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Walmsley T, McManus JW, Kumagai Y, Nagaya K, Harries J, Iwayama H, Ashfold MNR, Britton M, Bucksbaum PH, Downes-Ward B, Driver T, Heathcote D, Hockett P, Howard AJ, Lee JWL, Liu Y, Kukk E, Milesevic D, Minns RS, Niozu A, Niskanen J, Orr-Ewing AJ, Owada S, Robertson PA, Rolles D, Rudenko A, Ueda K, Unwin J, Vallance C, Brouard M, Burt M, Allum F, Forbes R. The Role of Momentum Partitioning in Covariance Ion Imaging Analysis. J Phys Chem A 2024. [PMID: 38713032 DOI: 10.1021/acs.jpca.4c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
We present results from a covariance ion imaging study, which employs extensive filtering, on the relationship between fragment momenta to gain deeper insight into photofragmentation dynamics. A new data analysis approach is introduced that considers the momentum partitioning between the fragments of the breakup of a molecular polycation to disentangle concurrent fragmentation channels, which yield the same ion species. We exploit this approach to examine the momentum exchange relationship between the products, which provides direct insight into the dynamics of molecular fragmentation. We apply these techniques to extensively characterize the dissociation of 1-iodopropane and 2-iodopropane dications prepared by site-selective ionization of the iodine atom using extreme ultraviolet intense femtosecond laser pulses with a photon energy of 95 eV. Our assignments are supported by classical simulations, using parameters largely obtained directly from the experimental data.
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Affiliation(s)
- Tiffany Walmsley
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Joseph W McManus
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Yoshiaki Kumagai
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Kiyonobu Nagaya
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - James Harries
- National Institutes for Quantum Science and Technology (QST), SPring-8, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Hiroshi Iwayama
- Institute for Molecular Science, Okazaki 444-8585, Japan
- Sokendai (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | | | - Mathew Britton
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Philip H Bucksbaum
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Briony Downes-Ward
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Taran Driver
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - David Heathcote
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Paul Hockett
- National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Andrew J Howard
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jason W L Lee
- Deutsches Elektronen-Synchrotron (DESY), Hamburg 22607, Germany
| | - Yusong Liu
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Edwin Kukk
- Department of Physics and Astronomy, University of Turku, Turku FI-20014, Finland
| | - Dennis Milesevic
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Russell S Minns
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Akinobu Niozu
- Graduate School of Advanced Science and Engineering, Hiroshima University, Hiroshima 739-8526, Japan
| | - Johannes Niskanen
- Department of Physics and Astronomy, University of Turku, Turku FI-20014, Finland
| | | | - Shigeki Owada
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198, Japan
| | - Patrick A Robertson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Daniel Rolles
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Artem Rudenko
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Kiyoshi Ueda
- Department of Chemistry, Tohoku University, Sendai 980-8578, Japan
| | - James Unwin
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Claire Vallance
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Mark Brouard
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Michael Burt
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Felix Allum
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Ruaridh Forbes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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2
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Jørgensen P, Olsen J, Johansen MB, von Buchwald TJ, Hillers-Bendtsen AE, Mikkelsen KV, Helgaker T. A variational reformulation of molecular properties in electronic-structure theory. Sci Adv 2024; 10:eadn3454. [PMID: 38657075 PMCID: PMC11042728 DOI: 10.1126/sciadv.adn3454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/19/2024] [Indexed: 04/26/2024]
Abstract
Conventional quantum-mechanical calculations of molecular properties, such as dipole moments and electronic excitation energies, give errors that depend linearly on the error in the wave function. An exception is the electronic energy, whose error depends quadratically on the error in wave function. We here describe how all properties may be calculated with a quadratic error, by setting up a variational Lagrangian for the property of interest. Because the construction of the Lagrangian is less expensive than the calculation of the wave function, this approach substantially improves the accuracy of quantum-chemical calculations without increasing cost. As illustrated for excitation energies, this approach enables the accurate calculation of molecular properties for larger systems, with a short time-to-solution and in a manner well suited for modern computer architectures.
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Affiliation(s)
- Poul Jørgensen
- Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Jeppe Olsen
- Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Magnus Bukhave Johansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Theo Juncker von Buchwald
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 260, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Trygve Helgaker
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P. O. Box 1033, Blindern, N-0315 Oslo, Norway
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3
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Jadoun D, Kowalewski M. Coherent x-ray spontaneous emission spectroscopy of conical intersections. J Chem Phys 2024; 160:094102. [PMID: 38426516 DOI: 10.1063/5.0180976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Conical intersections are known to play a vital role in many photochemical processes. The breakdown of the Born-Oppenheimer approximation in the vicinity of a conical intersection causes exciting phenomena, such as the ultrafast radiationless decay of excited states. The passage of a molecule through a conical intersection creates a coherent superposition of electronic states via nonadiabatic couplings. Detecting this coherent superposition may serve as a direct probe of the conical intersection. In this paper, we theoretically demonstrate the use of coherent spontaneous emission in samples with long-range order for probing the occurrence of a conical intersection in a molecule. Our simulations show that the spectrum contains clear signatures of the created coherent superposition of electronic states. We investigate the bandwidth requirements for the x-ray probes, which influence the observation of coherent superposition generated by the conical intersection.
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Affiliation(s)
- Deependra Jadoun
- Department of Physics, Stockholm University, Albanova University Centre, SE-106 91 Stockholm, Sweden
| | - Markus Kowalewski
- Department of Physics, Stockholm University, Albanova University Centre, SE-106 91 Stockholm, Sweden
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4
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Guo Z, Zhang M, Dong X, Wang J, Li Z, Liu Y. Probing Conical Intersection in the Multipathway Isomerization of CH 3Cl Using Coulomb Explosion. J Phys Chem Lett 2024; 15:2369-2374. [PMID: 38393833 DOI: 10.1021/acs.jpclett.3c03404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Ubiquitous ultrafast isomerization is paramount in photoexcited molecules, in which non-adiabatic coupling among multiple electronic states can occur. We use the pump-probe Coulomb explosion imaging method to study the isomerization of CH3Cl molecules. We find that the isomerization under our strong field pump-probe scheme proceeds along multiple pathways, which are encoded in several distinct branches of the time-resolved kinetic energy release spectra for the CH2++HCl+ Coulomb explosion channel. Apart from the isomerized dissociative pathway in neutral and cationic excited states, the pump laser can also induce coherent vibrational dynamics in two coupled intermediate states and set up the initial conditions for the two concurrently proceeding isomerization pathways. The isomerization of CH3Cl provides an intriguing example of a chemical reaction consisting of multiple pathways and non-adiabatic dynamics.
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Affiliation(s)
- Zhenning Guo
- State Key Laboratory for Mesoscopic Physics and Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Ming Zhang
- State Key Laboratory for Mesoscopic Physics and Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Xiaolong Dong
- State Key Laboratory for Mesoscopic Physics and Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Jiguo Wang
- State Key Laboratory for Mesoscopic Physics and Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Zheng Li
- State Key Laboratory for Mesoscopic Physics and Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Yangtze Delta Institute of Optoelectronics, Peking University, Nantong, Jiangsu 226010, China
| | - Yunquan Liu
- State Key Laboratory for Mesoscopic Physics and Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Center for Applied Physics and Technology, HEDPS, Peking University, Beijing 100871, China
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5
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Jadoun D, Zhang Z, Kowalewski M. Raman Spectroscopy of Conical Intersections Using Entangled Photons. J Phys Chem Lett 2024; 15:2023-2030. [PMID: 38349969 PMCID: PMC10895689 DOI: 10.1021/acs.jpclett.3c02852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/15/2024]
Abstract
Ultrafast Raman spectroscopy with attosecond pulses in the extreme ultraviolet and X-ray regime has been proposed theoretically for tracking the non-adiabatic dynamics of molecules in great detail. The large bandwidth of these pulses, which span several electronvolts within a couple of femtoseconds, provides a unique tool for tracking non-adiabatic phenomena. However, spectroscopy with classical light is limited by the time-bandwidth product of the probe laser pulse. In this work, we theoretically investigate an ultrafast Raman spectroscopy scheme that utilizes pairs of entangled photons. Our model simulations demonstrate that the dynamics in the vicinity of a conical intersection can be resolved with unprecedented resolution in the time and frequency domain.
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Affiliation(s)
- Deependra Jadoun
- Department
of Physics, Stockholm University, AlbaNova
University Center, SE-106 91 Stockholm, Sweden
| | - Zhedong Zhang
- Department
of Physics, City University of Hong Kong, Kowloon, Hong Kong SAR
- Shenzhen
Research Institute, City University of Hong
Kong, Shenzhen, Guangdong 518057, China
| | - Markus Kowalewski
- Department
of Physics, Stockholm University, AlbaNova
University Center, SE-106 91 Stockholm, Sweden
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6
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Garner SM, Haugen EA, Leone SR, Neuscamman E. Spin Coupling Effect on Geometry-Dependent X-Ray Absorption of Diradicals. J Am Chem Soc 2024; 146:2387-2397. [PMID: 38235992 DOI: 10.1021/jacs.3c08002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
We theoretically investigate the influence of diradical electron spin coupling on the time-resolved X-ray absorption spectra of the photochemical ring opening of furanone. We predict geometry-dependent carbon K-edge signals involving transitions from core orbitals to both singly and unoccupied molecular orbitals. The most obvious features of the ring opening come from the carbon atom directly involved in the bond breaking through its transition to both the newly formed singly occupied and the available lowest unoccupied molecular orbitals (SOMO and LUMO, respectively). In addition to this primary feature, the singlet spin coupling of four unpaired electrons that arises in the core-to-LUMO states creates additional geometry dependence in some spectral features with both oscillator strengths and relative excitation energies varying observably as a function of the ring opening. We attribute this behavior to a spin-occupancy-induced selection rule, which occurs when singlet spin coupling is enforced in the diradical state. Notably, one of these geometry-sensitive core-to-LUMO transitions excites core electrons from a backbone carbon not involved in the bond breaking, providing a novel nonlocal X-ray probe of chemical dynamics arising from electron spin coupling.
