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Martínez-Fernández L, Ranković ML, Canon F, Nahon L, Giuliani A, Milosavljević AR, Martin-Somer A. Photodissociation of leucine-enkephalin protonated peptide: an experimental and theoretical perspective. RSC Adv 2024; 14:16809-16820. [PMID: 38784408 PMCID: PMC11112675 DOI: 10.1039/d4ra01690d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Understanding the competing processes that govern far ultraviolet photodissociation (FUV-PD) of biopolymers such as proteins is a challenge. Here, we report a combined experimental and theoretical investigation of FUV-PD of protonated leucine-enkephalin pentapeptide ([YGGFL + H]+) in the gas-phase. Time-dependent density functional theory (TD-DFT) calculations in combination with experiments and previous results for amino acids and shorter peptides help in rationalizing the evolution of the excited states. The results confirm that fragmentation of [YGGFL + H]+ results mainly from vibrationally excited species in the ground electronic state, populated after internal conversion. We also propose fragmentation mechanisms for specific photo-fragments such as tyrosine side chain loss (with an extra hydrogen) or hydrogen loss. In general, we observe the same mechanisms as for smaller peptides or protonated Tyr and Phe, that are not quenched by the presence of other amino acids. Nevertheless, we also found some differences, as for H loss, in part due to the fact that the charge is solvated by the peptide chain and not only by the COOH terminal group.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física de Materiales, Instituto de Química Física Blas Cabrera, CSIC 28006 Madrid Spain
| | - Miloš Lj Ranković
- Institute of Physics Belgrade, University of Belgrade Pregrevica 118 11080 Belgrade Serbia
| | - Francis Canon
- SOLEIL l'Orme des Merisiers, St Aubin, BP48, F-91192 Gif sur Yvette Cedex France
| | - Laurent Nahon
- SOLEIL l'Orme des Merisiers, St Aubin, BP48, F-91192 Gif sur Yvette Cedex France
| | - Alexandre Giuliani
- SOLEIL l'Orme des Merisiers, St Aubin, BP48, F-91192 Gif sur Yvette Cedex France
- INRAE, Dpet. Transform UAR1008, Rue de la Géraudière, BP 71627 F-44316 Nantes France
| | | | - Ana Martin-Somer
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid Módulo 14 28049 Spain
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2
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Vandaele E, Mališ M, Luber S. A Local Diabatisation Method for Two-State Adiabatic Conical Intersections. J Chem Theory Comput 2024; 20:856-872. [PMID: 38174710 DOI: 10.1021/acs.jctc.3c01008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
A methodology to locally characterize conical intersections (CIs) between two adiabatic electronic states for which no nonadiabatic coupling (NAC) vectors are available is presented. Based on the Hessian and gradient at the CI, the branching space coordinates are identified. The potential energy surface around the CI in the branching space is expressed in the diabatic representation, from which the NAC vectors can be calculated in a wave-function-free, energy-based approach. To demonstrate the universality of the developed methodology, the minimum-energy CI (MECI) between the first (S1) and second (S2) singlet excited states of formamide is investigated at the state-averaged complete active space self-consistent field (SA-CASSCF) and extended multistate complete active space second-order perturbation theory (XMS-CASPT2) levels of theory. In addition, the asymmetrical MECI between the ground state (S0) and S1 of cyclopropanone is evaluated using SA-CASSCF, as well as (ME)CIs between the S1 and S2 states of benzene using SA-CASSCF and time-dependent density functional theory (TDDFT). Finally, a CI between the S1 and S2 excited states of thiophene was analyzed using TDDFT.
