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Borrego-Sánchez A, Zemmouche M, Carmona-García J, Francés-Monerris A, Mulet P, Navizet I, Roca-Sanjuán D. Multiconfigurational Quantum Chemistry Determinations of Absorption Cross Sections (σ) in the Gas Phase and Molar Extinction Coefficients (ε) in Aqueous Solution and Air-Water Interface. J Chem Theory Comput 2021; 17:3571-3582. [PMID: 33974417 PMCID: PMC8444339 DOI: 10.1021/acs.jctc.0c01083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Indexed: 11/29/2022]
Abstract
Theoretical determinations of absorption cross sections (σ) in the gas phase and molar extinction coefficients (ε) in condensed phases (water solution, interfaces or surfaces, protein or nucleic acids embeddings, etc.) are of interest when rates of photochemical processes, J = ∫ ϕ(λ) σ(λ) I(λ) dλ, are needed, where ϕ(λ) and I(λ) are the quantum yield of the process and the irradiance of the light source, respectively, as functions of the wavelength λ. Efficient computational strategies based on single-reference quantum-chemistry methods have been developed enabling determinations of line shapes or, in some cases, achieving rovibrational resolution. Developments are however lacking for strongly correlated problems, with many excited states, high-order excitations, and/or near degeneracies between states of the same and different spin multiplicities. In this work, we define and compare the performance of distinct computational strategies using multiconfigurational quantum chemistry, nuclear sampling of the chromophore (by means of molecular dynamics, ab initio molecular dynamics, or Wigner sampling), and conformational and statistical sampling of the environment (by means of molecular dynamics). A new mathematical approach revisiting previous absolute orientation algorithms is also developed to improve alignments of geometries. These approaches are benchmarked through the nπ* band of acrolein not only in the gas phase and water solution but also in a gas-phase/water interface, a common situation for instance in atmospheric chemistry. Subsequently, the best strategy is used to compute the absorption band for the adduct formed upon addition of an OH radical to the C6 position of uracil and compared with the available experimental data. Overall, quantum Wigner sampling of the chromophore with molecular dynamics sampling of the environment with CASPT2 electronic-structure determinations arise as a powerful methodology to predict meaningful σ(λ) and ε(λ) band line shapes with accurate absolute intensities.
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Affiliation(s)
- Ana Borrego-Sánchez
- Instituto
Andaluz de Ciencias de la Tierra, CSIC-University
of Granada, Av. de las
Palmeras 4, 18100 Armilla, Granada, Spain
| | - Madjid Zemmouche
- MSME,
Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris-Est Créteil 8208, F-77454 Marne-la-Vallée, France
| | - Javier Carmona-García
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, València, Spain
| | - Antonio Francés-Monerris
- Université
de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
- Departamento
de Química Física, Universitat
de València, C/Dr.
Moliner 50, 46100 Burjassot, Spain
| | - Pep Mulet
- Departamento
de Matemáticas Área de Matemática Aplicada Facultad
de Matemáticas C/Dr. Moliner, 50 46100 Burjassot, Spain
| | - Isabelle Navizet
- MSME,
Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris-Est Créteil 8208, F-77454 Marne-la-Vallée, France
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, València, Spain
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Aquilante F, Autschbach J, Baiardi A, Battaglia S, Borin VA, Chibotaru LF, Conti I, De Vico L, Delcey M, Fdez Galván I, Ferré N, Freitag L, Garavelli M, Gong X, Knecht S, Larsson ED, Lindh R, Lundberg M, Malmqvist PÅ, Nenov A, Norell J, Odelius M, Olivucci M, Pedersen TB, Pedraza-González L, Phung QM, Pierloot K, Reiher M, Schapiro I, Segarra-Martí J, Segatta F, Seijo L, Sen S, Sergentu DC, Stein CJ, Ungur L, Vacher M, Valentini A, Veryazov V. Modern quantum chemistry with [Open]Molcas. J Chem Phys 2020; 152:214117. [PMID: 32505150 DOI: 10.1063/5.0004835] [Citation(s) in RCA: 226] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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Affiliation(s)
- Francesco Aquilante
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, USA
| | - Alberto Baiardi
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stefano Battaglia
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Liviu F Chibotaru
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Mickaël Delcey
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Ignacio Fdez Galván
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Nicolas Ferré
- Aix-Marseille University, CNRS, Institut Chimie Radicalaire, Marseille, France
| | - Leon Freitag
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Xuejun Gong
- Department of Chemistry, University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Stefan Knecht
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Ernst D Larsson
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Roland Lindh
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Marcus Lundberg
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Per Åke Malmqvist
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Jesper Norell
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Odelius
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Thomas B Pedersen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Quan M Phung
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Kristine Pierloot
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Javier Segarra-Martí
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, United Kingdom
| | - Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Luis Seijo
- Departamento de Química, Instituto Universitario de Ciencia de Materiales Nicolás Cabrera, and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Saumik Sen
