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Curchod BFE, Orr-Ewing AJ. Perspective on Theoretical and Experimental Advances in Atmospheric Photochemistry. J Phys Chem A 2024; 128:6613-6635. [PMID: 39021090 PMCID: PMC11331530 DOI: 10.1021/acs.jpca.4c03481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
Research that explores the chemistry of Earth's atmosphere is central to the current understanding of global challenges such as climate change, stratospheric ozone depletion, and poor air quality in urban areas. This research is a synergistic combination of three established domains: earth observation, for example, using satellites, and in situ field measurements; computer modeling of the atmosphere and its chemistry; and laboratory measurements of the properties and reactivity of gas-phase molecules and aerosol particles. The complexity of the interconnected chemical and photochemical reactions which determine the composition of the atmosphere challenges the capacity of laboratory studies to provide the spectroscopic, photochemical, and kinetic data required for computer models. Here, we consider whether predictions from computational chemistry using modern electronic structure theory and nonadiabatic dynamics simulations are becoming sufficiently accurate to supplement quantitative laboratory data for wavelength-dependent absorption cross-sections, photochemical quantum yields, and reaction rate coefficients. Drawing on presentations and discussions from the CECAM workshop on Theoretical and Experimental Advances in Atmospheric Photochemistry held in March 2024, we describe key concepts in the theory of photochemistry, survey the state-of-the-art in computational photochemistry methods, and compare their capabilities with modern experimental laboratory techniques. From such considerations, we offer a perspective on the scope of computational (photo)chemistry methods based on rigorous electronic structure theory to become a fourth core domain of research in atmospheric chemistry.
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Hui CY, Ma BC, Hu SY, Wu C. Tailored bacteria tackling with environmental mercury: Inspired by natural mercuric detoxification operons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:123016. [PMID: 38008253 DOI: 10.1016/j.envpol.2023.123016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/30/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Mercury (Hg) and its inorganic and organic compounds significantly threaten the ecosystem and human health. However, the natural and anthropogenic Hg environmental inputs exceed 5000 metric tons annually. Hg is usually discharged in elemental or ionic forms, accumulating in surface water and sediments where Hg-methylating microbes-mediated biotransformation occurs. Microbial genetic factors such as the mer operon play a significant role in the complex Hg biogeochemical cycle. Previous reviews summarize the fate of environmental Hg, its biogeochemistry, and the mechanism of bacterial Hg resistance. This review mainly focuses on the mer operon and its components in detecting, absorbing, bioaccumulating, and detoxifying environmental Hg. Four components of the mer operon, including the MerR regulator, divergent mer promoter, and detoxification factors MerA and MerB, are rare bio-parts for assembling synthetic bacteria, which tackle pollutant Hg. Bacteria are designed to integrate synthetic biology, protein engineering, and metabolic engineering. In summary, this review highlights that designed bacteria based on the mer operon can potentially sense and bioremediate pollutant Hg in a green and low-cost manner.
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Affiliation(s)
- Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China.
| | - Bing-Chan Ma
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China
| | - Shun-Yu Hu
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Can Wu
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
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3
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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: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [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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Hewa Edirappulige DT, Kirby IJ, Beckett CK, Dibble TS. Atmospheric Chemistry of HOHg (II)O • Mimics That of a Hydroxyl Radical. J Phys Chem A 2023; 127:8392-8403. [PMID: 37769282 DOI: 10.1021/acs.jpca.3c04159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
HOHg(II)O•, formed from HOHg(I)• + O3, is a key intermediate in the OH-initiated oxidation of Hg(0) in the atmosphere. As no experimental data are available for HOHg(II)O•, we use computational chemistry (CCSD(T)//M06-2X/AVTZ) to characterize its reactions with atmospheric trace gases (NO, NO2, CH4, C2H4, CH2O and CO). In summary, HOHg(II)O•, like the analogous BrHg(II)O• radical, largely mimics the reactivity of •OH in reactions with NOx, alkanes, alkenes, and aldehydes. The rate constant for its reaction with methane (HOHg(II)O• + CH4 → Hg(II)(OH)2 + •CH3) is about four times higher than that of •OH at 298 K. All of these reactions maintain mercury as Hg(II), except for HOHg(II)O• + CO → HOHg(I)• + CO2. Considering only the six reactions studied here, we find that reduction by CO dominates the fate of HOHg(II)O• (79-93%) in many air masses (in the stratosphere and at ground level in rural, marine, and polluted urban regions) with only modest competition from HOHg(II)O• + CH4 (<15%). We expect that this work will help global modeling of atmospheric mercury chemistry.
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Affiliation(s)
- Darshi T Hewa Edirappulige
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York 13210, United States
| | - Ilena J Kirby
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York 13210, United States
| | - Camille K Beckett
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York 13210, United States
| | - Theodore S Dibble
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York 13210, United States
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5
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Prlj A, Hollas D, Curchod BFE. Deciphering the Influence of Ground-State Distributions on the Calculation of Photolysis Observables. J Phys Chem A 2023; 127:7400-7409. [PMID: 37556330 PMCID: PMC10493954 DOI: 10.1021/acs.jpca.3c02333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/17/2023] [Indexed: 08/11/2023]
Abstract
Nonadiabatic molecular dynamics offers a powerful tool for studying the photochemistry of molecular systems. Key to any nonadiabatic molecular dynamics simulation is the definition of its initial conditions (ICs), ideally representing the initial molecular quantum state of the system of interest. In this work, we provide a detailed analysis of how ICs may influence the calculation of experimental observables by focusing on the photochemistry of methylhydroperoxide (MHP), the simplest and most abundant organic peroxide in our atmosphere. We investigate the outcome of trajectory surface hopping simulations for distinct sets of ICs sampled from different approximate quantum distributions, namely harmonic Wigner functions and ab initio molecular dynamics using a quantum thermostat (QT). Calculating photoabsorption cross-sections, quantum yields, and translational kinetic energy maps from the results of these simulations reveals the significant effect of the ICs, in particular when low-frequency (∼ a few hundred cm-1) normal modes are connected to the photophysics of the molecule. Overall, our results indicate that sampling ICs from ab initio molecular dynamics using a QT is preferable for flexible molecules with photoactive low-frequency modes. From a photochemical perspective, our nonadiabatic dynamics simulations offer an explanation for a low-energy tail observed at high excitation energy in the translational kinetic energy map of MHP.
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Affiliation(s)
- Antonio Prlj
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
- Division
of Physical Chemistry, Ruđer Bošković
Institute, Zagreb 10000, Croatia
| | - Daniel Hollas
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Basile F. E. Curchod
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
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6
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Poirier CA, Guidry LM, Ratliff JM, Esposito VJ, Marchetti B, Karsili TNV. Modeling the Ground- and Excited-State Unimolecular Decay of the Simplest Fluorinated Criegee Intermediate, HFCOO, Formed from the Ozonolysis of Hydrofluoroolefin Refrigerants. J Phys Chem A 2023; 127:6377-6384. [PMID: 37523496 DOI: 10.1021/acs.jpca.3c01530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Hydrofluoroolefins (HFO) are fourth-generation refrigerants designed to function as efficient refrigerants with no ozone depletion potential and zero global warming potential. Despite extensive studies on their chemical and physical properties, the ground- and excited-state chemistry of their atmospheric oxidation products is less well understood. This study focuses on the ground- and excited-state chemistry of the simplest fluorinated Criegee intermediate (CI), fluoroformaldehyde oxide (HFCOO), which is the simplest fluorinated CI formed from the ozonolysis of HFOs. HFCOO contains syn- and anti-conformers, which have Boltzmann populations of, respectively, 87 and 13% at 298 K. For both conformers, the calculated ground-state reaction energy profiles associated with cyclization to form fluorodioxirane is lower than the equivalent unimolecular decay path in the simplest CI, H2COO, with anti-HFCOO returning a barrier height more than half of that of H2COO. The excited-state dynamics reveal that photoexcitation to the bright S2 state of syn-HFCOO and anti-HFCOO is expected to undergo a prompt O-O fission─with the former conformer expected to dissociate with an almost unity quantum yield and to form both O (1D) + HFCO (S0) and O (3P) + HFCO (T1) products. In contrast, photoexcitation of anti-HFCOO is expected to undergo an O-O bond fission with a non-unity quantum yield. The fraction of photoexcited anti-HFCOO that dissociates is predicted to exclusively form O (1D) + HFCO (S0) products, which is in sharp contrast to H2COO. The wider implications of our results are discussed from both physical and atmospheric chemistry perspectives.