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Affiliation(s)
- Eva Vandaele
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Momir Mališ
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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3
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Mejia-Rodriguez D, Aprà E, Autschbach J, Bauman NP, Bylaska EJ, Govind N, Hammond JR, Kowalski K, Kunitsa A, Panyala A, Peng B, Rehr JJ, Song H, Tretiak S, Valiev M, Vila FD. NWChem: Recent and Ongoing Developments. J Chem Theory Comput 2023; 19:7077-7096. [PMID: 37458314 DOI: 10.1021/acs.jctc.3c00421] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
This paper summarizes developments in the NWChem computational chemistry suite since the last major release (NWChem 7.0.0). Specifically, we focus on functionality, along with input blocks, that is accessible in the current stable release (NWChem 7.2.0) and in the "master" development branch, interfaces to quantum computing simulators, interfaces to external libraries, the NWChem github repository, and containerization of NWChem executable images. Some ongoing developments that will be available in the near future are also discussed.
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Affiliation(s)
- Daniel Mejia-Rodriguez
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Edoardo Aprà
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Nicholas P Bauman
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric J Bylaska
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Niranjan Govind
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jeff R Hammond
- Accelerated Computing, NVIDIA Helsinki Oy, Porkkalankatu 1, 00180 Helsinki, Finland
| | - Karol Kowalski
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Alexander Kunitsa
- Zapata Computing, Inc., 100 Federal Street, Boston, Massachusetts 02110, United States
| | - Ajay Panyala
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bo Peng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - John J Rehr
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Huajing Song
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Marat Valiev
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Fernando D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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4
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ThOgersen J, Weidner T, Jensen F. The primary photo-dissociation dynamics of aqueous formamide and dimethylformamide. Phys Chem Chem Phys 2022; 24:24695-24705. [DOI: 10.1039/d2cp03166c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study the primary dissociation dynamics of aqueous formamide (HCONH2) and dimethylformamide (HCON(CH3)2) induced by photo-excitation at λ = 200 nm. The photolysis is recorded with sub-picosecond time resolution by...
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5
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Song H, Freixas VM, Fernandez-Alberti S, White AJ, Zhang Y, Mukamel S, Govind N, Tretiak S. An Ab Initio Multiple Cloning Method for Non-Adiabatic Excited-State Molecular Dynamics in NWChem. J Chem Theory Comput 2021; 17:3629-3643. [PMID: 34014085 DOI: 10.1021/acs.jctc.1c00131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently developed ab initio multiple cloning (AIMC) approach based on the multiconfigurational Ehrenfest (MCE) method provides a powerful and accurate way of describing the excited-state dynamics of molecular systems. The AIMC method is a controlled approximation to nonadiabatic dynamics with a particular strength in the proper description of decoherence effects because of the branching of vibrational wavepackets at a level crossing. Here, we report a new implementation of the AIMC algorithm in the open source NWChem computational chemistry program. The framework combines linear-response time-dependent density functional theory with Ehrenfest mean-field theory to determine the equations of motion for classical trajectories. The multidimensional wave function is decomposed into a superposition of Gaussian coherent states guided by Ehrenfest trajectories (i.e., MCE approach), which can clone with fully quantum mechanical amplitudes and phases. By using an efficient time-derivative based nonadiabatic coupling approach within the AIMC method, all observables are calculated on-the-fly in the nonadiabatic molecular dynamics process. As a representative example, we apply our implementation to study the ultrafast photoinduced electronic and vibrational energy transfer in a pyridine molecule. The effects of the cloning procedure on electronic and vibrational coherence, relaxation and unidirectional energy transfer are discussed. This new AIMC implementation provides a high-level nonadiabatic molecular dynamics framework for simulating photoexcited dynamics in complex molecular systems and experimentally relevant ultrafast spectroscopic probes, such as nonlinear coherent optical and X-ray signals.
