1051
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Hégely B, Nagy PR, Ferenczy GG, Kállay M. Exact density functional and wave function embedding schemes based on orbital localization. J Chem Phys 2016. [DOI: 10.1063/1.4960177] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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1052
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Meitei OR, Heßelmann A. Molecular energies from an incremental fragmentation method. J Chem Phys 2016; 144:084109. [PMID: 26931683 DOI: 10.1063/1.4942189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.
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Affiliation(s)
- Oinam Romesh Meitei
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, D-91058 Erlangen, Germany
| | - Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, D-91058 Erlangen, Germany
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1053
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Abstract
We present an efficient implementation of the closed shell multilevel coupled cluster method where coupled cluster singles and doubles (CCSD) is used for the inactive orbital space and CCSD with perturbative triples (CC3) is employed for the smaller active orbital space. Using Cholesky orbitals, the active space can be spatially localized and the computational cost is greatly reduced compared to full CC3 while retaining the accuracy of CC3 excitation energies. For the small organic molecules considered we achieve up to two orders of magnitude reduction in the computational requirements.
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Affiliation(s)
- Rolf H Myhre
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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1054
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Dutta AK, Neese F, Izsák R. Towards a pair natural orbital coupled cluster method for excited states. J Chem Phys 2016; 145:034102. [DOI: 10.1063/1.4958734] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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1055
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Fiedler B, Coriani S, Friedrich J. Molecular Dipole Moments within the Incremental Scheme Using the Domain-Specific Basis-Set Approach. J Chem Theory Comput 2016; 12:3040-52. [PMID: 27300371 DOI: 10.1021/acs.jctc.6b00076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present the first implementation of the fully automated incremental scheme for CCSD unrelaxed dipole moments using the domain-specific basis-set approach. Truncation parameters are varied, and the accuracy of the method is statistically analyzed for a test set of 20 molecules. The local approximations introduce small errors at second order and negligible ones at third order. For a third-order incremental CCSD expansion with a CC2 error correction, a cc-pVDZ/SV domain-specific basis set (tmain = 3.5 Bohr), and the truncation parameter f = 30 Bohr, we obtain a mean error of 0.00 mau (-0.20 mau) and a standard deviation of 1.95 mau (2.17 mau) for the total dipole moments (Cartesian components of the dipole vectors). By analyzing incremental CCSD energies, we demonstrate that the MP2 and CC2 error correction schemes are an exclusive correction for the domain-specific basis-set error. Our implementation of the incremental scheme provides fully automated computations of highly accurate dipole moments at reduced computational cost and is fully parallelized in terms of the calculation of the increments. Therefore, one can utilize the incremental scheme, on the same hardware, to extend the basis set in comparison to standard CCSD and thus obtain a better total accuracy.
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Affiliation(s)
- Benjamin Fiedler
- Institute for Chemistry, Technische Universität Chemnitz , Straße der Nationen 62, D-09111 Chemnitz, Germany
| | - Sonia Coriani
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste , Via L. Giorgieri 1, I-34127 Trieste, Italy.,Aarhus Institute of Advanced Studies, Aarhus University , Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark
| | - Joachim Friedrich
- Institute for Chemistry, Technische Universität Chemnitz , Straße der Nationen 62, D-09111 Chemnitz, Germany
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1056
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Kats D. Speeding up local correlation methods: System-inherent domains. J Chem Phys 2016; 145:014103. [DOI: 10.1063/1.4954963] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Daniel Kats
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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1057
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Köppl C, Werner HJ. Parallel and Low-Order Scaling Implementation of Hartree–Fock Exchange Using Local Density Fitting. J Chem Theory Comput 2016; 12:3122-34. [DOI: 10.1021/acs.jctc.6b00251] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Köppl
- Institut
für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut
für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
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1058
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Duignan TJ, Autschbach J. Impact of the Kohn–Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide Complexes. J Chem Theory Comput 2016; 12:3109-21. [DOI: 10.1021/acs.jctc.6b00238] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas J. Duignan
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
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1059
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Riplinger C, Pinski P, Becker U, Valeev EF, Neese F. Sparse maps--A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory. J Chem Phys 2016; 144:024109. [PMID: 26772556 DOI: 10.1063/1.4939030] [Citation(s) in RCA: 667] [Impact Index Per Article: 83.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate previous implementation.
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Affiliation(s)
- Christoph Riplinger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Peter Pinski
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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1060
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Friedrich J, Fiedler B. Accurate calculation of binding energies for molecular clusters – Assessment of different models. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.02.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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1061
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Zhang J, Dolg M. Third-Order Incremental Dual-Basis Set Zero-Buffer Approach for Large High-Spin Open-Shell Systems. J Chem Theory Comput 2016; 11:962-8. [PMID: 26579750 DOI: 10.1021/ct501052e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The third-order incremental dual-basis set zero-buffer approach (inc3-db-B0) is an efficient, accurate, and black-box quantum chemical method for obtaining correlation energies of large systems, and it has been successfully applied to many real chemical problems. In this work, we extend this approach to high-spin open-shell systems. In the open-shell approach, we will first decompose the occupied orbitals of a system into several domains by a K-means clustering algorithm. The essential part is that we preserve the active (singly occupied) orbitals in all the calculations of the domain correlation energies. The duplicated contributions of the active orbitals to the correlation energy are subtracted from the incremental expansion. All techniques of truncating the virtual space such as the B0 approximation can be applied. This open-shell inc3-db-B0 approach is combined with the CCSD and CCSD(T) methods and applied to the computations of a singlet-triplet gap and an electron detachment process. Our approach exhibits an accuracy better than 0.6 kcal/mol or 0.3 eV compared with the standard implementation, while it saves a large amount of the computational time and can be efficiently parallelized.
