1
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Ghosh P. Investigation of the Nonradiative Photoprocesses of Unnatural DNA Base: 7-(2-Thienyl)-imidazo[4,5- b]pyridine (Ds)─A Computational Study. J Phys Chem A 2024; 128:8065-8071. [PMID: 39279655 PMCID: PMC11440586 DOI: 10.1021/acs.jpca.4c04070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
7-(2-Thienyl)-imidazo[4,5-b]pyridine (Ds) is an unnatural nucleic acid that forms a stable pair with pyrrole-2-carbaldehyde (Pa) in DNA. This Ds-Pa pair gets stabilized via van der Waals interaction and shape fitting. In our previous study [Ghosh, P. J. Phys. Chem. A 2021, 125, 5556-5561], we investigated the nonradiative photoprocesses of the unnatural DNA base Pa, and also there are some studies on its stability and reactivity in the ground state. But, to consider it as a good unnatural base pair, one has to understand its stability not only in the ground state but also in the excited states after absorbing ultraviolet (UV) radiation. Therefore, in this study, the excited-state photoprocesses of Ds on UV irradiation and its nonradiative decay channels have been investigated using state-of-the-art multireference methods, and this investigation finally leads the molecule to access the minimum energy crossing point (MECP) via a downhill pathway.
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Affiliation(s)
- Paulami Ghosh
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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2
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Vindel-Zandbergen P, González-Vázquez J. Non-adiabatic dynamics of photoexcited cyclobutanone: Predicting structural measurements from trajectory surface hopping with XMS-CASPT2 simulations. J Chem Phys 2024; 161:024104. [PMID: 38984954 DOI: 10.1063/5.0203722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
Over the years, theoretical calculations and scalable computer simulations have complemented ultrafast experiments, as they offer the advantage of overcoming experimental restrictions and having access to the whole dynamics. This synergy between theory and experiment promises to yield a deeper understanding of photochemical processes, offering valuable insights into the behavior of complex systems at the molecular level. However, the ability of theoretical models to predict ultrafast experimental outcomes has remained largely unexplored. In this work, we aim to predict the electron diffraction signals of an upcoming ultrafast photochemical experiment using high-level electronic structure calculations and non-adiabatic dynamics simulations. In particular, we perform trajectory surface hopping with extended multi-state complete active space with second order perturbation simulations for understanding the photodissociation of cyclobutanone (CB) upon excitation at 200 nm. Spin-orbit couplings are considered for investigating the role of triplet states. Our simulations capture the bond cleavage after ultrafast relaxation from the 3s Rydberg state, leading to the formation of the previously observed primary photoproducts: CO + cyclopropane/propene (C3 products), ketene, and ethene (C2 products). The ratio of the C3:C2 products is found to be about 1:1. Within 700 fs, the majority of trajectories transition to their electronic ground state, with a small fraction conserving the initial cyclobutanone ring structure. We found a minimal influence of triplet states during the early stages of the dynamics, with their significance increasing at later times. We simulate MeV-ultrafast electron diffraction (UED) patterns from our trajectory results, linking the observed features with specific photoproducts and the underlying structural dynamics. Our analysis reveals highly intense features in the UED signals corresponding to the photochemical processes of CB. These features offer valuable insights into the experimental monitoring of ring opening dynamics and the formation of C3 and C2 photoproducts.
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Affiliation(s)
| | - Jesús González-Vázquez
- Departamento de Química, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- Institute of Advanced Chemistry (IADChem), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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3
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Abma G, Parkes MA, Razmus WO, Zhang Y, Wyatt AS, Springate E, Chapman RT, Horke DA, Minns RS. Direct Observation of a Roaming Intermediate and Its Dynamics. J Am Chem Soc 2024; 146:12595-12600. [PMID: 38682306 PMCID: PMC11082896 DOI: 10.1021/jacs.4c01543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/01/2024]
Abstract
Chemical reactions are often characterized by their transition state, which defines the critical geometry the molecule must pass through to move from reactants to products. Roaming provides an alternative picture, where in a dissociation reaction, the bond breaking is frustrated and a loosely bound intermediate is formed. Following bond breaking, the two partners are seen to roam around each other at distances of several Ångstroms, forming a loosely bound, and structurally ill-defined, intermediate that can subsequently lead to reactive or unreactive collisions. Here, we present a direct and time-resolved experimental measurement of roaming. By measuring the photoelectron spectrum of UV-excited acetaldehyde with a femtosecond extreme ultraviolet pulse, we captured spectral signatures of all of the key reactive structures, including that of the roaming intermediate. This provided a direct experimental measurement of the roaming process and allowed us to identify the time scales by which the roaming intermediate is formed and removed and the electronic potential surfaces upon which roaming proceeds.
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Affiliation(s)
- Grite
L. Abma
- Institute
for Molecules and Materials, Radboud University, Heijendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Michael A. Parkes
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Weronika O. Razmus
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.
| | - Yu Zhang
- Central
Laser Facility, STFC Rutherford Appleton
Laboratory, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Adam S. Wyatt
- Central
Laser Facility, STFC Rutherford Appleton
Laboratory, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Emma Springate
- Central
Laser Facility, STFC Rutherford Appleton
Laboratory, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Richard T. Chapman
- Central
Laser Facility, STFC Rutherford Appleton
Laboratory, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Daniel A. Horke
- Institute
for Molecules and Materials, Radboud University, Heijendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Russell S. Minns
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.
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4
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Koga M, Kang DH, Heim ZN, Meyer P, Erickson BA, Haldar N, Baradaran N, Havenith M, Neumark DM. Extreme ultraviolet time-resolved photoelectron spectroscopy of adenine, adenosine and adenosine monophosphate in a liquid flat jet. Phys Chem Chem Phys 2024; 26:13106-13117. [PMID: 38629206 DOI: 10.1039/d4cp00856a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Time-resolved photoelectron spectroscopy using an extreme-ultraviolet (XUV) probe pulse was used to investigate the UV photoinduced dynamics of adenine (Ade), adenosine (Ado), and adenosine-5-monophosphate (AMP) in a liquid water jet. In contrast to previous studies using UV probe pulses, the XUV pulse at 21.7 eV can photoionize all excited states of a molecule, allowing for full relaxation pathways to be addressed after excitation at 4.66 eV. This work was carried out using a gas-dynamic flat liquid jet, resulting in considerably enhanced signal compared to a cylindrical jet. All three species decay on multiple time scales that are assigned based on their decay associated spectra; the fastest decay of ∼100 fs is assigned to ππ* decay to the ground state, while a smaller component with a lifetime of ∼500 fs is attributed to the nπ* state. An additional slower channel in Ade is assigned to the 7H Ade conformer, as seen previously. This work demonstrates the capability of XUV-TRPES to disentangle non-adiabatic dynamics in an aqueous solution in a state-specific manner and represents the first identification of the nπ* state in the relaxation dynamics of adenine and its derivatives.
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Affiliation(s)
- Masafumi Koga
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Do Hyung Kang
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Zachary N Heim
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Philipp Meyer
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801, Germany
| | - Blake A Erickson
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Neal Haldar
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Negar Baradaran
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801, Germany
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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5
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Coppola F, Cimino P, Petrone A, Rega N. Evidence of Excited-State Vibrational Mode Governing the Photorelaxation of a Charge-Transfer Complex. J Phys Chem A 2024; 128:1620-1633. [PMID: 38381887 DOI: 10.1021/acs.jpca.3c08366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Modern, nonlinear, time-resolved spectroscopic techniques have opened new doors for investigating the intriguing but complex world of photoinduced ultrafast out-of-equilibrium phenomena and charge dynamics. The interaction between light and matter introduces an additional dimension, where the complex interplay between electronic and vibrational dynamics needs the most advanced theoretical-computational protocols to be fully understood on the molecular scale. In this study, we showcase the capabilities of ab initio molecular dynamics simulation integrated with a multiresolution wavelet protocol to carefully investigate the excited-state relaxation dynamics in a noncovalent complex involving tetramethylbenzene (TMB) and tetracyanoquinodimethane (TCNQ) undergoing charge transfer (CT) upon photoexcitation. Our protocol provides an accurate description that facilitates a direct comparison between transient vibrational analysis and time-resolved spectroscopic signals. This molecular level perspective enhances our understanding of photorelaxation processes confined in the adiabatic regime and offers an improved interpretation of vibrational spectra. Furthermore, it enables the quantification of anharmonic vibrational couplings between high- and low-frequency modes, specifically the TCNQ "rocking" and "bending" modes. Additionally, it identifies the primary vibrational mode that governs the adiabaticity between the ground state and the CT state. This comprehensive understanding of photorelaxation processes holds significant importance in the rational design and precise control of more efficient photovoltaic and sensor devices.