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Affiliation(s)
- Huajing Song
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Victor M Freixas
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, B1876BXD, Bernal, Argentina
| | | | - Alexander J White
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Yu Zhang
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Shaul Mukamel
- Departments of Chemistry, Physics, and Astronomy, University of California, Irvine, California 92697, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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6
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Paterson MJ, Townsend D. Rydberg-to-valence evolution in excited state molecular dynamics. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1815389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Dave Townsend
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, UK
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7
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Song H, Fischer SA, Zhang Y, Cramer CJ, Mukamel S, Govind N, Tretiak S. First Principles Nonadiabatic Excited-State Molecular Dynamics in NWChem. J Chem Theory Comput 2020; 16:6418-6427. [DOI: 10.1021/acs.jctc.0c00295] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Huajing Song
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Sean A. Fischer
- Chemistry Division, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | - Yu Zhang
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Christopher J. Cramer
- Department of Chemistry, Supercomputing Institute and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Shaul Mukamel
- Departments of Chemistry, and physics and astronomy, University of California, Irvine, California 92697, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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8
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Zhang Y, Li L, Tretiak S, Nelson T. Nonadiabatic Excited-State Molecular Dynamics for Open-Shell Systems. J Chem Theory Comput 2020; 16:2053-2064. [DOI: 10.1021/acs.jctc.9b00928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yu Zhang
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Linqiu Li
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tammie Nelson
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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9
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Suwannakham P, Sagarik K. Unimolecular photolysis mechanisms of formamide: the effect of thermal energy. Phys Chem Chem Phys 2020; 22:25789-25802. [DOI: 10.1039/d0cp03718d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The C–N dissociation is the most favorable in S1 state, and radical products (1) are precursors in other channels.
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Affiliation(s)
- Parichart Suwannakham
- School of Chemistry
- Institute of Science, Suranaree University of Technology
- Nakhon Ratchasima 30000
- Thailand
| | - Kritsana Sagarik
- School of Chemistry
- Institute of Science, Suranaree University of Technology
- Nakhon Ratchasima 30000
- Thailand
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10
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Larsen MAB, Sølling TI, Forbes R, Boguslavskiy AE, Makhija V, Veyrinas K, Lausten R, Stolow A, Zawadzki MM, Saalbach L, Kotsina N, Paterson MJ, Townsend D. Vacuum ultraviolet excited state dynamics of small amides. J Chem Phys 2019; 150:054301. [DOI: 10.1063/1.5079721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Martin A. B. Larsen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Theis I. Sølling
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Ruaridh Forbes
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
| | - Andrey E. Boguslavskiy
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
- National Research Council Canada,
100 Sussex Drive, Ottawa, Ontario K1N 5A2, Canada
| | - Varun Makhija
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
| | - Kévin Veyrinas
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
| | - Rune Lausten
- National Research Council Canada,
100 Sussex Drive, Ottawa, Ontario K1N 5A2, Canada
| | - Albert Stolow
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
- National Research Council Canada,
100 Sussex Drive, Ottawa, Ontario K1N 5A2, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5,
Canada
| | - Magdalena M. Zawadzki
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Lisa Saalbach
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Nikoleta Kotsina
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Martin J. Paterson
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
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11
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Gahlaut A, Paranjothy M. Unimolecular decomposition of formamide via direct chemical dynamics simulations. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00541a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Classical chemical dynamics simulations show that formamide (NH2CHO) can dissociate via multiple pathways, either by direct dissociations or via intramolecular rearrangements to different isomers followed by dissociation.
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Affiliation(s)
- Anchal Gahlaut
- Department of Chemistry, Indian Institute of Technology Jodhpur
- Jodhpur
- India
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12
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Mališ M, Došlić N. Nonradiative Relaxation Mechanisms of UV Excited Phenylalanine Residues: A Comparative Computational Study. Molecules 2017; 22:E493. [PMID: 28335582 PMCID: PMC6155328 DOI: 10.3390/molecules22030493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/09/2017] [Accepted: 03/16/2017] [Indexed: 11/17/2022] Open
Abstract
The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory. The work emphasizes the role that excitation transfer from the phenylππ*to amidenπ*state plays in the deactivation of the three systems and shows how the ease of out-of-plane distortions of the amide group determines the rate of population transfer between the two electronic states. The subsequent dynamics on thenπ*state is barrierless along several pathways and leads to fast deactivation to the ground electronic state.
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Affiliation(s)
- Momir Mališ
- Ruđer Bošković Institute, HR-10000 Zagreb, Croatia.
- Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Nađa Došlić
- Ruđer Bošković Institute, HR-10000 Zagreb, Croatia.
