51
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Klawohn S, Kaupp M, Karton A. MVO-10: A Gas-Phase Oxide Benchmark for Localization/Delocalization in Mixed-Valence Systems. J Chem Theory Comput 2018; 14:3512-3523. [DOI: 10.1021/acs.jctc.8b00289] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sascha Klawohn
- Theoretische Chemie/Quantenchemie, Institut für Chemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Martin Kaupp
- Theoretische Chemie/Quantenchemie, Institut für Chemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Amir Karton
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, Australia
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52
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Barca GM, Loos PF. Recurrence Relations for Four-Electron Integrals Over Gaussian Basis Functions. ADVANCES IN QUANTUM CHEMISTRY 2018. [DOI: 10.1016/bs.aiq.2017.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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53
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Nunes CM, Reva I, Kozuch S, McMahon RJ, Fausto R. Photochemistry of 2-Formylphenylnitrene: A Doorway to Heavy-Atom Tunneling of a Benzazirine to a Cyclic Ketenimine. J Am Chem Soc 2017; 139:17649-17659. [DOI: 10.1021/jacs.7b10495] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Cláudio M. Nunes
- CQC, Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Igor Reva
- CQC, Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel
| | - Robert J. McMahon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1322, United States
| | - Rui Fausto
- CQC, Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
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54
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Sylvetsky N, Kesharwani MK, Martin JML. The aug-cc-pVnZ-F12 basis set family: Correlation consistent basis sets for explicitly correlated benchmark calculations on anions and noncovalent complexes. J Chem Phys 2017; 147:134106. [DOI: 10.1063/1.4998332] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Manoj K. Kesharwani
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
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55
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Pavošević F, Peng C, Ortiz JV, Valeev EF. Communication: Explicitly correlated formalism for second-order single-particle Green’s function. J Chem Phys 2017; 147:121101. [DOI: 10.1063/1.5000916] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Fabijan Pavošević
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Chong Peng
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - J. V. Ortiz
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, USA
| | - Edward F. Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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56
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57
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Mostafanejad M. Structure of free complement wavefunction for the ground and the first excited state of helium atom. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We review the fundamental ideas of free complement (FC) method through its application on both ground and first excited states of helium atom. We have found that lower energies can be obtained with fewer number of terms in the FC expansion of the ground state wavefunction. In this case, the optimization of orbital exponents was not necessary for achieving spectroscopic accuracy, especially at higher orders where the structure of the FC wavefunction converges to that of the exact one. We have discovered that permanents naturally appear in the FC expansion of the first triplet excited state wavefunction. Including permanents in the FC expansion is shown to be energetically important for the first triplet excited state of helium atom whereas it is not computationally favorable at higher orders. Finally, considering the group theoretical properties of the symmetric group [Formula: see text] and using immanants, a compact and more elegant form for the FC expansion of the first triplet excited state of the helium atom is achieved.
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Affiliation(s)
- Mohammad Mostafanejad
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
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58
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Vamhindi BSDR, Karton A. Can DFT and ab initio methods adequately describe binding energies in strongly interacting C6X6⋯C2X π–π complexes? Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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59
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Barca GMJ, Loos PF. Three- and four-electron integrals involving Gaussian geminals: Fundamental integrals, upper bounds, and recurrence relations. J Chem Phys 2017; 147:024103. [DOI: 10.1063/1.4991733] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Giuseppe M. J. Barca
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Pierre-François Loos
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, Toulouse, France
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60
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Chan B. How to computationally calculate thermochemical properties objectively, accurately, and as economically as possible. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-1116] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
We have developed the WnX series of quantum chemistry composite protocols for the computation of highly-accurate thermochemical quantities with advanced efficiency and applicability. The W1X-type methods have a general accuracy of ~3–4 kJ mol−1 and they can currently be applied to systems with ~20–30 atoms. Higher-level methods include W2X, W3X and W3X-L, with the most accurate of these being W3X-L. It can be applied to molecules with ~10–20 atoms and is generally accurate to ~1.5 kJ mol−1. The WnX procedures have opened up new possibilities for computational chemists in pursue of accurate thermochemical values in a highly-productive manner.