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Affiliation(s)
- Federico Coppola
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Paola Cimino
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Istituto Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italia
| | - Nadia Rega
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Istituto Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italia
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6
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Lamas I, Montero R, Martínez-Martínez V, Longarte A. Photodynamics of azaindoles in polar media: the influence of the environment. Phys Chem Chem Phys 2024; 26:3240-3252. [PMID: 38193884 DOI: 10.1039/d3cp03412g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
We have studied the relaxation dynamics of a family of azaindole (AI) structural isomers, 4-, 5-, 6- and 7-AI, by steady-state and time-resolved methods (fs-transient absorption and fluorescence up-conversion), in solvents of different polarity. The measurements in aprotic solvents show distinctive fluorescence yields and excited state lifetimes among the isomers, which are tuned by the polarity of the medium. Guided by simple TD-DFT calculations and based on the behavior observed in the isolated species, it has been possible to address the influence of the environment polarity on the relaxation route. According to the obtained picture, the energy of the nπ* state, which is strongly dependent on the position of the pyridinic nitrogen, controls the rate of the internal conversion channel that accounts for the distinctive photophysical behavior of the isomers. On the other hand, preliminary measurements in protic media (methanol) show a very different photodynamical behavior, in which the anomalous measured fluorescent patterns are very likely the result of reactive channels (proton transfer) triggered by the electronic excitation.
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Affiliation(s)
- Iker Lamas
- Departamento de Química-Física Facultad de Ciencia y Tecnología. Universidad del País Vasco (UPV/EHU) Apart. 644, 48080 Bilbao, Spain.
| | - Raúl Montero
- SGIKER Laser Facility Facultad de Ciencia y Tecnología. Universidad del País Vasco (UPV/EHU) 48940, Leioa, Spain.
| | - Virginia Martínez-Martínez
- Departamento de Química-Física Facultad de Ciencia y Tecnología. Universidad del País Vasco (UPV/EHU) Apart. 644, 48080 Bilbao, Spain.
| | - Asier Longarte
- Departamento de Química-Física Facultad de Ciencia y Tecnología. Universidad del País Vasco (UPV/EHU) Apart. 644, 48080 Bilbao, Spain.
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7
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Arribas EV, Ibele LM, Lauvergnat D, Maitra NT, Agostini F. Significance of Energy Conservation in Coupled-Trajectory Approaches to Nonadiabatic Dynamics. J Chem Theory Comput 2023; 19:7787-7800. [PMID: 37853509 DOI: 10.1021/acs.jctc.3c00845] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Through approximating electron-nuclear correlation terms in the exact factorization approach, trajectory-based methods have been derived and successfully applied to the dynamics of a variety of light-induced molecular processes, capturing quantum (de)coherence effects rigorously. These terms account for the coupling among the trajectories, recovering the nonlocal nature of quantum nuclear dynamics that is completely overlooked in traditional independent-trajectory algorithms. Nevertheless, some of the approximations introduced in the derivation of some of these methods do not conserve the total energy. We analyze energy conservation in the coupled-trajectory mixed quantum-classical (CTMQC) algorithm and explore the performance of a modified algorithm, CTMQC-E, where some of the terms are redefined to restore energy conservation. A set of molecular models is used as a test, namely, 2-cis-penta-2,4-dienimium cation, bis(methylene) adamantyl radical cation, butatriene cation, uracil radical cation, and neutral pyrazine.
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Affiliation(s)
| | - Lea M Ibele
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
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8
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Villaseco Arribas E, Vindel-Zandbergen P, Roy S, Maitra NT. Different flavors of exact-factorization-based mixed quantum-classical methods for multistate dynamics. Phys Chem Chem Phys 2023; 25:26380-26395. [PMID: 37750820 DOI: 10.1039/d3cp03464j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The exact factorization approach has led to the development of new mixed quantum-classical methods for simulating coupled electron-ion dynamics. We compare their performance for dynamics when more than two electronic states are occupied at a given time, and analyze: (1) the use of coupled versus auxiliary trajectories in evaluating the electron-nuclear correlation terms, (2) the approximation of using these terms within surface-hopping and Ehrenfest frameworks, and (3) the relevance of the exact conditions of zero population transfer away from nonadiabatic coupling regions and total energy conservation. Dynamics through the three-state conical intersection in the uracil radical cation as well as polaritonic models in one dimension are studied.
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Affiliation(s)
| | - Patricia Vindel-Zandbergen
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Saswata Roy
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
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9
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Kim J, Woo KC, Kang M, Kim SK. Dynamic Role of the Intramolecular Hydrogen Bonding in the S 1 State Relaxation Dynamics Revealed by the Direct Measurement of the Mode-Dependent Internal Conversion Rate of 2-Chlorophenol and 2-Chlorothiophenol. J Phys Chem Lett 2023; 14:8428-8436. [PMID: 37712655 DOI: 10.1021/acs.jpclett.3c02208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
The dynamic role of the intramolecular hydrogen bond in the S1 relaxation of cis-2-chlorophenol (2-CP) or cis-2-chlorothiophenol (2-CTP) has been investigated in a state-specific manner. Whereas ultrafast internal conversion is dominant for 2-CP, the H-tunneling competes with internal conversion for 2-CTP even at the S1 origin. The S0-S1 internal conversion rate of 2-CTP could be directly measured from the S1 lifetimes of 2-CTP-d1 (Cl-C6H4-SD) as the D-tunneling is kinetically blocked, allowing distinct estimations of tunneling and internal conversion rates with increasing the energy. The internal conversion rate of 2-CTP increases by two times at the out-of-plane torsional mode excitation, suggesting that the internal conversion is facilitated at the nonplanar geometry. It then sharply increases at ∼600 cm-1, indicating that the S1/S0 conical intersection is readily accessible at the extended C-Cl bond length. The strength of the intramolecular hydrogen bond should be responsible for the distinct dynamic behaviors of 2-CP and 2-CTP.
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Affiliation(s)
- Junggil Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Kyung Chul Woo
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Minseok Kang
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
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10
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Hartweg S, Hochlaf M, Garcia GA, Nahon L. Photoionization Dynamics and Proton Transfer within the Adenine-Thymine Nucleobase Pair. J Phys Chem Lett 2023; 14:3698-3705. [PMID: 37040591 DOI: 10.1021/acs.jpclett.3c00564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Studying the stability of hydrogen-bonded nucleobase pairs, at the heart of the genetic code, is of utmost importance for an in-depth understanding of basic mechanisms of life and biomolecular evolution. We present here a VUV single photon ionization dynamic study of the nucleobase pair adenine-thymine (AT), revealing its ionization and dissociative ionization thresholds via double imaging electron/ion coincidence spectroscopy. The experimental data, consisting of cluster mass-resolved threshold photoelectron spectra and photon energy-dependent ion kinetic energy release distributions, allow the unambiguous distinction of the dissociation of AT into protonated adenine AH+ and a dehydrogenated thymine radical T(-H) from dissociative ionization processes of other nucleobase clusters. Comparison to high-level ab initio calculations indicates that our experimental observations can be explained by a single hydrogen-bonded conformer present in our molecular beam and allows the estimation of an upper limit of the barrier of the proton transfer in the ionized AT pair.
