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Jaiswal VK, Montorsi F, Aleotti F, Segatta F, Keefer D, Mukamel S, Nenov A, Conti I, Garavelli M. Ultrafast photochemistry and electron-diffraction spectra in n → (3s) Rydberg excited cyclobutanone resolved at the multireference perturbative level. J Chem Phys 2024; 160:164316. [PMID: 38686819 DOI: 10.1063/5.0203624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
We study the ultrafast time evolution of cyclobutanone excited to the singlet n → Rydberg state through non-adiabatic surface-hopping simulationsperformed at extended multi-state complete active space second-order perturbation (XMS-CASPT2) level of theory. These dynamics predict relaxation to the ground-state with a timescale of 822 ± 45 fs with minimal involvement of the triplets. The major relaxation path to the ground-state involves a three-state degeneracy region and leads to a variety of fragmented photoproducts. We simulate the resulting time-resolved electron-diffraction spectra, which track the relaxation of the excited state and the formation of various photoproducts in the ground state.
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Affiliation(s)
- V K Jaiswal
- Dipartimento di Chimica industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - F Montorsi
- Dipartimento di Chimica industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - F Aleotti
- Dipartimento di Chimica industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - F Segatta
- Dipartimento di Chimica industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Daniel Keefer
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California Irvine, Irvine, California 92697, USA
| | - A Nenov
- Dipartimento di Chimica industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - I Conti
- Dipartimento di Chimica industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - M Garavelli
- Dipartimento di Chimica industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
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2
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Savino A, Rondonotti E, Rocchetto S, Piagnani A, Bina N, Di Domenico P, Segatta F, Radaelli F. GI genius endoscopy module: a clinical profile. Expert Rev Med Devices 2024:1-14. [PMID: 38618982 DOI: 10.1080/17434440.2024.2342508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
INTRODUCTION The identification of early-stage colorectal cancers (CRC) and the resection of pre-cancerous neoplastic lesions through colonoscopy allows to decrease both CRC incidence and mortality. However, colonoscopy miss rates up to 26% for adenomas and 9% for advanced adenomas have been reported. In recent years, artificial intelligence (AI) systems have been emerging as easy-to-use tools, potentially lowering the risk of missing lesions. AREAS COVERED This review paper focuses on GI Genius device (Medtronic Co. Minneapolis, MN, U.S.A.) a computer-assisted tool designed to assist endoscopists during standard white-light colonoscopies in detecting mucosal lesions. EXPERT OPINION Randomized controlled trials (RCTs) suggest that GI Genius is a safe and effective tool for improving adenoma detection, especially in CRC screening and surveillance colonoscopies. However, its impact seems to be less significant among experienced endoscopists and in real-world clinical scenarios compared to the controlled conditions of RCTs. Furthermore, it appears that GI Genius mainly enhances the detection of non-advanced, small polyps, but does not significantly impact the identification of advanced and difficult-to-detect adenoma. When using GI Genius, no complications were documented. Only a small number of studies reported an increased in withdrawal time or the removal of non-neoplastic lesions.
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Affiliation(s)
- Alberto Savino
- Division of Gastroenterology, Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
| | | | - Simone Rocchetto
- Gastroenterology Unit, Valduce Hospital, Como, Italy
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Gastroenterology and Hepatology, University of Milan, Milan, Italy
| | - Alessandra Piagnani
- Gastroenterology Unit, Valduce Hospital, Como, Italy
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Gastroenterology and Hepatology, University of Milan, Milan, Italy
| | - Niccolò Bina
- Gastroenterology Unit, Valduce Hospital, Como, Italy
| | - Pasquale Di Domenico
- Gastrointestinal Unit, Department of Medicine, Surgery & Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Francesco Segatta
- Gastroenterology Unit, Valduce Hospital, Como, Italy
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Gastroenterology and Hepatology, University of Milan, Milan, Italy
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3
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Segatta F, Aranda D, Aleotti F, Montorsi F, Mukamel S, Garavelli M, Santoro F, Nenov A. Time-Resolved X-ray Absorption Spectroscopy: An MCTDH Quantum Dynamics Protocol. J Chem Theory Comput 2024; 20:307-322. [PMID: 38101807 PMCID: PMC10782456 DOI: 10.1021/acs.jctc.3c00953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/04/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023]
Abstract
Expressions for linear and nonlinear spectroscopy simulation in the X-ray window in which the time evolution of a photoexcited molecular system is treated via quantum dynamics are derived. By leveraging on the peculiar properties of core-excited/ionized states, first- and third-order response functions are recast in the limit of time-scale separation between the extremely short core-state lifetime and the (comparably longer) electronic-state transfer and nuclear vibrational motion. This work is a natural extension of Segatta et al. (J. Chem. Theory Comput. 2023, 19, 2075-2091), in which some of the present authors coupled MCTDH quantum dynamics to spectroscopy simulation at different levels of sophistication. Full quantum dynamics and approximate expressions are compared by simulating X-ray transient absorption spectroscopy at the carbon K-edge in the pyrene molecule.