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Affiliation(s)
- Scott M Garner
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Eric A Haugen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stephen R Leone
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Physics, University of California, Berkeley, California 94720, United States
| | - Eric Neuscamman
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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7
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Arias-Martinez JE, Wu H, Head-Gordon M. Generalization of One-Center Nonorthogonal Configuration Interaction Singles to Open-Shell Singlet Reference States: Theory and Application to Valence-Core Pump-Probe States in Acetylacetone. J Chem Theory Comput 2024; 20:752-766. [PMID: 38164934 DOI: 10.1021/acs.jctc.3c01139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
We formulate a one-center nonorthogonal configuration interaction singles (1C-NOCIS) theory for the computation of core excited states of an initial singlet state with two unpaired electrons. This model, which we refer to as 1C-NOCIS two-electron open-shell (2eOS), is appropriate for computing the K-edge near-edge X-ray absorption spectra (NEXAS) of the valence excited states of closed-shell molecules relevant to pump-probe time-resolved (TR) NEXAS experiments. With the inclusion of core-hole relaxation effects and explicit spin adaptation, 1C-NOCIS 2eOS requires mild shifts to match experiment, is free of artifacts due to spin contamination, and can capture the high-energy region of the spectrum beyond the transitions into the singly occupied molecular orbitals (SOMOs). Calculations on water and thymine illustrate the different key features of excited-state NEXAS, namely, the core-to-SOMO transitions as well as shifts and spin-splittings in the transitions analogous to those of the ground state. Simulations of the TR-NEXAS of acetylacetone after excitation to its π → π* singlet excited state at the carbon K-edge, an experiment carried out recently, showcase the ability of 1C-NOCIS 2eOS to efficiently simulate NEXAS based on nonadiabatic molecular dynamics simulations.
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Affiliation(s)
- Juan E Arias-Martinez
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hamlin Wu
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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8
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Garratt D, Matthews M, Marangos J. Toward ultrafast soft x-ray spectroscopy of organic photovoltaic devices. Struct Dyn 2024; 11:010901. [PMID: 38250136 PMCID: PMC10799687 DOI: 10.1063/4.0000214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/17/2023] [Indexed: 01/23/2024]
Abstract
Novel ultrafast x-ray sources based on high harmonic generation and at x-ray free electron lasers are opening up new opportunities to resolve complex ultrafast processes in condensed phase systems with exceptional temporal resolution and atomic site specificity. In this perspective, we present techniques for resolving charge localization, transfer, and separation processes in organic semiconductors and organic photovoltaic devices with time-resolved soft x-ray spectroscopy. We review recent results in ultrafast soft x-ray spectroscopy of these systems and discuss routes to overcome the technical challenges in performing time-resolved x-ray experiments on photosensitive materials with poor thermal conductivity and low pump intensity thresholds for nonlinear effects.
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9
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Cuéllar-Zuquin J, Pepino AJ, Fdez. Galván I, Rivalta I, Aquilante F, Garavelli M, Lindh R, Segarra-Martí J. Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size. J Chem Theory Comput 2023; 19:8258-8272. [PMID: 37882796 PMCID: PMC10851440 DOI: 10.1021/acs.jctc.3c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
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Affiliation(s)
- Juliana Cuéllar-Zuquin
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Ana Julieta Pepino
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Ignacio Fdez. Galván
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Francesco Aquilante
- Theory
and Simulation of Materials (THEOS), and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Roland Lindh
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Javier Segarra-Martí
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
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Bäuml L, Rott F, Schnappinger T, de Vivie-Riedle R. Following the Nonadiabatic Ultrafast Dynamics of Uracil via Simulated X-ray Absorption Spectra. J Phys Chem A 2023; 127:9787-9796. [PMID: 37955656 DOI: 10.1021/acs.jpca.3c06509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The nucleobase uracil exhibits high photostability due to ultrafast relaxation processes mediated by conical intersections (CoIns), where the interplay between nuclear and electron dynamics becomes crucial. In our previous study, we observed seemingly long-lived traces of electronic coherence for the relaxation process through the S2/S1 CoIn by applying our ansatz for coupled nuclear and electron dynamics in molecules (NEMol). In this work, we theoretically investigate how time-dependent transient X-ray absorption spectroscopy can be used to observe this ultrafast dynamics. Therefore, we calculated X-ray absorption spectra (XAS) for the oxygen K-edge, using a multireference protocol in combination with NEMol dynamics. Thus, we have access to both the transient XAS based on the nuclear wavepacket dynamics and the modulation of the signals caused by the electronic coherence induced by the excitation process and the presence of a CoIn seam. In both cases, we were able to qualitatively predict its influence on the resulting XAS.
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Affiliation(s)
- Lena Bäuml
- Department of Chemistry, LMU Munich, Munich 81377, Germany
| | - Florian Rott
- Department of Chemistry, LMU Munich, Munich 81377, Germany
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11
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Komarov K, Park W, Lee S, Huix-Rotllant M, Choi CH. Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory. J Chem Theory Comput 2023; 19:7671-7684. [PMID: 37844129 DOI: 10.1021/acs.jctc.3c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.
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Affiliation(s)
- Konstantin Komarov
- Center for Quantum Dynamics, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul, 151-747, South Korea
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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12
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Bain M, Godínez Castellanos JL, Bradforth SE. High-Throughput Screening for Ultrafast Photochemical Reaction Discovery. J Phys Chem Lett 2023; 14:9864-9871. [PMID: 37890453 DOI: 10.1021/acs.jpclett.3c02389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
High-repetition-rate lasers present an opportunity to extend ultrafast spectroscopy from a detailed probe of singular model photochemical systems to a routine analysis technique in training machine learning models to aid the design cycle of photochemical syntheses. We bring together innovations in line scan cameras and micro-electro-mechanical grating modulators with sample delivery via high-pressure liquid chromatography pumps to demonstrate a transient absorption spectrometer that can characterize photoreactions initiated with ultrashort ultraviolet pulses in a time scale of minutes. Furthermore, we demonstrate that the ability to rapidly screen an important class of photochemical system, pyrimidine nucleosides, can be used to explore the effect of conformational modification on the evolution of excited-state processes.
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Affiliation(s)
- Matthew Bain
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - José L Godínez Castellanos
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Stephen E Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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13
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Park W, Komarov K, Lee S, Choi CH. Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory: Multireference Advantages with the Practicality of Linear Response Theory. J Phys Chem Lett 2023; 14:8896-8908. [PMID: 37767969 PMCID: PMC10561896 DOI: 10.1021/acs.jpclett.3c02296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
The density functional theory (DFT) and linear response (LR) time-dependent (TD)-DFT are of the utmost importance for routine computations. However, the single reference formulation of DFT suffers in the description of open-shell singlet systems such as diradicals and bond-breaking. LR-TDDFT, on the other hand, finds difficulties in the modeling of conical intersections, doubly excited states, and core-level excitations. In this Perspective, we demonstrate that many of these limitations can be overcome by recently developed mixed-reference (MR) spin-flip (SF)-TDDFT, providing an alternative yet accurate route for such challenging situations. Empowered by the practicality of the LR formalism, it is anticipated that MRSF-TDDFT can become one of the major workhorses for general routine tasks.
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Affiliation(s)
- Woojin Park
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Konstantin Komarov
- Center
for Quantum Dynamics, Pohang University
of Science and Technology, Pohang 37673, South Korea
| | - Seunghoon Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Cheol Ho Choi
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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14
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Kaczun T, Dempwolff AL, Huang X, Gelin MF, Domcke W, Dreuw A. Tuning UV Pump X-ray Probe Spectroscopy on the Nitrogen K Edge Reveals the Radiationless Relaxation of Pyrazine: Ab Initio Simulations Using the Quasiclassical Doorway-Window Approximation. J Phys Chem Lett 2023:5648-5656. [PMID: 37310800 DOI: 10.1021/acs.jpclett.3c01018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Transient absorption UV pump X-ray probe spectroscopy has been established as a versatile technique for the exploration of ultrafast photoinduced dynamics in valence-excited states. In this work, an ab initio theoretical framework for the simulation of time-resolved UV pump X-ray probe spectra is presented. The method is based on the description of the radiation-matter interaction in the classical doorway-window approximation and a surface-hopping algorithm for the nonadiabatic nuclear excited-state dynamics. Using the second-order algebraic-diagrammatic construction scheme for excited states, UV pump X-ray probe signals were simulated for the carbon and nitrogen K edges of pyrazine, assuming a duration of 5 fs of the UV pump and X-ray probe pulses. It is predicted that spectra measured at the nitrogen K edge carry much richer information about the ultrafast nonadiabatic dynamics in the valence-excited states of pyrazine than those measured at the carbon K edge.