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Affiliation(s)
- Courtney A Poirier
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
- Regional Application Center, NASA/University of Louisiana at Lafayette, Lafayette, Louisiana 70506, United States
| | - Lily M Guidry
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Jordyn M Ratliff
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Vincent J Esposito
- NASA Postdoctoral Program Fellow, NASA Ames Research Center, Moffett Field, California 94035-1000, United States
| | - Barbara Marchetti
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Tolga N V Karsili
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
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7
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Ali E, Patel N, Patel S, Asaduzzaman A. Quantum Chemical Investigation of Snow-Mercury Interactions and Their Implication of Mercury Deposition in the Arctic. J Phys Chem A 2023; 127:2554-2563. [PMID: 36917741 DOI: 10.1021/acs.jpca.2c08551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Elemental gaseous Hg is emitted into the atmosphere through various anthropogenic and natural processes. Mercury's different species and respective transport ranges, atmospheric physical and chemical transformations, and interaction with the earth's surfaces all contribute to the global cycling of toxic mercury. Under sunlight, halogens, ozone, and nitro species oxidize the emitted elemental Hg to gaseous Hg (II) molecules, which deposit onto the snow and ice surfaces in the Arctic. To investigate the fate of deposited mercury, a quantum chemical investigation was conducted using first-principles density functional theory (DFT) to analyze the interaction between various mercury molecules and snow clusters of differing sizes. Results show that all oxidized mercury molecules: XHgY, BrHgOX, BrHgXO XHgOH, XHgO2H, and XHgNO2, with X, Y = Cl, Br, and I atoms have thermodynamically stable interactions with snow clusters. Further, the adsorption energy of all mercury molecules increases with increasing size of snow clusters. Additionally, the orientations of deposited mercury molecules on the cluster surface also influence the mercury-snow interactions.
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Affiliation(s)
- Emaan Ali
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- School of Science, Engineering and Technology, Pennsylvania State University - Harrisburg, Middletown, Pennsylvania 17057, United States
| | - Nandini Patel
- School of Science, Engineering and Technology, Pennsylvania State University - Harrisburg, Middletown, Pennsylvania 17057, United States
| | - Shrina Patel
- School of Science, Engineering and Technology, Pennsylvania State University - Harrisburg, Middletown, Pennsylvania 17057, United States
| | - Abu Asaduzzaman
- School of Science, Engineering and Technology, Pennsylvania State University - Harrisburg, Middletown, Pennsylvania 17057, United States
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8
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Li T, Mao H, Wang Z, Yu JZ, Li S, Nie X, Herrmann H, Wang Y. Field Evidence for Asian Outflow and Fast Depletion of Total Gaseous Mercury in the Polluted Coastal Atmosphere. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4101-4112. [PMID: 36847858 DOI: 10.1021/acs.est.2c07551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Atmospheric mercury (Hg) cycling in polluted coastal atmosphere is complicated and not fully understood. Here, we present measurements of total gaseous mercury (TGM) monitored at a coastal mountaintop in Hong Kong downwind of mainland China. Sharp TGM peaks during cold front passages were frequently observed due to Asian pollution outflow with typical TGM/CO slopes of 6.8 ± 2.2 pg m-3 ppbv-1. Contrary to the daytime maximums of other air pollutants, TGM exhibited a distinct diurnal variation with a midday minimum. Moreover, we observed four cases of extremely fast TGM depletion after sunrise, during which TGM concentrations rapidly dipped to 0.3-0.6 ng m-3 accompanied by other pollutants on the rise. Simulated meteorological fields revealed that morning upslope flow transporting anthropogenically polluted but TGM-depleted air masses from the mixed layer caused morning TGM depletion at the mountaintop location. The TGM-depleted air masses were hypothesized to result mainly from fast photooxidation of Hg after sunrise with minor contributions from dry deposition (5.0%) and nocturnal oxidation (0.6%). A bromine-induced two-step oxidation mechanism involving abundant pollutants (NO2, O3, etc.) was estimated to play a dominant role, contributing 55%-60% of depleted TGM and requiring 0.20-0.26 pptv Br, an amount potentially available through sea salt aerosol debromination. Our findings suggest significant effects of the interaction between anthropogenic pollution and marine halogen chemistry on atmospheric Hg cycling in the coastal areas.
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Affiliation(s)
- Tao Li
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, Shandong University, Qingdao 266237, China
| | - Huiting Mao
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, United States
| | - Zhe Wang
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Kowloon, Hong Kong 999077, China
| | - Jian Zhen Yu
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Kowloon, Hong Kong 999077, China
| | - Shuwen Li
- Laboratory of Cloud-Precipitation Physics and Severe Storms (LACS), Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China
| | - Xiaoling Nie
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, Shandong University, Qingdao 266237, China
| | - Hartmut Herrmann
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, Shandong University, Qingdao 266237, China
- Atmospheric Chemistry Department (ACD), Leibniz Institute for Tropospheric Research (TROPOS), D-04318 Leipzig, Germany
| | - Yan Wang
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, Shandong University, Qingdao 266237, China
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9
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Hui CY, Hu SY, Li LM, Yun JP, Zhang YF, Yi J, Zhang NX, Guo Y. Metabolic engineering of the carotenoid biosynthetic pathway toward a specific and sensitive inorganic mercury biosensor. RSC Adv 2022; 12:36142-36148. [PMID: 36545109 PMCID: PMC9756418 DOI: 10.1039/d2ra06764a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The toxicity of mercury (Hg) mainly depends on its form. Whole-cell biosensors respond selectively to toxic Hg(ii), efficiently transformed by environmental microbes into methylmercury, a highly toxic form that builds up in aquatic animals. Metabolically engineered Escherichia coli (E. coli) have successfully produced rainbow colorants. By de novo reconstruction of the carotenoid synthetic pathway, the Hg(ii)-responsive production of lycopene and β-carotene enabled programmed E. coli to potentially become an optical biosensor for the qualitative and quantitative detection of ecotoxic Hg(ii). The red color of the lycopene-based biosensor cell pellet was visible upon exposure to 49 nM Hg(ii) and above. The orange β-carotene-based biosensor responded to a simple colorimetric assay as low as 12 nM Hg(ii). A linear response was observed at Hg(ii) concentrations ranging from 12 to 195 nM. Importantly, high specificity and good anti-interference capability suggested that metabolic engineering of the carotenoid biosynthesis was an alternative to developing a visual platform for the rapid analysis of the concentration and toxicity of Hg(ii) in environmentally polluted water.