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Affiliation(s)
- Jun Zhang
- Institute for Theoretical Chemistry, University of Cologne , Greinstraße 4, D-50939 Cologne, Germany
| | - Michael Dolg
- Institute for Theoretical Chemistry, University of Cologne , Greinstraße 4, D-50939 Cologne, Germany
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1062
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Simm GN, Reiher M. Systematic Error Estimation for Chemical Reaction Energies. J Chem Theory Comput 2016; 12:2762-73. [PMID: 27159007 DOI: 10.1021/acs.jctc.6b00318] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
For a theoretical understanding of the reactivity of complex chemical systems, accurate relative energies between intermediates and transition states are required. Despite its popularity, density functional theory (DFT) often fails to provide sufficiently accurate data, especially for molecules containing transition metals. Due to the huge number of intermediates that need to be studied for all but the simplest chemical processes, DFT is, to date, the only method that is computationally feasible. Here, we present a Bayesian framework for DFT that allows for error estimation of calculated properties. Since the optimal choice of parameters in present-day density functionals is strongly system dependent, we advocate for a system-focused reparameterization. While, at first sight, this approach conflicts with the first-principles character of DFT that should make it, in principle, system independent, we deliberately introduce system dependence to be able to assign a stochastically meaningful error to the system-dependent parametrization, which makes it nonarbitrary. By reparameterizing a functional that was derived on a sound physical basis to a chemical system of interest, we obtain a functional that yields reliable confidence intervals for reaction energies. We demonstrate our approach on the example of catalytic nitrogen fixation.
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Affiliation(s)
- Gregor N Simm
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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1063
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Mondal B, Neese F, Ye S. Toward Rational Design of 3d Transition Metal Catalysts for CO2 Hydrogenation Based on Insights into Hydricity-Controlled Rate-Determining Steps. Inorg Chem 2016; 55:5438-44. [PMID: 27163654 DOI: 10.1021/acs.inorgchem.6b00471] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbon dioxide functionalization attracts much interest due to the current environmental and energy challenges. Our earlier work (Mondal, B.; Neese, F.; Ye, S. Inorg. Chem. 2015, 54, 7192-7198) demonstrated that CO2 hydrogenation mediated by base metal catalysts [M(H)(η(2)-H2)(PP3(Ph))](n+) (M = Co(III) and Fe(II), n = 1, 2; PP3(Ph) = tris(2-(diphenylphosphino)phenyl)phosphine) features discrete rate-determining steps (RDSs). Specifically, the reaction with [Co(III)(H)(η(2)-H2)(PP3(Ph))](2+) passes through a hydride-transfer RDS, whereas the conversion with [Fe(II)(H)(η(2)-H2)(PP3(Ph))](+) traverses a H2-splitting RDS. More importantly, we found that the nature and barrier of the RDS likely correlate with the hydride affinity or hydricity of the dihydride intermediate [M(H)2(PP3(Ph))]((n-1)+) generated by H2-splitting. In the present contribution, following this notion we design a series of potential Fe(II) and Co(III) catalysts, for which the respective dihydride species possess differential hydricities, and computationally investigated their reactivity toward CO2 hydrogenation. Our results reveal that lowering the hydrictiy of [Co(III)(H)2(PP3(Ph))](+) by introducing anionic anchors in PP3(Ph) dramatically decreases the hydride-transfer RDS barrier, as shown for the enhanced reactivity of [Co(H)(η(2)-H2)(CP3(Ph))](+) and [Co(H)(η(2)-H2)(SiP3(Ph))](+) (CP3(Ph) = tris(2-(diphenylphosphino)phenyl)methyl, SiP3(Ph) = tris(2-(diphenylphosphino)phenyl)silyl), while the same ligand modification increases the H2-splitting RDS barriers for [Fe(H)(η(2)-H2)(CP3(Ph))] and [Fe(H)(η(2)-H2)(SiP3(Ph))] relative to that for [Fe(H)(η(2)-H2)(PP3(Ph))](+). Conversely, upon increasing the hydricity of [Fe(II)(H)2(PP3(Ph))] by adding an electron-withdrawing group to PP3(Ph), the transformation with [Fe(H)(η(2)-H2)(PP3(PhNO2))](+) (PP3(PhNO2) = tris(2-(diphenylphosphino)-4-nitrophenyl)phosphine) is predicted to encounter a lower barrier for H2-splitting and a higher barrier for hydride transfer than those for [Fe(H)(η(2)-H2)(PP3(Ph))](+). Thus, we have shown that hydricity can be used as a guide to direct the rational design and development of more efficient catalysts.
