QSimulate, Cambridge, Massachusetts 02139, USA
| | - R Atta-Fynn
- Department of Physics, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - J Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - N P Bauman
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - J C Becca
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - D E Bernholdt
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | | | - S Bogatko
- 4G Clinical, Wellesley, Massachusetts 02481, USA
| | - P Borowski
- Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - J Boschen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - J Brabec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 18223 Prague 8, Czech Republic
| | - A Bruner
- Department of Chemistry and Physics, University of Tennessee at Martin, Martin, Tennessee 38238, USA
| | - E Cauët
- Service de Chimie Quantique et Photophysique (CP 160/09), Université libre de Bruxelles, B-1050 Brussels, Belgium
| | - Y Chen
- Facebook, Menlo Park, California 94025, USA
| | - G N Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region 142290, Russia
| | - C J Cramer
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Daily
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M J O Deegan
- SKAO, Jodrell Bank Observatory, Macclesfield SK11 9DL, United Kingdom
| | - T H Dunning
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - M Dupuis
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - K G Dyall
- Dirac Solutions, Portland, Oregon 97229, USA
| | - G I Fann
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - S A Fischer
- Chemistry Division, U. S. Naval Research Laboratory, Washington, DC 20375, USA
| | - A Fonari
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - H Früchtl
- EaStCHEM and School of Chemistry, University of St. Andrews, St. Andrews KY16 9ST, United Kingdom
| | - L Gagliardi
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Garza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Col. Vicentina, Iztapalapa, C.P. 09340 Ciudad de México, Mexico
| | - N Gawande
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - S Ghosh
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 5545, USA
| | - K Glaesemann
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A W Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - J Hammond
- Intel Corporation, Santa Clara, California 95054, USA
| | - V Helms
- Center for Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany
| | - E D Hermes
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA
| | - K Hirao
- Next-generation Molecular Theory Unit, Advanced Science Institute, RIKEN, Saitama 351-0198, Japan
| | - S Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - M Jacquelin
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - L Jensen
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - B G Johnson
- Acrobatiq, Pittsburgh, Pennsylvania 15206, USA
| | - H Jónsson
- Faculty of Physical Sciences, University of Iceland, Reykjavík, Iceland and Department of Applied Physics, Aalto University, FI-00076 Aalto, Espoo, Finland
| | - R A Kendall
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Klemm
- Intel Corporation, Santa Clara, California 95054, USA
| | - R Kobayashi
- ANU Supercomputer Facility, Australian National University, Canberra, Australia
| | - V Konkov
- Chemistry Program, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - S Krishnamoorthy
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M Krishnan
- Facebook, Menlo Park, California 94025, USA
| | - Z Lin
- Department of Physics, University of Science and Technology of China, Hefei, China
| | - R D Lins
- Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | | | - A J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, Wales CF10 3AT, United Kingdom
| | - K Lopata
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - W Ma
- Institute of Software, Chinese Academy of Sciences, Beijing, China
| | - A V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Martin Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, México City, Mexico
| | - D Mejia-Rodriguez
- Quantum Theory Project, Department of Physics, University of Florida, Gainesville, Florida 32611, USA
| | - J E Moore
- Intel Corporation, Santa Clara, California 95054, USA
| | - J M Mullin
- DCI-Solutions, Aberdeen Proving Ground, Maryland 21005, USA
| | - T Nakajima
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - D R Nascimento
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - J A Nichols
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - P J Nichols
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - J Nieplocha
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - B Palmer
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A Panyala
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - T Pirojsirikul
- Department of Chemistry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - B Peng
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - R Peverati
- Chemistry Program, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J Pittner
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., 18223 Prague 8, Czech Republic
| | - L Pollack
- StudyPoint, Boston, Massachusetts 02114, USA
| | | | - P Sadayappan
- School of Computing, University of Utah, Salt Lake City, Utah 84112, USA
| | - G C Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - W A Shelton
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | | | - D M A Smith
- Intel Corporation, Santa Clara, California 95054, USA
| | - T A Soares
- Dept. of Fundamental Chemistry, Universidade Federal de Pernambuco, Recife, Brazil
| | - D Song
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M Swart
- ICREA, 08010 Barcelona, Spain and Universitat Girona, Institut de Química Computacional i Catàlisi, Campus Montilivi, 17003 Girona, Spain
| | - H L Taylor
- CD-adapco/Siemens, Melville, New York 11747, USA
| | - G S Thomas
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - V Tipparaju
- Cray Inc., Bloomington, Minnesota 55425, USA
| | - D G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | - T Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Á Vázquez-Mayagoitia
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - P Verma
