1
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Achazi AJ, Fataj X, Rohland P, Hager MD, Schubert US, Mollenhauer D. Development of a multi-step screening procedure for redox active molecules in organic radical polymer anodes and as redox flow anolytes. J Comput Chem 2024; 45:1112-1129. [PMID: 38258532 DOI: 10.1002/jcc.27299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Benzo[d]-X-zolyl-pyridinyl (XO, S, NH) radicals represent a promising class of redox-active molecules for organic batteries. We present a multistep screening procedure to identify the most promising radical candidates. Experimental investigations and highly correlated wave function-based calculations are performed to determine benchmark redox potentials. Based on these, the accuracies of different methods (semi-empirical, density functional theory, wave function-based), solvent models, dispersion corrections, and basis sets are evaluated. The developed screening procedure consists of three steps: First, a conformer search is performed with CREST. The molecules are selected based on the redox potentials calculated using GFN2-xTB. Second, HOMO energies calculated with reparametrized B3LYP-D3(BJ) and the def2-SVP basis set are used as selection criteria. The final molecules are selected based on the redox potentials calculated from Gibbs energies using BP86-D3(BJ)/def2-TZVP. With this multistep screening approach, promising molecules can be suggested for synthesis, and structure-property relationships can be derived.
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Affiliation(s)
- Andreas J Achazi
- Physikalisch-Chemisches Institut, Justus-Liebig-Universität Gießen, Gießen, Germany
- Zentrum für Materialforschung, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Xhesilda Fataj
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Jena, Germany
| | - Philip Rohland
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Jena, Germany
| | - Martin D Hager
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Jena, Germany
| | - Ulrich S Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Jena, Germany
| | - Doreen Mollenhauer
- Physikalisch-Chemisches Institut, Justus-Liebig-Universität Gießen, Gießen, Germany
- Zentrum für Materialforschung, Justus-Liebig-Universität Gießen, Gießen, Germany
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2
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Urban L, Laqua H, Thompson TH, Ochsenfeld C. Efficient Exploitation of Numerical Quadrature with Distance-Dependent Integral Screening in Explicitly Correlated F12 Theory: Linear Scaling Evaluation of the Most Expensive RI-MP2-F12 Term. J Chem Theory Comput 2024; 20:3706-3718. [PMID: 38626443 PMCID: PMC11099969 DOI: 10.1021/acs.jctc.4c00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
We present a linear scaling atomic orbital based algorithm for the computation of the most expensive exchange-type RI-MP2-F12 term by employing numerical quadrature in combination with CABS-RI to avoid six-center-three-electron integrals. Furthermore, a robust distance-dependent integral screening scheme, based on integral partition bounds [Thompson, T. H.; Ochsenfeld, C. J. Chem. Phys. 2019, 150, 044101], is used to drastically reduce the number of the required three-center-one-electron integrals substantially. The accuracy of our numerical quadrature/CABS-RI approach and the corresponding integral screening is thoroughly assessed for interaction and isomerization energies across a variety of numerical integration grids. Our method outperforms the standard density fitting/CABS-RI approach with errors below 1 μEh even for small grid sizes and moderate screening thresholds. The choice of the grid size and screening threshold allows us to tailor our ansatz to a desired accuracy and computational efficiency. We showcase the approach's effectiveness for the chemically relevant system valinomycin, employing a triple-ζ F12 basis set combination (C54H90N6O18, 5757 AO basis functions, 10,266 CABS basis functions, 735,783 grid points). In this context, our ansatz achieves higher accuracy combined with a 135× speedup compared to the classical density fitting based variant, requiring notably less computation time than the corresponding RI-MP2 calculation. Additionally, we demonstrate near-linear scaling through calculations on linear alkanes. We achieved an 817-fold acceleration for C80H162 and an extrapolated 28,765-fold acceleration for C200H402, resulting in a substantially reduced computational time for the latter─from 229 days to just 11.5 min. Our ansatz may also be adapted to the remaining MP2-F12 terms, which will be the subject of future work.
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Affiliation(s)
- Lars Urban
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
- Max
Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Henryk Laqua
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Travis H. Thompson
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
- Max
Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
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3
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Mester D, Kállay M. Basis Set Limit of CCSD(T) Energies: Explicit Correlation Versus Density-Based Basis-Set Correction. J Chem Theory Comput 2023; 19:8210-8222. [PMID: 37950703 PMCID: PMC10688194 DOI: 10.1021/acs.jctc.3c00979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/13/2023]
Abstract
A thorough comparison is carried out for explicitly correlated and density-based basis-set correction approaches, which were primarily developed to mitigate the basis-set incompleteness error of wave function methods. An efficient implementation of the density-based scheme is also presented, utilizing the density-fitting approximation. The performance of these approaches is comprehensively tested for the second-order Møller-Plesset (MP2), coupled-cluster singles and doubles (CCSD), and CCSD with perturbative triples [CCSD(T)] methods with respect to the corresponding complete basis set references. It is demonstrated that the density-based correction together with complementary auxiliary basis set (CABS)-corrected Hartree-Fock energies is highly robust and effectively reduces the error of the standard approaches; however, it does not outperform the corresponding explicitly correlated methods. Nevertheless, what still makes the density-corrected CCSD and CCSD(T) methods competitive is that their computational costs are roughly half of those of the corresponding explicitly correlated variants. Additionally, an incremental approach for standard CCSD and CCSD(T) is introduced. In this simple scheme, the total energies are corrected with the CABS correction and explicitly correlated MP2 contributions. As demonstrated, the resulting methods yield surprisingly good results, below 1 kcal/mol for thermochemical properties even with a double-ζ basis, while their computational expenses are practically identical to those of the density-based basis-set correction approaches.
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Affiliation(s)
- Dávid Mester
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
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4
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Franzke Y, Holzer C, Andersen JH, Begušić T, Bruder F, Coriani S, Della Sala F, Fabiano E, Fedotov DA, Fürst S, Gillhuber S, Grotjahn R, Kaupp M, Kehry M, Krstić M, Mack F, Majumdar S, Nguyen BD, Parker SM, Pauly F, Pausch A, Perlt E, Phun GS, Rajabi A, Rappoport D, Samal B, Schrader T, Sharma M, Tapavicza E, Treß RS, Voora V, Wodyński A, Yu JM, Zerulla B, Furche F, Hättig C, Sierka M, Tew DP, Weigend F. TURBOMOLE: Today and Tomorrow. J Chem Theory Comput 2023; 19:6859-6890. [PMID: 37382508 PMCID: PMC10601488 DOI: 10.1021/acs.jctc.3c00347] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Indexed: 06/30/2023]
Abstract
TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light-matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE's functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches. Select features under development are reviewed to illustrate the continuous growth of the program suite, including nuclear electronic orbital methods, Hartree-Fock-based adiabatic connection models, simplified time-dependent density functional theory, relativistic effects and magnetic properties, and multiscale modeling of optical properties.