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Affiliation(s)
- Tobias Kaczun
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg D-69120, Germany
| | - Adrian L Dempwolff
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg D-69120, Germany
| | - Xiang Huang
- Department of Chemistry, Technical University of Munich, Garching D-85747, Germany
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching D-85747, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg D-69120, Germany
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15
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Schnack-Petersen AK, Pápai M, Coriani S, Møller KB. A theoretical study of the time-resolved x-ray absorption spectrum of the photoionized BT-1T cation. Struct Dyn 2023; 10:034102. [PMID: 37250952 PMCID: PMC10224778 DOI: 10.1063/4.0000183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/01/2023] [Indexed: 05/31/2023]
Abstract
The time-resolved x-ray absorption spectrum of the BT-1T cation (BT-1T+) is theoretically simulated in order to investigate the charge transfer reaction of the system. We employ both trajectory surface hopping and quantum dynamics to simulate the structural evolution over time and the changes in the state populations. To compute the static x-ray absorption spectra (XAS) of the ground and excited states, we apply both the time-dependent density functional theory and the coupled cluster singles and doubles method. The results obtained are in good agreement between the methods. It is, furthermore, found that the small structural changes that occur during the reaction have little effect on the static XAS. Hence, the tr-XAS can be computed based on the state populations determined from a nuclear dynamics simulation and one set of static XAS calculations, utilizing the ground state optimized geometry. This approach can save considerable computational resources, as the static spectra need not to be calculated for all geometries. As BT-1T is a relatively rigid molecule, the outlined approach should only be considered when investigating non-radiative decay processes in the vicinity of the Franck-Condon point.
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Affiliation(s)
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Klaus Braagaard Møller
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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16
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Keefer D, Cavaletto SM, Rouxel JR, Garavelli M, Yong H, Mukamel S. Ultrafast X-Ray Probes of Elementary Molecular Events. Annu Rev Phys Chem 2023; 74:73-97. [PMID: 37093660 DOI: 10.1146/annurev-physchem-062322-051532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Elementary events that determine photochemical outcomes and molecular functionalities happen on the femtosecond and subfemtosecond timescales. Among the most ubiquitous events are the nonadiabatic dynamics taking place at conical intersections. These facilitate ultrafast, nonradiative transitions between electronic states in molecules that can outcompete slower relaxation mechanisms such as fluorescence. The rise of ultrafast X-ray sources, which provide intense light pulses with ever-shorter durations and larger observation bandwidths, has fundamentally revolutionized our spectroscopic capabilities to detect conical intersections. Recent theoretical studies have demonstrated an entirely new signature emerging once a molecule traverses a conical intersection, giving detailed insights into the coupled nuclear and electronic motions that underlie, facilitate, and ultimately determine the ultrafast molecular dynamics. Following a summary of current sources and experiments, we survey these techniques and provide a unified overview of their capabilities. We discuss their potential to dramatically increase our understanding of ultrafast photochemistry.
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Affiliation(s)
- Daniel Keefer
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA; ,
| | - Stefano M Cavaletto
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA; ,
- Current affiliation: Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Jérémy R Rouxel
- Université de Lyon, UJM-Saint-Etienne, IOGS, Laboratoire Hubert Curien, UMR CNRS 5516, Saint-Etienne, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Haiwang Yong
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA; ,
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA; ,
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17
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Cavaletto SM, Nam Y, Rouxel JR, Keefer D, Yong H, Mukamel S. Attosecond Monitoring of Nonadiabatic Molecular Dynamics by Transient X-ray Transmission Spectroscopy. J Chem Theory Comput 2023; 19:2327-2339. [PMID: 37015111 DOI: 10.1021/acs.jctc.3c00062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Tracing the evolution of molecular coherences can provide a direct, unambiguous probe of nonadiabatic molecular processes, such as the passage through conical intersections of electronic states. Two techniques, attosecond transient absorption spectroscopy (ATAS) and Transient Redistribution of Ultrafast Electronic Coherences in Attosecond Raman Signals (TRUECARS), have been used or proposed for monitoring nonadiabatic molecular dynamics. Both techniques employ the transmission of a weak attosecond extreme-ultraviolet or X-ray probe to interrogate the molecule at controllable time delays with respect to an optical pump, thereby extracting dynamical information from transient spectral features. The connection between these techniques has not been firmly established yet. In this theoretical study, we provide a unified description of both transient transmission techniques, establishing their relationship as limits of the same pump-probe spectroscopy technique for different pulse parameter regimes. We demonstrate this by quantum dynamical simulations of thiophenol photodissociation and show how complementary coherence information can be revealed by the two techniques.
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Affiliation(s)
- Stefano M Cavaletto
- Department of Chemistry and Department of Physics & Astronomy, University of California Irvine, Irvine, California 92697, United States
| | - Yeonsig Nam
- Department of Chemistry and Department of Physics & Astronomy, University of California Irvine, Irvine, California 92697, United States
| | - Jérémy R Rouxel
- Department of Chemistry and Department of Physics & Astronomy, University of California Irvine, Irvine, California 92697, United States
- Université de Lyon, UJM-Saint-Étienne, CNRS, IOGS, Laboratoire Hubert Curien UMR 5516, Saint-Étienne 42023, France
| | - Daniel Keefer
- Department of Chemistry and Department of Physics & Astronomy, University of California Irvine, Irvine, California 92697, United States
| | - Haiwang Yong
- Department of Chemistry and Department of Physics & Astronomy, University of California Irvine, Irvine, California 92697, United States
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics & Astronomy, University of California Irvine, Irvine, California 92697, United States
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18
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Orimo N, Yamamoto YI, Karashima S, Boyer A, Suzuki T. Ultrafast Electronic Relaxation in 6-Methyluracil and 5-Fluorouracil in Isolated and Aqueous Conditions: Substituent and Solvent Effects. J Phys Chem Lett 2023; 14:2758-2763. [PMID: 36897645 DOI: 10.1021/acs.jpclett.3c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report ultrafast extreme ultraviolet photoelectron spectroscopy of 6-methyluracil (6mUra) and 5-fluorouracil (5FUra) in the gas phase and 6mUra and 5-fluorouridine in an aqueous environment. In the gas phase, internal conversion (IC) occurs from 1ππ* to 1nπ* states in tens of femtoseconds, followed by intersystem crossing to the 3ππ* state in several picoseconds. In an aqueous solution, 6mUra undergoes IC almost exclusively to the ground state (S0) in about 100 fs, which is essentially the same process as that for unsubstituted uracil, but much faster than that for thymine (5-methyluracil). The different dynamics for C5 and C6 methylation suggest that IC from 1ππ* to S0 is facilitated by out-of-plane (OOP) motion of the C5 substituent. The slow IC for C5-substituted molecules in an aqueous environment is ascribed to the solvent reorganization that is required for this OOP motion to occur. The slow rate for 5FUrd may arise in part from an increased barrier height due to C5 fluorination.
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Affiliation(s)
- Natsumi Orimo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Yo-Ichi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Shutaro Karashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Alexie Boyer
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
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19
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Karak P, Moitra T, Ruud K, Chakrabarti S. Photophysics of uracil: an explicit time-dependent generating function-based method combining both nonadiabatic and spin-orbit coupling effects. Phys Chem Chem Phys 2023; 25:8209-8219. [PMID: 36881024 DOI: 10.1039/d2cp05955j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
We present a composite framework for calculating the rates of non-radiative deactivation processes, namely internal conversion (IC) and intersystem crossing (ISC), on an equal footing by explicitly computing the non-adiabatic coupling (NAC) and spin-orbit coupling (SOC) constants, respectively. The stationary-state approach uses a time-dependent generating function based on Fermi's golden rule. We validate the applicability of the framework by computing the rate of IC for azulene, obtaining comparable rates to experimental and previous theoretical results. Next, we investigate the photophysics associated with the complex photodynamics of the uracil molecule. Interestingly, our simulated rates corroborate experimental observations. Detailed analyses using Duschinsky rotation matrices, displacement vectors and NAC matrix elements are presented to interpret the findings alongside testing the suitability of the approach for such molecular systems. The suitability of the Fermi's golden rule based method is explained qualitatively in terms of single-mode potential energy surfaces.
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Affiliation(s)
- Pijush Karak
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
| | - Torsha Moitra
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway. .,Norwegian Defence Research Establishment, P.O.Box 25, 2027 Kjeller, Norway
| | - Swapan Chakrabarti
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
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20
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Miura Y, Yamamoto YI, Karashima S, Orimo N, Hara A, Fukuoka K, Ishiyama T, Suzuki T. Formation of Long-Lived Dark States during Electronic Relaxation of Pyrimidine Nucleobases Studied Using Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy. J Am Chem Soc 2023; 145:3369-3381. [PMID: 36724068 DOI: 10.1021/jacs.2c09803] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ultrafast electronic relaxation of nucleobases from 1ππ* states to the ground state (S0) is considered essential for the photostability of DNA. However, transient absorption spectroscopy (TAS) has indicated that some nucleobases in aqueous solutions create long-lived 1nπ*/3ππ* dark states from the 1ππ* states with a high quantum yield of 0.4-0.5. We investigated electronic relaxation in pyrimidine nucleobases in both aqueous solutions and the gas phase using extreme ultraviolet (EUV) time-resolved photoelectron spectroscopy. Femtosecond EUV probe pulses cause ionization from all electronic states involved in the relaxation process, providing a clear overview of the electronic dynamics. The 1nπ* quantum yields for aqueous cytidine and uracil (Ura) derivatives were found to be considerably lower (<0.07) than previous estimates reported by TAS. On the other hand, aqueous thymine (Thy) and thymidine exhibited a longer 1ππ* lifetime and a higher quantum yield (0.12-0.22) for the 1nπ* state. A similar trend was found for isolated Thy and Ura in the gas phase: the 1ππ* lifetimes are 39 and 17 fs and the quantum yield for 1nπ* are 1.0 and 0.45 for Thy and Ura, respectively. The result indicates that single methylation to the C5 position hinders the out-of-plane deformation that drives the system to the conical intersection region between 1ππ* and S0, providing a large impact on the photophysics/photochemistry of a pyrimidine nucleobase. The significant reduction of 1nπ* yield in aqueous solution is ascribed to the destabilization of the 1nπ* state induced by hydrogen bonding.