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Affiliation(s)
- Francesco Segatta
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Daniel Aranda
- ICMol, Universidad de Valencia, c/Catedrático José
Beltrán,
2, 46980 Paterna, Spain
- Istituto
di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via
Moruzzi 1, I-56124 Pisa, Italy
| | - Flavia Aleotti
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Francesco Montorsi
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, 92697 California, United States
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Fabrizio Santoro
- Istituto
di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via
Moruzzi 1, I-56124 Pisa, Italy
| | - Artur Nenov
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
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4
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Li Manni G, Fdez. Galván I, Alavi A, Aleotti F, Aquilante F, Autschbach J, Avagliano D, Baiardi A, Bao JJ, Battaglia S, Birnoschi L, Blanco-González A, Bokarev SI, Broer R, Cacciari R, Calio PB, Carlson RK, Carvalho Couto R, Cerdán L, Chibotaru LF, Chilton NF, Church JR, Conti I, Coriani S, Cuéllar-Zuquin J, Daoud RE, Dattani N, Decleva P, de Graaf C, Delcey M, De Vico L, Dobrautz W, Dong SS, Feng R, Ferré N, Filatov(Gulak) M, Gagliardi L, Garavelli M, González L, Guan Y, Guo M, Hennefarth MR, Hermes MR, Hoyer CE, Huix-Rotllant M, Jaiswal VK, Kaiser A, Kaliakin DS, Khamesian M, King DS, Kochetov V, Krośnicki M, Kumaar AA, Larsson ED, Lehtola S, Lepetit MB, Lischka H, López Ríos P, Lundberg M, Ma D, Mai S, Marquetand P, Merritt ICD, Montorsi F, Mörchen M, Nenov A, Nguyen VHA, Nishimoto Y, Oakley MS, Olivucci M, Oppel M, Padula D, Pandharkar R, Phung QM, Plasser F, Raggi G, Rebolini E, Reiher M, Rivalta I, Roca-Sanjuán D, Romig T, Safari AA, Sánchez-Mansilla A, Sand AM, Schapiro I, Scott TR, Segarra-Martí J, Segatta F, Sergentu DC, Sharma P, Shepard R, Shu Y, Staab JK, Straatsma TP, Sørensen LK, Tenorio BNC, Truhlar DG, Ungur L, Vacher M, Veryazov V, Voß TA, Weser O, Wu D, Yang X, Yarkony D, Zhou C, Zobel JP, Lindh R. The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry. J Chem Theory Comput 2023; 19:6933-6991. [PMID: 37216210 PMCID: PMC10601490 DOI: 10.1021/acs.jctc.3c00182] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 05/24/2023]
Abstract
The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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Affiliation(s)
- Giovanni Li Manni
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Ignacio Fdez. Galván
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Ali Alavi
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Yusuf Hamied
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Flavia Aleotti
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - 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, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Davide Avagliano
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Alberto Baiardi
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jie J. Bao
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Stefano Battaglia
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Letitia Birnoschi
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | - Alejandro Blanco-González
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - Sergey I. Bokarev
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
- Chemistry
Department, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Ria Broer
- Theoretical
Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Roberto Cacciari
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Paul B. Calio
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Rebecca K. Carlson
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Rafael Carvalho Couto
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Luis Cerdán
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
- Instituto
de Óptica (IO−CSIC), Consejo
Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Liviu F. Chibotaru
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Nicholas F. Chilton
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | | | - Irene Conti
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Sonia Coriani
- Department
of Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, 2800 Kongens Lyngby, Denmark
| | - Juliana Cuéllar-Zuquin
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Razan E. Daoud
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Nike Dattani
- HPQC Labs, Waterloo, N2T 2K9 Ontario Canada
- HPQC College, Waterloo, N2T 2K9 Ontario Canada
| | - Piero Decleva
- Istituto
Officina dei Materiali IOM-CNR and Dipartimento di Scienze Chimiche
e Farmaceutiche, Università degli
Studi di Trieste, I-34121 Trieste, Italy
| | - Coen de Graaf
- Department
of Physical and Inorganic Chemistry, Universitat
Rovira i Virgili, Tarragona 43007, Spain
- ICREA, Pg. Lluís
Companys 23, 08010 Barcelona, Spain
| | - Mickaël
G. Delcey
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Luca De Vico
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Werner Dobrautz
- Chalmers
University of Technology, Department of Chemistry
and Chemical Engineering, 41296 Gothenburg, Sweden
| | - Sijia S. Dong
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry and Chemical Biology, Department of Physics, and Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rulin Feng
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Nicolas Ferré
- Institut
de Chimie Radicalaire (UMR-7273), Aix-Marseille
Univ, CNRS, ICR 13013 Marseille, France
| | | | - Laura Gagliardi
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Marco Garavelli
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Yafu Guan
- State Key
Laboratory of Molecular Reaction Dynamics and Center for Theoretical
Computational Chemistry, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Meiyuan Guo
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Matthew R. Hennefarth