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Affiliation(s)
- Yannick
J. Franzke
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Christof Holzer
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Josefine H. Andersen
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Tomislav Begušić
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Florian Bruder
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Sonia Coriani
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabio Della Sala
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Eduardo Fabiano
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Daniil A. Fedotov
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Susanne Fürst
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Sebastian Gillhuber
- Institute
of Inorganic Chemistry, Karlsruhe Institute
of Technology (KIT), Engesserstr. 15, 76131 Karlsruhe, Germany
| | - Robin Grotjahn
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Martin Kaupp
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Max Kehry
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Marjan Krstić
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Fabian Mack
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Sourav Majumdar
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Brian D. Nguyen
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Shane M. Parker
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106 United States
| | - Fabian Pauly
- Institute
of Physics, University of Augsburg, Universitätsstr. 1, 86159 Augsburg, Germany
| | - Ansgar Pausch
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Eva Perlt
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Gabriel S. Phun
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Ahmadreza Rajabi
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Dmitrij Rappoport
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Bibek Samal
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Tim Schrader
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Manas Sharma
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Enrico Tapavicza
- Department
of Chemistry and Biochemistry, California
State University, Long Beach, 1250 Bellflower Boulevard, Long
Beach, California 90840-9507, United States
| | - Robert S. Treß
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vamsee Voora
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Artur Wodyński
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Jason M. Yu
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Benedikt Zerulla
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz-Platz
1, 76344 Eggenstein-Leopoldshafen Germany
| | - Filipp Furche
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Christof Hättig
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Marek Sierka
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - David P. Tew
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
| | - Florian Weigend
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
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5
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Wenz J, Pazdera TM, Golka L, Olzmann M. Pyrolysis of Methyl Formate and the Reaction of Methyl Formate with H Atoms: Shock Tube Experiments and Statistical Rate Theory. J Phys Chem A 2023; 127:1036-1045. [PMID: 36683280 DOI: 10.1021/acs.jpca.2c07053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Methyl formate (MF) is the smallest carboxylic ester and currently considered a promising alternative fuel. It can also serve as a model compound to study the combustion chemistry of the ester group, which is a typical structural feature in many biodiesel components. In the present work, the pyrolysis of MF was investigated behind reflected shock waves at temperatures between 1430 and 2070 K at a nominal pressure of 1.1 bar. Both time-resolved hydrogen atom resonance absorption spectroscopy (H-ARAS) and time-resolved time-of-flight mass spectrometry (TOF-MS) were used for species detection. Additionally, the reaction of MF and perdeuterated MF-d4 with H atoms was investigated at temperatures between 1000 and 1300 K at nominal pressures of 0.4 and 1.1 bar with H-ARAS. In the latter experiments, ethyl iodide served as precursor for H atoms. Rate coefficients of seven parallel unimolecular decomposition channels of MF and five parallel reaction channels of the MF + H reaction were calculated from statistical rate theory on the basis of molecular and transition state data from quantum chemical calculations. These calculated rate coefficients were implemented into an MF pyrolysis/oxidation mechanism from the literature, and the experimental concentration-time profiles of H (from ARAS) as well as MF, CH3OH, HCHO, and CO (from TOF-MS) were modeled. It turned out that the literature mechanism, which was originally validated against flow-reactor experiments, ignition delay times, and laminar burning velocities, was generally able to fit also the concentration-time profiles from the shock tube experiments reasonably well. The agreement could still be improved by substituting the original rate coefficients, which were estimated from structure-reactivity relationships, by the values calculated from statistical rate theory in the present work. Details of the channel branching are discussed, and the updated mechanism is given, also in machine-readable form.
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Affiliation(s)
- Johannes Wenz
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Tobias M Pazdera
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Leonie Golka
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Matthias Olzmann
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Kaiserstr. 12, 76131 Karlsruhe, Germany
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6
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Kállay M, Horváth RA, Gyevi-Nagy L, Nagy PR. Basis Set Limit CCSD(T) Energies for Extended Molecules via a Reduced-Cost Explicitly Correlated Approach. J Chem Theory Comput 2022; 19:174-189. [PMID: 36576419 PMCID: PMC9835832 DOI: 10.1021/acs.jctc.2c01031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Several approximations are introduced and tested to reduce the computational expenses of the explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)] method for both closed and open-shell species. First, the well-established frozen natural orbital (FNO) technique is adapted to explicitly correlated CC approaches. Second, our natural auxiliary function (NAF) scheme is employed to reduce the size of the auxiliary basis required for the density fitting approximation regularly used in explicitly correlated calculations. Third, a new approach, termed the natural auxiliary basis (NAB) approximation, is proposed to decrease the size of the auxiliary basis needed for the expansion of the explicitly correlated geminals. The performance of the above approximations and that of the combined FNO-NAF-NAB approach are tested for atomization and reaction energies. Our results show that overall speedups of 7-, 5-, and 3-times can be achieved with double-, triple-, and quadruple-ζ basis sets, respectively, without any loss in accuracy. The new method can provide, e.g., reaction energies and barrier heights well within chemical accuracy for molecules with more than 40 atoms within a few days using a few dozen processor cores, and calculations with 50+ atoms are still feasible. These routinely affordable computations considerably extend the reach of explicitly correlated CCSD(T).
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Affiliation(s)
- Mihály Kállay
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary,ELKH-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary,MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary,
| | - Réka A. Horváth
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary,ELKH-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary,MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - László Gyevi-Nagy
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary,ELKH-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary,MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Péter R. Nagy
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary,ELKH-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary,MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
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7
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Jensen AB, Kubečka J, Schmitz G, Christiansen O, Elm J. Massive Assessment of the Binding Energies of Atmospheric Molecular Clusters. J Chem Theory Comput 2022; 18:7373-7383. [PMID: 36417753 DOI: 10.1021/acs.jctc.2c00825] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Quantum chemical studies of the formation and growth of atmospheric molecular clusters are important for understanding aerosol particle formation. However, the search for the lowest free-energy cluster configuration is extremely time consuming. This makes high-level benchmark data sets extremely valuable in the quest for the global minimum as it allows the identification of cost-efficient computational methodologies, as well as the development of high-level machine learning (ML) models. Herein, we present a highly versatile quantum chemical data set comprising a total of 11 749 (acid)1-2(base)1-2 cluster configurations, containing up to 44 atoms. Utilizing the LUMI supercomputer, we calculated highly accurate PNO-CCSD(F12*)(T)/cc-pVDZ-F12 binding energies of the full set of cluster configurations leading to an unprecedented data set both in regard to sheer size and with respect to the level of theory. We employ the constructed benchmark set to assess the performance of various semiempirical and density functional theory methods. In particular, we find that the r2-SCAN-3c method shows excellent performance across the data set related to both accuracy and CPU time, making it a promising method to employ during cluster configurational sampling. Furthermore, applying the data sets, we construct ML models based on Δ-learning and provide recommendations for future application of ML in cluster configurational sampling.