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Affiliation(s)
- Bhaskar Mondal
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Shengfa Ye
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
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1064
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Tobisch S. CuH-Catalysed Hydroamination of Styrene with Hydroxylamine Esters: A Coupled Cluster Scrutiny of Mechanistic Pathways. Chemistry 2016; 22:8290-300. [DOI: 10.1002/chem.201600230] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Sven Tobisch
- University of St. Andrews; School of Chemistry; Purdie Building, North Haugh St. Andrews Fife KY16 9ST UK
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1065
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Ettenhuber P, Baudin P, Kjærgaard T, Jørgensen P, Kristensen K. Orbital spaces in the divide-expand-consolidate coupled cluster method. J Chem Phys 2016; 144:164116. [DOI: 10.1063/1.4947019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Patrick Ettenhuber
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Pablo Baudin
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Thomas Kjærgaard
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Poul Jørgensen
- 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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1066
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Isegawa M, Neese F, Pantazis DA. Ionization Energies and Aqueous Redox Potentials of Organic Molecules: Comparison of DFT, Correlated ab Initio Theory and Pair Natural Orbital Approaches. J Chem Theory Comput 2016; 12:2272-84. [PMID: 27065224 DOI: 10.1021/acs.jctc.6b00252] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The calculation of redox potentials involves large energetic terms arising from gas phase ionization energies, thermodynamic contributions, and solvation energies of the reduced and oxidized species. In this work we study the performance of a wide range of wave function and density functional theory methods for the prediction of ionization energies and aqueous one-electron oxidation potentials of a set of 19 organic molecules. Emphasis is placed on evaluating methods that employ the computationally efficient local pair natural orbital (LPNO) approach, as well as several implementations of coupled cluster theory and explicitly correlated F12 methods. The electronic energies are combined with implicit solvation models for the solvation energies. With the exception of MP2 and its variants, which suffer from enormous errors arising at least partially from the poor Hartree-Fock reference, ionization energies can be systematically predicted with average errors below 0.1 eV for most of the correlated wave function based methods studies here, provided basis set extrapolation is performed. LPNO methods are the most efficient way to achieve this type of accuracy. DFT methods show in general larger errors and suffer from inconsistent behavior. The only exception is the M06-2X functional which is found to be competitive with the best LPNO-based approaches for ionization energies. Importantly, the limiting factor for the calculation of accurate redox potentials is the solvation energy. The errors in the predicted solvation energies by all continuum solvation models tested in this work dominate the final computed reduction potential, resulting in average errors typically in excess of 0.3 V and hence obscuring the gains that arise from choosing a more accurate electronic structure method.
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Affiliation(s)
- Miho Isegawa
- Max Planck Institute for Chemical Energy Conversion, Stiftrasse 34-38, 45470 Mülheim and der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftrasse 34-38, 45470 Mülheim and der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max Planck Institute for Chemical Energy Conversion, Stiftrasse 34-38, 45470 Mülheim and der Ruhr, Germany
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1067
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Ortuño MA, Dereli B, Cramer CJ. Mechanism of Pd-Catalyzed Decarbonylation of Biomass-Derived Hydrocinnamic Acid to Styrene following Activation as an Anhydride. Inorg Chem 2016; 55:4124-31. [DOI: 10.1021/acs.inorgchem.5b02664] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel A. Ortuño
- Department of Chemistry,
Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Büşra Dereli
- Department of Chemistry,
Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher J. Cramer
- Department of Chemistry,
Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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1068
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Anacker T, Hill JG, Friedrich J. Optimized Basis Sets for the Environment in the Domain-Specific Basis Set Approach of the Incremental Scheme. J Phys Chem A 2016; 120:2443-58. [DOI: 10.1021/acs.jpca.6b01097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Tony Anacker
- Department
of Theoretical Chemistry, Chemnitz University of Technology, Straße
der Nationen 62, D-09111 Chemnitz, Germany
| | - J. Grant Hill
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Joachim Friedrich
- Department
of Theoretical Chemistry, Chemnitz University of Technology, Straße
der Nationen 62, D-09111 Chemnitz, Germany
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1069
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Liakos DG, Sparta M, Kesharwani MK, Martin JML, Neese F. Exploring the Accuracy Limits of Local Pair Natural Orbital Coupled-Cluster Theory. J Chem Theory Comput 2016; 11:1525-39. [PMID: 26889511 DOI: 10.1021/ct501129s] [Citation(s) in RCA: 479] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The domain based local pair natural orbital coupled cluster method with single-, double-, and perturbative triple excitations (DLPNO–CCSD(T)) is an efficient quantum chemical method that allows for coupled cluster calculations on molecules with hundreds of atoms. Because coupled-cluster theory is the method of choice if high-accuracy is needed, DLPNO–CCSD(T) is very promising for large-scale chemical application. However, the various approximations that have to be introduced in order to reach near linear scaling also introduce limited deviations from the canonical results. In the present work, we investigate how far the accuracy of the DLPNO–CCSD(T) method can be pushed for chemical applications. We also address the question at which additional computational cost improvements, relative to the previously established default scheme, come. To answer these questions, a series of benchmark sets covering a broad range of quantum chemical applications including reaction energies, hydrogen bonds, and other noncovalent interactions, conformer energies, and a prototype organometallic problem were selected. An accuracy of 1 kcal/mol or better can readily be obtained for all data sets using the default truncation scheme, which corresponds to the stated goal of the original implementation. Tightening of the three thresholds that control DLPNO leads to mean absolute errors and standard deviations from the canonical results of less than 0.25 kcal/mol (<1 kJ/mol). The price one has then to pay is an increased computational time by a factor close to 3. The applicability of the method is shown to be independent of the nature of the reaction. On the basis of the careful analysis of the results, three different sets of truncation thresholds (termed “LoosePNO”, “NormalPNO”, and “TightPNO”) have been chosen for “black box” use of DLPNO–CCSD(T). This will allow users of the method to optimally balance performance and accuracy.
