1
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Kumar G, Kellogg M, Dey S, Oliver TAA, Bradforth SE. Unraveling the Photoionization Dynamics of Indole in Aqueous and Ethanol Solutions. J Phys Chem B 2024; 128:4158-4170. [PMID: 38655896 DOI: 10.1021/acs.jpcb.4c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The photoionization dynamics of indole, the ultraviolet-B chromophore of tryptophan, were explored in water and ethanol using ultrafast transient absorption spectroscopy with 292, 268, and 200 nm excitation. By studying the femtosecond-to-nanosecond dynamics of indole in two different solvents, a new photophysical model has been generated that explains many previously unsolved facets of indole's complex solution phase photochemistry. Photoionization is only an active pathway for indole in aqueous solution, leading to a reduction in the fluorescence quantum yield in water-rich environments, which is frequently used in biophysical experiments as a key signature of the protein-folded state. Photoionization of indole in aqueous solution was observed for all three pump wavelengths but via two different mechanisms. For 200 nm excitation, electrons are ballistically ejected directly into the bulk solvent. Conversely, 292 and 268 nm excitation populates an admixture of two 1ππ* states, which form a dynamic equilibrium with a tightly bound indole cation and electron-ion pair. The ion pair dissociates on a nanosecond time scale, generating separated solvated electrons and indole cations. The charged species serve as important precursors to triplet indole production and greatly enhance the overall intersystem crossing rate. Our proposed photophysical model for indole in aqueous solution is the most appropriate for describing photoinduced dynamics of tryptophan in polypeptide sequences; tryptophan in aqueous pH 7 solution is zwitterionic, unlike in peptides, and resultantly has a competitive excited state proton transfer pathway that quenches the tryptophan fluorescence.
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Affiliation(s)
- Gaurav Kumar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Michael Kellogg
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shivalee Dey
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Thomas A A Oliver
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, U.K
| | - Stephen E Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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2
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Vandaele E, Mališ M, Luber S. The Role of Aqueous Solvation on the Intersystem Crossing of Nitrophenols. J Chem Theory Comput 2024; 20:3258-3272. [PMID: 38606908 PMCID: PMC11044273 DOI: 10.1021/acs.jctc.3c01400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024]
Abstract
The photochemistry of nitrophenols is a source of smog as nitrous acid is formed from their photolysis. Nevertheless, computational studies of the photochemistry of these widespread toxic molecules are scarce. In this work, the initial photodeactivation of ortho-nitrophenol and para-nitrophenol is modeled, both in gas phase and in aqueous solution to simulate atmospheric and aerosol environments. A large number of excited states, six for ortho-nitrophenol and 11 for para-nitrophenol, have been included and were all populated during the decay. Moreover, periodic time-dependent density functional theory (TDDFT) is used for both the explicitly included solvent and the solute. A comparison to periodic QM/MM (TDDFT/MM), with electrostatic embedding, is made, showing notable differences between the decays of solvated nitrophenols simulated with QM/MM and full (TD)DFT. A reduced intersystem crossing in aqueous solution could be observed thanks to the surface hopping approach using explicit, periodic TDDFT solvation including spin-orbit couplings.
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Affiliation(s)
- Eva Vandaele
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Momir Mališ
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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3
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Lamas I, González J, Longarte A, Montero R. Influence of H-bonds on the photoionization of aromatic chromophores in water: The aniline molecule. J Chem Phys 2023; 158:2890456. [PMID: 37184001 DOI: 10.1063/5.0147503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/01/2023] [Indexed: 05/16/2023] Open
Abstract
We have conducted time-resolved experiments (pump-probe and pump-repump-probe) on a model aromatic chromophore, aniline, after excitation in water at 267 nm. In the initial spectra recorded, in addition to the absorption corresponding to the bright ππ* excitation, the fingerprint of a transient state with the electron located on the solvent molecule is identified. We postulate that the latter corresponds to the πσ* state along the N-H bond, whose complete relaxation with a ∼500 ps lifetime results in the formation of the fully solvated electron and cation. This ionization process occurs in parallel with the ππ* photophysical channel that yields the characteristic ∼1 ns fluorescence lifetime. The observed branched pathway is rationalized in terms of the different H-bonds that the water establishes with the amino group. The proposed mechanism could be common for aromatics in water containing N-H or O-H bonds and would allow the formation of separated charges after excitation at the threshold of their electronic absorptions.