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Affiliation(s)
- Yuta Miura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Yo-Ichi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Shutaro Karashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Natsumi Orimo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Ayano Hara
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Kanae Fukuoka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama930-8555, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
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21
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Carlini L, Montorsi F, Wu Y, Bolognesi P, Borrego-Varillas R, Casavola AR, Castrovilli MC, Chiarinelli J, Mocci D, Vismarra F, Lucchini M, Nisoli M, Mukamel S, Garavelli M, Richter R, Nenov A, Avaldi L. Electron and ion spectroscopy of azobenzene in the valence and core shells. J Chem Phys 2023; 158:054201. [PMID: 36754795 DOI: 10.1063/5.0133824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Azobenzene is a prototype and a building block of a class of molecules of extreme technological interest as molecular photo-switches. We present a joint experimental and theoretical study of its response to irradiation with light across the UV to x-ray spectrum. The study of valence and inner shell photo-ionization and excitation processes combined with measurement of valence photoelectron-photoion coincidence and mass spectra across the core thresholds provides a detailed insight into the site- and state-selected photo-induced processes. Photo-ionization and excitation measurements are interpreted via the multi-configurational restricted active space self-consistent field method corrected by second order perturbation theory. Using static modeling, we demonstrate that the carbon and nitrogen K edges of azobenzene are suitable candidates for exploring its photoinduced dynamics thanks to the transient signals appearing in background-free regions of the NEXAFS and XPS.
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Affiliation(s)
- L Carlini
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - F Montorsi
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - Y Wu
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - P Bolognesi
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - R Borrego-Varillas
- CNR-Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, Milano, Italy
| | - A R Casavola
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - M C Castrovilli
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - J Chiarinelli
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - D Mocci
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - F Vismarra
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - M Lucchini
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - M Nisoli
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - S Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - M Garavelli
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - R Richter
- Elettra Sincrotrone Trieste, Area Science Park, Basovizza, Italy
| | - A Nenov
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - L Avaldi
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
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22
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Haugen EA, Hait D, Scutelnic V, Xue T, Head-Gordon M, Leone SR. Ultrafast X-ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron-Withdrawing Groups. J Phys Chem A 2023; 127:634-644. [PMID: 36638240 DOI: 10.1021/acs.jpca.2c06044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. We observe the excited state dynamics following excitation with 266 nm UV light to the 1ππ* (S2) state with element and site-specificity using a broadband soft X-ray pulse produced by high harmonic generation. These results are compared to X-ray spectra computed from orbital optimized density functional theory methods. It is found that the electron-withdrawing fluorine atoms decongest the X-ray absorption spectrum by enhancing separation between features originating from different carbon atoms. This facilitates the elucidation of structural and electronic dynamics at the chromophore. The evolution of the core-to-valence resonances at the carbon K-edge reveals an ultrafast population transfer between the 1nπ* (S1) and 3ππ* (T1) states on a 1.6 ± 0.4 ps time scale, which is similar to the 1.5 ps time scale earlier observed for acetylacetone [ J. Am. Chem. Soc. 2017, 139, 16576-16583, DOI: 10.1021/jacs.7b07532]. It therefore appears that terminal fluorination has little influence on the intersystem crossing rate of the acetylacetone chromophore. In addition, the significant role of hydrogen-bond opened and twisted rotational isomers is elucidated in the excited state dynamics by comparison of the experimental transient X-ray spectra with theory.
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Affiliation(s)
- Eric A Haugen
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Valeriu Scutelnic
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tian Xue
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stephen R Leone
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Department of Physics, University of California, Berkeley, California 94720, United States
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23
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Huix-Rotllant M, Schwinn K, Pomogaev V, Farmani M, Ferré N, Lee S, Choi CH. Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT. J Chem Theory Comput 2023; 19:147-156. [PMID: 36574493 DOI: 10.1021/acs.jctc.2c01010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.
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Affiliation(s)
| | - Karno Schwinn
- Aix-Marseille Univ, CNRS, ICR, Marseille13013, France
| | - Vladimir Pomogaev
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Maryam Farmani
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, Marseille13013, France
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
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24
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Park W, Alías-Rodríguez M, Cho D, Lee S, Huix-Rotllant M, Choi CH. Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory for Accurate X-ray Absorption Spectroscopy. J Chem Theory Comput 2022; 18:6240-6250. [PMID: 36166346 DOI: 10.1021/acs.jctc.2c00746] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is demonstrated that the challenging core-hole particle (CHP) orbital relaxation for core electron spectra can be readily achieved by the mixed-reference spin-flip (MRSF)-time-dependent density functional theory (TDDFT). With the additional scalar relativistic effects on K-edge excitation energies of 24 second- and 17 third-row molecules, the particular ΔCHP-MRSF(R) exhibited near perfect predictions with RMSE ∼0.5 eV, featuring a median value of 0.3 and an interquartile range of 0.4. Overall, the CHP effect is 2-4 times stronger than relativistic ones, contributing more than 20 eV in the cases of sulfur and chlorine third-row atoms. Such high precision allows to explain the splitting and spectral shapes of O, N, and C atom K-edges in the ground state of thymine with atom as well as orbital specific accuracy. The same protocol with a double hole particle relaxation also produced remarkably accurate K-edge spectra of core to valence hole excitation energies from the first (nO8π*) and second (ππ*) excited states of thymine, confirming the assignment of 1s → n excitation for the experimentally observed 526.4 eV peak. Regarding both accuracy and practicality, therefore, MRSF-TDDFT provides a promising protocol for core electron spectra of both ground and excited electronic states alike.
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Affiliation(s)
- Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Marc Alías-Rodríguez
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, Marseille 13284, France
| | - Daeheum Cho
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Miquel Huix-Rotllant
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, Marseille 13284, France
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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25
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Pant R, Ranga S, Bachhar A, Dutta AK. Pair Natural Orbital Equation-of-Motion Coupled-Cluster Method for Core Binding Energies: Theory, Implementation, and Benchmark. J Chem Theory Comput 2022; 18:4660-4673. [PMID: 35786933 DOI: 10.1021/acs.jctc.2c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the theory and implementation of a lower scaling core-valence separated equation-of-motion coupled-cluster approach based on domain-based local pair natural orbitals for core binding energies. The accuracy of the new method has been compared with that of the standard equation-of-motion coupled-cluster method and experimentally measured results. The use of pair natural orbitals significantly reduces the computation cost and can be applied to large molecules.
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Affiliation(s)
- Rakesh Pant
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Santosh Ranga
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Arnab Bachhar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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26
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Walter P, Osipov T, Lin MF, Cryan J, Driver T, Kamalov A, Marinelli A, Robinson J, Seaberg MH, Wolf TJA, Aldrich J, Brown N, Champenois EG, Cheng X, Cocco D, Conder A, Curiel I, Egger A, Glownia JM, Heimann P, Holmes M, Johnson T, Lee L, Li X, Moeller S, Morton DS, Ng ML, Ninh K, O’Neal JT, Obaid R, Pai A, Schlotter W, Shepard J, Shivaram N, Stefan P, Van X, Wang AL, Wang H, Yin J, Yunus S, Fritz D, James J, Castagna JC. The time-resolved atomic, molecular and optical science instrument at the Linac Coherent Light Source. J Synchrotron Radiat 2022; 29:957-968. [PMID: 35787561 PMCID: PMC9255571 DOI: 10.1107/s1600577522004283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
The newly constructed time-resolved atomic, molecular and optical science instrument (TMO) is configured to take full advantage of both linear accelerators at SLAC National Accelerator Laboratory, the copper accelerator operating at a repetition rate of 120 Hz providing high per-pulse energy as well as the superconducting accelerator operating at a repetition rate of about 1 MHz providing high average intensity. Both accelerators power a soft X-ray free-electron laser with the new variable-gap undulator section. With this flexible light source, TMO supports many experimental techniques not previously available at LCLS and will have two X-ray beam focus spots in line. Thereby, TMO supports atomic, molecular and optical, strong-field and nonlinear science and will also host a designated new dynamic reaction microscope with a sub-micrometer X-ray focus spot. The flexible instrument design is optimized for studying ultrafast electronic and molecular phenomena and can take full advantage of the sub-femtosecond soft X-ray pulse generation program.