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1070
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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: 6.6] [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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1071
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Minenkov Y, Chermak E, Cavallo L. Troubles in the Systematic Prediction of Transition Metal Thermochemistry with Contemporary Out-of-the-Box Methods. J Chem Theory Comput 2016; 12:1542-60. [DOI: 10.1021/acs.jctc.5b01163] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yury Minenkov
- King Abdullah University of Science and Technology (KAUST), Physical
Science and Engineering Division (PSE), KAUST Catalysis Center (KCC), Thuwal 23955-6900, Saudi Arabia
| | - Edrisse Chermak
- King Abdullah University of Science and Technology (KAUST), Physical
Science and Engineering Division (PSE), KAUST Catalysis Center (KCC), Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical
Science and Engineering Division (PSE), KAUST Catalysis Center (KCC), Thuwal 23955-6900, Saudi Arabia
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1072
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Elm J, Myllys N, Luy JN, Kurtén T, Vehkamäki H. The Effect of Water and Bases on the Clustering of a Cyclohexene Autoxidation Product C6H8O7 with Sulfuric Acid. J Phys Chem A 2016; 120:2240-9. [PMID: 26954007 DOI: 10.1021/acs.jpca.6b00677] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the molecular interaction between sulfuric acid and a C6H8O7 ketodiperoxy acid compound (a proxy for highly oxidized products of, e.g., monoterpene autoxidation) in the presence of water, ammonia, or dimethylamine. The molecular geometries are obtained using density functional theory (M06-2X, PW91, and ωB97X-D) with the 6-31++G(d,p) basis set, and the binding energy is corrected utilizing a high-level DLPNO-CCSD(T)/def2-QZVPP calculation. The formation free energies were calculated (ΔG at 298 K and 1 atm), and the stability of the molecular clusters was evaluated. The presence of bases is found to enhance the interaction between ketodiperoxy acid compounds and sulfuric acid. The addition of C6H8O7 compounds to (H2SO4)(NH3) or (H2SO4)((CH3)2NH) clusters is, however, not able to compete with the corresponding uptake of another sulfuric acid molecule, even at a high loading of organic compounds. We furthermore investigate the origin of the weak binding of peroxyacid compounds using atoms in molecules and natural bonding orbital analysis. The weak binding is caused by an internal hydrogen bond and the lack of a strong hydrogen bond acceptor in the peroxyacid group. These findings indicate that autoxidation products containing solely or mainly hydroperoxide and carbonyl functional groups do not participate in the initial step of new particle formation and thereby only contribute to the growth of atmospheric particles.
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Affiliation(s)
| | | | - Jan-Niclas Luy
- Department of Chemistry, Philipps University , Marburg, Germany
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1073
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Segarra-Martí J, Garavelli M, Aquilante F. Multiconfigurational Second-Order Perturbation Theory with Frozen Natural Orbitals Extended to the Treatment of Photochemical Problems. J Chem Theory Comput 2016; 11:3772-84. [PMID: 26574459 DOI: 10.1021/acs.jctc.5b00479] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new flavor of the frozen natural orbital complete active space second-order perturbation theory method (FNO-CASPT2, Aquilante et al., J. Chem. Phys. 131, 034113) is proposed herein. In this new implementation, the virtual space in Cholesky decomposition-based CASPT2 computations (CD-CASPT2) is truncated by excluding those orbitals that contribute the least toward preserving a predefined value of the trace of an approximate density matrix, as that represents a measure of the amount of dynamic correlation retained in the model. In this way, the amount of correlation included is practically constant at all nuclear arrangements, thus allowing for the computation of smooth electronic states surfaces and energy gradients-essential requirements for theoretical studies in photochemistry. The method has been benchmarked for a series of relevant biochromophores for which large speed-ups have been recorded while retaining the accuracy achieved in the corresponding CD-CASPT2 calculations. Both vertical excitation energies and gradient calculations have been carried out to establish general guidelines as to how much correlation needs to be retained in the calculation for the results to be consistent with the CD-CASPT2 findings. Our results feature errors within a tenth of an eV for the most difficult cases and have been validated to be used for gradient computations where an up to 3-fold speed-up is observed depending on the size of the system and the basis set employed.
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Affiliation(s)
- Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy.,Université de Lyon, CNRS , Institut de Chimie de Lyon, École Normale Supérieure de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France
| | - Francesco Aquilante
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy
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1074
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Mullinax JW, Sokolov AY, Schaefer HF. Can density cumulant functional theory describe static correlation effects? J Chem Theory Comput 2016; 11:2487-95. [PMID: 26575548 DOI: 10.1021/acs.jctc.5b00346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We evaluate the performance of density cumulant functional theory (DCT) for capturing static correlation effects. In particular, we examine systems with significant multideterminant character of the electronic wave function, such as the beryllium dimer, diatomic carbon, m-benzyne, 2,6-pyridyne, twisted ethylene, as well as the barrier for double-bond migration in cyclobutadiene. We compute molecular properties of these systems using the ODC-12 and DC-12 variants of DCT and compare these results to multireference configuration interaction and multireference coupled-cluster theories, as well as single-reference coupled-cluster theory with single, double (CCSD), and perturbative triple excitations [CCSD(T)]. For all systems the DCT methods show intermediate performance between that of CCSD and CCSD(T), with significant improvement over the former method. In particular, for the beryllium dimer, m-benzyne, and 2,6-pyridyne, the ODC-12 method along with CCSD(T) correctly predict the global minimum structures, while CCSD predictions fail qualitatively, underestimating the multireference effects. Our results suggest that the DC-12 and ODC-12 methods are capable of describing emerging static correlation effects but should be used cautiously when highly accurate results are required. Conveniently, the appearance of multireference effects in DCT can be diagnosed by analyzing the DCT natural orbital occupations, which are readily available at the end of the energy computation.