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Affiliation(s)
- Chang-ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Shun-yu Hu
- Department of Toxicology, School of Public Health, Southern Medical UniversityGuangzhou 510515China
| | - Li-mei Li
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Jian-pei Yun
- Physical & Chemical Testing Laboratory, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Yan-fang Zhang
- Physical & Chemical Testing Laboratory, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Nai-xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Yan Guo
- Department of Toxicology, School of Public Health, Southern Medical UniversityGuangzhou 510515China,National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
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10
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Castro PJ, Kellö V, Cernušák I, Dibble TS. Together, Not Separately, OH and O 3 Oxidize Hg (0) to Hg (II) in the Atmosphere. J Phys Chem A 2022; 126:8266-8279. [DOI: 10.1021/acs.jpca.2c04364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pedro J. Castro
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York13210, United States
| | - Vladimir Kellö
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 84215Bratislava, Slovakia
| | - Ivan Cernušák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 84215Bratislava, Slovakia
| | - Theodore S. Dibble
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York13210, United States
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11
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Sun G, Feng X, Yin R, Wang F, Lin CJ, Li K, Sommar JO. Dissociation of Mercuric Oxides Drives Anomalous Isotope Fractionation during Net Photo-oxidation of Mercury Vapor in Air. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13428-13438. [PMID: 35960609 DOI: 10.1021/acs.est.2c02722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The atmosphere is the primary medium for long-distance transport and transformation of elemental mercury (Hg), a potent neurotoxin. The recent discovery of mass-independent fractionation (MIF) of even-mass Hg isotopes (even-MIF, measured as Δ200Hg and Δ204Hg) in the atmosphere is surprising and can potentially serve as a powerful tracer in understanding Hg biogeochemistry. Far-ultraviolet (UVC) light-induced gas-phase reactions have been suspected as a likely cause for even-MIF, yet the mechanism remains unknown. Here, we present the first experimental evidence of large-scale even-MIF caused by UVC-induced (wavelength: 254 nm) Hg oxidation in synthetic air at the pressure (46-88 kPa) and temperature (233-298 K) resembling those of the lower atmosphere. We observe negatively correlated Δ200Hg and Δ204Hg signatures with values as low as -50‰ and as high as 550‰, respectively, in the remaining atomic Hg pool. The magnitude of even-MIF signatures decreases with decreasing pressure with the Δ200Hg/Δ204Hg ratio being similar to that observed in global precipitation. This even-MIF can be explained by photodissociation of mercuric oxides that are photochemically formed in the UVC-irradiated Hg-O2 system. We propose that similar processes occurring in the atmosphere, where mercuric oxide species serve as intermediates, are responsible for the observed even-MIF in the environment.
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Affiliation(s)
- Guangyi Sun
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
- Center for Excellence in Quaternary Science and Global Change, Chinese Academy of Sciences, Xian 710061, China
| | - Runsheng Yin
- State Key Laboratory of Ore Deposit Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Feiyue Wang
- Centre for Earth Observation Science, and Department of Environment and Geography, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Che-Jen Lin
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
- Center for Advances in Water and Air Quality, Lamar University, Beaumont, Texas 777100, United States
| | - Kai Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
- University of Chinese Academy of Sciences, Beijing 100045, China
| | - Jonas Olof Sommar
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
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12
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Francés-Monerris A, Carmona-García J, Trabelsi T, Saiz-Lopez A, Lyons JR, Francisco JS, Roca-Sanjuán D. Photochemical and thermochemical pathways to S 2 and polysulfur formation in the atmosphere of Venus. Nat Commun 2022; 13:4425. [PMID: 35907911 PMCID: PMC9338966 DOI: 10.1038/s41467-022-32170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Polysulfur species have been proposed to be the unknown near-UV absorber in the atmosphere of Venus. Recent work argues that photolysis of one of the (SO)2 isomers, cis-OSSO, directly yields S2 with a branching ratio of about 10%. If correct, this pathway dominates polysulfur formation by several orders of magnitude, and by addition reactions yields significant quantities of S3, S4, and S8. We report here the results of high-level ab-initio quantum-chemistry computations that demonstrate that S2 is not a product in cis-OSSO photolysis. Instead, we establish a novel mechanism in which S2 is formed in a two-step process. Firstly, the intermediate S2O is produced by the coupling between the S and Cl atmospheric chemistries (in particular, SO reaction with ClS) and in a lesser extension by O-abstraction reactions from cis-OSSO. Secondly, S2O reacts with SO. This modified chemistry yields S2 and subsequent polysulfur abundances comparable to the photolytic cis-OSSO mechanism through a more plausible pathway. Ab initio quantification of the photodissociations at play fills a critical data void in current atmospheric models of Venus. Polysulfur compounds have been ascribed as the unknown near-UV absorbers in Venusian atmosphere and play a key role in the sulfur chemical cycle of this planet. Here, authors establish their production from (SO)2 on the grounds of quantifications of photochemical and thermal pathways involved in the sulfur chemical cycle of the planet.
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Affiliation(s)
| | - Javier Carmona-García
- Institut de Ciència Molecular, Universitat de València, 46071, València, Spain.,Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, 28006, Madrid, Spain
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, 28006, Madrid, Spain
| | | | - Joseph S Francisco
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, 46071, València, Spain.
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13
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Marsili E, Prlj A, Curchod BFE. A Theoretical Perspective on the Actinic Photochemistry of 2-Hydroperoxypropanal. J Phys Chem A 2022; 126:5420-5433. [PMID: 35900368 PMCID: PMC9393889 DOI: 10.1021/acs.jpca.2c03783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The photochemical reactions triggered by the sunlight
absorption
of transient volatile organic compounds in the troposphere are notoriously
difficult to characterize experimentally due to the unstable and short-lived
nature of these organic molecules. Some members of this family of
compounds are likely to exhibit a rich photochemistry given the diversity
of functional groups they can bear. Even more interesting is the photochemical
fate of volatile organic compounds bearing more than one functional
group that can absorb light—this is the case, for example,
of α-hydroperoxycarbonyls, which are formed during the oxidation
of isoprene. Experimental observables characterizing the photochemistry
of these molecules like photoabsorption cross-sections or photolysis
quantum yields are currently missing, and we propose here to leverage
a recently developed computational protocol to predict in silico the
photochemical fate of 2-hydroperoxypropanal (2-HPP) in the actinic
region. We combine different levels of electronic structure methods—SCS-ADC(2)
and XMS-CASPT2—with the nuclear ensemble approach and trajectory
surface hopping to understand the mechanistic details of the possible
nonradiative processes of 2-HPP. In particular, we predict the photoabsorption
cross-section and the wavelength-dependent quantum yields for the
observed photolytic pathways and combine them to determine in silico
photolysis rate constants. The limitations of our protocol and possible
future improvements are discussed.