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61
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Lasar C, Klüner T. Explicitly Correlated Orbital Optimized Contracted Pair Correlation Methods: A Short Overview. J Phys Chem A 2017; 121:4707-4711. [PMID: 28570077 DOI: 10.1021/acs.jpca.7b03960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Designing efficient algorithms to apply highly accurate pair correlation methods to large molecules of scientific interest has remained an important field of research for a long period of time. We present a new approach toward fast algorithms, which represents an interesting alternative and extension to currently existing methods. The presented new contraction scheme saves a significant amount of memory and can be easily combined with efficient linear scaling algorithms. Additionally, the extension to orbital optimization and explicitly correlated f12-theory is demonstrated to further improve accuracy and applicablility.
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Affiliation(s)
- Christian Lasar
- Department of Chemistry, Carl von Ossietzky University Oldenburg , 26111 Oldenburg, Germany
| | - Thorsten Klüner
- Department of Chemistry, Carl von Ossietzky University Oldenburg , 26111 Oldenburg, Germany
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62
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Abstract
We have devised the composite procedures WG and WGh to unify the W1X and the (computationally more economical) G4(MP2)-6X protocols. The WG procedure employs a combination of MP2, MP2-F12, CCSD-F12b, and CCSD(T) to approximate the all-electron scalar-relativistic CCSD(T)/CBS energy. In addition, it incorporates features such as the scaling of the energy components and an empirical "higher-level-correction" term. The WGh protocol represents a somewhat more economical variant of WG with partial removal of diffuse functions. Our benchmark shows that, in general, both WG and WGh have similar performance to that for W1X-2, with WGh (predictably) performing somewhat less well for electron affinities. In terms of computational efficiency, WG is approximately an order of magnitude less costly than W1X-2, while WGh gives not only a further slight savings in computer time but also a notably reduced disk requirement.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University , Bunkyo 1-14, Nagasaki 852-8521, Japan
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63
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Grundei MMJ, Burow AM. Random Phase Approximation for Periodic Systems Employing Direct Coulomb Lattice Summation. J Chem Theory Comput 2017; 13:1159-1175. [DOI: 10.1021/acs.jctc.6b01146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin M. J. Grundei
- Department of Chemistry, Ludwig-Maximilians-Universität (LMU) Munich, Butenandtstrasse 7, D-81377 Munich, Germany
| | - Asbjörn M. Burow
- Department of Chemistry, Ludwig-Maximilians-Universität (LMU) Munich, Butenandtstrasse 7, D-81377 Munich, Germany
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64
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Grüneis A, Hirata S, Ohnishi YY, Ten-no S. Perspective: Explicitly correlated electronic structure theory for complex systems. J Chem Phys 2017; 146:080901. [DOI: 10.1063/1.4976974] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andreas Grüneis
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart,
Germany
- Department Chemie, Technische Universität München (TUM), Lichtenbergstrasse 4, D-85747 Garching,
Germany
- Graduate School of Science, Technology, and Innovation,
Kobe University, Nada-ku, Kobe 657-8501,
Japan
| | - So Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yu-ya Ohnishi
- Graduate School of System Informatics, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Seiichiro Ten-no
- Graduate School of Science, Technology, and Innovation,
Kobe University, Nada-ku, Kobe 657-8501,
Japan
- Graduate School of System Informatics, Kobe University, Nada-ku, Kobe 657-8501, Japan
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65
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Sarrami F, Yu LJ, Karton A. Thermochemistry of icosahedral closo-dicarboranes: a composite ab initio quantum-chemical perspective. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We obtained accurate thermochemical properties for the ortho-, meta-, and para-dicarborane isomers (C2B10H12) by means of explicitly correlated high-level thermochemical procedures. The thermochemical properties include heats of formation, isomerization energies, C–H and B–H bond dissociation energies (BDEs), and ionization potentials. Of these only the ionization potentials are known experimentally. Our best theoretical ionization potentials, obtained by means of the ab initio W1–F12 thermochemical protocol, was 241.50 kcal mol–1 (para-dicarborane), 238.45 kcal mol–1 (meta-dicarborane), and 236.54 kcal mol–1 (ortho-dicarborane). These values agree with the experimental values adopted by the National Institute of Standards and Technology (NIST) thermochemical tables to within overlapping uncertainties. However, they suggest that the experimental values may represent significant underestimations. For all isomers, the C–H BDEs are systematically higher than the B–H BDEs because of the relative stability of the boron-centred radicals. The C–H BDEs for the three isomers cluster within a narrow energetic interval, namely between 110.8 kcal mol–1 (para-dicarborane) and 111.7 kcal mol–1 (meta-dicarborane). The B–H BDEs cluster within a larger interval ranging between 105.8 and 108.1 kcal mol–1 (both obtained for ortho-dicarborane). We used our benchmark W1–F12 data to assess the performance of a number of lower cost composite ab initio methods. We found that the Gaussian-3 procedures (G3(MP2)B3 and G3B3) result in excellent performance with overall root-mean-square deviations (RMSDs) of 0.3–0.4 kcal mol–1 for the isomerization, ionization, and bond dissociation energies. However, the Gaussian-4 procedures (G4, G4(MP2), and G4(MP2)-6X) showed relatively poor performance with overall RMSDs of 1.3–3.7 kcal mol–1.
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Affiliation(s)
- Farzaneh Sarrami
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Li-Juan Yu
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Amir Karton
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
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66
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Johnson CM, Doran AE, Zhang J, Valeev EF, Hirata S. Monte Carlo explicitly correlated second-order many-body perturbation theory. J Chem Phys 2016; 145:154115. [DOI: 10.1063/1.4964854] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Cole M. Johnson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Alexander E. Doran
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jinmei Zhang
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Edward F. Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - So Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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67
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Spackman PR, Jayatilaka D, Karton A. Basis set convergence of CCSD(T) equilibrium geometries using a large and diverse set of molecular structures. J Chem Phys 2016; 145:104101. [DOI: 10.1063/1.4962168] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peter R. Spackman
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Amir Karton
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
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68
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Pavošević F, Pinski P, Riplinger C, Neese F, Valeev EF. SparseMaps--A systematic infrastructure for reduced-scaling electronic structure methods. IV. Linear-scaling second-order explicitly correlated energy with pair natural orbitals. J Chem Phys 2016; 144:144109. [PMID: 27083710 DOI: 10.1063/1.4945444] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a formulation of the explicitly correlated second-order Møller-Plesset (MP2-F12) energy in which all nontrivial post-mean-field steps are formulated with linear computational complexity in system size. The two key ideas are the use of pair-natural orbitals for compact representation of wave function amplitudes and the use of domain approximation to impose the block sparsity. This development utilizes the concepts for sparse representation of tensors described in the context of the domain based local pair-natural orbital-MP2 (DLPNO-MP2) method by us recently [Pinski et al., J. Chem. Phys. 143, 034108 (2015)]. Novel developments reported here include the use of domains not only for the projected atomic orbitals, but also for the complementary auxiliary basis set (CABS) used to approximate the three- and four-electron integrals of the F12 theory, and a simplification of the standard B intermediate of the F12 theory that avoids computation of four-index two-electron integrals that involve two CABS indices. For quasi-1-dimensional systems (n-alkanes), the ON DLPNO-MP2-F12 method becomes less expensive than the conventional ON(5) MP2-F12 for n between 10 and 15, for double- and triple-zeta basis sets; for the largest alkane, C200H402, in def2-TZVP basis, the observed computational complexity is N(∼1.6), largely due to the cubic cost of computing the mean-field operators. The method reproduces the canonical MP2-F12 energy with high precision: 99.9% of the canonical correlation energy is recovered with the default truncation parameters. Although its cost is significantly higher than that of DLPNO-MP2 method, the cost increase is compensated by the great reduction of the basis set error due to explicit correlation.