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Affiliation(s)
- Sebastian Hartweg
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
- University of Freiburg, Institute of Physics, Hermann-Herder-Straße 3, 79104 Freiburg, Germany
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454 Champs sur Marne, France
| | - Gustavo A Garcia
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
| | - Laurent Nahon
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
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11
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Kim J, Woo KC, Kim SK. Mode-dependent H atom tunneling dynamics of the S 1 phenol is resolved by the simple topographic view of the potential energy surfaces along the conical intersection seam. J Chem Phys 2023; 158:104301. [PMID: 36922134 DOI: 10.1063/5.0143655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
Mode-dependent H atom tunneling dynamics of the O-H bond predissociation of the S1 phenol has been theoretically analyzed. As the tunneling is governed by the complicated multi-dimensional potential energy surfaces that are dynamically shaped by the upper-lying S1(ππ*)/S2(πσ*) conical intersection, the mode-specific tunneling dynamics of phenol (S1) has been quite formidable to be understood. Herein, we have examined the topography of the potential energy surface along the particular S1 vibrational mode of interest at the nuclear configurations of the S1 minimum and S1/S2 conical intersection. The effective adiabatic tunneling barrier experienced by the reactive flux at the particular S1 vibrational mode excitation is then uniquely determined by the topographic shape of the potential energy surface extended along the conical intersection seam coordinate associated with the particular vibrational mode. The resultant multi-dimensional coupling of the specific vibrational mode to the tunneling coordinate is then reflected in the mode-dependent tunneling rate as well as nonadiabatic transition probability. Remarkably, the mode-specific experimental result of the S1 phenol tunneling reaction [K. C. Woo and S. K. Kim, J. Phys. Chem. A 123, 1529-1537 (2019)] (in terms of the qualitative and relative mode-dependent dynamic behavior) could be well rationalized by semi-classical calculations based on the mode-specific topography of the effective tunneling barrier, providing the clear conceptual insight that the skewed potential energy surfaces along the conical intersection seam (strongly or weakly coupled to the tunneling reaction coordinate) may dictate the tunneling dynamics in the proximity of the conical intersection.
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Affiliation(s)
- Junggil Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Kyung Chul Woo
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
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12
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Kim J, Woo KC, Kim KK, Kim SK. πσ*-Mediated Nonadiabatic Tunneling Dynamics of Thiophenols in S 1: The Semiclassical Approaches. J Phys Chem A 2022; 126:9594-9604. [PMID: 36534791 DOI: 10.1021/acs.jpca.2c05861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The S-H bond tunneling predissociation dynamics of thiophenol and its ortho-substituted derivatives (2-fluorothiophenol, 2-methoxythiophenol, and 2-chlorothiphenol) in S1 (ππ*) where the H atom tunneling is mediated by the nearby S2 (πσ*) state (which is repulsive along the S-H bond extension coordinate) have been investigated in a state-specific way using the picosecond time-resolved pump-probe spectroscopy for the jet-cooled molecules. The effects of the specific vibrational mode excitations and the SH/SD substitutions on the S-H(D) bond rupture tunneling dynamics have been interrogated, giving deep insights into the multidimensional aspects of the S1/S2 conical intersection, which also shapes the underlying adiabatic tunneling potential energy surfaces (PESs). The semiclassical tunneling rate calculations based on the Wentzel-Kramers-Brillouin (WKB) approximation or Zhu-Nakamura (ZN) theory have been carried out based on the ab initio PESs calculated in the (one, two, or three) reduced dimensions to be compared with the experiment. Though the quantitative experimental results could not be reproduced satisfactorily by the present calculations, the qualitative trends among different molecules in terms of the behavior of the tunneling rate versus the (adiabatic) barrier height or the number of PES dimensions could be rationalized. Most interestingly, the H/D kinetic isotope effect observed in the tunneling rate could be much better explained by the ZN theory compared to the WKB approximation, indicating that the nonadiabatic coupling matrix elements should be invoked for understanding the tunneling dynamics taking place in the proximity of the conical intersection.
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Affiliation(s)
- Junggil Kim
- Department of Chemistry, KAIST, Daejeon34141, Republic of Korea
| | - Kyung Chul Woo
- Department of Chemistry, KAIST, Daejeon34141, Republic of Korea
| | - Kuk Ki Kim
- Department of Chemistry, KAIST, Daejeon34141, Republic of Korea
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon34141, Republic of Korea
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13
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Heim ZN, Neumark DM. Nonadiabatic Dynamics Studied by Liquid-Jet Time-Resolved Photoelectron Spectroscopy. Acc Chem Res 2022; 55:3652-3662. [PMID: 36480155 DOI: 10.1021/acs.accounts.2c00609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The development of the liquid microjet technique by Faubel and co-workers has enabled the investigation of high vapor pressure liquids and solutions utilizing high-vacuum methods. One such method is photoelectron spectroscopy (PES), which allows one to probe the electronic properties of a sample through ionization in a state-specific manner. Liquid microjets consisting of pure solvents and solute-solvent systems have been studied with great success utilizing PES and, more recently, time-resolved PES (TRPES). Here, we discuss progress made over recent years in understanding the solvation and excited state dynamics of the solvated electron and nucleic acid constituents (NACs) using these methods, as well as the prospect for their future.The solvated electron is of particular interest in liquid microjet experiments as it represents the simplest solute system. Despite this simplicity, there were still many unresolved questions about its binding energy and excited state relaxation dynamics that are ideal problems for liquid microjet PES. In the work discussed in this Account, accurate binding energies were measured for the solvated electron in multiple high vapor pressure solvents. The advantages of liquid jet PES were further highlighted in the femtosecond excited state relaxation studies on the solvated electron in water where a 75 ± 20 fs lifetime attributable to internal conversion from the excited p-state to a hot ground state was measured, supporting a nonadiabatic relaxation mechanism.Nucleic acid constituents represent a class of important solutes with several unresolved questions that the liquid microjet PES method is uniquely suited to address. As TRPES is capable of tracking dynamics with state-specificity, it is ideal for instances where there are multiple excited states potentially involved in the dynamics. Time-resolved studies of NAC relaxation after excitation using ultraviolet light identified relaxation lifetimes from multiple excited states. The state-specific nature of the TRPES method allowed us to identify the lack of any signal attributable to the 1nπ* state in thymine derived NACs. The femtosecond time resolution of the technique also aided in identifying differences between the excited state lifetimes of thymidine and thymidine monophosphate. These have been interpreted, aided by molecular dynamics simulations, as an influence of conformational differences leading to a longer excited state lifetime in thymidine monophosphate.Finally, we discuss advances in tabletop light sources extending into the extreme ultraviolet and soft X-ray regimes that allow expansion of liquid jet TRPES to full valence band and potentially core level studies of solutes and pure liquids in liquid microjets. As most solutes have ground state binding energies in the range of 10 eV, observation of both excited state decay and ground state recovery using ultraviolet pump-ultraviolet probe TRPES has been intractable. With high-harmonic generation light sources, it will be possible to not only observe complete relaxation pathways for valence level dynamics but to also track dynamics with element specificity by probing core levels of the solute of interest.
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Affiliation(s)
- Zachary N Heim
- Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
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14
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Mandal S, Srinivasan V. Rationalizing the Unexpected Sensitivity in Excited State Lifetimes of Adenine to Tautomerization by Nonadiabatic Molecular Dynamics. J Phys Chem B 2022; 126:7077-7087. [PMID: 36083211 DOI: 10.1021/acs.jpcb.2c03178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The remarkable photostability of canonical nucleobases makes them ideal building blocks for DNA and RNA. Even minor structural changes are expected to lead to drastic alteration of their subpicosecond excited state lifetimes. However, it is interesting to note that while the 9H- and 7H-amino tautomers of adenine possess drastically different lifetimes, 9H- and 7H-keto guanine possess similar excited state lifetimes. With an aim to explain this unexpected difference in sensitivity of lifetimes to tautomerization, we have investigated the excited state relaxation mechanism of UV-excited adenine and guanine tautomers using surface hopping based nonadiabatic molecular dynamics. We find that internal conversion in both guanine tautomers is almost barrierless while both adenine tautomers encounter significant barriers before they can deactivate. Moreover, the major deactivation channel (C2-puckering) in 9H-amino adenine is overall more efficient than the one (C6-puckering) in the 7H-amino form. We trace this difference to the frequent rotation of the amino group which disrupts its conjugation with the heterocyclic ring thereby reducing the strength of nonadiabatic coupling and, hence, delaying internal conversion.