- 1QBit, Vancouver, British Columbia V6E 4B1, Canada
| | - O Villa
- NVIDIA, Santa Clara, California 95051, USA
| | - A Vishnu
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - K D Vogiatzis
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - D Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong 250014, China
| | - J H Weare
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - M J Williamson
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - T L Windus
- Department of Chemistry, Iowa State University and Ames Laboratory, Ames, Iowa 50011, USA
| | - K Woliński
- Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - A T Wong
- Qwil, San Francisco, California 94107, USA
| | - Q Wu
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C Yang
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Q Yu
- AMD, Santa Clara, California 95054, USA
| | - M Zacharias
- Department of Physics, Technical University of Munich, 85748 Garching, Germany
| | - Z Zhang
- Stanford Research Computing Center, Stanford University, Stanford, California 94305, USA
| | - Y Zhao
- State Key Laboratory of Silicate Materials for Architectures, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - R J Harrison
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
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15
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Jørgensen MW, Faber R, Ligabue A, Sauer SPA. Benchmarking Correlated Methods for Frequency-Dependent Polarizabilities: Aromatic Molecules with the CC3, CCSD, CC2, SOPPA, SOPPA(CC2), and SOPPA(CCSD) Methods. J Chem Theory Comput 2020; 16:3006-3018. [DOI: 10.1021/acs.jctc.9b01300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria W. Jørgensen
- Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
| | - Rasmus Faber
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Andrea Ligabue
- Game Science Research Center, University of Modena and Reggio Emilia, Modena 41121, Italy
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16
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Lesiuk M. A straightforward a posteriori method for reduction of density-fitting error in coupled-cluster calculations. J Chem Phys 2020; 152:044104. [PMID: 32007079 DOI: 10.1063/1.5129883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a simple method for a posteriori removal of a significant fraction of the density-fitting error from the calculated total coupled-cluster energies. The method treats the difference between the exact and density-fitted integrals as a perturbation, and simplified response-like equations allow us to calculate improved amplitudes and the corresponding energy correction. The proposed method is tested at the coupled-cluster singles and doubles level of theory for a diverse set of moderately-sized molecules. On average, error reductions by a factor of approximately 10 and 20 are observed in double-zeta and triple-zeta basis sets, respectively. Similar reductions are observed in calculations of interaction energies of several model complexes. The computational cost of the procedure is small in comparison with the preceding coupled-cluster iterations. The applicability of this method is not limited to the density-fitting approximation; in principle, it can be used in conjunction with an arbitrary decomposition scheme of the electron repulsion integrals.
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Affiliation(s)
- Michał Lesiuk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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17
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Mester D, Nagy PR, Kállay M. Reduced-Scaling Correlation Methods for the Excited States of Large Molecules: Implementation and Benchmarks for the Second-Order Algebraic-Diagrammatic Construction Approach. J Chem Theory Comput 2019; 15:6111-6126. [DOI: 10.1021/acs.jctc.9b00735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dávid Mester
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, H-1521 Budapest, P.O. Box 91, Hungary
| | - Péter R. Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, H-1521 Budapest, P.O. Box 91, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, H-1521 Budapest, P.O. Box 91, Hungary
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18
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Zhang T, Li C, Evangelista FA. Improving the Efficiency of the Multireference Driven Similarity Renormalization Group via Sequential Transformation, Density Fitting, and the Noninteracting Virtual Orbital Approximation. J Chem Theory Comput 2019; 15:4399-4414. [PMID: 31268704 DOI: 10.1021/acs.jctc.9b00353] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study examines several techniques to improve the efficiency of the linearized multireference driven similarity renormalization group truncated to one- and two-body operators [MR-LDSRG(2)]. We propose a sequential MR-LDSRG(2) [sq-MR-LDSRG(2)] scheme, in which one-body substitutions are folded exactly into the Hamiltonian. This new approach is combined with density fitting (DF) to reduce the storage cost of two-electron integrals. To further avoid storage of large four-index intermediates, we propose a noninteracting virtual orbital (NIVO) approximation of the Baker-Campbell-Hausdorff series that neglects commutators terms with three and four virtual indices. The NIVO approximation reduces the computational prefactor of the MR-LDSRG(2), bringing it closer to that of coupled cluster with singles and doubles (CCSD). We test the effect of the DF and NIVO approximations on the MR-LDSRG(2) and sq-MR-LDSRG(2) methods by computing properties of eight diatomic molecules. The diatomic constants obtained by DF-sq-MR-LDSRG(2)+NIVO are found to be as accurate as those from the original MR-LDSRG(2) and coupled cluster theory with singles, doubles, and perturbative triples. Finally, we demonstrate that the DF-sq-MR-LDSRG(2)+NIVO scheme can be applied to chemical systems with more than 550 basis functions by computing the automerization energy of cyclobutadiene with a quintuple-ζ basis set. The predicted automerization energy is found to be similar to the value computed with Mukherjee's state-specific multireference coupled cluster theory with singles and doubles.