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Affiliation(s)
| | - Jakub Kubečka
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Gunnar Schmitz
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Ove Christiansen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.,Department of Chemistry, iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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8
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Mehta N, Martin JML. Reduced-Scaling Double Hybrid Density Functional Theory with Rapid Basis Set Convergence through Localized Pair Natural Orbital F12. J Phys Chem Lett 2022; 13:9332-9338. [PMID: 36178852 PMCID: PMC9575149 DOI: 10.1021/acs.jpclett.2c02620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Following earlier work [Mehta, N.; Martin, J. M. L. J. Chem. Theory Comput.2022, 10.1021/acs.jctc.2c00426] that showed how the slow basis set convergence of the double hybrid density functional theory can be obviated by the use of F12 explicit correlation in the GLPT2 step (second order Görling-Levy perturbation theory), we demonstrate here for the very large and chemically diverse GMTKN55 benchmark suite that the CPU time scaling of this step can be reduced (asymptotically linearized) using the localized pair natural orbital (PNO-L) approximation at negligible cost in accuracy.
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9
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Chaussy L, Hagebaum-Reignier D, Humbel S, Nava P. Accurate computed singlet-triplet energy differences for cobalt systems: implication for two-state reactivity. Phys Chem Chem Phys 2022; 24:21841-21852. [PMID: 36065755 DOI: 10.1039/d2cp03291k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate singlet-triplet energy differences for cobalt and rhodium complexes were calculated by using several wave function methods, such as MRCISD, CASPT2, CCSD(T) and BCCD(T). Relaxed energy differences were obtained by considering the singlet and triplet complexes, each at the minimum of their potential energy surfaces. Active spaces for multireference calculations were carefully checked to provide accurate results. The considered systems are built by increasing progressively the first coordination sphere around the metal. We included in our set two CpCoX complexes (Cp = cyclopentadienyl, X = alkenyl ligand), which have been suggested as intermediates in cycloaddition reactions. Indeed, cobalt systems have been used for more than a decade as active species in this kind of transformations, for which a two-state reactivity has been proposed. Most of the considered systems display a triplet ground state. However, in the case of a reaction intermediate, while a triplet ground state was predicted on the basis of Density Functional Theory results, our calculations suggest a singlet ground state. This stems from the competition between the exchange term (stabilising the triplet) and the accessibility of an intramolecular coordination (stabilising the singlet). This finding has an impact on the general mechanism of the cycloaddition reaction. Analogous rhodium systems were also studied and, as expected, they have a larger tendency to electron pairing than cobalt species.
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Affiliation(s)
- Léo Chaussy
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | | | - Stéphane Humbel
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | - Paola Nava
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
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10
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Quesada JV, Chmela J, Greisch JF, Klopper W, Harding ME. A litmus test for the balanced description of dispersion interactions and coordination chemistry of lanthanoids. Phys Chem Chem Phys 2022; 24:25106-25117. [PMID: 35920212 DOI: 10.1039/d2cp01414a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of long-range interactions on the structure of complexes of Eu(III) with four 9-hydroxy-phenalen-1-one ligands (HPLN) and one alkaline earth metal dication [Eu(PLN)4AE]+ (AE: Mg, Ca, Sr, and Ba) is analyzed. Through the [Eu(PLN)4Ca]+ complex, which is a charged complex with two metals-one of them a lanthanoid-and with four relatively fluxional π-ligands, the difficulties of describing such systems are identified. The inclusion of the D3(BJ) or D4 corrections to different density functionals introduces significant changes in the structure, which are shown to stem from the interaction between pairs of PLN ligands. This interaction is studied further with a variety of density functionals, wave-function based methods, and by means of the random phase approximation. By comparing the computed results with those from experimental evidence of gas-phase photoluminescence and ion mobility measurements it is concluded that the inclusion of dispersion corrections does not always yield structures that are in agreement with the experimental findings.
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Affiliation(s)
- Juana Vázquez Quesada
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany.
| | - Jiří Chmela
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany.
| | - Jean-François Greisch
- Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
| | - Wim Klopper
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany. .,Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
| | - Michael E Harding
- Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
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11
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Urban L, Laqua H, Ochsenfeld C. Highly Efficient and Accurate Computation of Multiple Orbital Spaces Spanning Fock Matrix Elements on Central and Graphics Processing Units for Application in F12 Theory. J Chem Theory Comput 2022; 18:4218-4228. [PMID: 35674337 DOI: 10.1021/acs.jctc.2c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We employ our recently published highly efficient seminumerical exchange (sn-LinK) [Laqua, H.; Thompson, T. H.; Kussmann, J.; Ochsenfeld, C. J. Chem. Theory Comput. 2020, 16, 1456-1468] and integral-direct resolution of the identity Coulomb (RI-J) [Kussmann, J.; Laqua, H.; Ochsenfeld, C. J. Chem. Theory Comput. 2021, 17, 1512-1521] methods to significantly accelerate the computation of the demanding multiple orbital spaces spanning Fock matrix elements present in R12/F12 theory on central and graphics processing units. The errors introduced by RI-J and sn-LinK into the RI-MP2-F12 energy are thoroughly assessed for a variety of basis sets and integration grids. We find that these numerical errors are always below "chemical accuracy" (∼1 mH) even for the coarsest settings and can easily be reduced below 1 μH by employing only moderately large integration grids and RI-J basis sets. Since the number of basis functions of the multiple orbital spaces is notably larger compared with conventional Hartree-Fock theory, the efficiency gains from the superior basis scaling of RI-J and sn-LinK (O(Nbas2) instead of O(Nbas4) for both) are even more significant, with maximum speedup factors of 37 000 for RI-J and 4500 for sn-LinK. In total, the multiple orbital spaces spanning Fock matrix evaluation of the largest tested structure using a triple-ζ F12 basis set (5058 AO basis functions, 9267 CABS basis functions) is accelerated over 1575× using CPUs and over 4155× employing GPUs.