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew R. Hermes
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chad E. Hoyer
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miquel Huix-Rotllant
- Institut
de Chimie Radicalaire (UMR-7273), Aix-Marseille
Univ, CNRS, ICR 13013 Marseille, France
| | - Vishal Kumar Jaiswal
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Andy Kaiser
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Danil S. Kaliakin
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - Marjan Khamesian
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Daniel S. King
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vladislav Kochetov
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Marek Krośnicki
- Institute
of Theoretical Physics and Astrophysics, Faculty of Mathematics, Physics
and Informatics, University of Gdańsk, ul Wita Stwosza 57, 80-952, Gdańsk, Poland
| | | | - Ernst D. Larsson
- Division
of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Susi Lehtola
- Molecular
Sciences Software Institute, Blacksburg, Virginia 24061, United States
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 University of Helsinki, Finland
| | - Marie-Bernadette Lepetit
- Condensed
Matter Theory Group, Institut Néel, CNRS UPR 2940, 38042 Grenoble, France
- Theory
Group, Institut Laue Langevin, 38042 Grenoble, France
| | - Hans Lischka
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409-1061, United States
| | - Pablo López Ríos
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Marcus Lundberg
- Department
of Chemistry − Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
| | - Dongxia Ma
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | | | - Francesco Montorsi
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Maximilian Mörchen
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Artur Nenov
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Vu Ha Anh Nguyen
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Yoshio Nishimoto
- Graduate
School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Meagan S. Oakley
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Markus Oppel
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Daniele Padula
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Riddhish Pandharkar
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Quan Manh Phung
- Department
of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Felix Plasser
- Department
of Chemistry, Loughborough University, Loughborough, LE11 3TU, U.K.
| | - Gerardo Raggi
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
- Quantum
Materials and Software LTD, 128 City Road, London, EC1V 2NX, United Kingdom
| | - Elisa Rebolini
- Scientific
Computing Group, Institut Laue Langevin, 38042 Grenoble, France
| | - Markus Reiher
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Ivan Rivalta
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Thies Romig
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Arta Anushirwan Safari
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Aitor Sánchez-Mansilla
- Department
of Physical and Inorganic Chemistry, Universitat
Rovira i Virgili, Tarragona 43007, Spain
| | - Andrew M. Sand
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Igor Schapiro
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Thais R. Scott
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Javier Segarra-Martí
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Francesco Segatta
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Dumitru-Claudiu Sergentu
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
- Laboratory
RA-03, RECENT AIR, A. I. Cuza University of Iaşi, RA-03 Laboratory (RECENT AIR), Iaşi 700506, Romania
| | - Prachi Sharma
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Ron Shepard
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, USA
| | - Yinan Shu
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Jakob K. Staab
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | - Tjerk P. Straatsma
- National
Center for Computational Sciences, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831-6373, United States
- Department
of Chemistry and Biochemistry, University
of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | | | - Bruno Nunes Cabral Tenorio
- Department
of Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, 2800 Kongens Lyngby, Denmark
| | - Donald G. Truhlar
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Liviu Ungur
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Morgane Vacher
- Nantes
Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France
| | - Valera Veryazov
- Division
of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Torben Arne Voß
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Oskar Weser
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Dihua Wu
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Xuchun Yang
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - David Yarkony
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chen Zhou
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - J. Patrick Zobel
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Roland Lindh
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
- Uppsala
Center for Computational Chemistry (UC3), Uppsala University, PO Box 576, SE-751 23 Uppsala. Sweden
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5
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Segatta F, Ruiz DA, Aleotti F, Yaghoubi M, Mukamel S, Garavelli M, Santoro F, Nenov A. Nonlinear Molecular Electronic Spectroscopy via MCTDH Quantum Dynamics: From Exact to Approximate Expressions. J Chem Theory Comput 2023; 19:2075-2091. [PMID: 36961952 PMCID: PMC10100531 DOI: 10.1021/acs.jctc.2c01059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