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Affiliation(s)
- Tianyuan Zhang
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation , Emory University , Atlanta , Georgia 30322 , United States
| | - Chenyang Li
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation , Emory University , Atlanta , Georgia 30322 , United States
| | - Francesco A Evangelista
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation , Emory University , Atlanta , Georgia 30322 , United States
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19
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Folkestad SD, Kjønstad EF, Koch H. An efficient algorithm for Cholesky decomposition of electron repulsion integrals. J Chem Phys 2019; 150:194112. [DOI: 10.1063/1.5083802] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Sarai D. Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
- Scuola Normale Superiore, Piazza dei Cavaleri 7, 56126 Pisa, Italy
| | - Eirik F. Kjønstad
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
- Scuola Normale Superiore, Piazza dei Cavaleri 7, 56126 Pisa, Italy
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
- Scuola Normale Superiore, Piazza dei Cavaleri 7, 56126 Pisa, Italy
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20
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Howard JC, Sowndarya S. V. S, Ansari IM, Mach TJ, Baranowska-Łączkowska A, Crawford TD. Performance of Property-Optimized Basis Sets for Optical Rotation with Coupled Cluster Theory. J Phys Chem A 2018; 122:5962-5969. [DOI: 10.1021/acs.jpca.8b04183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Coleman Howard
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - Imaad M. Ansari
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Taylor J. Mach
- Concordia University, St. Paul, Minnesota 55104, United States
| | | | - T. Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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21
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Peng B, Kowalski K. Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations. J Chem Theory Comput 2017; 13:4179-4192. [DOI: 10.1021/acs.jctc.7b00605] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bo Peng
- William R. Wiley Environmental
Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P. O. Box 999, Richland, Washington 99352, United States
| | - Karol Kowalski
- William R. Wiley Environmental
Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P. O. Box 999, Richland, Washington 99352, United States
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22
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Haghdani S, Hoff BH, Koch H, Åstrand PO. Solvent Effects on Optical Rotation: On the Balance between Hydrogen Bonding and Shifts in Dihedral Angles. J Phys Chem A 2017; 121:4765-4777. [DOI: 10.1021/acs.jpca.6b12149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shokouh Haghdani
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Bård Helge Hoff
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Per-Olof Åstrand
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
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23
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Mester D, Nagy PR, Kállay M. Reduced-cost linear-response CC2 method based on natural orbitals and natural auxiliary functions. J Chem Phys 2017; 146:194102. [PMID: 28527453 DOI: 10.1063/1.4983277] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A reduced-cost density fitting (DF) linear-response second-order coupled-cluster (CC2) method has been developed for the evaluation of excitation energies. The method is based on the simultaneous truncation of the molecular orbital (MO) basis and the auxiliary basis set used for the DF approximation. For the reduction of the size of the MO basis, state-specific natural orbitals (NOs) are constructed for each excited state using the average of the second-order Møller-Plesset (MP2) and the corresponding configuration interaction singles with perturbative doubles [CIS(D)] density matrices. After removing the NOs of low occupation number, natural auxiliary functions (NAFs) are constructed [M. Kállay, J. Chem. Phys. 141, 244113 (2014)], and the NAF basis is also truncated. Our results show that, for a triple-zeta basis set, about 60% of the virtual MOs can be dropped, while the size of the fitting basis can be reduced by a factor of five. This results in a dramatic reduction of the computational costs of the solution of the CC2 equations, which are in our approach about as expensive as the evaluation of the MP2 and CIS(D) density matrices. All in all, an average speedup of more than an order of magnitude can be achieved at the expense of a mean absolute error of 0.02 eV in the calculated excitation energies compared to the canonical CC2 results. Our benchmark calculations demonstrate that the new approach enables the efficient computation of CC2 excitation energies for excited states of all types of medium-sized molecules composed of up to 100 atoms with triple-zeta quality basis sets.
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Affiliation(s)
- Dávid Mester
- 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
| | - 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
| | - 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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24
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Aquilante F, Delcey MG, Pedersen TB, Fdez. Galván I, Lindh R. Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1284354] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Francesco Aquilante
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Bologna, Italy
| | - Mickaël G. Delcey
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, CA, USA
| | - Thomas Bondo Pedersen
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, Blindern, Oslo, Norway
| | - Ignacio Fdez. Galván
- Department of Chemistry – Ångström, The Theoretical Chemistry Programme, Uppsala University, Uppsala, Sweden
- Uppsala Center for Computational Chemistry – UC3, Uppsala University, Uppsala, Sweden
| | - Roland Lindh
- Department of Chemistry – Ångström, The Theoretical Chemistry Programme, Uppsala University, Uppsala, Sweden
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25
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Haghdani S, Hoff BH, Koch H, Åstrand PO. Optical Rotation Calculations for Fluorinated Alcohols, Amines, Amides, and Esters. J Phys Chem A 2016; 120:7973-7986. [DOI: 10.1021/acs.jpca.6b08899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shokouh Haghdani
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Bård Helge Hoff
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Per-Olof Åstrand
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
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26
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Haghdani S, Gautun OR, Koch H, Åstrand PO. Optical Rotation Calculations for a Set of Pyrrole Compounds. J Phys Chem A 2016; 120:7351-60. [PMID: 27571252 DOI: 10.1021/acs.jpca.6b07004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optical rotation of 14 molecules containing the pyrrole group is calculated by employing both time-dependent density functional theory (TDDFT) with the CAM-B3LYP functional and the second-order approximate coupled-cluster singles and doubles (CC2) method. All optical rotations have been provided using the aug-cc-pVDZ basis set at λ = 589 nm. The two methods predict similar results for both sign and magnitude for the optical rotation of all molecules. The obtained signs are consistent with experiments as well, although several conformers for four molecules needed to be studied to reproduce the experimental sign. We have also calculated excitation energies and rotatory strengths for the six lowest lying electronic transitions for several conformers of the two smallest molecules and found that each rotatory strength has various contributions for each conformer which can cause different optical rotations for different conformers of a molecule. Our results illustrate that both methods are able to reproduce the experimental optical rotations, and that the CAM-B3LYP functional, the least computationally expensive method used here, is an applicable and reliable method to predict the optical rotation for these molecules in line with previous studies.