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Affiliation(s)
- Lars Urban
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany.,Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Henryk Laqua
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany.,Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
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12
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Pazdera TM, Wenz J, Olzmann M. The unimolecular decomposition of dimethoxymethane: channel switching as a function of temperature and pressure. Faraday Discuss 2022; 238:665-681. [DOI: 10.1039/d2fd00039c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Branching ratios of competing unimolecular reactions often exhibit a complicated temperature and pressure dependence that makes modeling of complex reaction systems in the gas phase difficult. In particular, the competition...
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13
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Sulzer D, Bihlmeier A. Tailoring the Gibbs Free Energy of the Nitroxide Exchange Reaction: Substituent and Solvent Effects. J Phys Chem A 2021; 125:7616-7624. [PMID: 34459589 DOI: 10.1021/acs.jpca.1c04864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A quantum chemical study of the nitroxide exchange reaction is presented. Inspired by the recent use of this reaction in the synthesis of dynamic covalent polymer networks, we studied the influence of substituents and solvents on the Gibbs free energy, which plays a crucial role for both the reversibility of the reaction and the extent of product formation. We provide accurate benchmark values based on CCSD(T) and COSMO-RS theory for a series of structural modifications and make suggestions for improving the molecular building blocks used so far.
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Affiliation(s)
- David Sulzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Angela Bihlmeier
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany
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14
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Gawrilow M, Suhm MA. Quantifying Conformational Isomerism in Chain Molecules by Linear Raman Spectroscopy: The Case of Methyl Esters. Molecules 2021; 26:molecules26154523. [PMID: 34361676 PMCID: PMC8348275 DOI: 10.3390/molecules26154523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 02/01/2023] Open
Abstract
The conformational preferences of the ester group have the potential to facilitate the large amplitude folding of long alkyl chains in the gas phase. They are monitored by Raman spectroscopy in supersonic jet expansions for the model system methyl butanoate, after establishing a quantitative relationship with quantum-chemical predictions for methyl methanoate. This requires a careful analysis of experimental details, and a simulation of the rovibrational contours for near-symmetric top molecules. The technique is shown to be complementary to microwave spectroscopy in quantifying coexisting conformations. It confirms that a C-O-C(=O)-C-C chain segment can be collapsed into a single all-trans conformation by collisional cooling, whereas alkyl chain isomerism beyond this five-membered chain largely survives the jet expansion. This sets the stage for the investigation of linear alkyl alkanoates in terms of dispersion-induced stretched-chain to hairpin transitions by Raman spectroscopy.
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15
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Kállay M, Horváth RA, Gyevi-Nagy L, Nagy PR. Size-consistent explicitly correlated triple excitation correction. J Chem Phys 2021; 155:034107. [PMID: 34293884 DOI: 10.1063/5.0057426] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A new approach is proposed to reduce the basis set incompleteness error of the triple excitation correction in explicitly correlated coupled-cluster singles and doubles with perturbative triples calculations. Our method is similar to the intuitive triples correction approach of Knizia et al. [J. Chem. Phys. 130, 054104 (2009)] but, in contrast to the latter, is size-consistent. The new approximation is easy to implement, and its overhead is negligible with respect to the conventional (T) correction. The performance of the approach is assessed for atomization, reaction, and interaction energies as well as for bond lengths and harmonic vibrational frequencies. The advantages of its size consistency are also demonstrated.
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Affiliation(s)
- Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, Budapest H-1521, Hungary
| | - Réka A Horváth
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, Budapest H-1521, Hungary
| | - László Gyevi-Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, Budapest H-1521, Hungary
| | - Péter R Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, Budapest H-1521, Hungary
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16
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Irmler A, Gallo A, Grüneis A. Focal-point approach with pair-specific cusp correction for coupled-cluster theory. J Chem Phys 2021; 154:234103. [PMID: 34241257 DOI: 10.1063/5.0050054] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a basis set correction scheme for the coupled-cluster singles and doubles (CCSD) method. The scheme is based on employing frozen natural orbitals (FNOs) and diagrammatically decomposed contributions to the electronic correlation energy, which dominate the basis set incompleteness error (BSIE). As recently discussed in the work of Irmler et al. [Phys. Rev. Lett. 123, 156401 (2019)], the BSIE of the CCSD correlation energy is dominated by the second-order Møller-Plesset (MP2) perturbation energy and the particle-particle ladder term. Here, we derive a simple approximation to the BSIE of the particle-particle ladder term that effectively corresponds to a rescaled pair-specific MP2 BSIE, where the scaling factor depends on the spatially averaged correlation hole depth of the coupled-cluster and first-order pair wavefunctions. The evaluation of the derived expressions is simple to implement in any existing code. We demonstrate the effectiveness of the method for the uniform electron gas. Furthermore, we apply the method to coupled-cluster theory calculations of atoms and molecules using FNOs. Employing the proposed correction and an increasing number of FNOs per occupied orbital, we demonstrate for a test set that rapidly convergent closed and open-shell reaction energies, atomization energies, electron affinities, and ionization potentials can be obtained. Moreover, we show that a similarly excellent trade-off between required virtual orbital basis set size and remaining BSIEs can be achieved for the perturbative triples contribution to the CCSD(T) energy employing FNOs and the (T*) approximation.
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Affiliation(s)
- Andreas Irmler
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | - Alejandro Gallo
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | - Andreas Grüneis
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
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17
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Gutten O, Jurečka P, Aliakbar Tehrani Z, Buděšínský M, Řezáč J, Rulíšek L. Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments. Phys Chem Chem Phys 2021; 23:7280-7294. [PMID: 33876088 DOI: 10.1039/d0cp05993e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Performance of computational methods in modelling cyclic dinucleotides - an important and challenging class of compounds - has been evaluated by two different benchmarks: (1) gas-phase conformational energies and (2) qualitative agreement with NMR observations of the orientation of the χ-dihedral angle in solvent. In gas-phase benchmarks, where CCSD(T) and DLPNO-CCSD(T) methods have been used as the reference, most of the (dispersion corrected) density functional approximations are accurate enough to justify prioritizing computational cost and compatibility with other modelling options as the criterion of choice. NMR experiments of 3'3'-c-di-AMP, 3'3'-c-GAMP, and 3'3'-c-di-GMP show the overall prevalence of the anti-conformation of purine bases, but some population of syn-conformations is observed for guanines. Implicit solvation models combined with quantum-chemical methods struggle to reproduce this behaviour, probably due to a lack of dynamics and explicitly modelled solvent, leading to structures that are too compact. Molecular dynamics simulations overrepresent the syn-conformation of guanine due to the overestimation of an intramolecular hydrogen bond. Our combination of experimental and computational benchmarks provides "error bars" for modelling cyclic dinucleotides in solvent, where such information is generally difficult to obtain, and should help gauge the interpretability of studies dealing with binding of cyclic dinucleotides to important pharmaceutical targets. At the same time, the presented analysis calls for improvement in both implicit solvation models and force-field parameters.