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Affiliation(s)
- J Wayne Mullinax
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - Alexander Yu Sokolov
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States.,Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
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1075
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Trouillas P, Sancho-García JC, De Freitas V, Gierschner J, Otyepka M, Dangles O. Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment. Chem Rev 2016; 116:4937-82. [PMID: 26959943 DOI: 10.1021/acs.chemrev.5b00507] [Citation(s) in RCA: 312] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Natural anthocyanin pigments/dyes and phenolic copigments/co-dyes form noncovalent complexes, which stabilize and modulate (in particular blue, violet, and red) colors in flowers, berries, and food products derived from them (including wines, jams, purees, and syrups). This noncovalent association and their electronic and optical implications constitute the copigmentation phenomenon. Over the past decade, experimental and theoretical studies have enabled a molecular understanding of copigmentation. This review revisits this phenomenon to provide a comprehensive description of the nature of binding (the dispersion and electrostatic components of π-π stacking, the hydrophobic effect, and possible hydrogen-bonding between pigment and copigment) and of spectral modifications occurring in copigmentation complexes, in which charge transfer plays an important role. Particular attention is paid to applications of copigmentation in food chemistry.
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Affiliation(s)
- Patrick Trouillas
- INSERM UMR 850, Univ. Limoges , Faculty of Pharmacy, 2 rue du Dr. Marcland, F-87025 Limoges, France.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Juan C Sancho-García
- Departamento de Química Física, Universidad de Alicante , Apartado de Correos 99, E-03080 Alicante, Spain
| | - Victor De Freitas
- REQUIMTE/LAQV - Research Unit, Faculty of Science, Porto University , Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Johannes Gierschner
- Madrid Institute for Advanced Studies - IMDEA Nanoscience , C/Faraday 9, Ciudad Universitaria de Cantoblanco, E-28049 Madrid, Spain
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Olivier Dangles
- University of Avignon, INRA, UMR408 SQPOV , F-84000 Avignon, France
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1076
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Guo Y, Sivalingam K, Valeev EF, Neese F. SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory. J Chem Phys 2016; 144:094111. [DOI: 10.1063/1.4942769] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yang Guo
- Max Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Kantharuban Sivalingam
- Max Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F. Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24014, USA
| | - Frank Neese
- Max Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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1077
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Zulfikri H, Amovilli C, Filippi C. Multiple-Resonance Local Wave Functions for Accurate Excited States in Quantum Monte Carlo. J Chem Theory Comput 2016; 12:1157-68. [DOI: 10.1021/acs.jctc.5b01077] [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)
- Habiburrahman Zulfikri
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE
Enschede, The Netherlands
| | - Claudio Amovilli
- Department
of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe
Moruzzi 13, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE
Enschede, The Netherlands
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1078
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Myllys N, Elm J, Halonen R, Kurtén T, Vehkamäki H. Coupled Cluster Evaluation of the Stability of Atmospheric Acid–Base Clusters with up to 10 Molecules. J Phys Chem A 2016; 120:621-30. [DOI: 10.1021/acs.jpca.5b09762] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nanna Myllys
- University of Helsinki, Department of Physics, FIN-00014 Helsinki, Finland
| | - Jonas Elm
- University of Helsinki, Department of Physics, FIN-00014 Helsinki, Finland
| | - Roope Halonen
- University of Helsinki, Department of Physics, FIN-00014 Helsinki, Finland
| | - Theo Kurtén
- University of Helsinki, Department of Chemistry, FIN-00014 Helsinki, Finland
| | - Hanna Vehkamäki
- University of Helsinki, Department of Physics, FIN-00014 Helsinki, Finland
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1079
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Brabec J, Yang C, Epifanovsky E, Krylov AI, Ng E. Reduced‐cost sparsity‐exploiting algorithm for solving coupled‐cluster equations. J Comput Chem 2016; 37:1059-67. [DOI: 10.1002/jcc.24293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/21/2015] [Accepted: 12/17/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Jiri Brabec
- Computational Research DivisionLawrence Berkeley National LaboratoryBerkeley California94720
| | - Chao Yang
- Computational Research DivisionLawrence Berkeley National LaboratoryBerkeley California94720
| | - Evgeny Epifanovsky
- Department of ChemistryUniversity of Southern CaliforniaLos Angeles California90089‐0482
- Q‐Chem IncSuite 105 Pleasanton California94588
| | - Anna I. Krylov
- Department of ChemistryUniversity of Southern CaliforniaLos Angeles California90089‐0482
| | - Esmond Ng
- Computational Research DivisionLawrence Berkeley National LaboratoryBerkeley California94720
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1080
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Iyer S, Lopez-Hilfiker F, Lee BH, Thornton JA, Kurtén T. Modeling the Detection of Organic and Inorganic Compounds Using Iodide-Based Chemical Ionization. J Phys Chem A 2016; 120:576-87. [DOI: 10.1021/acs.jpca.5b09837] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Siddharth Iyer
- Department
of Chemistry, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Felipe Lopez-Hilfiker
- Department
of Atmospheric Sciences, University of Washington, Seattle, Washington 98195-1640, United States
| | - Ben H. Lee
- Department
of Atmospheric Sciences, University of Washington, Seattle, Washington 98195-1640, United States
| | - Joel A. Thornton
- Department
of Atmospheric Sciences, University of Washington, Seattle, Washington 98195-1640, United States
| | - Theo Kurtén
- Department
of Chemistry, University of Helsinki, Helsinki, FIN-00014, Finland
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1081
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Dutta AK, Neese F, Izsák R. Speeding up equation of motion coupled cluster theory with the chain of spheres approximation. J Chem Phys 2016; 144:034102. [DOI: 10.1063/1.4939844] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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1082
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Pykal M, Jurečka P, Karlický F, Otyepka M. Modelling of graphene functionalization. Phys Chem Chem Phys 2016; 18:6351-72. [DOI: 10.1039/c5cp03599f] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This perspective describes the available theoretical methods and models for simulating graphene functionalization based on quantum and classical mechanics.