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Affiliation(s)
- Satyajit Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462 066, India
| | - Varadharajan Srinivasan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462 066, India
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15
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de Vries MS. Understanding How a New Hachimoji Nucleobase Alters Photodynamics of Genetic Building Blocks. Photochem Photobiol 2022; 99:857-859. [PMID: 36062299 DOI: 10.1111/php.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022]
Abstract
This article is a highlight of the paper by Krul et al. in this issue of Photochemistry and Photobiology. It describes the excited state dynamics of 5-aza-7-deazaguanine (5N7C G), which has recently been proposed as an alternative nucleobase. Upon UV absorption to the lowest energy 1 ππ* state, 5N7C G returns to the electronic ground state an order of magnitude more slowly than guanine with a corresponding greater fluorescence quantum yield. These findings are significant because they suggest that 5N7C G is less UV photostable that its canonical nucleobase equivalent, which would have been a selective disadvantage in prebiotic conditions.
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Affiliation(s)
- Mattanjah S de Vries
- Department of Chemistry and Biochemistry, University of California Santa Barbara, CA, 93106-9510, USA
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16
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Fu TH, Lin MY, Fu CB, Yu XF, Xiao B, Cheng JB, Li Q. The role of nitro group on the excited-state relaxation mechanism of P-Z base pair. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120549. [PMID: 34810098 DOI: 10.1016/j.saa.2021.120549] [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: 05/25/2021] [Revised: 09/09/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
DNAs' photostability is significant to the normal function of organisms. P-Z is a hydrogen bonded artificial DNA base pair, where P and Z represent 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one and 6-amino-5nitro-2(1H)-pyridone, respectively. The excited-state relaxation mechanism of P-Z pair is investigated using static TDDFT calculations combined with the non-adiabatic dynamic simulations at TDDFT level. The roles of nitro rotation, nitro out-of-plane deformation, and single proton transfer (SPT) along hydrogen bond are revealed. The results of potential energy profile calculations demonstrate that the SPT processes along the hydrogen bonds are unfavorable to occur statically, which is in great contrast to the natural base pair. The non-adiabatic dynamic simulations show that the excited-state nitro rotation and nitro out-of-plane deformation are the two important relaxation channels which lead to the fast internal conversion to S0 state. The SPT from Z to P is also observed, followed by distortion on P, inducing the fast internal conversion to S0 state. However, this channel (decay via SPT process) plays minor roles on the excited-state relaxation mechanism statistically. This work shows the great differences of the excited-state relaxation mechanism between the natural base pairs and artificial base pair, also sheds new light into the role of hydrogen bond and nitro group in P-Z base pair.
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Affiliation(s)
- Ting-He Fu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China
| | - Man-Yu Lin
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China
| | - Cheng-Bin Fu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China
| | - Xue-Fang Yu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Bo Xiao
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China
| | - Jian-Bo Cheng
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China
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17
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Kim J, Woo KC, Kim KK, Kang M, Kim SK. Tunneling dynamics dictated by the multidimensional conical intersection seam in the πσ*‐mediated photochemistry of heteroaromatic molecules. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Junggil Kim
- Department of Chemistry, KAIST Daejeon Republic of Korea
| | - Kyung Chul Woo
- Department of Chemistry, KAIST Daejeon Republic of Korea
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences Nanyang Technological University Singapore Singapore
| | - Kuk Ki Kim
- Department of Chemistry, KAIST Daejeon Republic of Korea
| | - Minseok Kang
- Department of Chemistry, KAIST Daejeon Republic of Korea
| | - Sang Kyu Kim
- Department of Chemistry, KAIST Daejeon Republic of Korea
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18
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Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code. Acta Biotheor 2021; 69:745-767. [PMID: 34283307 DOI: 10.1007/s10441-021-09420-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature Tm, the Tm:M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single -C=C bond and two nitrogen atoms in each heterocycle involved in C-N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of -C=O and/or -NH2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M-Tm diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, Tm, photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code.
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19
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Laamiri K, Garcia GA, Nahon L, Ben Houria A, Feifel R, Hochlaf M. Threshold photoelectron spectroscopy of 9-methyladenine: theory and experiment. Phys Chem Chem Phys 2021; 24:3523-3531. [PMID: 34676858 DOI: 10.1039/d1cp03729c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present a combined experimental and theoretical study of single-photon ionization of 9-methyladenine (9MA) in the gas phase. In addition to tautomerism, several rotamers due to the rotation of the methyl group may exist. Computations show, however, that solely one rotamer contributes because of low population in the molecular beam and/or unfavorable Franck-Condon factors upon ionization. Experimentally, we used VUV radiation available at the DESIRS beamline of the synchrotron radiation facility SOLEIL to record the threshold photoelectron spectrum of this molecule between 8 and 11 eV. This spectrum consists of a well-resolved band assigned mainly to vibronic levels of the D0 cationic state, plus a contribution from the D1 state, and two large bands corresponding to the D1, D2 and D3 electronically excited states. The adiabatic ionization energy of 9MA is measured at 8.097 ± 0.005 eV in close agreement with the computed value using the explicitly correlated coupled cluster approach including core valence, scalar relativistic and zero-point vibrational energy corrections. This work sheds light on the complex pattern of the lowest doublet electronic states of 9MA+. The comparison to canonical adenine reveals that methylation induces further electronic structure complication that may be important to understand the effects of ionizing radiation and the charge distribution in these biological entities at different time scales.
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Affiliation(s)
- K Laamiri
- Université Gustave Eiffel, COSYS/LISIS, 5 Bd Descartes 77454, Champs-sur-Marne, France. .,Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA, Université de Tunis El Manar, Tunis, Tunisia
| | - G A Garcia
- Synchrotron SOLEIL, L'orme des Merisiers, Saint-Aubin - BP 48 - 91192 Gif-sur-Yvette Cedex, France
| | - L Nahon
- Synchrotron SOLEIL, L'orme des Merisiers, Saint-Aubin - BP 48 - 91192 Gif-sur-Yvette Cedex, France
| | - A Ben Houria
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA, Université de Tunis El Manar, Tunis, Tunisia
| | - R Feifel
- University of Gothenburg, Department of Physics, 412 58 Gothenburg, Sweden
| | - M Hochlaf
- Université Gustave Eiffel, COSYS/LISIS, 5 Bd Descartes 77454, Champs-sur-Marne, France.
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20
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Ullah N, Chen S, Zhang R. Adenine ultrafast photorelaxation via electron-driven proton transfer. Phys Chem Chem Phys 2021; 23:23090-23095. [PMID: 34617085 DOI: 10.1039/d1cp03162g] [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
Photorelaxation of adenine in water was reported to be ultrafast (within 180 fs) primarily due to radiationless relaxation. However, in the last two decades, several experimental and theoretical investigations on photoexcitation of adenine have revealed diverse types of decay mechanisms. Using time-dependent density functional excited-state nonadiabatic dynamics simulations we show that it is the water to adenine electron-driven proton transfer (EDPT) barrierless reaction responsible for the ultrafast component of the adenine relaxation, which, however, occurred only in the case of the 7H isomer of adenine with five water molecules. This result reveals a known reaction pathway, however not found in previous simulations, with inference for the ultrafast relaxation mechanisms of adenine reported in experiments. The 9H isomer of adenine with six water molecules relaxing in a water cluster followed the previously known structural distortion (C2) decay pathway. The observations of the adenine EDPT reaction with water provide the origin of the experimental ultrafast adenine decay component and present a possible method to tackle future computational challenges in molecular-level biological processes.