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Affiliation(s)
- Emanuele Marsili
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Antonio Prlj
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
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14
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Abdelgawwad AMA, Monari A, Tuñón I, Francés-Monerris A. Spatial and Temporal Resolution of the Oxygen-Independent Photoinduced DNA Interstrand Cross-Linking by a Nitroimidazole Derivative. J Chem Inf Model 2022; 62:3239-3252. [PMID: 35771238 PMCID: PMC9277591 DOI: 10.1021/acs.jcim.2c00460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA damage is ubiquitous in nature and is at the basis of emergent treatments such as photodynamic therapy, which is based on the activation of highly oxidative reactive oxygen species by photosensitizing O2. However, hypoxia observed in solid tumors imposes the necessity to devise oxygen-independent modes of action able to induce DNA damage under a low oxygen concentration. The complexity of these DNA damage mechanisms in realistic environments grows exponentially when taking into account light absorption and subsequent excited-state population, photochemical and (photo)-redox reactions, the multiple species involved in different electronic states, noncovalent interactions, multiple reaction steps, and the large number of DNA reactive sites. This work tackles all the intricate reactivity of a photosensitizer based on a nitroimidazole derivative reacting toward DNA in solution under UV light exposition. This is performed through a combination of ground- and excited-state quantum chemistry, classical molecular dynamics, and hybrid QM/MM simulations to rationalize in detail the formation of DNA interstrand cross-links (ICLs) exerted by the noncanonical noncovalent photosensitizer. Unprecedented spatial and temporal resolution of these phenomena is achieved, revealing that the ICL is sequence-specific and that the fastest reactions take place at AT, GC, and GT steps involving either the opposite nucleobases or adjacent Watson-Crick base pairs. The N7 and O6 positions of guanine, the N7 and N3 sites of adenine, the N4 position of cytosine, and the O2 atom of thymine are deemed as the most nucleophile sites and are positively identified to participate in the ICL productions. This work provides a multiscale computational protocol to study DNA reactivity with noncovalent photosensitizers, and contributes to the understanding of therapies based on photoinduced DNA damage at molecular and electronic levels. In addition, we believe the depth understanding of these processes should assist the design of new photosensitizers considering their molecular size, electronic properties, and the observed regioselectivity toward nucleic acids.
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Affiliation(s)
| | - Antonio Monari
- Université Paris Cité, CNRS, ITODYS, F-75006 Paris, France.,Université de Lorraine and CNRS, UMR 7019 LPCT, F-5400 Nancy, France
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
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15
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Saiz‐Lopez A, Acuña AU, Mahajan AS, Dávalos JZ, Feng W, Roca‐Sanjuán D, Carmona‐García J, Cuevas CA, Kinnison DE, Gómez Martín JC, Francisco JS, Plane JMC. The Chemistry of Mercury in the Stratosphere. GEOPHYSICAL RESEARCH LETTERS 2022; 49:e2022GL097953. [PMID: 35860422 PMCID: PMC9285414 DOI: 10.1029/2022gl097953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Mercury, a global contaminant, enters the stratosphere through convective uplift, but its chemical cycling in the stratosphere is unknown. We report the first model of stratospheric mercury chemistry based on a novel photosensitized oxidation mechanism. We find two very distinct Hg chemical regimes in the stratosphere: in the upper stratosphere, above the ozone maximum concentration, Hg0 oxidation is initiated by photosensitized reactions, followed by second-step chlorine chemistry. In the lower stratosphere, ground-state Hg0 is oxidized by thermal reactions at much slower rates. This dichotomy arises due to the coincidence of the mercury absorption at 253.7 nm with the ozone Hartley band maximum at 254 nm. We also find that stratospheric Hg oxidation, controlled by chlorine and hydroxyl radicals, is much faster than previously assumed, but moderated by efficient photo-reduction of mercury compounds. Mercury lifetime shows a steep increase from hours in the upper-middle stratosphere to years in the lower stratosphere.
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Affiliation(s)
- Alfonso Saiz‐Lopez
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSICMadridSpain
| | - A. Ulises Acuña
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSICMadridSpain
| | - Anoop S. Mahajan
- Centre for Climate Change ResearchIndian Institute of Tropical MeteorologyMinistry of Earth SciencesPuneIndia
| | - Juan Z. Dávalos
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSICMadridSpain
| | - Wuhu Feng
- School of ChemistryUniversity of LeedsLeedsUK
- NCASSchool of Earth and EnvironmentUniversity of LeedsLeedsUK
| | | | - Javier Carmona‐García
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSICMadridSpain
- Institut de Ciència MolecularUniversitat de ValènciaValènciaSpain
| | - Carlos A. Cuevas
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSICMadridSpain
| | | | | | - Joseph S. Francisco
- Department of Earth and Environmental Science and Department of ChemistryUniversity of PennsylvaniaPhiladelphiaPAUSA
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16
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Wu R, Castro PJ, Gaito C, Beiter K, Dibble TS, Wang C. Combined Experimental and Computational Kinetics Studies for the Atmospherically Important BrHg Radical Reacting with NO and O 2. J Phys Chem A 2022; 126:3914-3925. [PMID: 35686857 DOI: 10.1021/acs.jpca.2c02531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report on the first experimental determination of the absolute rate constant of the reaction of BrHg + NO in N2 bath gas using a laser photolysis-laser-induced fluorescence (LP-LIF) system. The rate constant of the reaction of BrHg + NO is determined to be 7.0-0.9+1.3 × 10-12 cm3 molecule-1 s-1 over 50-700 Torr and 315-353 K. The absence of a pressure or temperature dependence suggests that this reaction leads mainly to mercury reduction (Hg + BrNO) rather than mercury oxidation (BrHgNO). Our theoretical calculations using NEVPT2 energies on density functional theory (DFT) geometries are consistent with a barrierless reaction to form Hg + BrNO. The equilibrium constants and the rate constants of the reaction BrHg + O2 ⇌ BrHgOO are computed theoretically because they are too low to be measured in the LP-LIF system. Molecular oxygen quenches the LIF signal of BrHg with a large rate constant of (1.7 ± 0.1) × 10-10 cm3 molecule-1 s-1. Thus, different techniques that capture the absolute [BrHg(X̃)] would be advantageous for kinetics studies of BrHg reactions in the presence of O2. The computed equilibrium constant suggests a non-negligible upper limit of the fraction of BrHg stored as BrHgOO (up to 0.5) at low-temperature conditions, e.g., in the upper troposphere and in polar winters at ground level. Preliminary results indicate that BrHgOO behaves like HOO or organic peroxy radicals in reactions with atmospheric radicals.
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Affiliation(s)
- Rongrong Wu
- Department of Physics and Astronomy, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Pedro J Castro
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210, United States
| | - Cameron Gaito
- Department of Physics and Astronomy, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Kyle Beiter
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210, United States
| | - Theodore S Dibble
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210, United States
| | - Chuji Wang
- Department of Physics and Astronomy, Mississippi State University, Mississippi State, Mississippi 39762, United States
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17
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Cerdán L, Roca-Sanjuán D. Reconstruction of Nuclear Ensemble Approach Electronic Spectra Using Probabilistic Machine Learning. J Chem Theory Comput 2022; 18:3052-3064. [PMID: 35481363 PMCID: PMC9097286 DOI: 10.1021/acs.jctc.2c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Indexed: 11/29/2022]
Abstract
The theoretical prediction of molecular electronic spectra by means of quantum mechanical (QM) computations is fundamental to gain a deep insight into many photophysical and photochemical processes. A computational strategy that is attracting significant attention is the so-called Nuclear Ensemble Approach (NEA), that relies on generating a representative ensemble of nuclear geometries around the equilibrium structure and computing the vertical excitation energies (ΔE) and oscillator strengths (f) and phenomenologically broadening each transition with a line-shaped function with empirical full-width δ. Frequently, the choice of δ is carried out by visually finding the trade-off between artificial vibronic features (small δ) and over-smoothing of electronic signatures (large δ). Nevertheless, this approach is not satisfactory, as it relies on a subjective perception and may lead to spectral inaccuracies overall when the number of sampled configurations is limited due to an excessive computational burden (high-level QM methods, complex systems, solvent effects, etc.). In this work, we have developed and tested a new approach to reconstruct NEA spectra, dubbed GMM-NEA, based on the use of Gaussian Mixture Models (GMMs), a probabilistic machine learning algorithm, that circumvents the phenomenological broadening assumption and, in turn, the use of δ altogether. We show that GMM-NEA systematically outperforms other data-driven models to automatically select δ overall for small datasets. In addition, we report the use of an algorithm to detect anomalous QM computations (outliers) that can affect the overall shape and uncertainty of the NEA spectra. Finally, we apply GMM-NEA to predict the photolysis rate for HgBrOOH, a compound involved in Earth's atmospheric chemistry.