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Affiliation(s)
- Iker Lamas
- Facultad de Ciencia y Tecnología, Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apart. 644, 48080 Bilbao, Spain
| | - Jorge González
- Facultad de Ciencia y Tecnología, Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apart. 644, 48080 Bilbao, Spain
| | - Asier Longarte
- Facultad de Ciencia y Tecnología, Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apart. 644, 48080 Bilbao, Spain
| | - Raúl Montero
- Facultad de Ciencia y Tecnología, SGIKER Laser Facility, UPV/EHU, Sarriena, S/N, 48940 Leioa, Spain
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4
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Manian A, Hudson RJ, Ramkissoon P, Smith TA, Russo SP. Interexcited State Photophysics I: Benchmarking Density Functionals for Computing Nonadiabatic Couplings and Internal Conversion Rate Constants. J Chem Theory Comput 2023; 19:271-292. [PMID: 36490305 DOI: 10.1021/acs.jctc.2c00888] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the first benchmarking study of nonadiabatic matrix coupling elements (NACMEs) calculated using different density functionals. Using the S1 → S0 transition in perylene solvated in toluene as a case study, we calculate the photophysical properties and corresponding rate constants for a variety of density functionals from each rung of Jacob's ladder. The singlet photoluminescence quantum yield (sPLQY) is taken as a measure of accuracy, measured experimentally here as 0.955. Important quantum chemical parameters such as geometries, absorption, emission, and adiabatic energies, NACMEs, Hessians, and transition dipole moments were calculated for each density functional basis set combination (data set) using density functional theory based multireference configuration interaction (DFT/MRCI) and compared to experiment where possible. We were able to derive simple relations between the TDDFT and DFT/MRCI photophysical properties; with semiempirical damping factors of ∼0.843 ± 0.017 and ∼0.954 ± 0.064 for TDDFT transition dipole moments and energies to DFT/MRCI level approximations, respectively. NACMEs were dominated by out-of-plane derivative components belonging to the center-most ring atoms with weaker contributions from perturbations along the transverse and longitudinal axes. Calculated theoretical spectra compared well to both experiment and literature, with fluorescence lifetimes between 7.1 and 12.5 ns, agreeing within a factor of 2 with experiment. Internal conversion (IC) rates were then calculated and were found to vary wildly between 106-1016 s-1 compared with an experimental rate of the order 107 s-1. Following further testing by mixing data sets, we found a strong dependence on the method used to obtain the Hessian. The 5 characterized data sets ranked in order of most promising are PBE0/def2-TZVP, ωB97XD/def2-TZVP, HCTH407/TZVP, PBE/TZVP, and PBE/def2-TZVP.
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Affiliation(s)
- Anjay Manian
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne3000, Australia
| | - Rohan J Hudson
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville3010, Australia
| | - Pria Ramkissoon
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville3010, Australia
| | - Trevor A Smith
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville3010, Australia
| | - Salvy P Russo
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne3000, Australia
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5
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Jaiswal VK, Kabaciński P, Nogueira de Faria BE, Gentile M, de Paula AM, Borrego-Varillas R, Nenov A, Conti I, Cerullo G, Garavelli M. Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan. J Am Chem Soc 2022; 144:12884-12892. [PMID: 35796759 PMCID: PMC9305959 DOI: 10.1021/jacs.2c04565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
By combining UV transient
absorption spectroscopy with sub-30-fs
temporal resolution and CASPT2/MM calculations, we present a complete
description of the primary photoinduced processes in solvated tryptophan.
Our results shed new light on the role of the solvent in the relaxation
dynamics of tryptophan. We unveil two consecutive coherent population
transfer events involving the lowest two singlet excited states: a
sub-50-fs nonadiabatic La → Lb transfer
through a conical intersection and a subsequent 220 fs reverse Lb → La transfer due to solvent-assisted adiabatic
stabilization of the La state. Vibrational fingerprints
in the transient absorption spectra provide compelling evidence of
a vibronic coherence established between the two excited states from
the earliest times after photoexcitation and lasting until the back-transfer
to La is complete. The demonstration of response to the
environment as a driver of coherent population dynamics among the
excited states of tryptophan closes the long debate on its solvent-assisted
relaxation mechanisms and extends its application as a local probe
of protein dynamics to the ultrafast time scales.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Piotr Kabaciński
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | | | - Marziogiuseppe Gentile
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
| | - Rocio Borrego-Varillas
- Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.,Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
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6
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Liang W, Pei Z, Mao Y, Shao Y. Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges. J Chem Phys 2022; 156:210901. [PMID: 35676148 PMCID: PMC9162785 DOI: 10.1063/5.0088271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/15/2022] [Indexed: 01/04/2023] Open
Abstract
Time-dependent density functional theory (TDDFT) based approaches have been developed in recent years to model the excited-state properties and transition processes of the molecules in the gas-phase and in a condensed medium, such as in a solution and protein microenvironment or near semiconductor and metal surfaces. In the latter case, usually, classical embedding models have been adopted to account for the molecular environmental effects, leading to the multi-scale approaches of TDDFT/polarizable continuum model (PCM) and TDDFT/molecular mechanics (MM), where a molecular system of interest is designated as the quantum mechanical region and treated with TDDFT, while the environment is usually described using either a PCM or (non-polarizable or polarizable) MM force fields. In this Perspective, we briefly review these TDDFT-related multi-scale models with a specific emphasis on the implementation of analytical energy derivatives, such as the energy gradient and Hessian, the nonadiabatic coupling, the spin-orbit coupling, and the transition dipole moment as well as their nuclear derivatives for various radiative and radiativeless transition processes among electronic states. Three variations of the TDDFT method, the Tamm-Dancoff approximation to TDDFT, spin-flip DFT, and spin-adiabatic TDDFT, are discussed. Moreover, using a model system (pyridine-Ag20 complex), we emphasize that caution is needed to properly account for system-environment interactions within the TDDFT/MM models. Specifically, one should appropriately damp the electrostatic embedding potential from MM atoms and carefully tune the van der Waals interaction potential between the system and the environment. We also highlight the lack of proper treatment of charge transfer between the quantum mechanics and MM regions as well as the need for accelerated TDDFT modelings and interpretability, which calls for new method developments.