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Affiliation(s)
- Naeem Ullah
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China.
| | - Shunwei Chen
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ruiqin Zhang
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China. .,Beijing Computational Science Research Center, Beijing 100193, China
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21
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Hervé M, Boyer A, Brédy R, Compagnon I, Allouche AR, Lépine F. Controlled ultrafast ππ*-πσ* dynamics in tryptophan-based peptides with tailored micro-environment. Commun Chem 2021; 4:124. [PMID: 36697624 PMCID: PMC9814788 DOI: 10.1038/s42004-021-00557-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/26/2021] [Indexed: 01/28/2023] Open
Abstract
Ultrafast charge, energy and structural dynamics in molecules are driven by the topology of the multidimensional potential energy surfaces that determines the coordinated electronic and nuclear motion. These processes are also strongly influenced by the interaction with the molecular environment, making very challenging a general understanding of these dynamics on a microscopic level. Here we use electrospray and mass spectrometry technologies to produce isolated molecular ions with a controlled micro-environment. We measure ultrafast photo-induced ππ*-πσ* dynamics in tryptophan species in the presence of a single, charged adduct. A striking increase of the timescale by more than one order of magnitude is observed when changing the added adduct atom. A model is proposed to rationalize the results, based on the localized and delocalized effects of the adduct on the electronic structure of the molecule. These results offer perspectives to control ultrafast molecular processes by designing the micro-environment on the Angström length scale.
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Affiliation(s)
- Marius Hervé
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Alexie Boyer
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Richard Brédy
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Isabelle Compagnon
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Abdul-Rahman Allouche
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Franck Lépine
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
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22
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Yu XF, Fu TH, Xiao B, Yu HY, Li Q. A theoretical study on the excited-state deactivation paths for the A-5FU dimer. Phys Chem Chem Phys 2021; 23:16089-16106. [PMID: 34291779 DOI: 10.1039/d1cp00030f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The photostability of DNA plays a key role in the normal function of organisms. A-5FU is a base pair derivative of the A-T dimer where the methyl group is replaced by a F atom. Here, accurate static TDDFT calculations and non-adiabatic dynamic simulations are used to systematically investigate the excited-state decay paths of the A-5FU dimer related to the proton transfer and the out-of-plane twisting deformation motion of A and 5FU in the 1ππ* and 1nπ* states. CC2 is used to check the accuracy of the current TDDFT calculations. Our results show that the deformation of the C[double bond, length as m-dash]C or C[double bond, length as m-dash]N double bond in A and 5FU provides an efficient pathway for the depopulation of the lowest excited states, which can compete with the excited-state proton transfer paths in the dimer. This finding indicates that monomer-like decay paths could be important for the photostability of weakly hydrogen-bonded DNA base pairs and provide a new insight into the excited-state decay paths in base pairs and their analogues.
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Affiliation(s)
- Xue-Fang Yu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
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23
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Castellani ME, Avagliano D, Verlet JRR. Ultrafast Dynamics of the Isolated Adenosine-5'-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging. J Phys Chem A 2021; 125:3646-3652. [PMID: 33882670 DOI: 10.1021/acs.jpca.1c01646] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The excited state dynamics of the doubly deprotonated dianion of adenosine-5'-triphosphate, [ATP-H2]2-, has been spectroscopically explored by time-resolved photoelectron spectroscopy following excitation at 4.66 eV. Time-resolved photoelectron spectra show that two competing processes occur for the initially populated 1ππ* state. The first is rapid electron emission by tunneling through a repulsive Coulomb barrier as the 1ππ* state is a resonance. The second is nuclear motion on the 1ππ* state surface leading to an intermediate that no longer tunnels and subsequently decays by internal conversion to the ground electronic state. The spectral signatures of the features are similar to those observed for other adenine-derivatives, suggesting that this nucleobase is quite insensitive to the nearby negative charges localized on the phosphates, except of course for the appearance of the additional electron tunneling channel, which is open in the dianion.
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Affiliation(s)
| | - Davide Avagliano
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17 1090 Vienna, Austria
| | - Jan R R Verlet
- Department of Chemistry, Durham University, DH1 3LE Durham, U.K
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24
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Chan RCT, Chan CTL, Ma C, Gu KY, Xie HX, Wong AKW, Xiong QW, Wang ML, Kwok WM. Long living excited state of protonated adenosine unveiled by ultrafast fluorescence spectroscopy and density functional theoretical study. Phys Chem Chem Phys 2021; 23:6472-6480. [PMID: 33729247 DOI: 10.1039/d0cp06439d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenosine (Ado) possesses ultrafast nonradiative dynamics accounting for its remarkably high photostability. The deactivation dynamics of Ado after protonation in an aqueous solution remains an elusive issue. Herein we report an investigation of the excited state dynamics of protonated Ado (AdoH+) performed using ultrafast time-resolved fluorescence spectroscopy combined with density functional theoretical calculation. The result obtained from comparison of conformers with protonation at different sites revealed that the syn-conformer with protonation occurring at the N3 position (syn-N3) is the predominant form of AdoH+ in the ground state, similar to that of Ado. In contrast, the fluorescence of AdoH+ with maximum intensity at 385 nm, significantly red-shifted from that of Ado, displaying decay dynamics composed of an ultrafast component with the lifetime of ∼0.5 ps and a slower one of ∼2.9 ns. The former is because of the decay of the syn-N3 conformer, similar to that reported for AdoH+ under the gas phase condition. The latter is due to the syn-N1 conformer formed via ultrafast proton transfer of the syn-N3. The excited state of syn-N1 has a peculiar nonplanar conformation over the purine molecule, which is responsible for the substantial Stokes shift showed in the fluorescence spectrum and correlates with a large energy barrier for nonradiative decay likely involving a reversed proton transfer. This study demonstrates the importance of protonation and solvent environment in altering dramatically the excited states of Ado, providing insight for better understanding nonradiative dynamics of both the monomeric bases and the oligomeric or polymeric DNAs.
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Affiliation(s)
- Ruth Chau-Ting Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China.
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25
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Castellani ME, Avagliano D, González L, Verlet JRR. Site-Specific Photo-oxidation of the Isolated Adenosine-5'-triphosphate Dianion Determined by Photoelectron Imaging. J Phys Chem Lett 2020; 11:8195-8201. [PMID: 32886886 DOI: 10.1021/acs.jpclett.0c02089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Photoelectron imaging of the isolated adenosine-5'-triphosphate dianion excited to the 1ππ* states reveals that electron emission is predominantly parallel to the polarization axis of the light and arises from subpicosecond electron tunneling through the repulsive Coulomb barrier (RCB). The computed RCB shows that the most probable electron emission site is on the amino group of adenine. This is consistent with the photoelectron imaging: excitation to the 1ππ* states leads to an aligned ensemble distributed predominantly parallel to the long axis of adenine; the subsequent electron tunneling site is along this axis; and the negatively charged phosphate groups guide the outgoing electron mostly along this axis at long range. Imaging of electron tunneling from polyanions combined with computational chemistry may offer a general route for probing the intrinsic photo-oxidation site and dynamics as well as the overall structure of complex isolated species.
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Affiliation(s)
| | - Davide Avagliano
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
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26
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Lamas I, Montero R, Martínez-Martínez V, Longarte A, Blancafort L. An nπ* gated decay mediates excited-state lifetimes of isolated azaindoles. Phys Chem Chem Phys 2020; 22:18639-18645. [PMID: 32789383 DOI: 10.1039/d0cp02635b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aiming to serve as a guide to understand the relaxation mechanisms of more complex aza-aromatic compounds, such as purine bases, we have studied the non-radiative channels of a set of azaindole structural isomers: 4-, 5-, 6- and 7-azaindole (AI). The relaxation of the isolated molecules, after excitation at the low energy portion of their spectra, has been tracked by femtosecond time-resolved ionization, and the decay paths have been obtained with MS-CASPT2//TD-DFT calculations. Although the ultrashort measured lifetimes for 5- and 6-AI are in contrast to the long-living excited state found in 7-AI, the calculations describe a common relaxation pathway. Along it, the initially excited ππ* states decay to the ground state through a conical intersection accessed through an nπ* state that functions as a gate state. The work reveals that the position of the nitrogen atoms in the purine ring determines the barrier to access the gate state and therefore, the rate of the non-radiative relaxation.
