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Olsen JMH, Reine S, Vahtras O, Kjellgren E, Reinholdt P, Hjorth Dundas KO, Li X, Cukras J, Ringholm M, Hedegård ED, Di Remigio R, List NH, Faber R, Cabral Tenorio BN, Bast R, Pedersen TB, Rinkevicius Z, Sauer SPA, Mikkelsen KV, Kongsted J, Coriani S, Ruud K, Helgaker T, Jensen HJA, Norman P. Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems. J Chem Phys 2020; 152:214115. [PMID: 32505165 DOI: 10.1063/1.5144298] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.
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Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Simen Reine
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, N-0315 Oslo, Norway
| | - Olav Vahtras
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Erik Kjellgren
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Karen Oda Hjorth Dundas
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Xin Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Janusz Cukras
- Department of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Magnus Ringholm
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Erik D Hedegård
- Division of Theoretical Chemistry, Lund University, SE-223 62 Lund, Sweden
| | - Roberto Di Remigio
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Nanna H List
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Rasmus Faber
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | | | - Radovan Bast
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Thomas Bondo Pedersen
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, N-0315 Oslo, Norway
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Kenneth Ruud
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Trygve Helgaker
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, N-0315 Oslo, Norway
| | - Hans Jørgen Aa Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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Krivdin LB. Computational protocols for calculating 13C NMR chemical shifts. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 112-113:103-156. [PMID: 31481156 DOI: 10.1016/j.pnmrs.2019.05.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 06/10/2023]
Abstract
The most recent results dealing with the computation of 13C NMR chemical shifts in chemistry (small molecules, saturated, unsaturated and aromatic compounds, heterocycles, functional derivatives, coordination complexes, carbocations, and natural products) are reviewed, paying special attention to theoretical background and accuracy, the latter involving solvent effects, vibrational corrections, and relativistic effects.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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Stoychev GL, Auer AA, Izsák R, Neese F. Self-Consistent Field Calculation of Nuclear Magnetic Resonance Chemical Shielding Constants Using Gauge-Including Atomic Orbitals and Approximate Two-Electron Integrals. J Chem Theory Comput 2018; 14:619-637. [DOI: 10.1021/acs.jctc.7b01006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Georgi L. Stoychev
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Alexander A. Auer
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
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Reiter K, Mack F, Weigend F. Calculation of Magnetic Shielding Constants with meta-GGA Functionals Employing the Multipole-Accelerated Resolution of the Identity: Implementation and Assessment of Accuracy and Efficiency. J Chem Theory Comput 2017; 14:191-197. [DOI: 10.1021/acs.jctc.7b01115] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Reiter
- Institut
für Nanotechnologie, Karlsruher Institut für Technologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Fabian Mack
- Institut
für Physikalische Chemie, Abteilung für Theoretische
Chemie, Karlsruher Institut für Technologie, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Florian Weigend
- Institut
für Nanotechnologie, Karlsruher Institut für Technologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institut
für Physikalische Chemie, Abteilung für Theoretische
Chemie, Karlsruher Institut für Technologie, Kaiserstraße 12, 76131 Karlsruhe, Germany
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