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Affiliation(s)
- Martin Pykal
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacký University Olomouc
- 771 46 Olomouc
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacký University Olomouc
- 771 46 Olomouc
| | - František Karlický
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacký University Olomouc
- 771 46 Olomouc
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacký University Olomouc
- 771 46 Olomouc
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1083
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Ertem MZ, Himeda Y, Fujita E, Muckerman JT. Interconversion of Formic Acid and Carbon Dioxide by Proton-Responsive, Half-Sandwich Cp*IrIII Complexes: A Computational Mechanistic Investigation. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01663] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mehmed Z. Ertem
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - Yuichiro Himeda
- National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
- Japan Science and Technology Agency, ACT-C, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Etsuko Fujita
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - James T. Muckerman
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
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1084
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McAlexander HR, Crawford TD. A Comparison of Three Approaches to the Reduced-Scaling Coupled Cluster Treatment of Non-Resonant Molecular Response Properties. J Chem Theory Comput 2015; 12:209-22. [DOI: 10.1021/acs.jctc.5b00898] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - T. Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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1085
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Baldauf C, Rossi M. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:493002. [PMID: 26598600 DOI: 10.1088/0953-8984/27/49/493002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.
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Affiliation(s)
- Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
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1086
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Anacker T, Tew DP, Friedrich J. First UHF Implementation of the Incremental Scheme for Open-Shell Systems. J Chem Theory Comput 2015; 12:65-78. [PMID: 26605975 DOI: 10.1021/acs.jctc.5b00933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The incremental scheme makes it possible to compute CCSD(T) correlation energies to high accuracy for large systems. We present the first extension of this fully automated black-box approach to open-shell systems using an Unrestricted Hartree-Fock (UHF) wave function, extending the efficient domain-specific basis set approach to handle open-shell references. We test our approach on a set of organic and metal organic structures and molecular clusters and demonstrate standard deviations from canonical CCSD(T) values of only 1.35 kJ/mol using a triple ζ basis set. We find that the incremental scheme is significantly more cost-effective than the canonical implementation even for relatively small systems and that the ease of parallelization makes it possible to perform high-level calculations on large systems in a few hours on inexpensive computers. We show that the approximations that make our approach widely applicable are significantly smaller than both the basis set incompleteness error and the intrinsic error of the CCSD(T) method, and we further demonstrate that incremental energies can be reliably used in extrapolation schemes to obtain near complete basis set limit CCSD(T) reaction energies for large systems.
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Affiliation(s)
- Tony Anacker
- Institute for Chemistry, Chemnitz University of Technology , Straße der Nationen 62, D-09111 Chemnitz, Sachsen, Germany
| | - David P Tew
- School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Joachim Friedrich
- Institute for Chemistry, Chemnitz University of Technology , Straße der Nationen 62, D-09111 Chemnitz, Sachsen, Germany
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1087
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Ly HGT, Mihaylov T, Absillis G, Pierloot K, Parac-Vogt TN. Reactivity of Dimeric Tetrazirconium(IV) Wells-Dawson Polyoxometalate toward Dipeptide Hydrolysis Studied by a Combined Experimental and Density Functional Theory Approach. Inorg Chem 2015; 54:11477-92. [PMID: 26599585 DOI: 10.1021/acs.inorgchem.5b02122] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Detailed kinetic studies on the hydrolysis of glycylglycine (Gly-Gly) in the presence of the dimeric tetrazirconium(IV)-substituted Wells-Dawson-type polyoxometalate Na14[Zr4(P2W16O59)2(μ3-O)2(OH)2(H2O)4] · 57H2O (1) were performed by a combination of (1)H, (13)C, and (31)P NMR spectroscopies. The catalyst was shown to be stable under a broad range of reaction conditions. The effect of pD on the hydrolysis of Gly-Gly showed a bell-shaped profile with the fastest hydrolysis observed at pD 7.4. The observed rate constant for the hydrolysis of Gly-Gly at pD 7.4 and 60 °C was 4.67 × 10(-7) s(-1), representing a significant acceleration as compared to the uncatalyzed reaction. (13)C NMR data were indicative for coordination of Gly-Gly to 1 via its amide oxygen and amine nitrogen atoms, resulting in a hydrolytically active complex. Importantly, the effective hydrolysis of a series of Gly-X dipeptides with different X side chain amino acids in the presence of 1 was achieved, and the observed rate constant was shown to be dependent on the volume, chemical nature, and charge of the X amino acid side chain. To give a mechanistic explanation of the observed catalytic hydrolysis of Gly-Gly, a detailed quantum-chemical study was performed. The theoretical results confirmed the nature of the experimentally suggested binding mode in the hydrolytically active complex formed between Gly-Gly and 1. To elucidate the role of 1 in the hydrolytic process, both the uncatalyzed and the polyoxometalate-catalyzed reactions were examined. In the rate-determining step of the uncatalyzed Gly-Gly hydrolysis, a carboxylic oxygen atom abstracts a proton from a solvent water molecule and the nascent OH nucleophile attacks the peptide carbon atom. Analogous general-base activity of the free carboxylic group was found to take place also in the case of polyoxometalate-catalyzed hydrolysis as the main catalytic effect originates from the -C═O···Zr(IV) binding.