We present an accurate and efficient approach to computing the linear and nonlinear optical spectroscopy of a closed quantum system subject to impulsive interactions with an incident electromagnetic field. It incorporates the effect of ultrafast nonadiabatic dynamics by means of explicit numerical propagation of the nuclear wave packet. The fundamental expressions for the evaluation of first- and higher-order response functions are recast in a general form that can be used with any quantum dynamics code capable of computing the overlap of nuclear wave packets evolving in different states. Here we present the evaluation of these expressions with the multiconfiguration time-dependent Hartree (MCTDH) method. Application is made to pyrene, excited to its lowest bright excited state S2 which exhibits a sub-100-fs nonadiabatic decay to a dark state S1. The system is described by a linear vibronic coupling Hamiltonian, parametrized with multiconfiguration electronic structure methods. We show that the ultrafast nonadiabatic dynamics can have a remarkable effect on the spectral line shapes that goes beyond simple lifetime broadening. Furthermore, a widely employed approximate expression based on the time scale separation of dephasing and population relaxation is recast in the same theoretical framework. Application to pyrene shows the range of validity of such approximations.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Daniel Aranda Ruiz
- ICMol, Universidad de Valencia, Catedrático José Beltrán Martínez, 2, 46980 Paterna, Spain
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Martha Yaghoubi
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
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6
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Montorsi F, Segatta F, Nenov A, Mukamel S, Garavelli M. Soft X-ray Spectroscopy Simulations with Multiconfigurational Wave Function Theory: Spectrum Completeness, Sub-eV Accuracy, and Quantitative Reproduction of Line Shapes. J Chem Theory Comput 2022; 18:1003-1016. [PMID: 35073066 PMCID: PMC8830047 DOI: 10.1021/acs.jctc.1c00566] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Francesco Montorsi
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Francesco Segatta
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Artur Nenov
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics & Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Marco Garavelli
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
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7
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Nam Y, Keefer D, Nenov A, Conti I, Aleotti F, Segatta F, Lee JY, Garavelli M, Mukamel S. Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy. J Phys Chem Lett 2021; 12:12300-12309. [PMID: 34931839 DOI: 10.1021/acs.jpclett.1c03814] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Conical intersections (CoIns) play an important role in ultrafast relaxation channels. Their monitoring remains a formidable experimental challenge. We theoretically compare the probing of the S2 → S1 CoIn passage in 4-thiouracil by monitoring its vibronic coherences, using off-resonant X-ray-stimulated Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). The quantum nuclear wavepacket (WP) dynamics provides an accurate picture of the photoinduced dynamics. Upon photoexcitation, the WP oscillates among the Franck-Condon point, the S2 minimum, and the CoIn with a 70 fs period. A vibronic coherence first emerges at 20 fs and can be observed until the S2 state is fully depopulated. The distribution of the vibronic frequencies involved in the coherence is recorded by the TRUECARS spectrogram. The TRXD signal provides spatial images of electron densities associated with the CoIn. In combination, the two signals provide a complementary picture of the nonadiabatic passage, which helps in the study of the underlying photophysics in thiobases.
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Affiliation(s)
- Yeonsig Nam
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
- Convergence Research Center for Energy and Environmental Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Daniel Keefer
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Jin Yong Lee
- Convergence Research Center for Energy and Environmental Sciences, Sungkyunkwan University, Suwon 16419, Korea
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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8
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Segatta F, Russo M, Nascimento DR, Presti D, Rigodanza F, Nenov A, Bonvicini A, Arcioni A, Mukamel S, Maiuri M, Muccioli L, Govind N, Cerullo G, Garavelli M. In Silico Ultrafast Nonlinear Spectroscopy Meets Experiments: The Case of Perylene Bisimide Dye. J Chem Theory Comput 2021; 17:7134-7145. [PMID: 34676761 PMCID: PMC8582250 DOI: 10.1021/acs.jctc.1c00570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Indexed: 11/30/2022]
Abstract
Spectroscopy simulations are of paramount importance for the interpretation of experimental electronic spectra, the disentangling of overlapping spectral features, and the tracing of the microscopic origin of the observed signals. Linear and nonlinear simulations are based on the results drawn from electronic structure calculations that provide the necessary parameterization of the molecular systems probed by light. Here, we investigate the applicability of excited-state properties obtained from linear-response time-dependent density functional theory (TDDFT) in the description of nonlinear spectra by employing the pseudowavefunction approach and compare them with benchmarks from highly accurate RASSCF/RASPT2 calculations and with high temporal resolution experimental results. As a test case, we consider the prediction of femtosecond transient absorption and two-dimensional electronic spectroscopy of a perylene bisimide dye in solution. We find that experimental signals are well reproduced by both theoretical approaches, showing that the computationally cheaper TDDFT can be a suitable option for the simulation of nonlinear spectroscopy of molecular systems that are too large to be treated with higher-level RASSCF/RASPT2 methods.