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Affiliation(s)
- Fabijan Pavošević
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Peter Pinski
- Max Planch Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Christoph Riplinger
- Max Planch Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planch Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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69
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Ohnishi YY, Ten-no S. Explicitly correlated frequency-independent second-order green's function for accurate ionization energies. J Comput Chem 2016; 37:2447-53. [DOI: 10.1002/jcc.24468] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Yu-ya Ohnishi
- Graduate School of System Informatics; Kobe University; Nada-Ku Kobe 657-8501 Japan
| | - Seiichiro Ten-no
- Graduate School of System Informatics; Kobe University; Nada-Ku Kobe 657-8501 Japan
- Graduate School of Science; Technology, and Innovation, Kobe University; Nada-Ku Kobe 657-8501 Japan
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70
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Kaupp M, Karton A, Bischoff FA. [Al2O4](-), a Benchmark Gas-Phase Class II Mixed-Valence Radical Anion for the Evaluation of Quantum-Chemical Methods. J Chem Theory Comput 2016; 12:3796-806. [PMID: 27434425 DOI: 10.1021/acs.jctc.6b00594] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The radical anion [Al2O4](-) has been identified as a rare example of a small gas-phase mixed-valence system with partially localized, weakly coupled class II character in the Robin/Day classification. It exhibits a low-lying C2v minimum with one terminal oxyl radical ligand and a high-lying D2h minimum at about 70 kJ/mol relative energy with predominantly bridge-localized-hole character. Two identical C2v minima and the D2h minimum are connected by two C2v-symmetrical transition states, which are only ca. 6-10 kJ/mol above the D2h local minimum. The small size of the system and the absence of environmental effects has for the first time enabled the computation of accurate ab initio benchmark energies, at the CCSDT(Q)/CBS level using W3-F12 theory, for a class-II mixed-valence system. These energies have been used to evaluate wave function-based methods [CCSD(T), CCSD, SCS-MP2, MP2, UHF] and density functionals ranging from semilocal (e.g., BLYP, PBE, M06L, M11L, N12) via global hybrids (B3LYP, PBE0, BLYP35, BMK, M06, M062X, M06HF, PW6B95) and range-separated hybrids (CAM-B3LYP, ωB97, ωB97X-D, LC-BLYP, LC-ωPBE, M11, N12SX), the B2PLYP double hybrid, and some local hybrid functionals. Global hybrids with about 35-43% exact-exchange (EXX) admixture (e.g., BLYP35, BMK), several range hybrids (CAM-B3LYP, ωB97X-D, ω-B97), and a local hybrid provide good to excellent agreement with benchmark energetics. In contrast, too low EXX admixture leads to an incorrect delocalized class III picture, while too large EXX overlocalizes and gives too large energy differences. These results provide support for previous method choices for mixed-valence systems in solution and for the treatment of oxyl defect sites in alumosilicates and SiO2. Vibrational gas-phase spectra at various computational levels have been compared directly to experiment and to CCSD(T)/aug-cc-pV(T+d)Z data.