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Affiliation(s)
- Shokouh Haghdani
- Department of Chemistry, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Odd R Gautun
- Department of Chemistry, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Per-Olof Åstrand
- Department of Chemistry, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
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27
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Haghdani S, Åstrand PO, Koch H. Optical Rotation from Coupled Cluster and Density Functional Theory: The Role of Basis Set Convergence. J Chem Theory Comput 2016; 12:535-48. [DOI: 10.1021/acs.jctc.5b00721] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shokouh Haghdani
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Per-Olof Åstrand
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Henrik Koch
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
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28
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Avramopoulos A, Otero N, Karamanis P, Pouchan C, Papadopoulos MG. A Computational Study of the Interaction and Polarization Effects of Complexes Involving Molecular Graphene and C60 or a Nucleobases. J Phys Chem A 2016; 120:284-98. [PMID: 26690053 DOI: 10.1021/acs.jpca.5b09813] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A systematic analysis of the molecular structure, energetics, electronic (hyper)polarizabilities and their interaction-induced counterparts of C60 with a series of molecular graphene (MG) models, CmHn, where m = 24, 84, 114, 222, 366, 546 and n = 12, 24, 30, 42, 54, 66, was performed. All the reported data were computed by employing density functional theory and a series of basis sets. The main goal of the study is to investigate how alteration of the size of the MG model affects the strength of the interaction, charge rearrangement, and polarization and interaction-induced polarization of the complex, C60-MG. A Hirshfeld-based scheme has been employed in order to provide information on the intrinsic polarizability density representations of the reported complexes. It was found that the interaction energy increases approaching a limit of -26.98 kcal/mol for m = 366 and 546; the polarizability and second hyperpolarizability increase with increasing the size of MG. An opposite trend was observed for the dipole moment. Interestingly, the variation of the first hyperpolarizability is relatively small with m. Since polarizability is a key factor for the stability of molecular graphene with nucleobases (NB), a study of the magnitude of the interaction-induced polarizability of C84H24-NB complexes is also reported, aiming to reveal changes of its magnitude with the type of NB. The binding strength of C84H24-NB complexes is also computed and found to be in agreement with available theoretical and experimental data. The interaction involved in C60 B12N12H24-NB complexes has also been considered, featuring the effect of contamination on the binding strength between MG and NBs.
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Affiliation(s)
- Aggelos Avramopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Nicolás Otero
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Panaghiotis Karamanis
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Claude Pouchan
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Manthos G Papadopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
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Aquilante F, Malmqvist PÅ, Pedersen TB, Ghosh A, Roos BO. Cholesky Decomposition-Based Multiconfiguration Second-Order Perturbation Theory (CD-CASPT2): Application to the Spin-State Energetics of Co(III)(diiminato)(NPh). J Chem Theory Comput 2015; 4:694-702. [PMID: 26621084 DOI: 10.1021/ct700263h] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The electronic structure and low-lying electronic states of a Co(III)(diiminato)(NPh) complex have been studied using multiconfigurational wave function theory (CASSCF/CASPT2). The results have been compared to those obtained with density functional theory. The best agreement with ab initio results is obtained with a modified B3LYP functional containing a reduced amount (15%) of Hartree-Fock exchange. A relativistic basis set with 869 functions has been employed in the most extensive ab initio calculations, where a Cholesky decomposition technique was used to overcome problems arising from the large size of the two-electron integral matrix. It is shown that this approximation reproduces results obtained with the full integral set to a high accuracy, thus opening the possibility to use this approach to perform multiconfigurational wave-function-based quantum chemistry on much larger systems relative to what has been possible until now.
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Affiliation(s)
- Francesco Aquilante
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Per-Åke Malmqvist
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Thomas Bondo Pedersen
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Abhik Ghosh
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Björn Olof Roos
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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30
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Kállay M. A systematic way for the cost reduction of density fitting methods. J Chem Phys 2015; 141:244113. [PMID: 25554139 DOI: 10.1063/1.4905005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We present a simple approach for the reduction of the size of auxiliary basis sets used in methods exploiting the density fitting (resolution of identity) approximation for electron repulsion integrals. Starting out of the singular value decomposition of three-center two-electron integrals, new auxiliary functions are constructed as linear combinations of the original fitting functions. The new functions, which we term natural auxiliary functions (NAFs), are analogous to the natural orbitals widely used for the cost reduction of correlation methods. The use of the NAF basis enables the systematic truncation of the fitting basis, and thereby potentially the reduction of the computational expenses of the methods, though the scaling with the system size is not altered. The performance of the new approach has been tested for several quantum chemical methods. It is demonstrated that the most pronounced gain in computational efficiency can be expected for iterative models which scale quadratically with the size of the fitting basis set, such as the direct random phase approximation. The approach also has the promise of accelerating local correlation methods, for which the processing of three-center Coulomb integrals is a bottleneck.