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13
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Crespo-Otero R, Mardykov A, Sanchez-Garcia E, Sander W, Barbatti M. Photo-stability of peptide-bond aggregates: N-methylformamide dimers. Phys Chem Chem Phys 2015; 16:18877-87. [PMID: 25081138 DOI: 10.1039/c4cp02518k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The formation of weakly-bound dimers of N-methylformamide (NMF) and the photochemistry of these dimers after irradiation at 248 nm were explored using matrix-isolation spectroscopy. Calculations were used to characterize the diverse isomers and assign their IR spectra; non-adiabatic dynamics was simulated to understand their photo-deactivation mechanism. The most stable dimers, and , were obtained by trans-trans aggregation (N-HO[double bond, length as m-dash]C interactions) and could be identified in the matrix. The main products formed after irradiation are the trans-cis dimers ( and ), also stabilized by N-HO[double bond, length as m-dash]C interactions. In contrast to the photochemistry of the monomers, no dissociative products were observed after 248 nm irradiation of the dimers. The absence of dissociative products can be explained by a proton-transfer mechanism in the excited state that is faster than the photo-dissociative mechanism. The fact that hydrogen bonding has such a significant effect on the photochemical stability of NMF has important implications to understand the stability of peptide-bonded systems to UV irradiation.
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Affiliation(s)
- Rachel Crespo-Otero
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilheim-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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14
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Meteorite-catalyzed syntheses of nucleosides and of other prebiotic compounds from formamide under proton irradiation. Proc Natl Acad Sci U S A 2015; 112:E2746-55. [PMID: 25870268 DOI: 10.1073/pnas.1422225112] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Liquid formamide has been irradiated by high-energy proton beams in the presence of powdered meteorites, and the products of the catalyzed resulting syntheses were analyzed by mass spectrometry. Relative to the controls (no radiation, or no formamide, or no catalyst), an extremely rich, variegate, and prebiotically relevant panel of compounds was observed. The meteorites tested were representative of the four major classes: iron, stony iron, chondrites, and achondrites. The products obtained were amino acids, carboxylic acids, nucleobases, sugars, and, most notably, four nucleosides: cytidine, uridine, adenosine, and thymidine. In accordance with theoretical studies, the detection of HCN oligomers suggests the occurrence of mechanisms based on the generation of radical cyanide species (CN·) for the synthesis of nucleobases. Given that many of the compounds obtained are key components of extant organisms, these observations contribute to outline plausible exogenous high-energy-based prebiotic scenarios and their possible boundary conditions, as discussed.
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15
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Xia SH, Liu XY, Fang Q, Cui G. Excited-State Ring-Opening Mechanism of Cyclic Ketones: A MS-CASPT2//CASSCF Study. J Phys Chem A 2015; 119:3569-76. [DOI: 10.1021/acs.jpca.5b00302] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shu-Hua Xia
- Key Laboratory of
Theoretical and Computational Photochemistry, Ministry of Education,
College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yang Liu
- Key Laboratory of
Theoretical and Computational Photochemistry, Ministry of Education,
College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiu Fang
- Key Laboratory of
Theoretical and Computational Photochemistry, Ministry of Education,
College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of
Theoretical and Computational Photochemistry, Ministry of Education,
College of Chemistry, Beijing Normal University, Beijing 100875, China
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16
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Zámečníková M, Nachtigallová D. Photodynamic behavior of electronic coupling in a N-methylformamide dimer. Phys Chem Chem Phys 2015; 17:12356-64. [DOI: 10.1039/c4cp04573d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the bridging water molecules has been studied during the excited state photodynamics of a N-methylformamide dimer in complex with water molecules employing the complete active space self-consistent field (CASSCF) and CAS perturbation theory (CASPT2) methods.