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Affiliation(s)
- Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie Technische, Sekr. C7, Universität Berlin , Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Amir Karton
- School of Chemistry and Biochemistry, The University of Western Australia , 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Florian A Bischoff
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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71
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Zhang J, Calvin JA, Valeev EF. Anatomy of molecular properties evaluated with explicitly correlated electronic wave functions. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1200754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Jinmei Zhang
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
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72
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Roskop LB, Valeev EF, Carter EA, Gordon MS, Windus TL. Spin-Free [2]R12 Basis Set Incompleteness Correction to the Local Multireference Configuration Interaction and the Local Multireference Average Coupled Pair Functional Methods. J Chem Theory Comput 2016; 12:3176-84. [DOI: 10.1021/acs.jctc.6b00315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luke B. Roskop
- Department
of Chemistry, Iowa State University, Ames, Iowa 50010, United States
| | - Edward F. Valeev
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Emily A. Carter
- Department
of Mechanical and Aerospace Engineering, Program in Applied and Computational
Mathematics, and Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
| | - Mark S. Gordon
- Department
of Chemistry, Iowa State University, Ames, Iowa 50010, United States
| | - Theresa L. Windus
- Department
of Chemistry, Iowa State University, Ames, Iowa 50010, United States
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73
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Sylvetsky N, Peterson KA, Karton A, Martin JML. Toward a W4-F12 approach: Can explicitly correlated and orbital-based ab initio CCSD(T) limits be reconciled? J Chem Phys 2016; 144:214101. [DOI: 10.1063/1.4952410] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Kirk A. Peterson
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, USA
| | - Amir Karton
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
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74
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Rasmussen TH, Wang YM, Kjærgaard T, Kristensen K. The explicitly correlated same number of optimized parameters (SNOOP-F12) scheme for calculating intermolecular interaction energies. J Chem Phys 2016; 144:204102. [DOI: 10.1063/1.4950846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Troels Hels Rasmussen
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Yang Min Wang
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Thomas Kjærgaard
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Kasper Kristensen
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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75
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Wang YM, Hättig C, Reine S, Valeev E, Kjærgaard T, Kristensen K. Explicitly correlated second-order Møller-Plesset perturbation theory in a Divide-Expand-Consolidate (DEC) context. J Chem Phys 2016; 144:204112. [DOI: 10.1063/1.4951696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yang Min Wang
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Simen Reine
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033, N-1315 Blindern, Norway
| | - Edward Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Thomas Kjærgaard
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Kasper Kristensen
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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76
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Frey JA, Holzer C, Klopper W, Leutwyler S. Experimental and Theoretical Determination of Dissociation Energies of Dispersion-Dominated Aromatic Molecular Complexes. Chem Rev 2016; 116:5614-41. [DOI: 10.1021/acs.chemrev.5b00652] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jann A. Frey
- Departement
für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Samuel Leutwyler
- Departement
für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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77
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Barca GMJ, Loos PF, Gill PMW. Many-Electron Integrals over Gaussian Basis Functions. I. Recurrence Relations for Three-Electron Integrals. J Chem Theory Comput 2016; 12:1735-40. [DOI: 10.1021/acs.jctc.6b00130] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giuseppe M. J. Barca
- Research School of Chemistry, Australian National University, Australian Capital Territory 2601, Australia
| | - Pierre-François Loos
- Research School of Chemistry, Australian National University, Australian Capital Territory 2601, Australia
| | - Peter M. W. Gill
- Research School of Chemistry, Australian National University, Australian Capital Territory 2601, Australia
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78
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Řezáč J, Hobza P. Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications. Chem Rev 2016; 116:5038-71. [DOI: 10.1021/acs.chemrev.5b00526] [Citation(s) in RCA: 281] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
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79
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General Coalescence Conditions for the Exact Wave Functions. ADVANCES IN QUANTUM CHEMISTRY 2016. [DOI: 10.1016/bs.aiq.2015.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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80