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Affiliation(s)
- Francesco Segatta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Mattia Russo
- IFN-CNR,
Dipartimento di Fisica, Politecnico di Milano, P. Leonardo da Vinci 32, Milan I-20133, Italy
| | - Daniel R. Nascimento
- Physical
and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department
of Chemistry, The University of Memphis, Memphis, Tennessee 38152, United States
| | - Davide Presti
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Francesco Rigodanza
- Dipartimento
di Scienze Chimiche, Università degli
studi di Padova, Via
F. Marzolo, Padova I-35131, Italy
| | - Artur Nenov
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Andrea Bonvicini
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Alberto Arcioni
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Margherita Maiuri
- IFN-CNR,
Dipartimento di Fisica, Politecnico di Milano, P. Leonardo da Vinci 32, Milan I-20133, Italy
| | - Luca Muccioli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Niranjan Govind
- Physical
and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Giulio Cerullo
- IFN-CNR,
Dipartimento di Fisica, Politecnico di Milano, P. Leonardo da Vinci 32, Milan I-20133, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
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9
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Keefer D, Rouxel JR, Aleotti F, Segatta F, Garavelli M, Mukamel S. Diffractive Imaging of Conical Intersections Amplified by Resonant Infrared Fields. J Am Chem Soc 2021; 143:13806-13815. [PMID: 34402612 DOI: 10.1021/jacs.1c06068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The fate of virtually all photochemical reactions is determined by conical intersections. These are energetically degenerate regions of molecular potential energy surfaces that strongly couple electronic states, thereby enabling fast relaxation channels. Their direct spectroscopic detection relies on weak features that are often buried beneath stronger, less interesting contributions. For azobenzene photoisomerization, a textbook photochemical reaction, we demonstrate how a resonant infrared field can be employed during the conical intersection passage to significantly enhance its coherence signatures in time-resolved X-ray diffraction while leaving the product yield intact. This transition-state amplification holds promise to bring signals of conical intersections above the detection threshold.
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Affiliation(s)
- Daniel Keefer
- Departments of Chemistry and Physics & Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Jérémy R Rouxel
- University Lyon, UJM-Saint-Étienne, CNRS, Graduate School Optics Institute, Laboratoire Hubert Curien UMR 5516, Saint-Étienne 42023, France
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Shaul Mukamel
- Departments of Chemistry and Physics & Astronomy, University of California, Irvine, California 92697-2025, United States
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10
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Cavaletto SM, Keefer D, Rouxel JR, Aleotti F, Segatta F, Garavelli M, Mukamel S. Unveiling the spatial distribution of molecular coherences at conical intersections by covariance X-ray diffraction signals. Proc Natl Acad Sci U S A 2021; 118:e2105046118. [PMID: 34050030 PMCID: PMC8179141 DOI: 10.1073/pnas.2105046118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The outcomes and timescales of molecular nonadiabatic dynamics are decisively impacted by the quantum coherences generated at localized molecular regions. In time-resolved X-ray diffraction imaging, these coherences create distinct signatures via inelastic photon scattering, but they are buried under much stronger background elastic features. Here, we exploit the rich dynamical information encoded in the inelastic patterns, which we reveal by frequency-dispersed covariance ultrafast powder X-ray diffraction of stochastic X-ray free-electron laser pulses. This is demonstrated for the photoisomerization of azobenzene involving the passage through a conical intersection, where the nuclear wave packet branches and explores different quantum pathways. Snapshots of the coherence dynamics are obtained at high frequency shifts, not accessible with conventional diffraction measurements. These provide access to the timing and to the confined spatial distribution of the valence electrons directly involved in the conical intersection passage. This study can be extended to full three-dimensional imaging of conical intersections with ultrafast X-ray and electron diffraction.