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17
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Antol I, Glasovac Z, Crespo-Otero R, Barbatti M. Guanidine and guanidinium cation in the excited state--theoretical investigation. J Chem Phys 2014; 141:074307. [PMID: 25149786 DOI: 10.1063/1.4892569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Diverse ab initio and density-functional-theory methods were used to investigate geometries, energies, and electronic absorption spectra of guanidine and its protonated form, as well as their photo-deactivation processes. It was shown that the guanidine is a weakly absorbing species with the excitation spectrum consisting mostly of transitions to the Rydberg excited states and one valence n-π4 state. The lowest energy band has a maximum at ca. 6.9 eV (∼180 nm). The protonation of guanidine affects its excitation spectrum substantially. A major shift of the Rydberg states to higher energies is clearly visible and strongly absorbing transitions from the ground state to the π3-π4 and π2-π4 states appears at 7.8 eV (∼160 nm). Three low-lying conical intersections (two for guanidine and one for protonated guanidine) between the ground state and the first excited singlet state were located. They are accessible from the Franck-Condon region through amino N-H stretching and out-of-plane deformations in guanidine and protonated guanidine, respectively. The relaxation of the π3-3s Rydberg state via amino N-H bond stretching was hindered by a barrier. The nondissociated conical intersection in protonated guanidine mediates the radiationless deactivation of the compound after excitation into the π3-π4 state. This fact is detrimental for the photostability of guanidine, since its conjugate acid is stable in aqueous solution over a wide pH range and in protein environment, where guanidinium moiety in arginine is expected to be in a protonated form.
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Affiliation(s)
- Ivana Antol
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia
| | - Zoran Glasovac
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia
| | - Rachel Crespo-Otero
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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18
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Eckert-Maksić M, Antol I, Vazdar M. Acetamide as the model of the peptide bond: Nonadiabatic photodynamical simulations in the gas phase and in the argon matrix. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Nelson T, Fernandez-Alberti S, Roitberg AE, Tretiak S. Nonadiabatic excited-state molecular dynamics: modeling photophysics in organic conjugated materials. Acc Chem Res 2014; 47:1155-64. [PMID: 24673100 DOI: 10.1021/ar400263p] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To design functional photoactive materials for a variety of technological applications, researchers need to understand their electronic properties in detail and have ways to control their photoinduced pathways. When excited by photons of light, organic conjugated materials (OCMs) show dynamics that are often characterized by large nonadiabatic (NA) couplings between multiple excited states through a breakdown of the Born-Oppenheimer (BO) approximation. Following photoexcitation, various nonradiative intraband relaxation pathways can lead to a number of complex processes. Therefore, computational simulation of nonadiabatic molecular dynamics is an indispensable tool for understanding complex photoinduced processes such as internal conversion, energy transfer, charge separation, and spatial localization of excitons. Over the years, we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework that efficiently and accurately describes photoinduced phenomena in extended conjugated molecular systems. We use the fewest-switches surface hopping (FSSH) algorithm to treat quantum transitions among multiple adiabatic excited state potential energy surfaces (PESs). Extended molecular systems often contain hundreds of atoms and involve large densities of excited states that participate in the photoinduced dynamics. We can achieve an accurate description of the multiple excited states using the configuration interaction single (CIS) formalism with a semiempirical model Hamiltonian. Analytical techniques allow the trajectory to be propagated "on the fly" using the complete set of NA coupling terms and remove computational bottlenecks in the evaluation of excited-state gradients and NA couplings. Furthermore, the use of state-specific gradients for propagation of nuclei on the native excited-state PES eliminates the need for simplifications such as the classical path approximation (CPA), which only uses ground-state gradients. Thus, the NA-ESMD methodology offers a computationally tractable route for simulating hundreds of atoms on ~10 ps time scales where multiple coupled excited states are involved. In this Account, we review recent developments in the NA-ESMD modeling of photoinduced dynamics in extended conjugated molecules involving multiple coupled electronic states. We have successfully applied the outlined NA-ESMD framework to study ultrafast conformational planarization in polyfluorenes where the rate of torsional relaxation can be controlled based on the initial excitation. With the addition of the state reassignment algorithm to identify instances of unavoided crossings between noninteracting PESs, NA-ESMD can now be used to study systems in which these so-called trivial unavoided crossings are expected to predominate. We employ this technique to analyze the energy transfer between poly(phenylene vinylene) (PPV) segments where conformational fluctuations give rise to numerous instances of unavoided crossings leading to multiple pathways and complex energy transfer dynamics that cannot be described using a simple Förster model. In addition, we have investigated the mechanism of ultrafast unidirectional energy transfer in dendrimers composed of poly(phenylene ethynylene) (PPE) chromophores and have demonstrated that differential nuclear motion favors downhill energy transfer in dendrimers. The use of native excited-state gradients allows us to observe this feature.