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Christopher J Stein
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Liviu Ungur
- Department of Chemistry, University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Morgane Vacher
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 44300 Nantes, France
| | - Alessio Valentini
- Theoretical Physical Chemistry, Research Unit MolSys, Université de Liège, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Valera Veryazov
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
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Aquilante F, Autschbach J, Carlson RK, Chibotaru LF, Delcey MG, De Vico L, Fdez Galván I, Ferré N, Frutos LM, Gagliardi L, Garavelli M, Giussani A, Hoyer CE, Li Manni G, Lischka H, Ma D, Malmqvist PÅ, Müller T, Nenov A, Olivucci M, Pedersen TB, Peng D, Plasser F, Pritchard B, Reiher M, Rivalta I, Schapiro I, Segarra-Martí J, Stenrup M, Truhlar DG, Ungur L, Valentini A, Vancoillie S, Veryazov V, Vysotskiy VP, Weingart O, Zapata F, Lindh R. Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table. J Comput Chem 2015; 37:506-41. [PMID: 26561362 DOI: 10.1002/jcc.24221] [Citation(s) in RCA: 1105] [Impact Index Per Article: 122.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 12/17/2022]
Abstract
In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
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Affiliation(s)
- Francesco Aquilante
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden.,Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York, 14260-3000, USA
| | - Rebecca K Carlson
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA
| | - Liviu F Chibotaru
- Division of Quantum and Physical Chemistry, and INPAC, Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven Celestijnenlaan, 200F, 3001, Belgium
| | - Mickaël G Delcey
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden
| | - Luca De Vico
- Department of Chemistry, Copenhagen University, Universitetsparken 5, Copenhagen Ø, 2100, Denmark
| | - Ignacio Fdez Galván
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden.,Uppsala Center for Computational Chemistry - UC3, Uppsala University, Box 518, Uppsala, 751 20, Sweden
| | - Nicolas Ferré
- Université d'Aix-Marseille, CNRS, Institut de Chimie Radicalaire, Campus Étoile/Saint-Jérôme Case 521, Avenue Esc. Normandie Niemen, Marseille Cedex 20, 13397, France
| | - Luis Manuel Frutos
- Unidad Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Laura Gagliardi
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy.,Université de Lyon, CNRS, École Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon Cedex 07, F-69364, France
| | - Angelo Giussani
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy
| | - Chad E Hoyer
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA
| | - Giovanni Li Manni
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA.,Max Planck Institut für Festkörperforschung, Heisenbergstraße 1, Stuttgart, 70569, Germany
| | - Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle and Boston, Lubbock, Texas, 79409-1061, USA.,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, Vienna, A-1090, Austria
| | - Dongxia Ma
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA.,Max Planck Institut für Festkörperforschung, Heisenbergstraße 1, Stuttgart, 70569, Germany
| | - Per Åke Malmqvist
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O.B 124 S-221 00, Lund, Sweden
| | - Thomas Müller
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Institute for Advanced Simulation (IAS), Wilhelm-Johnen-Straße, Jülich, 52425, Germany
| | - Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena, 53100, Italy.,Chemistry Department, Bowling Green State University, 141 Overman Hall, Bowling Green, Ohio, 43403, USA.,Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504, 23 Rue du Loess, Strasbourg, 67034, France
| | - Thomas Bondo Pedersen
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, Oslo, 0315, Norway
| | - Daoling Peng
- College of Chemistry and Environment, South China Normal University, Guangzhou, 510006, China
| | - Felix Plasser
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, Vienna, A-1090, Austria
| | - Ben Pritchard
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York, 14260-3000, USA
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, Zurich, CH-8093, Switzerland
| | - Ivan Rivalta
- Université de Lyon, CNRS, École Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon Cedex 07, F-69364, France
| | - Igor Schapiro
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504, 23 Rue du Loess, Strasbourg, 67034, France.,Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy
| | - Michael Stenrup
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden.,Uppsala Center for Computational Chemistry - UC3, Uppsala University, Box 518, Uppsala, 751 20, Sweden
| | - Donald G Truhlar
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA
| | - Liviu Ungur
- Division of Quantum and Physical Chemistry, and INPAC, Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven Celestijnenlaan, 200F, 3001, Belgium
| | - Alessio Valentini
- Unidad Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.,Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena, 53100, Italy
| | - Steven Vancoillie
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O.B 124 S-221 00, Lund, Sweden
| | - Valera Veryazov
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O.B 124 S-221 00, Lund, Sweden
| | - Victor P Vysotskiy
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O.B 124 S-221 00, Lund, Sweden
| | - Oliver Weingart
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
| | - Felipe Zapata
- Unidad Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Roland Lindh
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden.,Uppsala Center for Computational Chemistry - UC3, Uppsala University, Box 518, Uppsala, 751 20, Sweden
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