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Affiliation(s)
- Iker Lamas
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apart. 644, 48080 Bilbao, Spain.
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27
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Kempfer-Robertson EM, Pike TD, Thompson LM. Difference projection-after-variation double-hybrid density functional theory applied to the calculation of vertical excitation energies. J Chem Phys 2020; 153:074103. [DOI: 10.1063/5.0017222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Thomas Dane Pike
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40205, USA
| | - Lee M. Thompson
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40205, USA
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28
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MacDonell RJ, Corrales ME, Boguslavskiy AE, Bañares L, Stolow A, Schuurman MS. Substituent effects on nonadiabatic excited state dynamics: Inertial, steric, and electronic effects in methylated butadienes. J Chem Phys 2020; 152:084308. [DOI: 10.1063/1.5139446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ryan J. MacDonell
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - María E. Corrales
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Luis Bañares
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Albert Stolow
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Michael S. Schuurman
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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29
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Xie C, Zhao B, Malbon CL, Yarkony DR, Xie D, Guo H. Insights into the Mechanism of Nonadiabatic Photodissociation from Product Vibrational Distributions. The Remarkable Case of Phenol. J Phys Chem Lett 2020; 11:191-198. [PMID: 31821757 DOI: 10.1021/acs.jpclett.9b03407] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The fate of a photoexcited molecule is often strongly influenced by electronic degeneracies, such as conical intersections, which break the Born-Oppenheimer separation of electronic and nuclear motion. Detailed information concerning internal energy redistribution in a nonadiabatic process can be extracted from the product state distribution of a photofragment in photodissociation. Here, we focus on the nonadiabatic photodissociation of phenol and discuss the internal excitation of the phenoxyl fragment using both symmetry analysis and wave packet dynamics. It is shown that unique and general selection rules exist, which can be attributed to the geometric phase in the adiabatic representation. Further, our results provide a reinterpretation of the experimental data, shedding light on the impact of conical intersections on the product state distribution.
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Affiliation(s)
- Changjian Xie
- Institute of Modern Physics, Shaanxi Key Laboratory for Theoretical Physics Frontiers , Northwest University , Xian , Shaanxi 710127 , China
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Bin Zhao
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Christopher L Malbon
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - David R Yarkony
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Hua Guo
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
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30
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Zhang X, Zhai J, Zhong Y, Yang X. Degradation and DBP formations from pyrimidines and purines bases during sequential or simultaneous use of UV and chlorine. WATER RESEARCH 2019; 165:115023. [PMID: 31472336 DOI: 10.1016/j.watres.2019.115023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Purine and pyrimidines are present an important pool of dissolved organic nitrogen in aqueous medias and also precursors of disinfection byproducts. The degradation kinetics of cytosine and adenine-model pyrimidine and purine compounds-were investigated along with their transformation pathways leading to the formation of disinfection byproducts during two typical multi-barrier disinfection processes: UV irradiation and UV/chlorine pretreatment followed by post-chlorination. UV irradiation followed by post-chlorination enhanced the degradation of cytosine and adenine (by 17.1 and 26.1%, respectively), but it also generated more byproduct precursors compared to chlorination alone. The presence of reactive species in the UV/chlorine treatment greatly enhanced cytosine and adenine degradation (by 61.8 and 123.0%) but generated even more disinfection byproducts. Compared to 24 h chlorination, the concentrations of byproducts increased by up to 361.6% for cytosine and 85.1% for adenine with longer UV/chlorine treatment (from 2 to 30 min). Thirty minutes of combined UV/chlorine treatment decreased the total organic chlorine produced from cytosine by 34.4% (from 233.8 to 153.3 μg Cl L-1) but it increased byproduct generation by 68.3% compared with 24 h of simple chlorination. The TOCl from adenine increased by 50.0% (from 9.2 to 18.4 μg Cl L-1) but byproduct generation was 11.0% less after 30 min of UV/chlorine pretreatment followed by 24 h of chlorination. The intermediates generated were analyzed in detail and multiple transformation pathways leading to byproduct formation are proposed.
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Affiliation(s)
- Xinran Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Jiaxin Zhai
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yu Zhong
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xin Yang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China.
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31
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Wolf TJA, Gühr M. Photochemical pathways in nucleobases measured with an X-ray FEL. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20170473. [PMID: 30929626 PMCID: PMC6452046 DOI: 10.1098/rsta.2017.0473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The conversion of light energy into other molecular energetic degrees of freedom is often dominated by ultrafast, non-adiabatic processes. Femtosecond spectroscopy with optical pulses has helped in shaping our understanding of crucial processes in molecular energy-conversion. The advent of new, ultrashort and bright X-ray free electron laser sources opens the possibility to use X-ray-typical element and site sensitivity for ultrafast molecular research. We present two types of spectroscopy, ultrafast Auger and ultrafast X-ray absorption spectroscopy, and discuss their sensitivity to molecular processes. While Auger spectroscopy is able to monitor bond distance changes in the vicinity of an X-ray created core hole, near-edge absorption spectroscopy can deliver high-fidelity information on non-adiabatic transitions involving lone-pair orbitals. We demonstrate these features on the example of the UV-excited nucleobase thymine, investigated at the oxygen K-edge. We find a C-O bond elongation in the Auger data in addition to ππ*/ nπ* non-adiabatic transition in X-ray near-edge absorption. We compare the results from both methods and draw a conclusive scenario of non-adiabatic molecular relaxation after UV excitation. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
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Affiliation(s)
- Thomas J. A. Wolf
- SLAC National Accelerator Laboratory, PULSE, 2575 Sand Hill Road, Menlo Park 94025, CA, USA
| | - Markus Gühr
- SLAC National Accelerator Laboratory, PULSE, 2575 Sand Hill Road, Menlo Park 94025, CA, USA
- Physics and Astronomy Institute, Universität Potsdam, Karl-Liebknecht-Strasse 24/25, Potsdam 14476, Germany
- e-mail:
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32
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MacDonell RJ, Schuurman MS. Site-Selective Isomerization of Cyano-Substituted Butadienes: Chemical Control of Nonadiabatic Dynamics. J Phys Chem A 2019; 123:4693-4701. [DOI: 10.1021/acs.jpca.9b02446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ryan J. MacDonell
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, D’Iorio Hall, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Michael S. Schuurman
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, D’Iorio Hall, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
- National Research of Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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33
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Ghosh J, Gajapathy H, Jayachandran A, Bernstein ER, Bhattacharya A. On the electronically nonadiabatic decomposition dynamics of furazan and triazole energetic molecules. J Chem Phys 2019; 150:164304. [PMID: 31042884 DOI: 10.1063/1.5088995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The combined results of ab initio electronic-structure calculations, nonadiabatic molecular dynamics simulations using ab initio multiple spawning, and previous spectroscopic investigations of jet-cooled molecules provide strong evidence of a (π,σ*)-mediated decomposition mechanism for the furazan and triazole energetic molecules. The importance of dissociative excited states formed by electron promotion from a π molecular orbital to a σ* molecular orbital is explored for the furazan and triazole energetic molecules. Dissociative (π,σ*) states of furazan and triazole energetic molecules can be populated by nonadiabatic surface jump from the (π,π*) or the (n,π*) state. Finally, conical intersections between (π,σ*) potential energy surfaces (PESs) and the ground PES influence the eventual fragmentation dynamics of the furazan and triazole energetic molecules. Due to structural similarity of the triazole molecule with the pyrrole molecule, a comparison of nonadiabatic dynamics of these two molecules is also presented. The N-N bond dissociation is found to be a barrierless pathway for the triazole molecule, whereas the N-H bond dissociation exhibits a barrierless pathway for the pyrrole molecule. The present work, thus, provides insights into the excited-state chemistry of furazan and triazole energetic functional groups. The same insight can also be relevant for other energetic molecules.