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Affiliation(s)
- Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic.
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18
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Urban L, Thompson TH, Ochsenfeld C. A scaled explicitly correlated F12 correction to second-order Møller-Plesset perturbation theory. J Chem Phys 2021; 154:044101. [PMID: 33514114 DOI: 10.1063/5.0033411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An empirically scaled version of the explicitly correlated F12 correction to second-order Møller-Plesset perturbation theory (MP2-F12) is introduced. The scaling eliminates the need for many of the most costly terms of the F12 correction while reproducing the unscaled explicitly correlated F12 interaction energy correction to a high degree of accuracy. The method requires a single, basis set dependent scaling factor that is determined by fitting to a set of test molecules. We present factors for the cc-pVXZ-F12 (X = D, T, Q) basis set family obtained by minimizing interaction energies of the S66 set of small- to medium-sized molecular complexes and show that our new method can be applied to accurately describe a wide range of systems. Remarkably good explicitly correlated corrections to the interaction energy are obtained for the S22 and L7 test sets, with mean percentage errors for the double-zeta basis of 0.60% for the F12 correction to the interaction energy, 0.05% for the total electron correlation interaction energy, and 0.03% for the total interaction energy, respectively. Additionally, mean interaction energy errors introduced by our new approach are below 0.01 kcal mol-1 for each test set and are thus negligible for second-order perturbation theory based methods. The efficiency of the new method compared to the unscaled F12 correction is shown for all considered systems, with distinct speedups for medium- to large-sized structures.
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Affiliation(s)
- L Urban
- Department of Chemistry, Ludwig-Maximilians-University Munich (LMU Munich), D-81377 Munich, Germany
| | - T H Thompson
- Department of Chemistry, Ludwig-Maximilians-University Munich (LMU Munich), D-81377 Munich, Germany
| | - C Ochsenfeld
- Department of Chemistry, Ludwig-Maximilians-University Munich (LMU Munich), D-81377 Munich, Germany
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19
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Tew DP. Principal domains in F12 explicitly correlated theory. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Sorathia K, Tew DP. Basis set extrapolation in pair natural orbital theories. J Chem Phys 2020; 153:174112. [PMID: 33167642 DOI: 10.1063/5.0022077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present the results of a benchmark study of the effect of Pair Natural Orbital (PNO) truncation errors on the performance of basis set extrapolation. We find that reliable conclusions from the application of Helgaker's extrapolation method are only obtained when using tight PNO thresholds of at least 10-7. The use of looser thresholds introduces a significant risk of observing a false basis set convergence and underestimating the residual basis set errors. We propose an alternative extrapolation approach based on the PNO truncation level that only requires a single basis set and show that it is a viable alternative to hierarchical basis set extrapolation methods.
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Affiliation(s)
- Kesha Sorathia
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, GermanyUniversity of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David P Tew
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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21
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Gratzfeld D, Heitkämper J, Debailleul J, Olzmann M. On the influence of water on urea condensation reactions: a theoretical study. Z PHYS CHEM 2020. [DOI: 10.1515/zpch-2020-1658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The influence of water molecules on the kinetics of urea condensation reactions was studied with high-level quantum chemical methods and statistical rate theory. The study focuses on the production of biuret, triuret, and cyanuric acid from urea because of their relevance as unwanted byproducts in the urea-based selective catalytic reduction (urea-SCR) exhaust after treatment of Diesel engines. In order to characterize the potential energy surfaces and molecular reaction pathways, calculations with explicitly-correlated coupled-cluster methods were performed. It turned out that the reactions proceed via pre-reactive complexes and the inclusion of one or two water molecules into the condensation mechanisms leads to a decrease of the energy barriers. This effect is particularly pronounced in the production of biuret. Due to the pre-reactive equilibria, the rates of the overall reactions can increase or decrease by incorporating water into the mechanism, depending on the temperature and water concentration. Under the conditions of urea-SCR, the studied reactions are too slow to contribute to the observed byproduct formation.
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Affiliation(s)
- Dennis Gratzfeld
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Juliane Heitkämper
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Julien Debailleul
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Matthias Olzmann
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
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22
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Gawrilow M, Suhm MA. 2-Methoxyethanol: harmonic tricks, anharmonic challenges and chirality-sensitive chain aggregation. Phys Chem Chem Phys 2020; 22:15303-15311. [PMID: 32626860 DOI: 10.1039/d0cp02488k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Raman spectrum of jet-cooled, nearly monoconformational 2-methoxyethanol reveals a strong, aggregation-sensitive resonance in the backbone stretching region and pronounced chirality-dependent dimerisation effects in the OH stretching region. These effects are disentangled by a dual-detection scheme which simultaneously probes the two spectral regions. The performance of mass-scaled harmonic wavenumber predictions and of vibrational perturbation theory in reproducing these spectral features is explored.
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Affiliation(s)
- Maxim Gawrilow
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany.
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23
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Balasubramani SG, Chen GP, Coriani S, Diedenhofen M, Frank MS, Franzke YJ, Furche F, Grotjahn R, Harding ME, Hättig C, Hellweg A, Helmich-Paris B, Holzer C, Huniar U, Kaupp M, Marefat Khah A, Karbalaei Khani S, Müller T, Mack F, Nguyen BD, Parker SM, Perlt E, Rappoport D, Reiter K, Roy S, Rückert M, Schmitz G, Sierka M, Tapavicza E, Tew DP, van Wüllen C, Voora VK, Weigend F, Wodyński A, Yu JM. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations. J Chem Phys 2020; 152:184107. [PMID: 32414256 PMCID: PMC7228783 DOI: 10.1063/5.0004635] [Citation(s) in RCA: 533] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE's functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE's current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE's development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.