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Affiliation(s)
- Hong Giang T Ly
- Laboratory of Bioinorganic Chemistry and ‡Laboratory of Computational Coordination Chemistry, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Tzvetan Mihaylov
- Laboratory of Bioinorganic Chemistry and ‡Laboratory of Computational Coordination Chemistry, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Gregory Absillis
- Laboratory of Bioinorganic Chemistry and ‡Laboratory of Computational Coordination Chemistry, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Kristine Pierloot
- Laboratory of Bioinorganic Chemistry and ‡Laboratory of Computational Coordination Chemistry, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Tatjana N Parac-Vogt
- Laboratory of Bioinorganic Chemistry and ‡Laboratory of Computational Coordination Chemistry, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium
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1088
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Gehrold AC, Bruhn T, Schneider H, Radius U, Bringmann G. Monomeric Chiral and Achiral Basket-Handle Porphyrins: Synthesis, Structural Features, and Arrested Tautomerism. J Org Chem 2015; 80:12359-78. [DOI: 10.1021/acs.joc.5b02259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas C. Gehrold
- Institute of Organic Chemistry and ‡Institute of Inorganic
Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Torsten Bruhn
- Institute of Organic Chemistry and ‡Institute of Inorganic
Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Heidi Schneider
- Institute of Organic Chemistry and ‡Institute of Inorganic
Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Udo Radius
- Institute of Organic Chemistry and ‡Institute of Inorganic
Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry and ‡Institute of Inorganic
Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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1089
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Zenkina OV, Gidron O, Shimon LJW, Iron MA, van der Boom ME. Mechanistic Aspects of Aryl-Halide Oxidative Addition, Coordination Chemistry, and Ring-Walking by Palladium. Chemistry 2015; 21:16113-25. [PMID: 26382568 DOI: 10.1002/chem.201501580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 07/17/2015] [Indexed: 11/07/2022]
Abstract
This contribution describes the reactivity of a zero-valent palladium phosphine complex with substrates that contain both an aryl halide moiety and an unsaturated carbon-carbon bond. Although η(2) -coordination of the metal center to a C=C or C≡C unit is kinetically favored, aryl halide bond activation is favored thermodynamically. These quantitative transformations proceed under mild reaction conditions in solution or in the solid state. Kinetic measurements indicate that formation of η(2) -coordination complexes are not nonproductive side-equilibria, but observable (and in several cases even isolated) intermediates en route to aryl halide bond cleavage. At the same time, DFT calculations show that the reaction with palladium may proceed through a dissociation-oxidative addition mechanism rather than through a haptotropic intramolecular process (i.e., ring walking). Furthermore, the transition state involves coordination of a third phosphine to the palladium center, which is lost during the oxidative addition as the C-halide bond is being broken. Interestingly, selective activation of aryl halides has been demonstrated by adding reactive aryl halides to the η(2) -coordination complexes. The product distribution can be controlled by the concentration of the reactants and/or the presence of excess phosphine.
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Affiliation(s)
- Olena V Zenkina
- Department of Organic Chemistry, The Weizmann Institute of Science, 76100 Rehovot (Israel).,Current address: Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON (Canada)
| | - Ori Gidron
- Department of Organic Chemistry, The Weizmann Institute of Science, 76100 Rehovot (Israel)
| | - Linda J W Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot (Israel)
| | - Mark A Iron
- Department of Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot (Israel)
| | - Milko E van der Boom
- Department of Organic Chemistry, The Weizmann Institute of Science, 76100 Rehovot (Israel).
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1090
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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: 6.3] [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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1091
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Kwan EE, Liu RY. Enhancing NMR Prediction for Organic Compounds Using Molecular Dynamics. J Chem Theory Comput 2015; 11:5083-9. [PMID: 26574306 DOI: 10.1021/acs.jctc.5b00856] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR spectroscopy is a crucial tool in organic chemistry for the routine characterization of small molecules, structural elucidation of natural products, and study of reaction mechanisms. Although there is evidence that thermal motions strongly affect observed resonances, conventional predictions are performed only on stationary structures. Here we show that quasiclassical molecular dynamics provides a highly accurate and broadly applicable method for improving shielding predictions. Gas-phase values of the absolute shieldings of protons and carbons are predicted to nearly within experimental uncertainty, while the chemical shifts of large systems such as natural products are closely reproduced. Importantly, these results are obtained without the use of any empirical corrections. Our analysis suggests that the linear scaling factors currently employed are primarily a correction for vibrational effects. As a result, our method extends the reach of prediction methods to the study of molecules with unusual dynamics such as the iconic and controversial [18]annulene. Our predictions agree closely with experiment at both low and high temperatures and provide strong evidence that the equilibrium structure of [18]annulene is planar and aromatic.