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Affiliation(s)
- Stefano M Cavaletto
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Physics & Astronomy, University of California, Irvine, CA 92697
| | - Daniel Keefer
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Physics & Astronomy, University of California, Irvine, CA 92697
| | - Jérémy R Rouxel
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Physics & Astronomy, University of California, Irvine, CA 92697
- University Lyon, UJM-Saint-Étienne, CNRS, Graduate School Optics Institute, Laboratoire Hubert Curien UMR 5516, Saint-Étienne 42023, France
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, CA 92697;
- Department of Physics & Astronomy, University of California, Irvine, CA 92697
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11
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Segatta F, Nenov A, Nascimento DR, Govind N, Mukamel S, Garavelli M. iSPECTRON: A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software. J Comput Chem 2021; 42:644-659. [PMID: 33556195 DOI: 10.1002/jcc.26485] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Calculations at two levels of electronic structure theory, time-dependent density functional theory (with NWChem) and RASSCF/RASPT2 (with OpenMolcas) are presented and compared where possible. The iSPECTRON program is available online at https://github.com/ispectrongit/iSPECTRON/ and distributed open source under the terms of the Educational Community License version 2.0 (ECL 2.0).
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
| | - Daniel R Nascimento
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
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12
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Gu B, Nenov A, Segatta F, Garavelli M, Mukamel S. Manipulating Core Excitations in Molecules by X-Ray Cavities. Phys Rev Lett 2021; 126:053201. [PMID: 33605757 DOI: 10.1103/physrevlett.126.053201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/02/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Core excitations on different atoms are highly localized and therefore decoupled. By placing molecules in an x-ray cavity the core transitions become coupled via the exchange of cavity photons and form delocalized hybrid light-matter excitations known as core polaritons. We demonstrate these effects for the two inequivalent carbon atoms in 1,1-difluoroethylene. Polariton signatures in the x-ray absorption, two-photon absorption, and multidimensional four-wave mixing signals are predicted.
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Affiliation(s)
- Bing Gu
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari," Università degli studi di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari," Università degli studi di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari," Università degli studi di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
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13
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Segatta F, Rogers DM, Dyer NT, Guest EE, Li Z, Do H, Nenov A, Garavelli M, Hirst JD. Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides. Molecules 2021; 26:E396. [PMID: 33451152 PMCID: PMC7828623 DOI: 10.3390/molecules26020396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Naomi T. Dyer
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Ellen E. Guest
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China;
| | - Hainam Do
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China;
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
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14
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Provazza J, Segatta F, Coker DF. Modeling Nonperturbative Field-Driven Vibronic Dynamics: Selective State Preparation and Nonlinear Spectroscopy. J Chem Theory Comput 2020; 17:29-39. [DOI: 10.1021/acs.jctc.0c01035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Justin Provazza
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Francesco Segatta
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Dipartimento di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - David F. Coker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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15
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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: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Alvertis A, Barford W, Bourne Worster S, Burghardt I, Datta A, Dijkstra A, Fay T, Ghosh S, Grünbaum T, Habershon S, Hore PJ, Hutchinson D, Iyengar S, Jones AR, Jones G, Komarova K, Lawrence J, Léonard J, Litman Y, Mannouch J, Manolopoulos D, Martens C, Mondelo-Martell M, Picconi D, Plant D, Sakaushi K, Saller MAC, Schile A, Scholes GD, Segarra-Martí J, Segatta F, Troisi A, Worth G. Quantum coherence in complex environments: general discussion. Faraday Discuss 2020; 221:168-201. [DOI: 10.1039/c9fd90076d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Alvertis A, Barford W, Bourne Worster S, Burghardt I, Chin A, Datta A, Dijkstra A, Fay T, Fielding H, Grünbaum T, Habershon S, Hammes-Schiffer S, Iyengar S, Jones AR, Komarova K, Léonard J, Litman Y, Picconi D, Plant D, Schile A, Scholes GD, Segarra-Martí J, Segatta F, Troisi A, Worth G. Spectroscopic signatures of quantum effects: general discussion. Faraday Discuss 2020; 221:322-349. [DOI: 10.1039/c9fd90074h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Segarra-Martí J, Segatta F, Mackenzie TA, Nenov A, Rivalta I, Bearpark MJ, Garavelli M. Modeling multidimensional spectral lineshapes from first principles: application to water-solvated adenine. Faraday Discuss 2020; 221:219-244. [DOI: 10.1039/c9fd00072k] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We theoretically describe spectral lineshape from first principles, providing insight into solvent–solute interactions in terms of static and dynamic disorder and how these shape experimental signals in linear and non-linear optical spectroscopies.