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Affiliation(s)
- Jayanta Ghosh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Harshad Gajapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ajay Jayachandran
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Elliot R Bernstein
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Atanu Bhattacharya
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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34
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Pitzer M, Ozga C, Küstner-Wetekam C, Reiß P, Knie A, Ehresmann A, Jahnke T, Giuliani A, Nahon L. State-Dependent Fragmentation of Protonated Uracil and Uridine. J Phys Chem A 2019; 123:3551-3557. [PMID: 30943036 DOI: 10.1021/acs.jpca.9b01822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Action spectroscopy using photon excitation in the VUV range (photon energy 4.5-9 eV) was performed on protonated uracil (UraH+) and uridine (UrdH+). The precursor ions with m/ z 113 and m/ z 245, respectively, were produced by an electrospray ionization source and accumulated inside a quadrupole ion trap mass spectrometer. After irradiation with tunable synchrotron radiation, product ion mass spectra were obtained. Fragment yields as a function of excitation energy show several maxima that can be attributed to the photoexcitation into different electronic states. For uracil, vertically excited states were calculated using the equation-of-motion coupled cluster approach and compared to the observed maxima. This allows to establish correlations between electronic states and the resulting fragment masses and can thus help to disentangle the complex de-excitation and fragmentation pathways of nucleic acid building blocks. Photofragmentation of the nucleoside uridine shows a significantly lower variety of fragments, indicating stabilization of the nucleobase by the attached sugar.
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Affiliation(s)
- Martin Pitzer
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel.,Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Christian Ozga
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Catmarna Küstner-Wetekam
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Philipp Reiß
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - André Knie
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Arno Ehresmann
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Till Jahnke
- Institute for Nuclear Physics , Goethe-University , 60438 Frankfurt , Germany
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35
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Sun Z, Wang C, Zhao W, Yang C. Mapping of the light-induced conical intersections in the photoelectron spectra of K 2 molecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 207:348-353. [PMID: 30268902 DOI: 10.1016/j.saa.2018.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/31/2018] [Accepted: 09/08/2018] [Indexed: 06/08/2023]
Abstract
In the strong field regime, exploring the physical nature of molecular dynamics is still a challenge due to the dramatic change of molecular potentials. Here, we perform a quantum wave packet study on the pump-probe ionization of K2 molecules and show how the light-induced conical intersections (LICIs) are imprinted into the molecular photoelectron spectra. We demonstrate that the energy and angular distributions of photoelectron spectra provide an accurate mapping of the electronic structure under the influence of the strong laser field. The determination of correct characterization of LICIs can help us to better explore alternative ways to control dynamics.
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Affiliation(s)
- Zhaopeng Sun
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.
| | - Chunyang Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Wenkai Zhao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Chuanlu Yang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.
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36
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Wu X, Ehrmaier J, Sobolewski AL, Karsili TNV, Domcke W. Mechanisms of photoreactivity in hydrogen-bonded adenine-H 2O complexes. Phys Chem Chem Phys 2019; 21:14238-14249. [PMID: 30543228 DOI: 10.1039/c8cp05305g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanisms of photoinduced reactions of adenine with water molecules in hydrogen-bonded adenine-water complexes were investigated with ab initio wave-function-based electronic-structure calculations. Two excited-state electron/proton transfer reaction mechanisms have been characterized: H-atom abstraction from water by photoexcited adenine as well as H-atom transfer from photoexcited adenine or the (adenine+H) radical to water. In the water-to-adenine H-atom transfer reaction, an electron from one of the p orbitals of the water molecule fills the hole in the n (π) orbital of the nπ* (ππ*) excited state of adenine, resulting in a charge-separated electronic state. The electronic charge separation is neutralized by the transfer of a proton from the water molecule to adenine, resulting in the (adenine+H)OH biradical in the electronic ground state. In the adenine-to-water H-atom transfer reaction, πσ* states localized at the acidic sites of adenine provide the mechanism for the photoejection of an electron from adenine, which is followed by proton transfer to the hydrogen-bonded water molecule, resulting in the (adenine-H)H3O biradical. The energy profiles of the photoreactions have been computed as relaxed scans with the ADC(2) electronic-structure method. These reactions, which involve the reactivity of adenine with hydrogen-bonded water molecules, compete with the well-established intrinsic excited-state deactivation mechanisms of adenine via ring-puckering or ring-opening conical intersections. By providing additional decay channels, the electron/proton exchange reactions with water can account for the observed significantly shortened excited-state lifetime of adenine in aqueous environments. These findings indicate that adenine possibly was not only a photostabilizer at the beginning of life, but also a primordial photocatalyst for water splitting.
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Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany.
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37
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Galli M, Wanie V, Månsson EP, Trabattoni A, Légaré F, Frassetto F, Poletto L, Nisoli M, Calegari F. A beamline for attosecond UV pump - XUV probe experiments. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920502017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A time resolved setup combining sub-2fs UV pump pulses with attosecond XUV probe pulses is presented. This scheme will allow the UV photo-induced electron dynamics in bio-chemically relevant molecules to be investigated with unprecedented time resolution.
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38
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Adachi S, Schatteburg T, Humeniuk A, Mitrić R, Suzuki T. Probing ultrafast dynamics during and after passing through conical intersections. Phys Chem Chem Phys 2019; 21:13902-13905. [PMID: 30259014 DOI: 10.1039/c8cp04426k] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved photoelectron spectroscopy using vacuum-UV probe pulses enables observing ultrafast dynamics during and after passing through conical intersections (CIs). The ring-puckering CI plays a prominent role following the ππ* photoexcitation of furan. More than 90% of the excited molecules safely return to the original ground state, while the remaining 10% transforms into isomers after passing through the puckering CI.
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Affiliation(s)
- Shunsuke Adachi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
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39
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Gate G, Szabla R, Haggmark MR, Šponer J, Sobolewski AL, de Vries MS. Photodynamics of alternative DNA base isoguanine. Phys Chem Chem Phys 2019; 21:13474-13485. [DOI: 10.1039/c9cp01622h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pump–probe experiments and quantum-chemical simulations of UV-excited isoguanine elucidate its tautomer dependent photochemical properties.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Rafał Szabla
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
- Institute of Biophysics of the Czech Academy of Sciences
| | - Michael R. Haggmark
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences
- 61265 Brno
- Czech Republic
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40
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Wu EC, Ge Q, Arsenault EA, Lewis NHC, Gruenke NL, Head-Gordon MJ, Fleming GR. Two-dimensional electronic-vibrational spectroscopic study of conical intersection dynamics: an experimental and electronic structure study. Phys Chem Chem Phys 2019; 21:14153-14163. [DOI: 10.1039/c8cp05264f] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relaxation from the lowest singlet excited state of the triphenylmethane dyes, crystal violet and malachite green, is studied via two-dimensional electronic-vibrational (2DEV) spectroscopy.