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Ohtsuka Y, Ten-no S. A study of potential energy curves from the model space quantum Monte Carlo method. J Chem Phys 2015; 143:214107. [DOI: 10.1063/1.4936412] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuhki Ohtsuka
- Department of Computational Sciences, Graduate School of System Informatics, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Seiichiro Ten-no
- Department of Computational Sciences, Graduate School of System Informatics, Kobe University, Nada-ku, Kobe 657-8501, Japan
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81
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Ma Q, Werner HJ. Scalable Electron Correlation Methods. 2. Parallel PNO-LMP2-F12 with Near Linear Scaling in the Molecular Size. J Chem Theory Comput 2015; 11:5291-304. [DOI: 10.1021/acs.jctc.5b00843] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qianli Ma
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Baden-Württemberg, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Baden-Württemberg, Germany
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82
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Wagner JP, Schreiner PR. London’sche Dispersionswechselwirkungen in der Molekülchemie - eine Neubetrachtung sterischer Effekte. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503476] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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83
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Wagner JP, Schreiner PR. London dispersion in molecular chemistry--reconsidering steric effects. Angew Chem Int Ed Engl 2015; 54:12274-96. [PMID: 26262562 DOI: 10.1002/anie.201503476] [Citation(s) in RCA: 673] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 12/15/2022]
Abstract
London dispersion, which constitutes the attractive part of the famous van der Waals potential, has long been underappreciated in molecular chemistry as an important element of structural stability, and thus affects chemical reactivity and catalysis. This negligence is due to the common notion that dispersion is weak, which is only true for one pair of interacting atoms. For increasingly larger structures, the overall dispersion contribution grows rapidly and can amount to tens of kcal mol(-1) . This Review collects and emphasizes the importance of inter- and intramolecular dispersion for molecules consisting mostly of first row atoms. The synergy of experiment and theory has now reached a stage where dispersion effects can be examined in fine detail. This forces us to reconsider our perception of steric hindrance and stereoelectronic effects. The quantitation of dispersion energy donors will improve our ability to design sophisticated molecular structures and much better catalysts.
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Affiliation(s)
- J Philipp Wagner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen (Germany)
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen (Germany).
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84
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Karton A, Schreiner PR, Martin JML. Heats of formation of platonic hydrocarbon cages by means of high-level thermochemical procedures. J Comput Chem 2015; 37:49-58. [DOI: 10.1002/jcc.23963] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/25/2015] [Accepted: 05/11/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Amir Karton
- School of Chemistry and Biochemistry; The University of Western Australia; Perth Western 6009 Australia
| | - Peter R. Schreiner
- Institute of Organic Chemistry; Justus-Liebig University; Heinrich-Buff-Ring 58 35392 Giessen Germany
| | - Jan M. L. Martin
- Department of Organic Chemistry; Weizmann Institute of Science; Reḥovot Israel
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85
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Peterson KA, Kesharwani MK, Martin JM. The cc-pV5Z-F12 basis set: reaching the basis set limit in explicitly correlated calculations. Mol Phys 2014. [DOI: 10.1080/00268976.2014.985755] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Kirk A. Peterson
- Department of Chemistry, Washington State University, Pullman, WA, USA
| | - Manoj K. Kesharwani
- Department of Organic Chemistry, Weizmann Institute of Science, Reḥovot, Israel
| | - Jan M.L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, Reḥovot, Israel
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86
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Yu LJ, Sarrami F, Karton A, O’Reilly RJ. An assessment of theoretical procedures forπ-conjugation stabilisation energies in enones. Mol Phys 2014. [DOI: 10.1080/00268976.2014.986238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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87
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Senn HM. Insights into enzymatic halogenation from computational studies. Front Chem 2014; 2:98. [PMID: 25426489 PMCID: PMC4227530 DOI: 10.3389/fchem.2014.00098] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/20/2014] [Indexed: 12/15/2022] Open
Abstract
The halogenases are a group of enzymes that have only come to the fore over the last 10 years thanks to the discovery and characterization of several novel representatives. They have revealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate halogens and introduce them into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these studies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein serve to illustrate some of the limitations of the current computational approaches and the challenges encountered in computational mechanistic enzymology.