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Affiliation(s)
- Javier Segarra-Martí
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Tristan A. Mackenzie
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Ivan Rivalta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
- Univ Lyon
| | - Michael J. Bearpark
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
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19
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Segatta F, Nenov A, Orlandi S, Arcioni A, Mukamel S, Garavelli M. Exploring the capabilities of optical pump X-ray probe NEXAFS spectroscopy to track photo-induced dynamics mediated by conical intersections. Faraday Discuss 2020; 221:245-264. [DOI: 10.1039/c9fd00073a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present contribution we introduce an accurate theoretical approach for the simulation of NEXAFS spectra of organic molecules, employing azobenzene as a test case.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Silvia Orlandi
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Alberto Arcioni
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Shaul Mukamel
- Department of Chemistry and Physics and Astronomy
- University of California
- Irvine
- USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
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20
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”, Università degli studi di Bologna, Viale del Risorgimento 4,
40136 Bologna, Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”, Università degli studi di Bologna, Viale del Risorgimento 4,
40136 Bologna, Italy
| | - Adam Bruner
- Department of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697,
USA
| | - Shaul Mukamel
- Department of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697,
USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Università degli studi di Bologna, Viale del Risorgimento 4,
40136 Bologna, Italy
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21
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Abstract
Multichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment-protein complexes to nucleic acids. The former are designed to capture, harvest, efficiently transport, and transform energy from sunlight for photosynthesis, while the latter should dissipate the absorbed radiation as quickly as possible to prevent photodamages and corruption of the carried genetic information. Because of the unique electronic and structural characteristics, the modeling of their photoinduced activity is a real challenge. Numerous approaches have been devised building on the theoretical development achieved for single chromophores and on model Hamiltonians that capture the essential features of the system. Still, a question remains: is a general strategy for the accurate modeling of multichromophoric systems possible? By using a quantum chemical point of view, here we review the advancements developed so far highlighting differences and similarities with the single chromophore treatment. Finally, we outline the important limitations and challenges that still need to be tackled to reach a complete and accurate picture of their photoinduced properties and dynamics.
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Affiliation(s)
- Francesco Segatta
- Dipartimento
di Chimica Industriale “Toso Montanari” University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, University
of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari” University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University
of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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22
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Nenov A, Borrego-Varillas R, Oriana A, Ganzer L, Segatta F, Conti I, Manzoni C, Cerullo G, Garavelli M. UV-light induced vibrational coherences explain Kasha rule violation in frans-azobenzene. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201920509016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sub-20-fs transient absorption spectroscopy and simulations show that CNN-bendings dominate the sub-ps dynamics of ππ*-excited trans-azobenzene, thereby driving the system to the ground state through a non-productive decay channel in violation of the Kasha rule.
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23
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento) I-38050, Italy
- European Center for Theoretical
Studies in Nuclear Physics and Related Areas (ECT*-FBK), 38123 Trento, Italy
- Dipartimento di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Gianluca Lattanzi
- Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento) I-38050, Italy
- Trento
Institute for Fundamental Physics and Applications (TIFPA), Via Sommarive 14, Povo (Trento) I-38050, Italy
| | - Pietro Faccioli
- Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento) I-38050, Italy
- Trento
Institute for Fundamental Physics and Applications (TIFPA), Via Sommarive 14, Povo (Trento) I-38050, Italy
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24
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Segatta F, Gdor I, Réhault J, Taioli S, Friedman N, Sheves M, Rivalta I, Ruhman S, Cerullo G, Garavelli M. Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two-Dimensional Electronic Spectroscopy. Chemistry 2018; 24:12084-12092. [PMID: 30048017 DOI: 10.1002/chem.201803525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/26/2018] [Indexed: 11/10/2022]
Abstract
By comparing two-dimensional electronic spectroscopy (2DES) and Pump-Probe (PP) measurements on xanthorhodopsin (XR) and reduced-xanthorhodopsin (RXR) complexes, the ultrafast carotenoid-to-retinal energy transfer pathway is revealed, at very early times, by an excess of signal amplitude at the associated cross-peak and by the carotenoid bleaching reduction due to its ground state recovery. The combination of the measured 2DES and PP spectroscopic data with theoretical modelling allows a clear identification of the main experimental signals and a comprehensive interpretation of their origin and dynamics. The remarkable velocity of the energy transfer, despite the non-negligible energy separation between the two chromophores, and the analysis of the underlying transport mechanism, highlight the role played by the ground state carotenoid vibrations in assisting the process.