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Affiliation(s)
- 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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Costa R, Valero R, Mañeru DR, Moreira IDPR, Illas F. Spin Adapted versus Broken Symmetry Approaches in the Description of Magnetic Coupling in Heterodinuclear Complexes. J Chem Theory Comput 2015; 11:1006-19. [DOI: 10.1021/ct5011483] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Rosendo Valero
- Center
for Superfunctional Materials, Department of Chemistry, School of
Natural Science, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 689-798, Korea
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32
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Kennedy MR, McDonald AR, DePrince AE, Marshall MS, Podeszwa R, Sherrill CD. Communication: resolving the three-body contribution to the lattice energy of crystalline benzene: benchmark results from coupled-cluster theory. J Chem Phys 2014; 140:121104. [PMID: 24697416 DOI: 10.1063/1.4869686] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Coupled-cluster theory including single, double, and perturbative triple excitations [CCSD(T)] has been applied to trimers that appear in crystalline benzene in order to resolve discrepancies in the literature about the magnitude of non-additive three-body contributions to the lattice energy. The present results indicate a non-additive three-body contribution of 0.89 kcal mol(-1), or 7.2% of the revised lattice energy of -12.3 kcal mol(-1). For the trimers for which we were able to compute CCSD(T) energies, we obtain a sizeable difference of 0.63 kcal mol(-1) between the CCSD(T) and MP2 three-body contributions to the lattice energy, confirming that three-body dispersion dominates over three-body induction. Taking this difference as an estimate of three-body dispersion for the closer trimers, and adding an Axilrod-Teller-Muto estimate of 0.13 kcal mol(-1) for long-range contributions yields an overall value of 0.76 kcal mol(-1) for three-body dispersion, a significantly smaller value than in several recent studies.
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Affiliation(s)
- Matthew R Kennedy
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Ashley Ringer McDonald
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - A Eugene DePrince
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Michael S Marshall
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Rafal Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006, Katowice, Poland
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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33
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Cuesta IG, Sánchez de Merás AMJ. Energy interactions in amyloid-like fibrils from NNQQNY. Phys Chem Chem Phys 2014; 16:4369-77. [PMID: 24458317 DOI: 10.1039/c3cp53551g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We use large-scale MP2 calculations to analyze the interactions appearing in amyloid fibers, which are difficult to determine experimentally. To this end, dimers and trimers of the hexapeptide NNQQNY from the yeast prion-like protein Sup35 were considered as model systems. We studied the energy interactions present in the three levels of organization in which the formation of amyloid fibrils is structured. The structural changes in the hydrogen bonds were studied too. It was found that the most energetic process is the formation of the β-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of the aromatic rings of tyrosine, the stability produced by the aromatics residues increasing with their aromaticity. The formation of the basic unit of the assembled proto-fiber, the steric zipper, is less energetic and is associated to both dispersion forces and hydrogen bonds. The interactions between pair of β-sheets across the peptide-to-peptide contact through the tyrosine rings are cooperative and due to dispersion effects. Moreover, the strength of this interaction can rationalize the variation of mobility of the aromatic ring in the tyrosine units found in solid NMR experiments.
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Affiliation(s)
- Inmaculada García Cuesta
- Instituto de Ciencia Molecular, Universidad de Valencia, P.O. Box 22085, E-46071 Valencia, Spain.
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34
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Bhaskaran-Nair K, Kowalski K, Moreno J, Jarrell M, Shelton WA. Equation of motion coupled cluster methods for electron attachment and ionization potential in fullerenes C60and C70. J Chem Phys 2014; 141:074304. [DOI: 10.1063/1.4891934] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Podlech J, Fleck SC, Metzler M, Bürck J, Ulrich AS. Determination of the absolute configuration of perylene quinone-derived mycotoxins by measurement and calculation of electronic circular dichroism spectra and specific rotations. Chemistry 2014; 20:11463-70. [PMID: 25056998 DOI: 10.1002/chem.201402567] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Indexed: 01/14/2023]
Abstract
Altertoxins I-III, alterlosins I and II, alteichin (alterperylenol), stemphyltoxins I-IV, stemphyperylenol, stemphytriol, 7-epi-8-hydroxyaltertoxin I, and 6-epi-stemphytriol are mycotoxins derived from perylene quinone, for which the absolute configuration was not known. Electronic circular dichroism (ECD) spectra were calculated for these compounds and compared with measured spectra of altertoxins I-III, alteichin, and stemphyltoxin III and with reported Cotton effects. Specific rotations were calculated and compared with reported specific rotations. The absolute configuration of all the toxins, except for stemphyltoxin IV, could thus be determined. The validity of the assignment was high whenever reported ECD data were available for comparison, and the validity was lower when the assignment was based only on the comparison of calculated and reported specific rotations. ECD spectra are intrinsically different for toxins with a biphenyl substructure and for toxins derived from dihydroanthracene.