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Affiliation(s)
- Luis Cerdán
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain
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18
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Cossa D, Knoery J, Bănaru D, Harmelin-Vivien M, Sonke JE, Hedgecock IM, Bravo AG, Rosati G, Canu D, Horvat M, Sprovieri F, Pirrone N, Heimbürger-Boavida LE. Mediterranean Mercury Assessment 2022: An Updated Budget, Health Consequences, and Research Perspectives. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3840-3862. [PMID: 35244390 DOI: 10.1021/acs.est.1c03044] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mercury (Hg) and especially its methylated species (MeHg) are toxic chemicals that contaminate humans via the consumption of seafood. The most recent UNEP Global Mercury Assessment stressed that Mediterranean populations have higher Hg levels than people elsewhere in Europe. The present Critical Review updates current knowledge on the sources, biogeochemical cycling, and mass balance of Hg in the Mediterranean and identifies perspectives for future research especially in the context of global change. Concentrations of Hg in the Western Mediterranean average 0.86 ± 0.27 pmol L-1 in the upper water layer and 1.02 ± 0.12 pmol L-1 in intermediate and deep waters. In the Eastern Mediterranean, Hg measurements are in the same range but are too few to determine any consistent oceanographical pattern. The Mediterranean waters have a high methylation capacity, with MeHg representing up to 86% of the total Hg, and constitute a source of MeHg for the adjacent North Atlantic Ocean. The highest MeHg concentrations are associated with low oxygen water masses, suggesting a microbiological control on Hg methylation, consistent with the identification of hgcA-like genes in Mediterranean waters. MeHg concentrations are twice as high in the waters of the Western Basin compared to the ultra-oligotrophic Eastern Basin waters. This difference appears to be transferred through the food webs and the Hg content in predators to be ultimately controlled by MeHg concentrations of the waters of their foraging zones. Many Mediterranean top-predatory fish still exceed European Union regulatory Hg thresholds. This emphasizes the necessity of monitoring the exposure of Mediterranean populations, to formulate adequate mitigation strategies and recommendations, without advising against seafood consumption. This review also points out other insufficiencies of knowledge of Hg cycling in the Mediterranean Sea, including temporal variations in air-sea exchange, hydrothermal and cold seep inputs, point sources, submarine groundwater discharge, and exchanges between margins and the open sea. Future assessment of global change impacts under the Minamata Convention Hg policy requires long-term observations and dedicated high-resolution Earth System Models for the Mediterranean region.
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Affiliation(s)
- Daniel Cossa
- Université Grenoble Alpes, ISTerre, CS 40700, 38058 Grenoble Cedex 9, France
| | - Joël Knoery
- Ifremer, Centre Atlantique de Nantes, BP 44311, 44980 Nantes, France
| | - Daniela Bănaru
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288 Marseille, France
| | - Mireille Harmelin-Vivien
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288 Marseille, France
| | - Jeroen E Sonke
- Géosciences Environnement Toulouse, CNRS/Observatoire Midi-Pyrénées (OMP)/Université de Toulouse, 31400 Toulouse, France
| | - Ian M Hedgecock
- Istituto sull'inquinamento atmosferico, CNR-IIA, 87036 Rende, Italy
| | | | - Ginevra Rosati
- Istituto Nazionale di Oceanografia e di Geofisca Sperimentale (OGS), 34010 Trieste, Italy
| | - Donata Canu
- Istituto Nazionale di Oceanografia e di Geofisca Sperimentale (OGS), 34010 Trieste, Italy
| | | | | | - Nicola Pirrone
- Istituto sull'inquinamento atmosferico, CNR-IIA, 87036 Rende, Italy
| | - Lars-Eric Heimbürger-Boavida
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288 Marseille, France
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19
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Simulating Electronic Absorption Spectra of Atmospherically Relevant Molecules: A Systematic Assignment for Enhancing Undergraduate STEM Education. EDUCATION SCIENCES 2022. [DOI: 10.3390/educsci12040252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Computational and atmospheric chemistry are two important branches of contemporary chemistry. With the present topical nature of climate change and global warming, it is more crucial than ever that students are aware of and exposed to atmospheric chemistry, with an emphasis on how modeling may aid in understanding how atmospherically relevant chemical compounds interact with incoming solar radiation. Nonetheless, computational and atmospheric chemistry are under-represented in most undergraduate chemistry curricula. In this manuscript, we describe a simple and efficient method for simulating the electronic absorption spectral profiles of atmospherically relevant molecules that may be utilized in an undergraduate computer laboratory. The laboratory results give students hands-on experience in computational and atmospheric chemistry, as well as electronic absorption spectroscopy.
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20
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McCoy JC, Léger SJ, Frey CF, Vansco MF, Marchetti B, Karsili TNV. Modeling the Conformer-Dependent Electronic Absorption Spectra and Photolysis Rates of Methyl Vinyl Ketone Oxide and Methacrolein Oxide. J Phys Chem A 2022; 126:485-496. [PMID: 35049299 DOI: 10.1021/acs.jpca.1c08381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Criegee intermediates are important atmospheric oxidants, formed via the reaction of ozone with volatile alkenes emitted into the troposphere. Small Criegee intermediates (e.g., CH2OO and CH3CHOO) are highly reactive, and their removal via unimolecular decay or bimolecular chemistry dominates their atmospheric lifetimes. As the molecular complexity of Criegee intermediates increases, their electronic absorption spectra show a bathochromic shift within the solar spectrum relevant to the troposphere. In these cases, solar photolysis may become a competitive contributor to their atmospheric removal. In this article, we report the conformer-dependent simulated electronic absorption spectra of two four-carbon-centered Criegee intermediates, methyl vinyl ketone oxide (MVK-oxide) and methacrolein oxide (MACR-oxide). Both MVK-oxide and MACR-oxide contain four low-energy conformers, which are convoluted in the experimentally measured spectra. Here, we deconvolute each conformer and estimate contributions from each of the four conformers to the experimentally measured spectra. We also estimate the photolysis rates and predict that solar photolysis should be a more competitive removal process for MVK-oxide and MACR-oxide (cf. CH2OO and CH3CHOO).