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Affiliation(s)
- Eric C. Wu
- Department of Chemistry
- University of California
- Berkeley
- USA
- Molecular Biophysics and Integrated Bioimaging Division
| | - Qinghui Ge
- Department of Chemistry
- University of California
- Berkeley
- USA
| | - Eric A. Arsenault
- Department of Chemistry
- University of California
- Berkeley
- USA
- Molecular Biophysics and Integrated Bioimaging Division
| | | | - Natalie L. Gruenke
- Department of Chemistry
- University of California
- Berkeley
- USA
- Molecular Biophysics and Integrated Bioimaging Division
| | | | - Graham R. Fleming
- Department of Chemistry
- University of California
- Berkeley
- USA
- Molecular Biophysics and Integrated Bioimaging Division
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41
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Stange UC, Temps F. Ultrafast electronic deactivation of UV-excited adenine and its ribo- and deoxyribonucleosides and -nucleotides: A comparative study. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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42
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Williams HL, Erickson BA, Neumark DM. Time-resolved photoelectron spectroscopy of adenosine and adenosine monophosphate photodeactivation dynamics in water microjets. J Chem Phys 2018; 148:194303. [PMID: 30307253 DOI: 10.1063/1.5027258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The excited state relaxation dynamics of adenosine and adenosine monophosphate were studied at multiple excitation energies using femtosecond time-resolved photoelectron spectroscopy in a liquid water microjet. At pump energies of 4.69-4.97 eV, the lowest ππ* excited state, S1, was accessed and its decay dynamics were probed via ionization at 6.20 eV. By reversing the role of the pump and probe lasers, a higher-lying ππ* state was excited at 6.20 eV and its time-evolving photoelectron spectrum was monitored at probe energies of 4.69-4.97 eV. The S1 ππ* excited state was found to decay with a lifetime ranging from ∼210 to 250 fs in adenosine and ∼220 to 250 fs in adenosine monophosphate. This lifetime drops with increasing pump photon energy. Signal from the higher-lying ππ* excited state decayed on a time scale of ∼320 fs and was measureable only in adenosine monophosphate.
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Affiliation(s)
- Holly L Williams
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Blake A Erickson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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43
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Zhao HY, Lau KC, Garcia GA, Nahon L, Carniato S, Poisson L, Schwell M, Al-Mogren MM, Hochlaf M. Unveiling the complex vibronic structure of the canonical adenine cation. Phys Chem Chem Phys 2018; 20:20756-20765. [PMID: 29989120 DOI: 10.1039/c8cp02930j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenine, a DNA base, exists as several tautomers and isomers that are closely lying in energy and that may form a mixture upon vaporization of solid adenine. Indeed, it is challenging to bring adenine into the gas phase, especially as a unique tautomer. The experimental conditions were tuned to prepare a jet-cooled canonical adenine (9H-adenine). This isolated DNA base was ionized by single VUV photons from a synchrotron beamline and the corresponding slow photoelectron spectrum was compared to ab initio computations of the neutral and ionic species. We report the vibronic structure of the X+ 2A'' (D0), A+ 2A' (D1) and B+ 2A'' (D2) electronic states of the 9H adenine cation, from the adiabatic ionization energy (AIE) up to AIE + 1.8 eV. Accurate AIEs are derived for the 9H-adenine (X[combining tilde] 1A') + hν → 9H-adenine+ (X+ 2A'', A+ 2A', B+ 2A'') + e- transitions. Close to the AIE, we fully assign the rich vibronic structure solely to the 9H-adenine (X 1A') + hν → 9H-adenine+ (X+ 2A'') transition. Importantly, we show that the lowest cationic electronic states of canonical adenine are coupled vibronically. The present findings are important for understanding the effects of ionizing radiation and the charge distribution on this elementary building block of life, at ultrafast, short, and long timescales.
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Affiliation(s)
- Hong Yan Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
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44
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von Conta A, Tehlar A, Schletter A, Arasaki Y, Takatsuka K, Wörner HJ. Conical-intersection dynamics and ground-state chemistry probed by extreme-ultraviolet time-resolved photoelectron spectroscopy. Nat Commun 2018; 9:3162. [PMID: 30089780 PMCID: PMC6082858 DOI: 10.1038/s41467-018-05292-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/15/2018] [Indexed: 11/09/2022] Open
Abstract
Time-resolved photoelectron spectroscopy (TRPES) is a useful approach to elucidate the coupled electronic-nuclear quantum dynamics underlying chemical processes, but has remained limited by the use of low photon energies. Here, we demonstrate the general advantages of XUV-TRPES through an application to NO2, one of the simplest species displaying the complexity of a non-adiabatic photochemical process. The high photon energy enables ionization from the entire geometrical configuration space, giving access to the true dynamics of the system. Specifically, the technique reveals dynamics through a conical intersection, large-amplitude motion and photodissociation in the electronic ground state. XUV-TRPES simultaneously projects the excited-state wave packet onto many final states, offering a multi-dimensional view of the coupled electronic and nuclear dynamics. Our interpretations are supported by ab initio wavepacket calculations on new global potential-energy surfaces. The presented results contribute to establish XUV-TRPES as a powerful technique providing a complete picture of ultrafast chemical dynamics from photoexcitation to the final products.
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Affiliation(s)
- A von Conta
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland
| | - A Tehlar
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland
| | - A Schletter
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland
| | - Y Arasaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto, 606-8103, Japan
| | - K Takatsuka
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto, 606-8103, Japan
| | - H J Wörner
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland.
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45
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Ling F, Li S, Wei J, Liu K, Wang Y, Zhang B. Unraveling the electronic relaxation dynamics in photoexcited 2,4-difluoroaniline via femtosecond time-resolved photoelectron imaging. J Chem Phys 2018; 148:144311. [DOI: 10.1063/1.5024255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Fengzi Ling
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Wei
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanmei Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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46
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Lee SY, Kang H. Nonresonant Contribution in Pump-Probe Transient Ion Signal of Adenine. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sang Yoon Lee
- Department of Biomedical Sciences and Chronic Inflammatory Disease Research Center; Ajou University School of Medicine; Suwon 16499 South Korea
| | - Hyuk Kang
- Department of Chemistry; Ajou University; Suwon 16499 South Korea
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47
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Marchetti B, Karsili TNV, Ashfold MNR, Domcke W. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs. Phys Chem Chem Phys 2018; 18:20007-27. [PMID: 26980149 DOI: 10.1039/c6cp00165c] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.
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Affiliation(s)
- Barbara Marchetti
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Tolga N V Karsili
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael N R Ashfold
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
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48
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Abstract
The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.
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Affiliation(s)
- Samuel Boldissar
- Department of Chemistry and Biochemistry University of California Santa Barbara
- USA
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49
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Lin GSM, Xie C, Xie D. Three-Dimensional Diabatic Potential Energy Surfaces for the Photodissociation of Thiophenol. J Phys Chem A 2017; 121:8432-8439. [DOI: 10.1021/acs.jpca.7b09070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guang-Shuang-Mu Lin
- Institute
of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic
Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Changjian Xie
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Daiqian Xie
- Institute
of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic
Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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50
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Dehez F, Gattuso H, Bignon E, Morell C, Dumont E, Monari A. Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates. Nucleic Acids Res 2017; 45:3654-3662. [PMID: 28334906 PMCID: PMC5397166 DOI: 10.1093/nar/gkx148] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/21/2017] [Indexed: 02/01/2023] Open
Abstract
DNA photolesions constitute a particularly deleterious class of molecular defects responsible for the insurgence of a vast majority of skin malignant tumors. Dimerization of two adjacent thymines or cytosines mostly gives rise to cyclobutane pyrimidine dimers (CPD) and pyrimidine(6-4)pyrimidone 64-PP as the most common defects. We perform all-atom classical simulations, up to 2 μs, of CPD and 64-PP embedded in a 16-bp duplex, which reveal the constrasted behavior of the two lesions. In particular we evidence a very limited structural deformation induced by CPD while 64-PP is characterized by a complex structural polymorphism. Our simulations also allow to unify the contrasting experimental structural results obtained by nuclear magnetic resonance or Förster Resonant Energy Transfer method, showing that both low and high bent structures are indeed accessible. These contrasting behaviors can also explain repair resistance or the different replication obstruction, and hence the genotoxicity of these two photolesions.
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Affiliation(s)
- François Dehez
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana Champaign
| | - Hugo Gattuso
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France
| | - Emmanuelle Bignon
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, ENS Lyon, Lyon, France.,Université de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F69342 Lyon, France
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, ENS Lyon, Lyon, France
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F69342 Lyon, France
| | - Antonio Monari
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France
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