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Affiliation(s)
- Tammie Nelson
- Los Alamos National Laboratory, Theoretical
Division, Los Alamos, New Mexico 87545, United States
| | | | - Adrian E. Roitberg
- Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Sergei Tretiak
- Los Alamos National Laboratory, Theoretical
Division, Los Alamos, New Mexico 87545, United States
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20
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Giegerich J, Petersen J, Mitrić R, Fischer I. Photodissociation dynamics of propargylene, HCCCH. Phys Chem Chem Phys 2014; 16:6294-302. [DOI: 10.1039/c3cp53213e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a joint theoretical and experimental study on the photodissociation of the C3H2 isomer propargylene, HCCCH, combining velocity map imaging with nonadiabatic surface hopping calculations.
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Affiliation(s)
- Jens Giegerich
- Institute of Physical and Theoretical Chemistry
- University of Würzburg
- D-97074 Würzburg, Germany
| | - Jens Petersen
- Institute of Physical and Theoretical Chemistry
- University of Würzburg
- D-97074 Würzburg, Germany
| | - Roland Mitrić
- Institute of Physical and Theoretical Chemistry
- University of Würzburg
- D-97074 Würzburg, Germany
| | - Ingo Fischer
- Institute of Physical and Theoretical Chemistry
- University of Würzburg
- D-97074 Würzburg, Germany
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21
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Nguyen HT, Nguyen VS, Trung NT, Havenith RWA, Nguyen MT. Decomposition pathways of the neutral and protonated formamide in some lower-lying excited states. J Phys Chem A 2013; 117:7904-17. [PMID: 23889466 DOI: 10.1021/jp405657y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unimolecular decompositions of neutral (NH2CHO) and protonated (NH3CHO(+)) formamide, an active precursor of biomolecules in prebiotic chemistry, are investigated in the ground (S0) and first triplet (T1) and singlet (S1) excited states. Different decomposition channels including the homolytic bond dissociations, dehydration, decarbonylation, dehydrogenation, etc., are explored using coupled-cluster theory (CCSD(T)/CBS method) for both S0 and T1 states and RASPT2(18,15)/6-31G(d,p) computations for the S1 state. On S1 and T1 energy surfaces, formamide preferentially follows C-N homolytic bond cleavages forming NH2 + HCO radical pairs. Formation of HCN and HNC from dehydration of neutral and protonated formamide via formimic acid and aminohydroxymethylene isomers has higher energy barriers. A strong stabilization upon triplet excitation of the two latter isomers significantly facilitates the interconversions between isomers, and thus considerably reduces the energy barriers for dehydration pathways. The most probable pathways for HCN and HNC generation are found to be dehydration of formamide in the T1 state. Dehydration pathways from the neutral S1 and protonated T1 forms lead to stable complexes of HCN and HNC with water but are associated with large energy barriers. Overall, in the lower-lying excited states of either neutral or protonated formamide, dehydration is not competitive with homolytic C-N bond cleavages, which finally lead to formation of CO.