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Affiliation(s)
- Joachim Podlech
- Institute for Organic Chemistry, Karlsruhe Institute for Technology (KIT), Campus South, Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany), Fax: (+49) 721-608-47652.
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36
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Baudin P, Marín JS, Cuesta IG, Sánchez de Merás AMJ. Calculation of excitation energies from the CC2 linear response theory using Cholesky decomposition. J Chem Phys 2014; 140:104111. [DOI: 10.1063/1.4867270] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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37
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DePrince, AE, Kennedy MR, Sumpter BG, Sherrill CD. Density-fitted singles and doubles coupled cluster on graphics processing units. Mol Phys 2014. [DOI: 10.1080/00268976.2013.874599] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Friese DH, Hättig C. Optical rotation calculations on large molecules using the approximate coupled cluster model CC2 and the resolution-of-the-identity approximation. Phys Chem Chem Phys 2014; 16:5942-51. [DOI: 10.1039/c3cp54338b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Beerepoot MTP, Friese DH, Ruud K. Intermolecular charge transfer enhances two-photon absorption in yellow fluorescent protein. Phys Chem Chem Phys 2014; 16:5958-64. [DOI: 10.1039/c3cp55205e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Aidas K, Angeli C, Bak KL, Bakken V, Bast R, Boman L, Christiansen O, Cimiraglia R, Coriani S, Dahle P, Dalskov EK, Ekström U, Enevoldsen T, Eriksen JJ, Ettenhuber P, Fernández B, Ferrighi L, Fliegl H, Frediani L, Hald K, Halkier A, Hättig C, Heiberg H, Helgaker T, Hennum AC, Hettema H, Hjertenæs E, Høst S, Høyvik IM, Iozzi MF, Jansík B, Jensen HJA, Jonsson D, Jørgensen P, Kauczor J, Kirpekar S, Kjærgaard T, Klopper W, Knecht S, Kobayashi R, Koch H, Kongsted J, Krapp A, Kristensen K, Ligabue A, Lutnæs OB, Melo JI, Mikkelsen KV, Myhre RH, Neiss C, Nielsen CB, Norman P, Olsen J, Olsen JMH, Osted A, Packer MJ, Pawlowski F, Pedersen TB, Provasi PF, Reine S, Rinkevicius Z, Ruden TA, Ruud K, Rybkin VV, Sałek P, Samson CCM, de Merás AS, Saue T, Sauer SPA, Schimmelpfennig B, Sneskov K, Steindal AH, Sylvester-Hvid KO, Taylor PR, Teale AM, Tellgren EI, Tew DP, Thorvaldsen AJ, Thøgersen L, Vahtras O, Watson MA, Wilson DJD, Ziolkowski M, Agren H. The Dalton quantum chemistry program system. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013; 4:269-284. [PMID: 25309629 PMCID: PMC4171759 DOI: 10.1002/wcms.1172] [Citation(s) in RCA: 917] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, Møller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.
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Affiliation(s)
- Kestutis Aidas
- Department of General Physics and Spectroscopy, Faculty of Physics, Vilnius University Vilnius, Lithuania
| | | | - Keld L Bak
- Aarhus University School of Engineering Aarhus, Denmark
| | - Vebjørn Bakken
- Faculty of Mathematics and Natural Sciences, University of Oslo Oslo, Norway
| | - Radovan Bast
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
| | | | | | | | - Sonia Coriani
- Department of Chemical and Pharmaceutical Sciences, University of Trieste Trieste, Italy
| | - Pål Dahle
- Norwegian Computing Center Oslo, Norway
| | | | - Ulf Ekström
- CTCC, Department of Chemistry, University of Oslo Oslo, Norway
| | - Thomas Enevoldsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense, Denmark
| | | | | | - Berta Fernández
- Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela Santiago de Compostela, Spain
| | - Lara Ferrighi
- CTCC, Department of Chemistry, UiT The Arctic University of Norway, Tromsø Norway
| | - Heike Fliegl
- CTCC, Department of Chemistry, University of Oslo Oslo, Norway
| | - Luca Frediani
- CTCC, Department of Chemistry, UiT The Arctic University of Norway, Tromsø Norway
| | | | | | - Christof Hättig
- Department of Theoretical Chemistry, Ruhr-University Bochum Bochum, Germany
| | | | - Trygve Helgaker
- CTCC, Department of Chemistry, University of Oslo Oslo, Norway
| | | | - Hinne Hettema
- Department of Philosophy, The University of Auckland Auckland, New Zealand
| | - Eirik Hjertenæs
- Department of Chemistry, Norwegian University of Science and Technology Trondheim, Norway
| | - Stinne Høst
- Department of Geoscience, Aarhus University Aarhus, Denmark
| | | | | | | | - Hans Jørgen Aa Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense, Denmark
| | - Dan Jonsson
- High-Performance Computing Group, UiT The Arctic University of Norway, Tromsø Norway
| | - Poul Jørgensen
- Department of Chemistry, Aarhus University Aarhus, Denmark
| | - Joanna Kauczor
- Department of Physics, Chemistry and Biology, Linköping University Linköping, Sweden
| | | | | | - Wim Klopper
- Institute of Physical Chemistry, Karlsruhe Institute of Technology Karlsruhe, Germany
| | - Stefan Knecht
- Laboratory of Physical Chemistry, ETH Zürich Zürich, Switzerland
| | - Rika Kobayashi
- Australian National University Supercomputer Facility Canberra, Australia
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology Trondheim, Norway
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense, Denmark
| | | | | | - Andrea Ligabue