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Affiliation(s)
- Sree Ganesh Balasubramani
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Guo P Chen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Michael Diedenhofen
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Marius S Frank
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Yannick J Franzke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Robin Grotjahn
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Arnim Hellweg
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Uwe Huniar
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Alireza Marefat Khah
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | | | - Thomas Müller
- Forschungszentrum Jülich, Jülich Supercomputer Centre, Wilhelm-Jonen Straße, 52425 Jülich, Germany
| | - Fabian Mack
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Brian D Nguyen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Shane M Parker
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Eva Perlt
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Dmitrij Rappoport
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kevin Reiter
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Saswata Roy
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Matthias Rückert
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Gunnar Schmitz
- Department of Chemistry, Aarhus Universitet, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Marek Sierka
- TURBOMOLE GmbH, Litzenhardtstraße 19, 76135 Karlsruhe, Germany
| | - Enrico Tapavicza
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, California 90840, USA
| | - David P Tew
- Max Planck Institute for Solid State Research, Heisenbergstaße 1, 70569 Stuttgart, Germany
| | - Christoph van Wüllen
- Fachbereich Chemie and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, Erwin-Schrödinger-Staße 52, 67663 Kaiserslautern, Germany
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Florian Weigend
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Artur Wodyński
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jason M Yu
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
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24
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Schmitz G, Elm J. Assessment of the DLPNO Binding Energies of Strongly Noncovalent Bonded Atmospheric Molecular Clusters. ACS OMEGA 2020; 5:7601-7612. [PMID: 32280904 PMCID: PMC7144154 DOI: 10.1021/acsomega.0c00436] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/11/2020] [Indexed: 05/03/2023]
Abstract
This work assesses the performance of DLPNO-CCSD(T0), DLPNO-MP2, and density functional theory methods in calculating the binding energies of a representative test set of 45 atmospheric acid-acid, acid-base, and acid-water dimer clusters. The performance of the approximate methods is compared to high level explicitly correlated CCSD(F12*)(T)/complete basis set (CBS) reference calculations. Out of the tested density functionals, ωB97X-D3(BJ) shows the best performance with a mean deviation of 0.09 kcal/mol and a maximum deviation of 0.83 kcal/mol. The RI-CC2/aug-cc-pV(T+d)Z level of theory severely overpredicts the cluster binding energies with a mean deviation of -1.31 kcal/mol and a maximum deviation up to -3.00 kcal/mol. Hence, RI-CC2/aug-cc-pV(T+d)Z should not be utilized for studying atmospheric molecular clusters. The DLPNO variants are tested both with and without the inclusion of explicit correlation (F12) in the wavefunction, with different pair natural orbital (PNO) settings (loosePNO, normalPNO, and tightPNO) and using both double and triple zeta basis sets. The performance of the DLPNO-MP2 methods is found to be independent of PNO settings and yield low mean deviations of -0.84 kcal/mol or below. However, DLPNO-MP2 requires explicitly correlated wavefunctions to yield maximum deviations below 1.40 kcal/mol. For obtaining high accuracy, with maximum deviation below ∼1.0 kcal/mol, either DLPNO-CCSD(T0)/aug-cc-pVTZ (normalPNO) calculations or DLPNO-CCSD(T0)-F12/cc-pVTZ-F12 (normalPNO) calculations are required. The most accurate level of theory is found to be DLPNO-CCSD(T0)-F12/cc-pVTZ-F12 using a tightPNO criterion which yields a mean deviation of 0.10 kcal/mol, with a maximum deviation of 0.20 kcal/mol, compared to the CCSD(F12*)(T)/CBS reference.
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Affiliation(s)
- Gunnar Schmitz
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department
of Chemistry and iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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25
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Kottmann JS, Bischoff FA, Valeev EF. Direct determination of optimal pair-natural orbitals in a real-space representation: The second-order Moller–Plesset energy. J Chem Phys 2020; 152:074105. [DOI: 10.1063/1.5141880] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jakob S. Kottmann
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin-Adlershof, Germany
| | - Florian A. Bischoff
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin-Adlershof, Germany
| | - Edward F. Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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26
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Golka L, Gratzfeld D, Weber I, Olzmann M. Temperature- and pressure-dependent kinetics of the competing C–O bond fission reactions of dimethoxymethane. Phys Chem Chem Phys 2020; 22:5523-5530. [DOI: 10.1039/d0cp00136h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Under typical shock tube conditions, dimethoxymethane decomposes mainly to give CH3 + OCH2OCH3.
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Affiliation(s)
- Leonie Golka
- Institut für Physikalische Chemie
- Karlsruher Institut für Technologie (KIT)
- 76131 Karlsruhe
- Germany
| | - Dennis Gratzfeld
- Institut für Physikalische Chemie
- Karlsruher Institut für Technologie (KIT)
- 76131 Karlsruhe
- Germany
| | - Isabelle Weber
- Institut für Physikalische Chemie
- Karlsruher Institut für Technologie (KIT)
- 76131 Karlsruhe
- Germany
| | - Matthias Olzmann
- Institut für Physikalische Chemie
- Karlsruher Institut für Technologie (KIT)
- 76131 Karlsruhe
- Germany
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27
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Klimeš J, Tew DP. Efficient and accurate description of adsorption in zeolites. J Chem Phys 2019; 151:234108. [PMID: 31864262 DOI: 10.1063/1.5123425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Accurate theoretical methods are needed to correctly describe adsorption on solid surfaces or in porous materials. The random phase approximation (RPA) with singles corrections scheme and the second order Møller-Plesset perturbation theory (MP2) are two schemes, which offer high accuracy at affordable computational cost. However, there is little knowledge about their applicability and reliability for different adsorbates and surfaces. Here, we calculate adsorption energies of seven different molecules in zeolite chabazite to show that RPA with singles corrections is superior to MP2, not only in terms of accuracy but also in terms of computer time. Therefore, RPA with singles is a suitable scheme for obtaining highly accurate adsorption energies in porous materials and similar systems.
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Affiliation(s)
- Jiří Klimeš
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, CZ-12116 Prague 2, Czech Republic
| | - David P Tew
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
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28
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Kodrycka M, Holzer C, Klopper W, Patkowski K. Explicitly Correlated Dispersion and Exchange Dispersion Energies in Symmetry-Adapted Perturbation Theory. J Chem Theory Comput 2019; 15:5965-5986. [PMID: 31503481 DOI: 10.1021/acs.jctc.9b00547] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The individual interaction energy terms in symmetry-adapted perturbation theory (SAPT) not only have different physical interpretations but also converge to their complete basis set (CBS) limit values at quite different rates. Dispersion energy is notoriously the slowest converging interaction energy contribution, and exchange dispersion energy, while smaller in absolute value, converges just as poorly in relative terms. To speed up the basis set convergence of the lowest-order SAPT dispersion and exchange dispersion energies, we borrow the techniques from explicitly correlated (F12) electronic structure theory and develop practical expressions for the closed-shell Edisp(20)-F12 and Eexch-disp(20)-F12 contributions. While the latter term has been derived and implemented for the first time, the former correction was recently proposed by Przybytek [ J. Chem. Theory Comput. 2018 , 14 , 5105 - 5117 ] using an Ansatz with a full optimization of the explicitly correlated amplitudes. In addition to reimplementing the fully optimized variant of Edisp(20)-F12, we propose three approximate Ansätze that substantially improve the scaling of the method and at the same time avoid the numerical instabilities of the unrestricted optimization. The performance of all four resulting flavors of Edisp(20)-F12 and Eexch-disp(20)-F12 is first tested on helium, neon, argon, water, and methane dimers, with orbital and auxiliary basis sets up to aug-cc-pV5Z and aug-cc-pV5Z-RI, respectively. The double- and triple-ζ basis set calculations are then extended to the entire A24 database of noncovalent interaction energies and compared with CBS estimates for Edisp(20) and Eexch-disp(20) computed using conventional SAPT with basis sets up to aug-cc-pV6Z with midbond functions. It is shown that the F12 treatment is highly successful in improving the basis set convergence of the SAPT terms, with the F12 calculations in an X-tuple ζ basis about as accurate as conventional calculations in bases with cardinal numbers (X + 2) for Edisp(20) and either (X + 1) or (X + 2) for Eexch-disp(20). While the full amplitude optimization affords the highest accuracy for both corrections, the much simpler and numerically stable optimized diagonal Ansatz is a very close second. We have also tested the performance of the simple F12 correction based on the second-order Møller-Plesset perturbation theory, SAPT-F12(MP2) [ Frey , J. A. ; Chem. Rev. 2016 , 116 , 5614 - 5641 ] and observed that it is also quite successful in speeding up the basis set convergence of conventional Edisp(20) + Eexch-disp(20), albeit with some outliers.