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Affiliation(s)
- Huyen Thi Nguyen
- Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium
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22
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Tapavicza E, Bellchambers GD, Vincent JC, Furche F. Ab initio non-adiabatic molecular dynamics. Phys Chem Chem Phys 2013; 15:18336-48. [DOI: 10.1039/c3cp51514a] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Mališ M, Loquais Y, Gloaguen E, Biswal HS, Piuzzi F, Tardivel B, Brenner V, Broquier M, Jouvet C, Mons M, Došlić N, Ljubić I. Unraveling the Mechanisms of Nonradiative Deactivation in Model Peptides Following Photoexcitation of a Phenylalanine Residue. J Am Chem Soc 2012; 134:20340-51. [DOI: 10.1021/ja3054942] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Momir Mališ
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Yohan Loquais
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Eric Gloaguen
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Himansu S. Biswal
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - François Piuzzi
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Benjamin Tardivel
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Valérie Brenner
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Michel Broquier
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Christophe Jouvet
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Michel Mons
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Nađa Došlić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Ivan Ljubić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
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24
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Ruzi M, Anderson DT. Photodissociation of N-methylformamide isolated in solid parahydrogen. J Chem Phys 2012. [DOI: 10.1063/1.4765372] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Crespo‐Otero R, Mardyukov A, Sanchez‐Garcia E, Barbatti M, Sander W. Photochemistry of
N
‐Methylformamide: Matrix Isolation and Nonadiabatic Dynamics. Chemphyschem 2012; 14:827-36. [DOI: 10.1002/cphc.201200573] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Rachel Crespo‐Otero
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Artur Mardyukov
- Lehrstuhl für Organische Chemie II, Ruhr Universität Bochum, Universitätsstraße 150 44801 Bochum (Germany), Fax: (+49) (0)234‐3214353
| | - Elsa Sanchez‐Garcia
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Mario Barbatti
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Wolfram Sander
- Lehrstuhl für Organische Chemie II, Ruhr Universität Bochum, Universitätsstraße 150 44801 Bochum (Germany), Fax: (+49) (0)234‐3214353
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26
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Lu Y, Lan Z, Thiel W. Monomeric adenine decay dynamics influenced by the DNA environment. J Comput Chem 2012; 33:1225-35. [DOI: 10.1002/jcc.22952] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/09/2012] [Accepted: 01/16/2012] [Indexed: 01/25/2023]
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27
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Nelson T, Fernandez-Alberti S, Chernyak V, Roitberg AE, Tretiak S. Nonadiabatic excited-state molecular dynamics: Numerical tests of convergence and parameters. J Chem Phys 2012; 136:054108. [DOI: 10.1063/1.3680565] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Plasser F, Barbatti M, Aquino AJA, Lischka H. Electronically excited states and photodynamics: a continuing challenge. Theor Chem Acc 2012. [DOI: 10.1007/s00214-011-1073-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Antol I, Eckert-Maksić M, Vazdar M, Ruckenbauer M, Lischka H. QM/MM non-adiabatic decay dynamics of formamide in polar and non-polar solvents. Phys Chem Chem Phys 2012; 14:13262-72. [DOI: 10.1039/c2cp41830d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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30
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Tapavicza E, Meyer AM, Furche F. Unravelling the details of vitamin D photosynthesis by non-adiabatic molecular dynamics simulations. Phys Chem Chem Phys 2011; 13:20986-98. [PMID: 22020179 DOI: 10.1039/c1cp21292c] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We investigate the photodynamics of vitamin D derivatives by a fully analytical implementation of the linear response time-dependent density functional theory surface hopping method (LR-TDDFT-SH). Our study elucidates the dynamics of the processes involved in vitamin D formation at the molecular level and with femtosecond resolution. We explain the major experimental findings and provide new insights that cannot directly be obtained from experiments: firstly, we investigate the dynamics of the photoinduced ring-opening of provitamin D (Pro) and cyclohexadiene (CHD) and the subsequent rotational isomerization. In agreement with recent experiments and CC2 calculations, only the bright S(1) state is involved in the ring-opening reaction. Our calculations confirm the experimentally reported 5 : 1 ratio between the excited state lifetimes of Pro and CHD. The longer lifetimes of Pro are attributed to steric constraints of the steroid skeleton and to temperature effects, both emerging directly from our simulations. For CHD and Pro, we present an explanation of the biexponential decay recently reported by Sension and coworkers [Tang et al., J. Phys. Chem., 2011, 134, 104503]: our calculations suggest that the fast and slow components arise from a reactive and an unreactive reaction pathway, respectively. Secondly, we assess the wavelength dependent photochemistry of previtamin D (Pre). Using replica exchange molecular dynamics we sample the Pre conformers present at thermal equilibrium. Based on this ensemble we explain the conformation dependent absorption and the essential features of Pre photochemistry. Consistent with the experiments, we find ring-closure to occur mostly after excitation of the cZc conformers and at lower energies, whereas Z/E isomerization of the central double bond preferably occurs after excitation at higher energies. For the isomerization we provide the first theoretical evidence of the proposed hula-twist mechanism. Our results show that LR-TDDFT-SH is a highly valuable tool for studying the photochemistry of moderately large systems, even though challenges remain in the vicinity of conical intersections.