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Affiliation(s)
- Hans M. Senn
- WestCHEM School of Chemistry, University of GlasgowGlasgow, UK
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88
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Ohnishi YY, Ishimura K, Ten-no S. Interaction Energy of Large Molecules from Restrained Denominator MP2-F12. J Chem Theory Comput 2014; 10:4857-61. [DOI: 10.1021/ct500738g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-ya Ohnishi
- Graduate
School of System Informatics, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Kazuya Ishimura
- Institute
for
Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - Seiichiro Ten-no
- Graduate
School of System Informatics, Kobe University, Nada-ku, Kobe 657-8501, Japan
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89
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Yu LJ, Karton A. Assessment of theoretical procedures for a diverse set of isomerization reactions involving double-bond migration in conjugated dienes. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.07.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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90
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Brauer B, Kesharwani MK, Martin JML. Some Observations on Counterpoise Corrections for Explicitly Correlated Calculations on Noncovalent Interactions. J Chem Theory Comput 2014; 10:3791-9. [PMID: 26588524 DOI: 10.1021/ct500513b] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The basis set convergence of explicitly correlated ab initio methods, when applied to noncovalent interactions, has been considered in the presence (and absence) of Boys-Bernardi counterpoise corrections, as well as using "half-counterpoise" (the average of raw and counterpoise-corrected values) as recently advocated in this journal [Burns, L. A.; Marshall, M. S.; Sherrill, C. D. J. Chem. Theory Comput. 2014, 10, 49-57]. Reference results were obtained using basis sets so large that BSSE (basis set superposition error) can be shown to be negligible. For the HF+CABS component, full counterpoise unequivocally exhibits the fastest basis set convergence. However, at the MP2-F12 and CCSD(T*)-F12b levels, surprisingly good uncorrected results can be obtained with small basis sets like cc-pVDZ-F12, owing to error compensation between basis set superposition error (which overbinds) and intrinsic basis set insufficiency (which underbinds). For intermediate sets like cc-pVTZ-F12, "half-half" averages work best, while for large basis sets like cc-pVQZ-F12, full counterpoise may be preferred but BSSE in uncorrected values is tolerably small for most purposes. A composite scheme in which CCSD(T)-MP2 "high level corrections" obtained at the CCSD(T*)-F12b/cc-pVDZ-F12 level are combined with "half-counterpoise" MP2-F12/cc-pVTZ-F12 interaction energies yields surprisingly good performance for standard benchmark sets like S22 and S66.
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Affiliation(s)
- Brina Brauer
- Department of Organic Chemistry, Weizmann Institute of Science , 76100 Reḥovot, Israel
| | - Manoj K Kesharwani
- Department of Organic Chemistry, Weizmann Institute of Science , 76100 Reḥovot, Israel
| | - Jan M L Martin
- Department of Organic Chemistry, Weizmann Institute of Science , 76100 Reḥovot, Israel
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91
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Kurokawa YI, Nakashima H, Nakatsuji H. General coalescence conditions for the exact wave functions. II. Higher-order relations for many-particle systems. J Chem Phys 2014; 140:214103. [DOI: 10.1063/1.4879266] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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92
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Karton A, Talbi D. Pinning the most stable HxCyOz isomers in space by means of high-level theoretical procedures. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.03.010] [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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93
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Karton A, Yu LJ, Kesharwani MK, Martin JML. Heats of formation of the amino acids re-examined by means of W1-F12 and W2-F12 theories. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1483-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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94
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The reaction of the benzene cation with acetylenes for the growth of PAHs in the interstellar medium. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.01.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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95
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Accurate atomization energies from combining coupled-cluster computations with interference-corrected explicitly correlated second-order perturbation theory. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1446-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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96
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97
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Karton A, Kettner M, Wild D. Sneaking up on the Criegee intermediate from below: Predicted photoelectron spectrum of the CH2OO− anion and W3-F12 electron affinity of CH2OO. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.08.075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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98
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Mehine MM, Losilla SA, Sundholm D. An efficient algorithm to calculate three-electron integrals for Gaussian-type orbitals using numerical integration. Mol Phys 2013. [DOI: 10.1080/00268976.2013.793847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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99
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Demel O, Kedžuch S, Noga J, Pittner J. Perturbative triples correction for explicitly correlated Mukherjee’s state-specific coupled cluster method. Mol Phys 2013. [DOI: 10.1080/00268976.2013.809488] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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100
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Ohnishi YY, Ten-no S. Alternative formulation of explicitly correlated third-order Møller–Plesset perturbation theory. Mol Phys 2013. [DOI: 10.1080/00268976.2013.793846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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