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Affiliation(s)
- Francesco Segatta
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK), 38123, Trento, Italy.,Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Itay Gdor
- Department of Physical Chemistry, The Hebrew University, Jerusalem, 9190401, Israel
| | - Julien Réhault
- Department für Chemie und Biochemie, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Simone Taioli
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK), 38123, Trento, Italy
| | - Noga Friedman
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ivan Rivalta
- Laboratoire de Chimie UMR 5182, Université Lyon, ENS de Lyon, CNRS, Unversité Lyon 1, Allée d'Italie 46, FR-69342, Lyon, France
| | - Sanford Ruhman
- Department of Physical Chemistry, The Hebrew University, Jerusalem, 9190401, Israel
| | - Giulio Cerullo
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Marco Garavelli
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
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25
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Nenov A, Borrego-Varillas R, Oriana A, Ganzer L, Segatta F, Conti I, Segarra-Marti J, Omachi J, Dapor M, Taioli S, Manzoni C, Mukamel S, Cerullo G, Garavelli M. UV-Light-Induced Vibrational Coherences: The Key to Understand Kasha Rule Violation in trans-Azobenzene. J Phys Chem Lett 2018; 9:1534-1541. [PMID: 29504764 DOI: 10.1021/acs.jpclett.8b00152] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We combine sub-20 fs transient absorption spectroscopy with state-of-the-art computations to study the ultrafast photoinduced dynamics of trans-azobenzene (AB). We are able to resolve the lifetime of the ππ* state, whose decay within ca. 50 fs is correlated to the buildup of the nπ* population and to the emergence of coherences in the dynamics, to date unobserved. Nonlinear spectroscopy simulations call for the CNN in-plane bendings as the active modes in the subps photoinduced coherent dynamics out of the ππ* state. Radiative to kinetic energy transfer into these modes drives the system to a high-energy planar nπ*/ground state conical intersection, inaccessible upon direct excitation of the nπ* state, that triggers an ultrafast (0.45 ps) nonproductive decay of the nπ* state and is thus responsible for the observed Kasha rule violation in UV excited trans-AB. On the other hand, cis-AB is built only after intramolecular vibrational energy redistribution and population of the NN torsional mode.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Rocio Borrego-Varillas
- IFN-CNR, Dipartimento di Fisica , Politecnico di Milano , Piazza Leonardo da Vinci 32 , I-20133 Milano , Italy
| | - Aurelio Oriana
- IFN-CNR, Dipartimento di Fisica , Politecnico di Milano , Piazza Leonardo da Vinci 32 , I-20133 Milano , Italy
| | - Lucia Ganzer
- IFN-CNR, Dipartimento di Fisica , Politecnico di Milano , Piazza Leonardo da Vinci 32 , I-20133 Milano , Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN) , 38123 Trento , Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Javier Segarra-Marti
- Laboratoire de Chimie UMR 5182 , Université Lyon, ENS de Lyon, CNRS, Université Lyon 1 , 46 Allée d'Italie , FR-69342 Lyon , France
| | - Junko Omachi
- Institute for Photon Science and Technology , University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Maurizio Dapor
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN) , 38123 Trento , Italy
| | - Simone Taioli
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN) , 38123 Trento , Italy
- Faculty of Mathematics and Physics , Charles University , Praha 8 , 180 00 Prague , Czech Republic
| | - Cristian Manzoni
- IFN-CNR, Dipartimento di Fisica , Politecnico di Milano , Piazza Leonardo da Vinci 32 , I-20133 Milano , Italy
| | - Shaul Mukamel
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica , Politecnico di Milano , Piazza Leonardo da Vinci 32 , I-20133 Milano , Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
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26
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Affiliation(s)
- Justin Provazza
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Francesco Segatta
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK), 38123 Trento, Italy
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - David F. Coker
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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27
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Segatta F, Cupellini L, Jurinovich S, Mukamel S, Dapor M, Taioli S, Garavelli M, Mennucci B. A Quantum Chemical Interpretation of Two-Dimensional Electronic Spectroscopy of Light-Harvesting Complexes. J Am Chem Soc 2017; 139:7558-7567. [DOI: 10.1021/jacs.7b02130] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Segatta
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), 38123 Trento, Italy
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi
13, 56124 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi
13, 56124 Pisa, Italy
| | - Shaul Mukamel
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Maurizio Dapor
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), 38123 Trento, Italy
| | - Simone Taioli
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), 38123 Trento, Italy
- Faculty
of Mathematics and Physics, Charles University, Prague 116 36, Czech Republic
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi
13, 56124 Pisa, Italy
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