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Affiliation(s)
- Enrico Tapavicza
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, California 92697-2025, USA.
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31
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Ončák M, Lischka H, Slavíček P. Photostability and solvation: photodynamics of microsolvated zwitterionic glycine. Phys Chem Chem Phys 2010; 12:4906-14. [DOI: 10.1039/b925246k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Eckert-Maksić M, Vazdar M, Ruckenbauer M, Barbatti M, Müller T, Lischka H. Matrix-controlled photofragmentation of formamide: dynamics simulation in argon by nonadiabatic QM/MM method. Phys Chem Chem Phys 2010; 12:12719-26. [DOI: 10.1039/c0cp00174k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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33
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Eckert-Maksić M, Antol I. Study of the Mechanism of the N−CO Photodissociation in N,N-Dimethylformamide by Direct Trajectory Surface Hopping Simulations. J Phys Chem A 2009; 113:12582-90. [DOI: 10.1021/jp9046177] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mirjana Eckert-Maksić
- Rudjer Bošković Institute, Division of Organic Chemistry and Biochemistry, POB 180, HR-10002 Zagreb, Croatia
| | - Ivana Antol
- Rudjer Bošković Institute, Division of Organic Chemistry and Biochemistry, POB 180, HR-10002 Zagreb, Croatia
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34
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Fernandez-Alberti S, Kleiman VD, Tretiak S, Roitberg AE. Nonadiabatic Molecular Dynamics Simulations of the Energy Transfer between Building Blocks in a Phenylene Ethynylene Dendrimer. J Phys Chem A 2009; 113:7535-42. [DOI: 10.1021/jp900904q] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Fernandez-Alberti
- Universidad Nacional de Quilmes, Roque Saenz Peña 352, B1876BXD Bernal, Argentina, Department of Chemistry, University of Florida, Gainesville, Florida 32611, Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Valeria D. Kleiman
- Universidad Nacional de Quilmes, Roque Saenz Peña 352, B1876BXD Bernal, Argentina, Department of Chemistry, University of Florida, Gainesville, Florida 32611, Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Sergei Tretiak
- Universidad Nacional de Quilmes, Roque Saenz Peña 352, B1876BXD Bernal, Argentina, Department of Chemistry, University of Florida, Gainesville, Florida 32611, Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Adrian E. Roitberg
- Universidad Nacional de Quilmes, Roque Saenz Peña 352, B1876BXD Bernal, Argentina, Department of Chemistry, University of Florida, Gainesville, Florida 32611, Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611
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Abstract
Combined complete active space perturbation theory (CASPT2) and multireference configuration interaction calculations with single and double excitations (MR-CISD) were performed in order to explore possible deactivation pathways of thymine after photoexcitation. Equilibrium geometries are reported together with a total of eight extremes (minima or maxima) on the crossing seam (MXS), through which such radiationless transitions may occur. Furthermore, conformational analysis allows grouping these conical intersections in five distinct types. Reaction paths were calculated connecting the S1 (1)n pi* minimum with the lowest-energy MXS of each group. Two distinct types of paths were observed, both with features that should delay the internal conversion to the ground state. This is shown to provide a possible explanation for the relatively long excited-state lifetime of thymine.
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Affiliation(s)
- Gunther Zechmann
- Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, UK.
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36
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Antol I, Vazdar M, Barbatti M, Eckert-Maksić M. The effect of protonation on the photodissociation processes in formamide – An ab initio surface hopping dynamics study. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.01.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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