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Affiliation(s)
- Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Timur Osipov
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ming-Fu Lin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - James Cryan
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Taran Driver
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrei Kamalov
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Agostino Marinelli
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Joe Robinson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matthew H. Seaberg
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas J. A. Wolf
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jeff Aldrich
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Nolan Brown
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Elio G. Champenois
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Xinxin Cheng
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniele Cocco
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alan Conder
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ivan Curiel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Adam Egger
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - James M. Glownia
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Philip Heimann
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael Holmes
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Tyler Johnson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Lance Lee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Xiang Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stefan Moeller
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel S. Morton
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - May Ling Ng
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kayla Ninh
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jordan T. O’Neal
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Razib Obaid
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Allen Pai
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - William Schlotter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jackson Shepard
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Niranjan Shivaram
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Peter Stefan
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Xiong Van
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Anna Li Wang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hengzi Wang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jing Yin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sameen Yunus
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - David Fritz
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Justin James
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jean-Charles Castagna
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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27
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Uemura Y, Ismail ASM, Park SH, Kwon S, Kim M, Elnaggar H, Frati F, Wadati H, Hirata Y, Zhang Y, Yamagami K, Yamamoto S, Matsuda I, Halisdemir U, Koster G, Milne C, Ammann M, Weckhuysen BM, de Groot FMF. Hole Dynamics in Photoexcited Hematite Studied with Femtosecond Oxygen K-edge X-ray Absorption Spectroscopy. J Phys Chem Lett 2022; 13:4207-4214. [PMID: 35512383 PMCID: PMC9125685 DOI: 10.1021/acs.jpclett.2c00295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/05/2022] [Indexed: 05/21/2023]
Abstract
Hematite (α-Fe2O3) is a photoelectrode for the water splitting process because of its relatively narrow bandgap and abundance in the earth's crust. In this study, the photoexcited state of a hematite thin film was investigated with femtosecond oxygen K-edge X-ray absorption spectroscopy (XAS) at the PAL-XFEL in order to follow the dynamics of its photoexcited states. The 200 fs decay time of the hole state in the valence band was observed via its corresponding XAS feature.
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Affiliation(s)
- Yohei Uemura
- Inorganic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitslaan 99, Utrecht, 3584 CG, The Netherlands
- Laboratory
of Environmental Chemistry, Energy and Environment Research Division, Paul Scherrer Institut, Villigen, 5232, Switzerland
- European
XFEL, Holzkoppel 4, Schenefeld, 22869, Germany
| | - Ahmed S. M. Ismail
- Inorganic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitslaan 99, Utrecht, 3584 CG, The Netherlands
| | - Sang Han Park
- PAL-XFEL, Pohang Accelerator Laboratory, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Soonnam Kwon
- PAL-XFEL, Pohang Accelerator Laboratory, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Minseok Kim
- PAL-XFEL, Pohang Accelerator Laboratory, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hebatalla Elnaggar
- Inorganic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitslaan 99, Utrecht, 3584 CG, The Netherlands
| | - Federica Frati
- Inorganic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitslaan 99, Utrecht, 3584 CG, The Netherlands
| | - Hiroki Wadati
- Institute
for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Graduate
School of Material Science, University of
Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yasuyuki Hirata
- Institute
for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Yujun Zhang
- Institute
for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Kohei Yamagami
- Institute
for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Susumu Yamamoto
- Institute
for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Iwao Matsuda
- Institute
for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Ufuk Halisdemir
- Faculty
of
Science and Technology and MESA + Institute for Nanotechnology, University of Twente, P.O. Box 2171, Enschede, 7500 AE, The Netherlands
| | - Gertjan Koster
- Faculty
of
Science and Technology and MESA + Institute for Nanotechnology, University of Twente, P.O. Box 2171, Enschede, 7500 AE, The Netherlands
| | - Christopher Milne
- European
XFEL, Holzkoppel 4, Schenefeld, 22869, Germany
- SwissFEL, Paul
Scherrer Institut, Villigen, 5232, Switzerland
| | - Markus Ammann
- Laboratory
of Environmental Chemistry, Energy and Environment Research Division, Paul Scherrer Institut, Villigen, 5232, Switzerland
| | - Bert M. Weckhuysen
- Inorganic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitslaan 99, Utrecht, 3584 CG, The Netherlands
| | - Frank M. F. de Groot
- Inorganic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitslaan 99, Utrecht, 3584 CG, The Netherlands
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28
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Restaino L, Jadoun D, Kowalewski M. Probing nonadiabatic dynamics with attosecond pulse trains and soft x-ray Raman spectroscopy. Struct Dyn 2022; 9:034101. [PMID: 35774244 PMCID: PMC9239728 DOI: 10.1063/4.0000146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/06/2022] [Indexed: 05/31/2023]
Abstract
Linear off-resonant x-ray Raman techniques are capable of detecting the ultrafast electronic coherences generated when a photoexcited wave packet passes through a conical intersection. A hybrid femtosecond or attosecond probe pulse is employed to excite the system and stimulate the emission of the signal photon, where both fields are components of a hybrid pulse scheme. In this paper, we investigate how attosecond pulse trains, as provided by high-harmonic generation processes, perform as probe pulses in the framework of this spectroscopic technique, instead of single Gaussian pulses. We explore different combination schemes for the probe pulse as well as the impact of parameters of the pulse trains on the signals. Furthermore, we show how Raman selection rules and symmetry consideration affect the spectroscopic signal, and we discuss the importance of vibrational contributions to the overall signal. We use two different model systems, representing molecules of different symmetries, and quantum dynamics simulations to study the difference in the spectra. The results suggest that such pulse trains are well suited to capture the key features associated with the electronic coherence.
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29
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Nam Y, Montorsi F, Keefer D, Cavaletto SM, Lee JY, Nenov A, Garavelli M, Mukamel S. Time-Resolved Optical Pump-Resonant X-ray Probe Spectroscopy of 4-Thiouracil: A Simulation Study. J Chem Theory Comput 2022; 18:3075-3088. [PMID: 35476905 DOI: 10.1021/acs.jctc.2c00064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We theoretically monitor the photoinduced ππ* → nπ* internal conversion process in 4-thiouracil (4TU), triggered by an optical pump. The element-sensitive spectroscopic signatures are recorded by a resonant X-ray probe tuned to the sulfur, oxygen, or nitrogen K-edge. We employ high-level electronic structure methods optimized for core-excited electronic structure calculation combined with quantum nuclear wavepacket dynamics computed on two relevant nuclear modes, fully accounting for their quantum nature of nuclear motions. We critically discuss the capabilities and limitations of the resonant technique. For sulfur and nitrogen, we document a pre-edge spectral window free from ground-state background and rich with ππ* and nπ* absorption features. The lowest sulfur K-edge shows strong absorption for both ππ* and nπ*. In the lowest nitrogen K-edge window, we resolve a state-specific fingerprint of the ππ* and an approximate timing of the conical intersection via its depletion. A spectral signature of the nπ* transition, not accessible by UV-vis spectroscopy, is identified. The oxygen K-edge is not sensitive to molecular deformations and gives steady transient absorption features without spectral dynamics. The ππ*/nπ* coherence information is masked by more intense contributions from populations. Altogether, element-specific time-resolved resonant X-ray spectroscopy provides a detailed picture of the electronic excited-state dynamics and therefore a sensitive window into the photophysics of thiobases.
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Affiliation(s)
- Yeonsig Nam
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States.,Convergence Research Center for Energy and Environmental Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Francesco Montorsi
- Dipartimento di Chimica Industriale "Toso Montanari", Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Daniel Keefer
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Stefano M Cavaletto
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Jin Yong Lee
- Convergence Research Center for Energy and Environmental Sciences, Sungkyunkwan University, Suwon 16419, Korea.,Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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30
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Manian A, Shaw RA, Lyskov I, Russo SP. Exciton Dynamics of a Diketo-Pyrrolopyrrole Core for All Low-Lying Electronic Excited States Using Density Functional Theory-Based Methods. J Chem Theory Comput 2022; 18:1838-1848. [PMID: 35196857 DOI: 10.1021/acs.jctc.2c00070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ab initio treatments of interexcited state internal conversion (IC) are more often than not missing from exciton dynamic descriptions, because of their inherent complexity. Here, we define "interexcited state IC" as a same-spin nonradiative transition between states i and j, where i ≠ j ≠ 0. Competing directly with multiexciton processes such as singlet fission or triplet photoupconversion, inclusion of this mechanism in the narrative of molecular photophysics would allow for strategic synthesis of chromophores for more efficient photon-harvesting applications. Herein, we present a robust formalism which can model these rates using density functional theory (DFT)-based methods within the Franck-Condon and Herzberg-Teller regime. Using an unsubstituted diketo-pyrrolopyrrole (DPP) core as a case study, we illustrate the exciton dynamics along the first four excited states for both singlet and triplet manifolds, showing ultrafast same-spin transfer mechanisms due to all excited states, excluding the first triplet level, being in close energetic proximity (within 0.8 eV of each other). The resulting electron same-spin rates outcompete the electron spin-flipping intersystem crossing (ISC) rates, with excitons firmly obeying Kasha's rule as they cascade down from the high-lying excited states toward the lower states. Furthermore, we calculated that only the first singlet excited state displayed a reasonable probability of triplet exciton generation, of ∼40%, with a near-zero chance of the exciton reverting to the singlet manifold once the electron-hole pair are of parallel spin.