- Computer Services: Networks and Systems, University of Modena and Reggio Emilia Modena, Italy
| | | | - Juan I Melo
- Physics Department, FCEyN-UBA and IFIBA-CONICET, Universidad de Buenos Aires Buenos Aires, Argentina
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Copenhagen Denmark
| | - Rolf H Myhre
- Department of Chemistry, Norwegian University of Science and Technology Trondheim, Norway
| | - Christian Neiss
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg Erlangen, Germany
| | | | - Patrick Norman
- Department of Physics, Chemistry and Biology, Linköping University Linköping, Sweden
| | - Jeppe Olsen
- Department of Chemistry, Aarhus University Aarhus, Denmark
| | - Jógvan Magnus H Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense, Denmark
| | | | - Martin J Packer
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense, Denmark
| | - Filip Pawlowski
- Institute of Physics, Kazimierz Wielki University Bydgoszcz, Poland
| | | | - Patricio F Provasi
- Department of Physics, University of Northeastern and IMIT-CONICET Corrientes, Argentina
| | - Simen Reine
- CTCC, Department of Chemistry, University of Oslo Oslo, Norway
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Biotechnology and Swedish e-Science Research Center (SeRC), KTH Royal Institute of Technology Stockholm, Sweden
| | | | - Kenneth Ruud
- CTCC, Department of Chemistry, UiT The Arctic University of Norway, Tromsø Norway
| | - Vladimir V Rybkin
- Institute of Physical Chemistry, Karlsruhe Institute of Technology Karlsruhe, Germany
| | | | - Claire C M Samson
- Institute of Physical Chemistry, Karlsruhe Institute of Technology Karlsruhe, Germany
| | | | - Trond Saue
- Paul Sabatier University Toulouse, France
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen Denmark
| | - Bernd Schimmelpfennig
- Institute for Nuclear Waste Disposal, Karlsruhe Institute of Technology Karlsruhe, Germany
| | | | - Arnfinn H Steindal
- CTCC, Department of Chemistry, UiT The Arctic University of Norway, Tromsø Norway
| | | | - Peter R Taylor
- VLSCI and School of Chemistry, University of Melbourne Parkville, Australia
| | - Andrew M Teale
- School of Chemistry, University of Nottingham Nottingham, UK
| | - Erik I Tellgren
- CTCC, Department of Chemistry, University of Oslo Oslo, Norway
| | - David P Tew
- School of Chemistry, University of Bristol Bristol, UK
| | | | | | - Olav Vahtras
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
| | - Mark A Watson
- Department of Chemistry, Princeton University Princeton, New Jersey
| | - David J D Wilson
- Department of Chemistry and La Trobe Institute for Molecular Sciences, La Trobe University Melbourne, Australia
| | - Marcin Ziolkowski
- CoE for Next Generation Computing, Clemson University Clemson, South Carolina
| | - Hans Agren
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
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41
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DePrince AE, Sherrill CD. Accuracy and Efficiency of Coupled-Cluster Theory Using Density Fitting/Cholesky Decomposition, Frozen Natural Orbitals, and a t1-Transformed Hamiltonian. J Chem Theory Comput 2013; 9:2687-96. [DOI: 10.1021/ct400250u] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Eugene DePrince
- Center for
Computational Molecular Science and Technology,
School of Chemistry and Biochemistry, and School of Computational
Science and Engineering, Georgia Institute of Technology, Atlanta,
Georgia 30332-0400, United States
| | - C. David Sherrill
- Center for
Computational Molecular Science and Technology,
School of Chemistry and Biochemistry, and School of Computational
Science and Engineering, Georgia Institute of Technology, Atlanta,
Georgia 30332-0400, United States
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42
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Kauczor J, Norman P, Saidi WA. Non-additivity of polarizabilities and van der Waals C6 coefficients of fullerenes. J Chem Phys 2013; 138:114107. [DOI: 10.1063/1.4795158] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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43
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Friese DH, Hättig C, Koβmann J. Analytic Molecular Hessian Calculations for CC2 and MP2 Combined with the Resolution of Identity Approximation. J Chem Theory Comput 2013; 9:1469-80. [DOI: 10.1021/ct400034t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel H. Friese
- Lehrstuhl für Theoretische
Chemie, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Christof Hättig
- Lehrstuhl für Theoretische
Chemie, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Jörg Koβmann
- Atomistic Modelling and Simulation,
ICAMS, Ruhr-Universität Bochum, D-44801 Bochum, Germany
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44
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Chwee TS, Lim GS, Fan WY, Sullivan MB. Computational study of molecular properties with dual basis sets. Phys Chem Chem Phys 2013; 15:16566-73. [DOI: 10.1039/c3cp51055g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Boström J, Aquilante F, Pedersen TB, Lindh R. Analytical Gradients of Hartree–Fock Exchange with Density Fitting Approximations. J Chem Theory Comput 2012; 9:204-12. [DOI: 10.1021/ct200836x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jonas Boström