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Affiliation(s)
- Julia C McCoy
- Department of Chemistry, University of Louisiana at Lafayette, Louisiana, Louisiana 70503, United States
| | - Spencer J Léger
- Department of Chemistry, University of Louisiana at Lafayette, Louisiana, Louisiana 70503, United States
| | - Conrad F Frey
- Department of Chemistry, University of Louisiana at Lafayette, Louisiana, Louisiana 70503, United States
| | - Michael F Vansco
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Barbara Marchetti
- Department of Chemistry, University of Louisiana at Lafayette, Louisiana, Louisiana 70503, United States
| | - Tolga N V Karsili
- Department of Chemistry, University of Louisiana at Lafayette, Louisiana, Louisiana 70503, United States
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21
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Prlj A, Marsili E, Hutton L, Hollas D, Shchepanovska D, Glowacki DR, Slavíček P, Curchod BFE. Calculating Photoabsorption Cross-Sections for Atmospheric Volatile Organic Compounds. ACS EARTH & SPACE CHEMISTRY 2022; 6:207-217. [PMID: 35087992 PMCID: PMC8785186 DOI: 10.1021/acsearthspacechem.1c00355] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 05/30/2023]
Abstract
Characterizing the photochemical reactivity of transient volatile organic compounds (VOCs) in our atmosphere begins with a proper understanding of their abilities to absorb sunlight. Unfortunately, the photoabsorption cross-sections for a large number of transient VOCs remain unavailable experimentally due to their short lifetime or high reactivity. While structure-activity relationships (SARs) have been successfully employed to estimate the unknown photoabsorption cross-sections of VOCs, computational photochemistry offers another promising strategy to predict not only the vertical electronic transitions of a given molecule but also the width and shape of the bands forming its absorption spectrum. In this work, we focus on the use of the nuclear ensemble approach (NEA) to determine the photoabsorption cross-section of four exemplary VOCs, namely, acrolein, methylhydroperoxide, 2-hydroperoxy-propanal, and (microsolvated) pyruvic acid. More specifically, we analyze the influence that different strategies for sampling the ground-state nuclear density-Wigner sampling and ab initio molecular dynamics with a quantum thermostat-can have on the simulated absorption spectra. We highlight the potential shortcomings of using uncoupled harmonic modes within Wigner sampling of nuclear density to describe flexible or microsolvated VOCs and some limitations of SARs for multichromophoric VOCs. Our results suggest that the NEA could constitute a powerful tool for the atmospheric community to predict the photoabsorption cross-section for transient VOCs.
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Affiliation(s)
- Antonio Prlj
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Emanuele Marsili
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Lewis Hutton
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Daniel Hollas
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, Prague 16628, Czech Republic
| | - Darya Shchepanovska
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.
| | - David R. Glowacki
- ArtSci
International Foundation, 5th Floor Mariner House, Bristol BS1 4QD, U.K.
- CiTIUS
Intelligent Technologies Research Centre, Rúa de Jenaro de La Fuente, s/n, Santiago de Compostela 15705, A Coruña, Spain
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, Prague 16628, Czech Republic
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22
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Abdelgawwad AMA, Xavier JAM, Roca-Sanjuán D, Viñas C, Teixidor F, Francés-Monerris A. Light-Induced On/Off Switching of the Surfactant Character of the o-Cobaltabis(dicarbollide) Anion with No Covalent Bond Alteration. Angew Chem Int Ed Engl 2021; 60:25753-25757. [PMID: 34562322 PMCID: PMC9297989 DOI: 10.1002/anie.202111493] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Indexed: 12/22/2022]
Abstract
Cobaltabis(dicarbollide) anion ([o‐COSAN]−) is a well‐known metallacarborane with multiple applications in a variety of fields. In aqueous solution, the cisoid rotamer is the most stable disposition in the ground state. The present work provides theoretical evidence on the possibility to photoinduce the rotation from the cisoid to the transoid rotamer, a conversion that can be reverted when the ground state is repopulated. The non‐radiative decay mechanisms proposed in this work are coherent with the lack of fluorescence observed in 3D fluorescence mapping experiments performed on [o‐COSAN]− and its derivatives. This phenomenon induced by light has the potential to destruct the vesicles and micelles cisoid [o‐COSAN]− typically forms in aqueous solution, which could lead to promising applications, particularly in the field of nanomedicine.
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Affiliation(s)
| | - Jewel Ann Maria Xavier
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus UAB, 08193, Bellaterra, Spain
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, 46071, València, Spain
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus UAB, 08193, Bellaterra, Spain
| | - Francesc Teixidor
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus UAB, 08193, Bellaterra, Spain
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23
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Abdelgawwad AMA, Xavier JAM, Roca‐Sanjuán D, Viñas C, Teixidor F, Francés‐Monerris A. Light‐Induced On/Off Switching of the Surfactant Character of the
o
‐Cobaltabis(dicarbollide) Anion with No Covalent Bond Alteration. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Jewel Ann Maria Xavier
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC Campus UAB 08193 Bellaterra Spain
| | | | - Clara Viñas
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC Campus UAB 08193 Bellaterra Spain
| | - Francesc Teixidor
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC Campus UAB 08193 Bellaterra Spain
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24
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Carmona-García J, Trabelsi T, Francés-Monerris A, Cuevas CA, Saiz-Lopez A, Roca-Sanjuán D, Francisco JS. Photochemistry of HOSO 2 and SO 3 and Implications for the Production of Sulfuric Acid. J Am Chem Soc 2021; 143:18794-18802. [PMID: 34726419 DOI: 10.1021/jacs.1c10153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sulfur trioxide (SO3) and the hydroxysulfonyl radical (HOSO2) are two key intermediates in the production of sulfuric acid (H2SO4) on Earth's atmosphere, one of the major components of acid rain. Here, the photochemical properties of these species are determined by means of high-level quantum chemical methodologies, and the potential impact of their light-induced reactivity is assessed within the context of the conventional acid rain generation mechanism. Results reveal that the photodissociation of HOSO2 occurs primarily in the stratosphere through the ejection of hydroxyl radicals (•OH) and sulfur dioxide (SO2). This may decrease the production rate of H2SO4 in atmospheric regions with low O2 concentration. In contrast, the photostability of SO3 under stratospheric conditions suggests that its removal efficiency, still poorly understood, is key to assess the H2SO4 formation in the upper atmosphere.
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Affiliation(s)
- Javier Carmona-García
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain.,Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Carlos A Cuevas
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain
| | - Joseph S Francisco
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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25
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Shah V, Jacob DJ, Thackray CP, Wang X, Sunderland EM, Dibble TS, Saiz-Lopez A, Černušák I, Kellö V, Castro PJ, Wu R, Wang C. Improved Mechanistic Model of the Atmospheric Redox Chemistry of Mercury. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14445-14456. [PMID: 34724789 DOI: 10.1021/acs.est.1c03160] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We present a new chemical mechanism for Hg0/HgI/HgII atmospheric cycling, including recent laboratory and computational data, and implement it in the GEOS-Chem global atmospheric chemistry model for comparison to observations. Our mechanism includes the oxidation of Hg0 by Br and OH, subsequent oxidation of HgI by ozone and radicals, respeciation of HgII in aerosols and cloud droplets, and speciated HgII photolysis in the gas and aqueous phases. The tropospheric Hg lifetime against deposition in the model is 5.5 months, consistent with observational constraints. The model reproduces the observed global surface Hg0 concentrations and HgII wet deposition fluxes. Br and OH make comparable contributions to global net oxidation of Hg0 to HgII. Ozone is the principal HgI oxidant, enabling the efficient oxidation of Hg0 to HgII by OH. BrHgIIOH and HgII(OH)2, the initial HgII products of Hg0 oxidation, respeciate in aerosols and clouds to organic and inorganic complexes, and volatilize to photostable forms. Reduction of HgII to Hg0 takes place largely through photolysis of aqueous HgII-organic complexes. 71% of model HgII deposition is to the oceans. Major uncertainties for atmospheric Hg chemistry modeling include Br concentrations, stability and reactions of HgI, and speciation and photoreduction of HgII in aerosols and clouds.