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Affiliation(s)
- Anjay Manian
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, 3000, Australia
| | - Robert A Shaw
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Igor Lyskov
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, 3000, Australia
| | - Salvy P Russo
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, 3000, Australia
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31
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Montorsi F, Segatta F, Nenov A, Mukamel S, Garavelli M. Soft X-ray Spectroscopy Simulations with Multiconfigurational Wave Function Theory: Spectrum Completeness, Sub-eV Accuracy, and Quantitative Reproduction of Line Shapes. J Chem Theory Comput 2022; 18:1003-1016. [PMID: 35073066 PMCID: PMC8830047 DOI: 10.1021/acs.jctc.1c00566] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Francesco Montorsi
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Francesco Segatta
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Artur Nenov
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics & Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Marco Garavelli
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
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32
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Mayer D, Lever F, Picconi D, Metje J, Alisauskas S, Calegari F, Düsterer S, Ehlert C, Feifel R, Niebuhr M, Manschwetus B, Kuhlmann M, Mazza T, Robinson MS, Squibb RJ, Trabattoni A, Wallner M, Saalfrank P, Wolf TJA, Gühr M. Following excited-state chemical shifts in molecular ultrafast x-ray photoelectron spectroscopy. Nat Commun 2022; 13:198. [PMID: 35017539 DOI: 10.1038/s41467-021-27908-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/20/2021] [Indexed: 01/08/2023] Open
Abstract
The conversion of photon energy into other energetic forms in molecules is accompanied by charge moving on ultrafast timescales. We directly observe the charge motion at a specific site in an electronically excited molecule using time-resolved x-ray photoelectron spectroscopy (TR-XPS). We extend the concept of static chemical shift from conventional XPS by the excited-state chemical shift (ESCS), which is connected to the charge in the framework of a potential model. This allows us to invert TR-XPS spectra to the dynamic charge at a specific atom. We demonstrate the power of TR-XPS by using sulphur 2p-core-electron-emission probing to study the UV-excited dynamics of 2-thiouracil. The method allows us to discover that a major part of the population relaxes to the molecular ground state within 220–250 fs. In addition, a 250-fs oscillation, visible in the kinetic energy of the TR-XPS, reveals a coherent exchange of population among electronic states. Imaging the charge flow in photoexcited molecules would provide key information on photophysical and photochemical processes. Here the authors demonstrate tracking in real time after photoexcitation the change in charge density at a specific site of 2-thiouracil using time-resolved X-ray photoelectron spectroscopy.
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33
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Stiel H, Braenzel J, Jonas A, Gnewkow R, Glöggler LT, Sommer D, Krist T, Erko A, Tümmler J, Mantouvalou I. Towards Understanding Excited-State Properties of Organic Molecules Using Time-Resolved Soft X-ray Absorption Spectroscopy. Int J Mol Sci 2021; 22:13463. [PMID: 34948258 PMCID: PMC8706469 DOI: 10.3390/ijms222413463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
The extension of the pump-probe approach known from UV/VIS spectroscopy to very short wavelengths together with advanced simulation techniques allows a detailed analysis of excited-state dynamics in organic molecules or biomolecular structures on a nanosecond to femtosecond time level. Optical pump soft X-ray probe spectroscopy is a relatively new approach to detect and characterize optically dark states in organic molecules, exciton dynamics or transient ligand-to-metal charge transfer states. In this paper, we describe two experimental setups for transient soft X-ray absorption spectroscopy based on an LPP emitting picosecond and sub-nanosecond soft X-ray pulses in the photon energy range between 50 and 1500 eV. We apply these setups for near-edge X-ray absorption fine structure (NEXAFS) investigations of thin films of a metal-free porphyrin, an aggregate forming carbocyanine and a nickel oxide molecule. NEXAFS investigations have been carried out at the carbon, nitrogen and oxygen K-edge as well as on the Ni L-edge. From time-resolved NEXAFS carbon, K-edge measurements of the metal-free porphyrin first insights into a long-lived trap state are gained. Our findings are discussed and compared with density functional theory calculations.
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Affiliation(s)
- Holger Stiel
- Berlin Laboratory for Innovative X-ray Technologies (BLiX), D-10623 Berlin, Germany; (J.B.); (A.J.); (R.G.); (L.T.G.); (J.T.); (I.M.)
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany;
| | - Julia Braenzel
- Berlin Laboratory for Innovative X-ray Technologies (BLiX), D-10623 Berlin, Germany; (J.B.); (A.J.); (R.G.); (L.T.G.); (J.T.); (I.M.)
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany;
| | - Adrian Jonas
- Berlin Laboratory for Innovative X-ray Technologies (BLiX), D-10623 Berlin, Germany; (J.B.); (A.J.); (R.G.); (L.T.G.); (J.T.); (I.M.)
- Analytical X-ray Physics, TU Berlin, D-10623 Berlin, Germany
| | - Richard Gnewkow
- Berlin Laboratory for Innovative X-ray Technologies (BLiX), D-10623 Berlin, Germany; (J.B.); (A.J.); (R.G.); (L.T.G.); (J.T.); (I.M.)
- Analytical X-ray Physics, TU Berlin, D-10623 Berlin, Germany
- Helmholtz Zentrum Berlin, D-12489 Berlin, Germany
| | - Lisa Theresa Glöggler
- Berlin Laboratory for Innovative X-ray Technologies (BLiX), D-10623 Berlin, Germany; (J.B.); (A.J.); (R.G.); (L.T.G.); (J.T.); (I.M.)
- Analytical X-ray Physics, TU Berlin, D-10623 Berlin, Germany
| | - Denny Sommer
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany;
| | - Thomas Krist
- NOB Nano Optics Berlin GmbH, D-10627 Berlin, Germany;
| | | | - Johannes Tümmler
- Berlin Laboratory for Innovative X-ray Technologies (BLiX), D-10623 Berlin, Germany; (J.B.); (A.J.); (R.G.); (L.T.G.); (J.T.); (I.M.)
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany;
| | - Ioanna Mantouvalou
- Berlin Laboratory for Innovative X-ray Technologies (BLiX), D-10623 Berlin, Germany; (J.B.); (A.J.); (R.G.); (L.T.G.); (J.T.); (I.M.)
- Analytical X-ray Physics, TU Berlin, D-10623 Berlin, Germany
- Helmholtz Zentrum Berlin, D-12489 Berlin, Germany
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34
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Hohenstein EG, Yu JK, Bannwarth C, List NH, Paul AC, Folkestad SD, Koch H, Martínez TJ. Predictions of Pre-edge Features in Time-Resolved Near-Edge X-ray Absorption Fine Structure Spectroscopy from Hole-Hole Tamm-Dancoff-Approximated Density Functional Theory. J Chem Theory Comput 2021; 17:7120-7133. [PMID: 34623139 DOI: 10.1021/acs.jctc.1c00478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Time-resolved near-edge X-ray absorption fine structure (TR-NEXAFS) spectroscopy is a powerful technique for studying photochemical reaction dynamics with femtosecond time resolution. In order to avoid ambiguity in TR-NEXAFS spectra from nonadiabatic dynamics simulations, core- and valence-excited states must be evaluated on equal footing and those valence states must also define the potential energy surfaces used in the nonadiabatic dynamics simulation. In this work, we demonstrate that hole-hole Tamm-Dancoff-approximated density functional theory (hh-TDA) is capable of directly simulating TR-NEXAFS spectroscopies. We apply hh-TDA to the excited-state dynamics of acrolein. We identify two pre-edge features in the oxygen K-edge TR-NEXAFS spectrum associated with the S2 (ππ*) and S1 (nπ*) excited states. We show that these features can be used to follow the internal conversion dynamics between the lowest three electronic states of acrolein. Due to the low, O(N2) apparent computational complexity of hh-TDA and our GPU-accelerated implementation, this method is promising for the simulation of pre-edge features in TR-NEXAFS spectra of large molecules and molecules in the condensed phase.
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Affiliation(s)
- Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Jimmy K Yu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States.,Biophysics Program, Stanford University, Stanford, California 94305, United States
| | - Christoph Bannwarth
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Nanna Holmgaard List
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Alexander C Paul
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway
| | - Sarai D Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavaleri 7, 56126 Pisa, Italy
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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35
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Lee S, Park W, Nakata H, Filatov M, Choi CH. Recent advances in ensemble density functional theory and linear response theory for strong correlation. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Seunghoon Lee
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena California USA
| | - Woojin Park
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Hiroya Nakata
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Michael Filatov
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Cheol Ho Choi
- Department of Chemistry Kyungpook National University Daegu South Korea
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36
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Abstract
Photoexcited molecules convert light into chemical and mechanical energy through changes in electronic and nuclear structure that take place on femtosecond timescales. Gas phase ultrafast electron diffraction (GUED) is an ideal tool to probe the nuclear geometry evolution of the molecules and complements spectroscopic methods that are mostly sensitive to the electronic state. GUED is a passive probing tool that does not alter the molecular properties during the probing process and is sensitive to the spatial distribution of charge in the molecule, including both electrons and nuclei. Improvements in temporal resolution have enabled GUED to capture coherent nuclear motions in molecules in the excited and ground electronic states with femtosecond and subangstrom resolution. Here we present the basic theory of GUED and explain what information is encoded in the diffraction signal, review how GUED has been used to observe coherent structural dynamics in recent experiments, and discuss the advantages and limitations of the method. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Martin Centurion
- Department of Physics and Astronomy, University of Nebraska, Lincoln, Nebraska, USA;
| | - Thomas J A Wolf
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA;
| | - Jie Yang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, China;
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37
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Lever F, Mayer D, Metje J, Alisauskas S, Calegari F, Düsterer S, Feifel R, Niebuhr M, Manschwetus B, Kuhlmann M, Mazza T, Robinson MS, Squibb RJ, Trabattoni A, Wallner M, Wolf TJA, Gühr M. Core-Level Spectroscopy of 2-Thiouracil at the Sulfur L 1- and L 2,3-Edges Utilizing a SASE Free-Electron Laser. Molecules 2021; 26:6469. [PMID: 34770877 DOI: 10.3390/molecules26216469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
In this paper, we report X-ray absorption and core-level electron spectra of the nucleobase derivative 2-thiouracil at the sulfur L1- and L2,3-edges. We used soft X-rays from the free-electron laser FLASH2 for the excitation of isolated molecules and dispersed the outgoing electrons with a magnetic bottle spectrometer. We identified photoelectrons from the 2p core orbital, accompanied by an electron correlation satellite, as well as resonant and non-resonant Coster–Kronig and Auger–Meitner emission at the L1- and L2,3-edges, respectively. We used the electron yield to construct X-ray absorption spectra at the two edges. The experimental data obtained are put in the context of the literature currently available on sulfur core-level and 2-thiouracil spectroscopy.