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124 S-221 00 Lund, Sweden
| | - Francesco Aquilante
- Center for Biomolecular Nanotechnologies @UNILE, Italian Institute of Technology (IIT), Via Barsanti, I-73010 Arnesano (LE), Italy
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
| | - Thomas Bondo Pedersen
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Roland Lindh
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
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Friese DH, Winter NOC, Balzerowski P, Schwan R, Hättig C. Large scale polarizability calculations using the approximate coupled cluster model CC2 and MP2 combined with the resolution-of-the-identity approximation. J Chem Phys 2012; 136:174106. [DOI: 10.1063/1.4704788] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Boström J, Pitoňák M, Aquilante F, Neogrády P, Pedersen TB, Lindh R. Coupled Cluster and Møller–Plesset Perturbation Theory Calculations of Noncovalent Intermolecular Interactions using Density Fitting with Auxiliary Basis Sets from Cholesky Decompositions. J Chem Theory Comput 2012; 8:1921-8. [DOI: 10.1021/ct3003018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jonas Boström
- Department
of Theoretical Chemistry,
Chemical Center, Lund University, P.O. Box 124 S-221 00 Lund, Sweden
| | - Michal Pitoňák
- Department of Physical and Theoretical
Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská
Dolina, SK-84215 Bratislava, Slovak Republic, and Computing Center
of the Slovak Academy of Sciences, Dúbravská cesta č.
9, SK-84535 Bratislava, Slovak Republic
| | - Francesco Aquilante
- Department of Chemistry—Ångström,
the Theoretical Chemistry Programme, Uppsala University, P.O. Box
518, SE-751 20 Uppsala, Sweden
| | - Pavel Neogrády
- Department of Physical and Theoretical
Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská
Dolina, SK-84215 Bratislava, Slovak Republic
| | - Thomas Bondo Pedersen
- Centre for Theoretical and Computational
Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033
Blindern, N-0315 Oslo, Norway
| | - Roland Lindh
- Department of Chemistry—Ångström,
the Theoretical Chemistry Programme, Uppsala University, P.O. Box
518, SE-751 20 Uppsala, Sweden
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Helgaker T, Coriani S, Jørgensen P, Kristensen K, Olsen J, Ruud K. Recent Advances in Wave Function-Based Methods of Molecular-Property Calculations. Chem Rev 2012; 112:543-631. [DOI: 10.1021/cr2002239] [Citation(s) in RCA: 463] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Trygve Helgaker
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Sonia Coriani
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Giorgieri 1, I-34127 Trieste, Italy
| | - Poul Jørgensen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kasper Kristensen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Jeppe Olsen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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Friese DH, Hättig C, Ruud K. Calculation of two-photon absorption strengths with the approximate coupled cluster singles and doubles model CC2 using the resolution-of-identity approximation. Phys Chem Chem Phys 2011; 14:1175-84. [PMID: 22130199 DOI: 10.1039/c1cp23045j] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An implementation of two-photon absorption matrix elements using the approximate second-order coupled-cluster singles and doubles model CC2 is presented. In this implementation we use the resolution-of-the-identity approximation for the two-electron repulsion integrals to reduce the computational cost. To avoid storage of large arrays we introduce in addition a numerical Laplace transformation of orbital energy denominators for the response of the doubles amplitudes. The error due to the numerical Laplace transformation is found to be negligible. Using this new implementation, we performed a series of benchmark calculations on substituted benzene and azobenzene derivatives to get reference values for TD-DFT results. We show that results obtained with the Coulomb-attenuated B3LYP functional are in reasonable agreement with the coupled-cluster results, whereas other density functionals which do not have a long-range correction give considerably less accurate results. Applications to the AF240 dye molecule and a weakly bound molecular tweezer complex demonstrate that this new RI-CC2 implementation allows for the first time to compute two-photon absorption cross sections with a correlated wave function method for molecules with more than 70 atoms and to apply this method for benchmarking TD-DFT calculations on molecules which are of particular relevance for experimental studies of two-photon absorption.
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Affiliation(s)
- Daniel H Friese
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44801 Bochum, Germany.
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Kumar A, Thakkar AJ. Dipole polarizability, sum rules, mean excitation energies, and long-range dispersion coefficients for buckminsterfullerene C60. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.080] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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