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Affiliation(s)
- Viral Shah
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Daniel J Jacob
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Colin P Thackray
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Xuan Wang
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Elsie M Sunderland
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts 02115, United States
| | - Theodore S Dibble
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, New York 13210, United States
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Ivan Černušák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Vladimir Kellö
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Pedro J Castro
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, New York 13210, United States
| | - Rongrong Wu
- Department of Physics and Astronomy, Mississippi State University, Starkville, Mississippi 39759, United States
| | - Chuji Wang
- Department of Physics and Astronomy, Mississippi State University, Starkville, Mississippi 39759, United States
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26
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Carmona-García J, Francés-Monerris A, Cuevas CA, Trabelsi T, Saiz-Lopez A, Francisco JS, Roca-Sanjuán D. Photochemistry and Non-adiabatic Photodynamics of the HOSO Radical. J Am Chem Soc 2021; 143:10836-10841. [PMID: 34270223 DOI: 10.1021/jacs.1c05149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydroxysulfinyl radical (HOSO) is important due to its involvement in climate geoengineering upon SO2 injection and generation of the highly hygroscopic H2SO4. Its photochemical behavior in the upper atmosphere is, however, uncertain. Here we present the ultraviolet-visible photochemistry and photodynamics of this species by simulating the atmospheric conditions with high-level quantum chemistry methods. Photocleavage to HO + SO arises as the major solar-induced channel, with a minor contribution of H + SO2 photoproducts. The efficient generation of SO is relevant due to its reactivity with O3 and the consequent depletion of ozone in the stratosphere.
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Affiliation(s)
- Javier Carmona-García
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain.,Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Antonio Francés-Monerris
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain.,Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Carlos A Cuevas
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Joseph S Francisco
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain
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27
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Taamalli S, Pitoňák M, Dibble TS, Černušák I, Louis F. Theoretical Study of the Monohydration of Mercury Compounds of Atmospheric Interest. J Phys Chem A 2021; 125:5819-5828. [PMID: 34180661 DOI: 10.1021/acs.jpca.1c02772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structures, vibrational frequencies, and model IR spectra of the monohydrates of oxygenated mercury compounds (BrHgO, BrHgOH, BrHgOOH, BrHgNO2, BrHgONO, and HgOH) have been theoretically studied using the ωB97X-D/aug-cc-pVTZ level of theory. The ground state potential energy surface exhibits several stable structures of these monohydrates. The thermodynamic properties of the hydration reactions have been calculated at different levels of theory including DFT and coupled-cluster calculations DK-CCSD(T) with the ANO-RCC-Large basis sets. Standard enthalpies and Gibbs free energies of hydration were computed. The temperature dependence of ΔrG°(T) was evaluated for the most stable complexes over the temperature range 200-400 K. Thermodynamic data revealed that the highest fraction hydrated at 298 K and 100% relative humidity will be BrHgNO2-H2O at ∼5%.
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Affiliation(s)
- Sonia Taamalli
- CNRS, UMR 8522 - PC2A - PhysicoChimie des Processus de Combustion et de l'Atmosphère, Université Lille, 59000 Lille, France
| | - Michal Pitoňák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia.,Computing Center, Centre of Operations of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 35 Bratislava, Slovakia
| | - Theodore S Dibble
- Department of Chemistry, State University of New York-College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York 13210, United States
| | - Ivan Černušák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Florent Louis
- CNRS, UMR 8522 - PC2A - PhysicoChimie des Processus de Combustion et de l'Atmosphère, Université Lille, 59000 Lille, France
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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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29
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McCoy JC, Marchetti B, Thodika M, Karsili TNV. A Simple and Efficient Method for Simulating the Electronic Absorption Spectra of Criegee Intermediates: Benchmarking on CH 2OO and CH 3CHOO. J Phys Chem A 2021; 125:4089-4097. [PMID: 33970629 DOI: 10.1021/acs.jpca.1c01074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Criegee intermediates (CIs) play a vital role in the atmosphere-known most prominently for enhancing the oxidizing capacity of the troposphere. Knowledge of their electronic absorption spectra is of vital importance for two reasons: (1) to aid experimentalists in detecting CIs and (2) in deciding if their removal is affected by solar photolysis. In this article we report a simple and efficient method based on the nuclear ensemble method that may be effectively used to compute the electronic absorption spectra of Criegee intermediates without the need for extensive computation of preparing the initial configurations of the starting geometry. We use this method to benchmark several excited-state electronic structure methods and their efficacy in reproducing the electronic absorption spectra of two well-known cases of CI: CH2OO and CH3CHOO. The success and computational feasibility of the methodology are crucial for its applicability to CIs of increasing molecular complexity, which have no known experimentally measured electronic absorption spectra, allowing a guide for experimentalists. Application of the methodology to more complex CIs (e.g., those with extended conjugation or those derived from endocyclic alkenes) will also reveal if solar photolysis becomes a competitive removal process when compared to unimolecular decay or bimolecular chemistry.
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Affiliation(s)
- Julia C McCoy
- University of Louisiana at Lafayette, Lafayette, Louisiana 70503, United States
| | - Barbara Marchetti
- University of Louisiana at Lafayette, Lafayette, Louisiana 70503, United States
| | - Mushir Thodika
- Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Tolga N V Karsili
- University of Louisiana at Lafayette, Lafayette, Louisiana 70503, United States
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30
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Mao N, Antley J, Cooper M, Shah N, Kadam A, Khalizov A. Heterogeneous Chemistry of Mercuric Chloride on Inorganic Salt Surfaces. J Phys Chem A 2021; 125:3943-3952. [PMID: 33914544 DOI: 10.1021/acs.jpca.1c02220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gaseous oxidized mercury (GOM) is a major chemical form responsible for deposition of atmospheric mercury, but its interaction with environmental surfaces is not well understood. To address this knowledge gap, we investigated the uptake of gaseous HgCl2, used as a GOM surrogate, by several inorganic salts representative of marine and urban aerosols. The process was studied in a fast flow reactor coupled to an ion drift-chemical ionization mass spectrometer, where gaseous HgCl2 was quantitatively detected as HgCl2·NO3-. Uptake curves showed a common behavior, where upon exposure of the salt surface to HgCl2, the gas-phase concentration of the latter dropped rapidly and then recovered gradually. None of the salts produced a full recovery of HgCl2, indicating the presence of an irreversible chemical reaction in addition to reversible adsorption, and all salts showed reactive behavior consistent with the presence of surface sites of a high and a low reactivity. On the basis of the decrease in the uptake coefficient with increasing concentration of gaseous HgCl2, we conclude that the interaction follows the Langmuir-Hinshelwood mechanism. The reactivity of a deactivated salt surface after uptake could be partially restored by cycling through an elevated relative humidity at atmospheric pressure. The overall surface reactivity decreased in the series Na2SO4 > NaCl > (NH4)2SO4 > NH4NO3. The uptake on NH4NO3 was nearly fully reversible, with low values of the initial (0.4 × 10-2) and steady-state (3.3 × 10-4) uptake coefficients, whereas Na2SO4 was significantly more reactive (3.1 × 10-2 and 1.7 × 10-3). Depending on the aerosol loading, the lifetimes of gaseous HgCl2 on dry urban and marine particles (as pure (NH4)2SO4 and NaCl, respectively) were estimated to range from half an hour to about a day.