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38
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Jouybari MY, Green JA, Improta R, Santoro F. The Ultrafast Quantum Dynamics of Photoexcited Adenine-Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model. J Phys Chem A 2021; 125:8912-8924. [PMID: 34609880 PMCID: PMC9281421 DOI: 10.1021/acs.jpca.1c08132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
this contribution we present a quantum dynamical study of the
photoexcited hydrogen bonded base pair adenine–thymine (AT)
in a Watson–Crick arrangement. To that end, we parametrize
Linear Vibronic Coupling (LVC) models with Time-Dependent Density
Functional Theory (TD-DFT) calculations, exploiting a fragment diabatization
scheme (FrD) we have developed to define diabatic states on the basis
of individual chromophores in a multichromophoric system. Wavepacket
propagations were run with the multilayer extension of the Multiconfiguration
Time-Dependent Hartree method. We considered excitations to the three
lowest bright states, a ππ* state of
thymine and two ππ* states (La and Lb) of adenine, and we found that on the 100 fs time
scale the main decay pathways involve intramonomer population transfers
toward nπ* states of the same nucleobase. In AT this transfer
is less effective than in the isolated nucleobases, because hydrogen
bonding destabilizes the nπ* states. The population transfer
to the A → T charge transfer state is negligible, making the
ultrafast (femtosecond) decay through the proton coupled electron
transfer mechanism unlikely, in line with experimental results in
apolar solvents. The excitation energy transfer is also very small.
We carefully compare the predictions of LVC Hamiltonians obtained
with different sets of diabatic states, defined so to match either
local states of the two separated monomers or the base pair adiabatic
states in the Franck–Condon region. To that end we also extend
the flexibility of the FrD-LVC approach, introducing a new strategy
to define fragments diabatic states that account for the effect of
the rest of the multichromohoric system through a Molecular Mechanics
potential.
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Affiliation(s)
- Martha Yaghoubi Jouybari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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39
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Tsuru S, Sharma B, Nagasaka M, Hättig C. Solvent Effects in the Ultraviolet and X-ray Absorption Spectra of Pyridazine in Aqueous Solution. J Phys Chem A 2021; 125:7198-7206. [PMID: 34379425 DOI: 10.1021/acs.jpca.1c05183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Electrostatic interaction of the solvent with the solute and fluctuations of the solvent configurations may make excitation energies of the solute different from those in the gas phase. These effects may dominate photoinduced or chemical reaction dynamics in solution systems and can be observed as shifts or broadening of peaks in absorption spectra. In this work, the nitrogen K-edge X-ray absorption spectra were measured for pyridazine in the gas phase and in aqueous solution. The ultraviolet and X-ray absorption spectra of pyridazine in aqueous solution, as well as those in the gas phase, were then calculated with models based on the algebraic-diagrammatic construction through second order [ADC(2)] with the resolution-of-identity (RI) approximation and compared with the spectra obtained in experiments. For aqueous solution, explicit local solvation structures were extracted from an ab initio molecular dynamics (AIMD) trajectory of pyridazine in bulk water, and RI-ADC(2) was combined with the conductor-like screening model (COSMO). The experimental absorption spectra of pyridazine in aqueous solution were reproduced with good accuracy by theoretical treatment of an ensemble containing the explicit local solvation structures of pyridazine with relevant water molecules combined with the COSMO solvation model of water for long-range solvation.
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Affiliation(s)
- Shota Tsuru
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Bikramjit Sharma
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Masanari Nagasaka
- Institute for Molecular Science and SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki 444-8585, Japan
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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41
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Jadoun D, Kowalewski M. Time-Resolved Photoelectron Spectroscopy of Conical Intersections with Attosecond Pulse Trains. J Phys Chem Lett 2021; 12:8103-8108. [PMID: 34410134 PMCID: PMC8404190 DOI: 10.1021/acs.jpclett.1c01843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/13/2021] [Indexed: 05/09/2023]
Abstract
Conical Intersections (CIs), which are believed to be ubiquitous in molecular and biological systems, open up ultrafast nonradiative decay channels. A superposition of electronic states is created when a molecule passes through a CI and the nuclear wave packet branches. The resulting electronic coherence can be considered a unique signature of the CI. The involved electronic states can be resolved in the energy domain with photoelectron spectroscopy using a femtosecond pulse as a probe. However, the observation of the created electronic coherence in the time domain requires probe pulses with several electron volts of bandwidth. Attosecond pulses can probe the electronic coherence but are unable to resolve the involved electronic states. In this Letter, we propose to address this restriction by using time-resolved photoelectron spectroscopy with an attosecond pulse train as a probe. We theoretically demonstrate that the resulting photoelectron spectrum may yield energy resolution as well as the information on the created coherences in the time domain.
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Affiliation(s)
- Deependra Jadoun
- Department of Physics, Stockholm University, Albanova University Centre, SE-106 91 Stockholm, Sweden
| | - Markus Kowalewski
- Department of Physics, Stockholm University, Albanova University Centre, SE-106 91 Stockholm, Sweden
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42
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Scutelnic V, Tsuru S, Pápai M, Yang Z, Epshtein M, Xue T, Haugen E, Kobayashi Y, Krylov AI, Møller KB, Coriani S, Leone SR. X-ray transient absorption reveals the 1A u (nπ*) state of pyrazine in electronic relaxation. Nat Commun 2021; 12:5003. [PMID: 34408141 PMCID: PMC8373973 DOI: 10.1038/s41467-021-25045-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Electronic relaxation in organic chromophores often proceeds via states not directly accessible by photoexcitation. We report on the photoinduced dynamics of pyrazine that involves such states, excited by a 267 nm laser and probed with X-ray transient absorption spectroscopy in a table-top setup. In addition to the previously characterized 1B2u (ππ*) (S2) and 1B3u (nπ*) (S1) states, the participation of the optically dark 1Au (nπ*) state is assigned by a combination of experimental X-ray core-to-valence spectroscopy, electronic structure calculations, nonadiabatic dynamics simulations, and X-ray spectral computations. Despite 1Au (nπ*) and 1B3u (nπ*) states having similar energies at relaxed geometry, their X-ray absorption spectra differ largely in transition energy and oscillator strength. The 1Au (nπ*) state is populated in 200 ± 50 femtoseconds after electronic excitation and plays a key role in the relaxation of pyrazine to the ground state.
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Affiliation(s)
- Valeriu Scutelnic
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Shota Tsuru
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark.,Ruhr-Universität, Bochum, Germany
| | - Mátyás Pápai
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark.,Wigner Research Centre for Physics, Budapest, Hungary
| | - Zheyue Yang
- Department of Chemistry, University of California, Berkeley, CA, USA.,, Shanghai, China
| | - Michael Epshtein
- Department of Chemistry, University of California, Berkeley, CA, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,, Beer-Sheva, Israel
| | - Tian Xue
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Eric Haugen
- Department of Chemistry, University of California, Berkeley, CA, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuki Kobayashi
- Department of Chemistry, University of California, Berkeley, CA, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Klaus B Møller
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stephen R Leone
- Department of Chemistry, University of California, Berkeley, CA, USA. .,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Physics, University of California, Berkeley, CA, USA.
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43
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Manian A, Shaw RA, Lyskov I, Wong W, Russo SP. Modeling radiative and non-radiative pathways at both the Franck-Condon and Herzberg-Teller approximation level. J Chem Phys 2021; 155:054108. [PMID: 34364347 DOI: 10.1063/5.0058643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Here, we present a concise model that can predict the photoluminescent properties of a given compound from first principles, both within and beyond the Franck-Condon approximation. The formalism required to compute fluorescence, Internal Conversion (IC), and Inter-System Crossing (ISC) is discussed. The IC mechanism, in particular, is a difficult pathway to compute due to difficulties associated with the computation of required bosonic configurations and non-adiabatic coupling elements. Here, we offer a discussion and breakdown on how to model these pathways at the Density Functional Theory (DFT) level with respect to its computational implementation, strengths, and current limitations. The model is then used to compute the photoluminescent quantum yield (PLQY) of a number of small but important compounds: anthracene, tetracene, pentacene, diketo-pyrrolo-pyrrole (DPP), and Perylene Diimide (PDI) within a polarizable continuum model. Rate constants for fluorescence, IC, and ISC compare well for the most part with respect to experiment, despite triplet energies being overestimated to a degree. The resulting PLQYs are promising with respect to the level of theory being DFT. While we obtained a positive result for PDI within the Franck-Condon limit, the other systems require a second order correction. Recomputing quantum yields with Herzberg-Teller terms yields PLQYs of 0.19, 0.08, 0.04, 0.70, and 0.99 for anthracene, tetracene, pentacene, DPP, and PDI, respectively. Based on these results, we are confident that the presented methodology is sound with respect to the level of quantum chemistry and presents an important stepping stone in the search for a tool to predict the properties of larger coupled systems.