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Affiliation(s)
- Eugene E Kwan
- Department of Chemistry & Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Richard Y Liu
- Department of Chemistry & Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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1092
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Haindl MH, Hioe J, Gschwind RM. The Proline Enamine Formation Pathway Revisited in Dimethyl Sulfoxide: Rate Constants Determined via NMR. J Am Chem Soc 2015; 137:12835-42. [DOI: 10.1021/jacs.5b03420] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Michael H. Haindl
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
| | - Johnny Hioe
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
| | - Ruth M. Gschwind
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
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1093
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Kruse H, Mladek A, Gkionis K, Hansen A, Grimme S, Sponer J. Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit. J Chem Theory Comput 2015; 11:4972-91. [PMID: 26574283 DOI: 10.1021/acs.jctc.5b00515] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have created a benchmark set of quantum chemical structure-energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0χOL3 force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ∼0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields.
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Affiliation(s)
- Holger Kruse
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Arnost Mladek
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Konstantinos Gkionis
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn , Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn , Beringstr. 4, D-53115 Bonn, Germany
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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1094
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Usvyat D, Maschio L, Schütz M. Periodic local MP2 method employing orbital specific virtuals. J Chem Phys 2015; 143:102805. [DOI: 10.1063/1.4921301] [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)
- Denis Usvyat
- Institute for Physical and Theoretical Chemistry, Universität Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Lorenzo Maschio
- Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino, Italy
| | - Martin Schütz
- Institute for Physical and Theoretical Chemistry, Universität Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
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1095
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Minenkov Y, Chermak E, Cavallo L. Accuracy of DLPNO–CCSD(T) Method for Noncovalent Bond Dissociation Enthalpies from Coinage Metal Cation Complexes. J Chem Theory Comput 2015; 11:4664-76. [DOI: 10.1021/acs.jctc.5b00584] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yury Minenkov
- KAUST Catalysis
Center (KCC), King Abdullah University of Science and Technology, Thuwal-23955-6900, Saudi Arabia
| | - Edrisse Chermak
- KAUST Catalysis
Center (KCC), King Abdullah University of Science and Technology, Thuwal-23955-6900, Saudi Arabia
| | - Luigi Cavallo
- KAUST Catalysis
Center (KCC), King Abdullah University of Science and Technology, Thuwal-23955-6900, Saudi Arabia
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1096
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Liakos DG, Neese F. Is It Possible To Obtain Coupled Cluster Quality Energies at near Density Functional Theory Cost? Domain-Based Local Pair Natural Orbital Coupled Cluster vs Modern Density Functional Theory. J Chem Theory Comput 2015; 11:4054-63. [DOI: 10.1021/acs.jctc.5b00359] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dimitrios G. Liakos
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 32-34, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 32-34, D-45470 Mülheim an der Ruhr, Germany
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1097
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Friedrich J. Efficient Calculation of Accurate Reaction Energies—Assessment of Different Models in Electronic Structure Theory. J Chem Theory Comput 2015; 11:3596-609. [DOI: 10.1021/acs.jctc.5b00087] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joachim Friedrich
- Institute for Chemistry, Chemnitz University of Technology, Straße der Nationen
62, 09111 Chemnitz, Germany
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1098
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Mondal B, Neese F, Ye S. Control in the Rate-Determining Step Provides a Promising Strategy To Develop New Catalysts for CO2 Hydrogenation: A Local Pair Natural Orbital Coupled Cluster Theory Study. Inorg Chem 2015. [PMID: 26204267 DOI: 10.1021/acs.inorgchem.5b00469] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of efficient catalysts with base metals for CO2 hydrogenation has always been a major thrust of interest. A series of experimental and theoretical work has revealed that the catalytic cycle typically involves two key steps, namely, base-promoted heterolytic H2 splitting and hydride transfer to CO2, either of which can be the rate-determining step (RDS) of the entire reaction. To explore the determining factor for the nature of RDS, we present herein a comparative mechanistic investigation on CO2 hydrogenation mediated by [M(H)(η(2)-H2)(PP3(Ph))](n+) (M = Fe(II), Ru(II), and Co(III); PP3(Ph) = tris(2-(diphenylphosphino)phenyl)phosphine) type complexes. In order to construct reliable free energy profiles, we used highly correlated wave function based ab initio methods of the coupled cluster type alongside the standard density functional theory. Our calculations demonstrate that the hydricity of the metal-hydride intermediate generated by H2 splitting dictates the nature of the RDS for the Fe(II) and Co(III) systems, while the RDS for the Ru(II) catalyst appears to be ambiguous. CO2 hydrogenation catalyzed by the Fe(II) complex that possesses moderate hydricity traverses an H2-splitting RDS, whereas the RDS for the high-hydricity Co(III) species is found to be the hydride transfer. Thus, our findings suggest that hydricity can be used as a practical guide in future catalyst design. Enhancing the electron-accepting ability of low-hydricity catalysts is likely to improve their catalytic performance, while increasing the electron-donating ability of high-hydricity complexes may speed up CO2 conversion. Moreover, we also established the active roles of base NEt3 in directing the heterolytic H2 splitting and assisting product release through the formation of an acid-base complex.
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Affiliation(s)
- Bhaskar Mondal
- Department of Molecular Theory and Spectroscopy, Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Department of Molecular Theory and Spectroscopy, Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Shengfa Ye
- Department of Molecular Theory and Spectroscopy, Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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1099
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Pinski P, Riplinger C, Valeev EF, Neese F. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals. J Chem Phys 2015. [DOI: 10.1063/1.4926879] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peter Pinski
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Christoph Riplinger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F. Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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1100
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Liu Z, Huntington LM, Nooijen M. Application of the multireference equation of motion coupled cluster method, including spin–orbit coupling, to the atomic spectra of Cr, Mn, Fe and Co. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1063730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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