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Affiliation(s)
- Na Mao
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - John Antley
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Matthew Cooper
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States.,Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Neil Shah
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Anuradha Kadam
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States.,New Jersey School of Architecture, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Alexei Khalizov
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States.,Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
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31
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Shchepanovska D, Shannon RJ, Curchod BFE, Glowacki DR. Nonadiabatic Kinetics in the Intermediate Coupling Regime: Comparing Molecular Dynamics to an Energy-Grained Master Equation. J Phys Chem A 2021; 125:3473-3488. [PMID: 33880919 DOI: 10.1021/acs.jpca.1c01260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We propose and test an extension of the energy-grained master equation (EGME) for treating nonadiabatic (NA) hopping between different potential energy surfaces, which enables us to model the competition between stepwise collisional relaxation and kinetic processes which transfer population between different electronic states of the same spin symmetry. By incorporating Zhu-Nakamura theory into the EGME, we are able to treat NA passages beyond the simple Landau-Zener approximation, along with the corresponding treatments of zero-point energy and tunneling probability. To evaluate the performance of this NA-EGME approach, we carried out detailed studies of the UV photodynamics of the volatile organic compound C6-hydroperoxy aldehyde (C6-HPALD) using on-the-fly ab initio molecular dynamics and trajectory surface hopping. For this multichromophore molecule, we show that the EGME is able to capture important aspects of the dynamics, including kinetic timescales, and diabatic trapping. Such an approach provides a promising and efficient strategy for treating the long-time dynamics of photoexcited molecules in regimes which are difficult to capture using atomistic on-the-fly molecular dynamics.
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Affiliation(s)
| | - Robin J Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | | | - David R Glowacki
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.,Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, U.K.,Department of Computer Science, University of Bristol, Bristol BS8 1UB, U.K
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32
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Amin S, Asif T, Khan M, Usinowicz E, Mitra D, Asaduzzaman A. Structural, energetic and vibrational properties of oxidized mercury in the gas and aqueous phases. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Borrego-Sánchez A, Giussani A, Rubio M, Roca-Sanjuán D. On the chemiluminescence emission of luminol: protic and aprotic solvents and encapsulation to improve the properties in aqueous solution. Phys Chem Chem Phys 2020; 22:27617-27625. [PMID: 33245300 DOI: 10.1039/d0cp04571c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Luminol is a popular molecule that is currently gaining further interest due to its potential role for non-invasive cancer treatments. Design of more efficient derivatives in this context would benefit from a clear knowledge on the origin of the distinct intensity and spectroscopic properties in protic and aprotic solvents observed experimentally, which are still not rationalized. By efficiently combining molecular dynamics, quantum methodologies based on density functional theory and multiconfigurational quantum chemistry and hybrid approaches, and developing herein a computational approach for accurately determining "molar negative extinction (or gain) coefficients of emission", we firstly demonstrate that the amino and imino forms of the 3-aminophthalate dianion are responsible for the chemiluminescence in protic and aprotic medium, respectively. Secondly, we show that the coupling between the adjacent amino and carboxylate groups of luminol existing in aprotic solvents must be kept in aqueous solution to increase the chemiexcitation and emission intensity. Thirdly, modifications of luminol are proposed and simulated showing improved performances as compared to the parent molecule (stronger emission electronic transition and longer emission wavelengths) under the physiological conditions of relevance in biological and medical applications.
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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
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34
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Saiz-Lopez A, Travnikov O, Sonke JE, Thackray CP, Jacob DJ, Carmona-García J, Francés-Monerris A, Roca-Sanjuán D, Acuña AU, Dávalos JZ, Cuevas CA, Jiskra M, Wang F, Bieser J, Plane JMC, Francisco JS. Photochemistry of oxidized Hg(I) and Hg(II) species suggests missing mercury oxidation in the troposphere. Proc Natl Acad Sci U S A 2020; 117:30949-30956. [PMID: 33229529 PMCID: PMC7733835 DOI: 10.1073/pnas.1922486117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 10/26/2020] [Indexed: 11/18/2022] Open
Abstract
Mercury (Hg), a global contaminant, is emitted mainly in its elemental form Hg0 to the atmosphere where it is oxidized to reactive HgII compounds, which efficiently deposit to surface ecosystems. Therefore, the chemical cycling between the elemental and oxidized Hg forms in the atmosphere determines the scale and geographical pattern of global Hg deposition. Recent advances in the photochemistry of gas-phase oxidized HgI and HgII species postulate their photodissociation back to Hg0 as a crucial step in the atmospheric Hg redox cycle. However, the significance of these photodissociation mechanisms on atmospheric Hg chemistry, lifetime, and surface deposition remains uncertain. Here we implement a comprehensive and quantitative mechanism of the photochemical and thermal atmospheric reactions between Hg0, HgI, and HgII species in a global model and evaluate the results against atmospheric Hg observations. We find that the photochemistry of HgI and HgII leads to insufficient Hg oxidation globally. The combined efficient photoreduction of HgI and HgII to Hg0 competes with thermal oxidation of Hg0, resulting in a large model overestimation of 99% of measured Hg0 and underestimation of 51% of oxidized Hg and ∼66% of HgII wet deposition. This in turn leads to a significant increase in the calculated global atmospheric Hg lifetime of 20 mo, which is unrealistically longer than the 3-6-mo range based on observed atmospheric Hg variability. These results show that the HgI and HgII photoreduction processes largely offset the efficiency of bromine-initiated Hg0 oxidation and reveal missing Hg oxidation processes in the troposphere.
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Affiliation(s)
- Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), 28006 Madrid, Spain;
| | - Oleg Travnikov
- Meteorological Synthesizing Centre-East of EMEP, 115419 Moscow, Russia;
| | - Jeroen E Sonke
- Géosciences Environnement Toulouse, CNRS/Observatoire Midi-Pyrénées (OMP)/Université de Toulouse, 31400 Toulouse, France
| | - Colin P Thackray
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Daniel J Jacob
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | | | - Antonio Francés-Monerris
- Departamento de Química Física, Universitat de València, 46100 València, Spain
- Université de Lorraine, CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), F-54000 Nancy, France
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, 46071 València, Spain
| | - A Ulises Acuña
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Juan Z Dávalos
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Carlos A Cuevas
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Martin Jiskra
- Géosciences Environnement Toulouse, CNRS/Observatoire Midi-Pyrénées (OMP)/Université de Toulouse, 31400 Toulouse, France
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Feiyue Wang
- Department of Environment and Geography, Centre for Earth Observation Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Johannes Bieser
- Helmholtz-Zentrum Geethacht, Institute of Coastal Research, 21502 Geesthacht, Germany
| | - John M C Plane
- School of Chemistry, University of Leeds, LS2 9TJ Leeds, United Kingdom
| | - Joseph S Francisco
- Department of Earth and Environmental Science,University of Pennsylvania, Philadelphia, PA 19104;
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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35
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Prlj A, Ibele LM, Marsili E, Curchod BFE. On the Theoretical Determination of Photolysis Properties for Atmospheric Volatile Organic Compounds. J Phys Chem Lett 2020; 11:5418-5425. [PMID: 32543205 PMCID: PMC7372557 DOI: 10.1021/acs.jpclett.0c01439] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Volatile organic compounds (VOCs) are ubiquitous atmospheric molecules that generate a complex network of chemical reactions in the troposphere, often triggered by the absorption of sunlight. Understanding the VOC composition of the atmosphere relies on our ability to characterize all of their possible reaction pathways. When considering reactions of (transient) VOCs with sunlight, the availability of photolysis rate constants, utilized in general atmospheric models, is often out of experimental reach due to the unstable nature of these molecules. Here, we show how recent advances in computational photochemistry allow us to calculate in silico the different ingredients of a photolysis rate constant, namely, the photoabsorption cross-section and wavelength-dependent quantum yields. The rich photochemistry of tert-butyl hydroperoxide, for which experimental data are available, is employed to test our protocol and highlight the strengths and weaknesses of different levels of electronic structure and nonadiabatic molecular dynamics to study the photochemistry of (transient) VOCs.
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