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Affiliation(s)
- A Manian
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT Univeristy, Melbourne 3000, Australia
| | - R A Shaw
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - I Lyskov
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT Univeristy, Melbourne 3000, Australia
| | - W Wong
- ARC Centre of Excellence in Exciton Science, School of Chemistry, The University of Melbourne, Parkville VIC 3052, Australia
| | - S P Russo
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT Univeristy, Melbourne 3000, Australia
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44
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Tenorio BNC, Oliveira RR, Coriani S. Insights on the site-selective fragmentation of CF2Cl2 and CH2Cl2 at the chlorine K-edge from ab initio calculations. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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45
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Sun X, Li L, Zhang H, Dong M, Wang J, Jia P, Bu T, Wang X, Wang L. Near-Infrared Light-Regulated Drug-Food Homologous Bioactive Molecules and Photothermal Collaborative Precise Antibacterial Therapy Nanoplatform with Controlled Release Property. Adv Healthc Mater 2021; 10:e2100546. [PMID: 34081401 DOI: 10.1002/adhm.202100546] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/30/2021] [Indexed: 12/28/2022]
Abstract
Herein, a collaborative precise antibacterial wound healing therapy nanoplatform integrating drug-food homologous bioactive molecule (cinnamaldehyde, CA) with photothermal therapy (PTT) is presented. Copper-gallic acids-cinnamaldehyde-polydopamine nanorods (Cu-GA-CA-PDA NRs) with near-infrared light (NIR)-controlled CA release property are fabricated, which also integrate CA and photothermal synergistic sterilization, as well as antioxidant, anti-inflammatory, and anti-infection capacities. The characteristics of NIR-mediated CA release and photothermal response of Cu-GA-CA-PDA NRs support their excellent sterilization performance in vitro/in vivo. In addition, under the guidance of NIR, Cu-GA-CA-PDA NRs can hinder the formation of inflammatory cells, reduce oxidative stress damage, accelerate the regeneration of skin tissues in S. aureus-infected wound sites, and achieve the goal of promoting wound healing. Therefore, NIR-mediated Cu-GA-CA-PDA NRs with multifunctional biological activities provide a highly competitive strategy for curing bacteria-infected wounds.
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Affiliation(s)
- Xinyu Sun
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
| | - Lihua Li
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
| | - Hui Zhang
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
| | - Mengna Dong
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
| | - Jiao Wang
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
| | - Pei Jia
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
| | - Tong Bu
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
| | - Xin Wang
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
| | - Li Wang
- College of Food Science and Engineering Northwest A&F University Yangling Shaanxi 712100 P. R. China
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Wolf TJA, Paul AC, Folkestad SD, Myhre RH, Cryan JP, Berrah N, Bucksbaum PH, Coriani S, Coslovich G, Feifel R, Martinez TJ, Moeller SP, Mucke M, Obaid R, Plekan O, Squibb RJ, Koch H, Gühr M. Transient resonant Auger-Meitner spectra of photoexcited thymine. Faraday Discuss 2021; 228:555-570. [PMID: 33566045 DOI: 10.1039/d0fd00112k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the first investigation of excited state dynamics by resonant Auger-Meitner spectroscopy (also known as resonant Auger spectroscopy) using the nucleobase thymine as an example. Thymine is photoexcited in the UV and probed with X-ray photon energies at and below the oxygen K-edge. After initial photoexcitation to a ππ* excited state, thymine is known to undergo internal conversion to an nπ* excited state with a strong resonance at the oxygen K-edge, red-shifted from the ground state π* resonances of thymine (see our previous study Wolf, et al., Nat. Commun., 2017, 8, 29). We resolve and compare the Auger-Meitner electron spectra associated both with the excited state and ground state resonances, and distinguish participator and spectator decay contributions. Furthermore, we observe simultaneously with the decay of the nπ* state signatures the appearance of additional resonant Auger-Meitner contributions at photon energies between the nπ* state and the ground state resonances. We assign these contributions to population transfer from the nπ* state to a ππ* triplet state via intersystem crossing on the picosecond timescale based on simulations of the X-ray absorption spectra in the vibrationally hot triplet state. Moreover, we identify signatures from the initially excited ππ* singlet state which we have not observed in our previous study.
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Affiliation(s)
- Thomas J A Wolf
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
| | - Alexander C Paul
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Sarai D Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Rolf H Myhre
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - James P Cryan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
| | - Nora Berrah
- Department of Physics, University of Connecticut Storrs, 2152 Hillside Road, Storrs, CT 06269, USA
| | - Phil H Bucksbaum
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA. and Departments of Physics and Applied Physics, Stanford University, 382 Via Pueblo Mall, Stanford, CA 94305, USA
| | - Sonia Coriani
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway and DTU Chemistry, Technical University of Denmark, Kongens Lyngby, DK-2800, Denmark
| | - Giacomo Coslovich
- Linac Coherent Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 58 Gothenburg, Sweden
| | - Todd J Martinez
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA. and Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305, USA
| | - Stefan P Moeller
- Linac Coherent Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Melanie Mucke
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Razib Obaid
- Department of Physics, University of Connecticut Storrs, 2152 Hillside Road, Storrs, CT 06269, USA
| | - Oksana Plekan
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Richard J Squibb
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 58 Gothenburg, Sweden
| | - Henrik Koch
- Scuola Normale Superiore, I-56126 Pisa, Italy.
| | - Markus Gühr
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Straßze 24/25, DE-14476 Potsdam, Germany.
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47
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Park W, Lee S, Huix-Rotllant M, Filatov M, Choi CH. Impact of the Dynamic Electron Correlation on the Unusually Long Excited-State Lifetime of Thymine. J Phys Chem Lett 2021; 12:4339-4346. [PMID: 33929858 DOI: 10.1021/acs.jpclett.1c00712] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Non-radiative relaxation of the photoexcited thymine in the gas phase shows an unusually long excited-state lifetime, and, over the years, a number of models, i.e., S1-trapping, S2-trapping, and S1&S2-trapping, have been put forward to explain its mechanism. Here, we investigate this mechanism using non-adiabatic molecular dynamics (NAMD) simulations in connection with the recently developed mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. We show that the previously predicted S2-trapping model was due to an artifact caused by an insufficient account of the dynamic electron correlation. The current work supports the S1-trapping mechanism with two lifetimes, τ1 = 30 ± 1 fs and τ2 = 6.1 ± 0.035 ps, quantitatively consistent with the recent time-resolved experiments. Upon excitation to the S2 (ππ*) state, thymine undergoes an ultrafast (ca. 30 fs) S2→S1 internal conversion and resides around the minimum on the S1 (nOπ*) surface, slowly decaying to the ground state (ca. 6.1 ps). While the S2→S1 internal conversion is mediated by fast bond length alternation distortion, the subsequent S1→S0 occurs through several conical intersections, involving a slow puckering motion.
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Affiliation(s)
- Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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48
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Rott F, Reduzzi M, Schnappinger T, Kobayashi Y, Chang KF, Timmers H, Neumark DM, de Vivie-Riedle R, Leone SR. Ultrafast strong-field dissociation of vinyl bromide: An attosecond transient absorption spectroscopy and non-adiabatic molecular dynamics study. Struct Dyn 2021; 8:034104. [PMID: 34169117 PMCID: PMC8208825 DOI: 10.1063/4.0000102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Attosecond extreme ultraviolet (XUV) and soft x-ray sources provide powerful new tools for studying ultrafast molecular dynamics with atomic, state, and charge specificity. In this report, we employ attosecond transient absorption spectroscopy (ATAS) to follow strong-field-initiated dynamics in vinyl bromide. Probing the Br M edge allows one to assess the competing processes in neutral and ionized molecular species. Using ab initio non-adiabatic molecular dynamics, we simulate the neutral and cationic dynamics resulting from the interaction of the molecule with the strong field. Based on the dynamics results, the corresponding time-dependent XUV transient absorption spectra are calculated by applying high-level multi-reference methods. The state-resolved analysis obtained through the simulated dynamics and related spectral contributions enables a detailed and quantitative comparison with the experimental data. The main outcome of the interaction with the strong field is unambiguously the population of the first three cationic states, D 1, D 2, and D 3. The first two show exclusively vibrational dynamics while the D 3 state is characterized by an ultrafast dissociation of the molecule via C-Br bond rupture within 100 fs in 50% of the analyzed trajectories. The combination of the three simulated ionic transient absorption spectra is in excellent agreement with the experimental results. This work establishes ATAS in combination with high-level multi-reference simulations as a spectroscopic technique capable of resolving coupled non-adiabatic electronic-nuclear dynamics in photoexcited molecules with sub-femtosecond resolution.
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Affiliation(s)
- Florian Rott
- Department of Chemistry, LMU Munich, 81377 Munich, Germany
| | - Maurizio Reduzzi
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Yuki Kobayashi
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Kristina F. Chang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Henry Timmers
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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49
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Bergmann U, Kern J, Schoenlein RW, Wernet P, Yachandra VK, Yano J. Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes. Nat Rev Phys 2021; 3:264-282. [PMID: 34212130 PMCID: PMC8245202 DOI: 10.1038/s42254-021-00289-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 05/14/2023]
Abstract
The metal centres in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.
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Affiliation(s)
- Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Physics, University of Wisconsin–Madison, Madison, WI, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert W. Schoenlein
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Philippe Wernet
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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50
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Green JA, Jouybari MY, Aranda D, Improta R, Santoro F. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules 2021; 26:1743. [PMID: 33804640 PMCID: PMC8003674 DOI: 10.3390/molecules26061743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.
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Affiliation(s)
- James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Martha Yaghoubi Jouybari
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Daniel Aranda
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Fabrizio Santoro
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
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