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Affiliation(s)
- Monika Kodrycka
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Christof Holzer
- Theoretical Chemistry Group, Institute of Physical Chemistry , Karlsruhe Institute of Technology (KIT) , KIT Campus South , P.O. Box 6980, D-76049 Karlsruhe , Germany
| | - Wim Klopper
- Theoretical Chemistry Group, Institute of Physical Chemistry , Karlsruhe Institute of Technology (KIT) , KIT Campus South , P.O. Box 6980, D-76049 Karlsruhe , Germany
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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29
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Höfener S, Schieschke N, Klopper W, Köhn A. The extended explicitly-correlated second-order approximate coupled-cluster singles and doubles ansatz suitable for response theory. J Chem Phys 2019; 150:184110. [DOI: 10.1063/1.5094434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sebastian Höfener
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), P.O. Box 6980, D-76049 Karlsruhe, Germany
| | - Nils Schieschke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), P.O. Box 6980, D-76049 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), P.O. Box 6980, D-76049 Karlsruhe, Germany
| | - Andreas Köhn
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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30
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Ganyecz Á, Kállay M, Csontos J. Thermochemistry of Uracil, Thymine, Cytosine, and Adenine. J Phys Chem A 2019; 123:4057-4067. [DOI: 10.1021/acs.jpca.9b02061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ádám Ganyecz
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, PO Box 91, H-1521, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, PO Box 91, H-1521, Hungary
| | - József Csontos
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, PO Box 91, H-1521, Hungary
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31
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Ganyecz Á, Kállay M, Csontos J. High Accuracy Quantum Chemical and Thermochemical Network Data for the Heats of Formation of Fluorinated and Chlorinated Methanes and Ethanes. J Phys Chem A 2018; 122:5993-6006. [PMID: 29939026 DOI: 10.1021/acs.jpca.8b00614] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reliable heats of formation are reported for numerous fluorinated and chlorinated methane and ethane derivatives by means of an accurate thermochemical protocol, which involves explicitly correlated coupled-cluster calculations augmented with anharmonic, scalar relativistic, and diagonal Born-Oppenheimer corrections. The theoretical results, along with additional experimental data, are further enhanced with the help of the thermochemical network approach. For 28 species, out of 50, this study presents the best estimates, and discrepancies with previous reports are also highlighted. Furthermore, the effects of the less accurate theoretical data on the results yielded by thermochemical networks are discussed.
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Affiliation(s)
- Ádám Ganyecz
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science , Budapest University of Technology and Economics , P.O. Box 91, Budapest , H-1521 Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science , Budapest University of Technology and Economics , P.O. Box 91, Budapest , H-1521 Hungary
| | - József Csontos
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science , Budapest University of Technology and Economics , P.O. Box 91, Budapest , H-1521 Hungary
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32
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Abstract
The requirement that the linear density fitting error in the integral exactly vanishes introduces unphysical long range contributions to the approximate density when the auxiliary basis is incomplete. A quasi-robust density fitting formulation is presented where spatial locality is recovered at the expense of permitting a linear error that is made small by the fitting procedure, which involves optimising the Coulomb potential of the approximate charge density. The method is shown to be stable and almost as accurate as standard robust density fitting without local approximations in practical calculations using standard density fitting basis sets.
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Affiliation(s)
- David P Tew
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom and Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
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33
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Řezáč J, Bím D, Gutten O, Rulíšek L. Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set. J Chem Theory Comput 2018; 14:1254-1266. [DOI: 10.1021/acs.jctc.7b01074] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jan Řezáč
- Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Daniel Bím
- Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Ondrej Gutten
- Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Lubomír Rulíšek
- Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
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34
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Fiedler B, Himmel D, Krossing I, Friedrich J. More Stable Template Localization for an Incremental Focal-Point Approach—Implementation and Application to the Intramolecular Decomposition of Tris-perfluoro- tert-butoxyalane. J Chem Theory Comput 2018; 14:557-571. [DOI: 10.1021/acs.jctc.7b00707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Fiedler
- Institut
für Chemie, Technische Universität Chemnitz, 09111 Chemnitz, Germany
| | - Daniel Himmel
- Institut
für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Ingo Krossing
- Institut
für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Joachim Friedrich
- Institut
für Chemie, Technische Universität Chemnitz, 09111 Chemnitz, Germany
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35
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Fiedler B, Schmitz G, Hättig C, Friedrich J. Combining Accuracy and Efficiency: An Incremental Focal-Point Method Based on Pair Natural Orbitals. J Chem Theory Comput 2017; 13:6023-6042. [PMID: 29045786 DOI: 10.1021/acs.jctc.7b00654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this work, we present a new pair natural orbitals (PNO)-based incremental scheme to calculate CCSD(T) and CCSD(T0) reaction, interaction, and binding energies. We perform an extensive analysis, which shows small incremental errors similar to previous non-PNO calculations. Furthermore, slight PNO errors are obtained by using TPNO = TTNO with appropriate values of 10-7 to 10-8 for reactions and 10-8 for interaction or binding energies. The combination with the efficient MP2 focal-point approach yields chemical accuracy relative to the complete basis-set (CBS) limit. In this method, small basis sets (cc-pVDZ, def2-TZVP) for the CCSD(T) part are sufficient in case of reactions or interactions, while some larger ones (e.g., (aug)-cc-pVTZ) are necessary for molecular clusters. For these larger basis sets, we show the very high efficiency of our scheme. We obtain not only tremendous decreases of the wall times (i.e., factors >102) due to the parallelization of the increment calculations as well as of the total times due to the application of PNOs (i.e., compared to the normal incremental scheme) but also smaller total times with respect to the standard PNO method. That way, our new method features a perfect applicability by combining an excellent accuracy with a very high efficiency as well as the accessibility to larger systems due to the separation of the full computation into several small increments.
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Affiliation(s)
- Benjamin Fiedler
- Institut für Chemie, Technische Universität Chemnitz , 09111 Chemnitz, Germany
| | - Gunnar Schmitz
- Institut for Kemi, Aarhus Universitet , 8000 Aarhus C, Denmark
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , 44801 Bochum, Germany
| | - Joachim Friedrich
- Institut für Chemie, Technische Universität Chemnitz , 09111 Chemnitz, Germany
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36
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Kottmann JS, Bischoff FA. Coupled-Cluster in Real Space. 1. CC2 Ground State Energies Using Multiresolution Analysis. J Chem Theory Comput 2017; 13:5945-5955. [PMID: 28902997 DOI: 10.1021/acs.jctc.7b00694] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A framework to calculate CC2 approximated coupled-cluster ground state correlation energies in a multiresolution basis is derived and implemented into the MADNESS library. The CC2 working equations are formulated in first quantization which makes them suitable for real-space methods. The first quantized equations can be interpreted diagrammatically using the usual diagrams from second quantization with adjusted interpretation rules. Singularities arising from the nuclear and electronic potentials are regularized by explicitly taking the nuclear and electronic cusps into account. The regularized three- and six-dimensional cluster functions are represented directly on an adaptive grid. The resulting equations are free of singularities and virtual orbitals, which results in a low intrinsic scaling. Correlation energies close to the basis set limit are computed for small molecules. This work is the first step toward CC2 excitation energies in a multiresolution basis.
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Affiliation(s)
- Jakob S Kottmann
- Institut für Chemie, Humboldt-Universität zu Berlin , Unter den Linden 6, D-10099 Berlin, Germany
| | - Florian A Bischoff
- Institut für Chemie, Humboldt-Universität zu Berlin , Unter den Linden 6, D-10099 Berlin, Germany
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37
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Ganyecz Á, Kállay M, Csontos J. Moderate-Cost Ab Initio Thermochemistry with Chemical Accuracy. J Chem Theory Comput 2017; 13:4193-4204. [DOI: 10.1021/acs.jctc.7b00607] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ádám Ganyecz
- MTA-BME Lendület Quantum
Chemistry Research Group, Department of Physical Chemistry and Materials
Science, Budapest University of Technology and Economics, Budapest, P.O. Box 91, H-1521 Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum
Chemistry Research Group, Department of Physical Chemistry and Materials
Science, Budapest University of Technology and Economics, Budapest, P.O. Box 91, H-1521 Hungary
| | - József Csontos
- MTA-BME Lendület Quantum
Chemistry Research Group, Department of Physical Chemistry and Materials
Science, Budapest University of Technology and Economics, Budapest, P.O. Box 91, H-1521 Hungary
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38
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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: 2.3] [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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39
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Höfener S, Klopper W. Natural transition orbitals for the calculation of correlation and excitation energies. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.083] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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Gas-phase standard enthalpies of formation of urea-derived compounds: A quantum-chemical study. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Schmitz G, Hättig C. Accuracy of Explicitly Correlated Local PNO-CCSD(T). J Chem Theory Comput 2017; 13:2623-2633. [DOI: 10.1021/acs.jctc.7b00180] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gunnar Schmitz
- Department
of Chemistry, Aarhus Universitet, Aarhus 8000, Denmark
| | - Christof Hättig
- Arbeitsgruppe
Quantenchemie, Ruhr-Universität, Bochum 44780, Germany
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42
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Stasyuk OA, Jakubec D, Vondrášek J, Hobza P. Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes. J Chem Theory Comput 2017; 13:877-885. [PMID: 27992205 DOI: 10.1021/acs.jctc.6b00775] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In view of the importance of protein-DNA interactions in biological processes, we extracted from the Protein Data Bank several one-to-one complexes of amino acids with nucleotides that matched certain geometric and energetic specificity criteria and investigated them using quantum chemistry methods. The CCSD(T)/CBS interaction energies were used as a benchmark to compare the performance of the MP2.5, MP2-F12, DFT-D3, and PM6-D3H4 methods. All methods yielded good agreement with the reference values, with declining accuracy from MP2.5 to PM6-D3H4. Regardless of the site of interaction, the minima found after full optimization in implicit solvent with high dielectric constant were close to the structures experimentally detected in protein-DNA complexes. According to DFT-SAPT analysis, the nature of noncovalent interactions strongly depends on the type of amino acid. The negatively charged sugar-phosphate backbone of DNA heavily influences the strength of interactions and must be included in the computational model, especially in the case of interactions with charged amino acids.
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Affiliation(s)
- Olga A Stasyuk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - David Jakubec
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague , Albertov 6, 128 43 Prague, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 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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43
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Mullaney JC, Medcraft C, Tew DP, Lewis-Borrell L, Golding BT, Walker NR, Legon AC. Cooperative hydrogen bonds form a pseudocycle stabilizing an isolated complex of isocyanic acid with urea. Phys Chem Chem Phys 2017; 19:25080-25085. [DOI: 10.1039/c7cp04315e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The structure and properties of a gas phase complex formed between urea and isocyanic acid are characterised through microwave spectroscopy andab initiocalculations at the CCSD(T)(F12*)/aug-cc-pVTZ level.
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Affiliation(s)
- John C. Mullaney
- School of Chemistry
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
- UK
| | - Chris Medcraft
- School of Chemistry
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
- UK
| | - David P. Tew
- School of Chemistry
- University of Bristol
- Bristol
- UK
| | - Luke Lewis-Borrell
- School of Chemistry
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
- UK
| | - Bernard T. Golding
- School of Chemistry
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
- UK
| | - Nicholas R. Walker
- School of Chemistry
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
- UK
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44
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Hehn AS, Holzer C, Klopper W. Explicitly-correlated ring-coupled-cluster-doubles theory: Including exchange for computations on closed-shell systems. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.09.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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45
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Tew DP. Explicitly correlated coupled-cluster theory with Brueckner orbitals. J Chem Phys 2016; 145:074103. [DOI: 10.1063/1.4960655] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David P. Tew
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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46
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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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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: 1.4] [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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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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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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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: 1.4] [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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