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Affiliation(s)
- WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Zheng Pei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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7
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Vandaele E, Mališ M, Luber S. The ΔSCF method for non-adiabatic dynamics of systems in the liquid phase. J Chem Phys 2022; 156:130901. [PMID: 35395890 DOI: 10.1063/5.0083340] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Computational studies of ultrafast photoinduced processes give valuable insights into the photochemical mechanisms of a broad range of compounds. In order to accurately reproduce, interpret, and predict experimental results, which are typically obtained in a condensed phase, it is indispensable to include the condensed phase environment in the computational model. However, most studies are still performed in vacuum due to the high computational cost of state-of-the-art non-adiabatic molecular dynamics (NAMD) simulations. The quantum mechanical/molecular mechanical (QM/MM) solvation method has been a popular model to perform photodynamics in the liquid phase. Nevertheless, the currently used QM/MM embedding techniques cannot sufficiently capture all solute-solvent interactions. In this Perspective, we will discuss the efficient ΔSCF electronic structure method and its applications with respect to the NAMD of solvated compounds, with a particular focus on explicit quantum mechanical solvation. As more research is required for this method to reach its full potential, some challenges and possible directions for future research are presented as well.
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Affiliation(s)
- Eva Vandaele
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Momir Mališ
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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8
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Manian A, Shaw RA, Lyskov I, Russo SP. The quantum chemical solvation of indole: accounting for strong solute-solvent interactions using implicit/explicit models. Phys Chem Chem Phys 2022; 24:3357-3369. [PMID: 35060986 DOI: 10.1039/d1cp05496a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we investigate the efficacy of different quantum chemical solvent modelling methods of indole in both water and methylcyclohexane solutions. The goal is to show that one can yield good photophysical properties in strongly coupled solute-solvent systems using standard DFT methods. We use standard and linearly-corrected Polarisable Continuum Models (PCM), as well as explicit solvation models, and compare the different model parameters, including the choice of density functional, basis set, and number of explicit solvent molecules. We demonstrate that implicit models overestimate energies and oscillator strengths. In particular, for indole-water, no level inversion is observed, suggesting a dielectric medium on its own is insufficient. In contrast, energies are seen to converge fairly rapidly with respect to cluster size towards experimentally measured properties in the explicit models. We find that the use of B3LYP with a diffuse basis set can adequately represent the photophysics of the system with a cluster size of between 9-12 explicit water molecules. Sampling of configurations from a molecular dynamics simulation suggests that the single point results are suitably representative of the solvated ensemble. For indole-water, we show that solvent reorganisation plays a significant role in stabilisation of the excited state energies. It is hoped that the findings and observations of this study will aid in the choice of solvation model parameters in future studies.
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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, UK
| | - 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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9
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Lin K, Hu D, Peng J, Xu C, Gu FL, Lan Z. Prediction of the excited-state reaction channels in photo-induced processes of nitrofurantoin using first-principle calculations and dynamics simulations. CHEMOSPHERE 2021; 281:130831. [PMID: 34289597 DOI: 10.1016/j.chemosphere.2021.130831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/25/2021] [Accepted: 05/06/2021] [Indexed: 06/13/2023]
Abstract
The understanding of the photochemistry of antibiotic compounds is important because it gives the direct information on the possible environmental pollution caused by them. Due to their large size, the theoretical studies of their excited-state reactions are rather challenging. In current work, we combined the on-the-fly trajectory surface-hopping dynamics, conical-intersection optimizations and excited-state pathway calculations to study the photochemistry of the trans-isomer of nitrofurantoin, a widely-used drug to treat the urinary tract infections. The dynamics-then-pathway approach was taken. First the trajectory surface hopping dynamics at the state-averaged complete-active-space self-consistent-field (SA-CASSCF) level with small active space and small basis sets were run. Second, the minimum-energy conical-intersection optimizations were performed. Finally the excited pathways from the Frank-Condon region to different reaction channels were built at the multi-state multi-reference second-order perturbation (MS-CASPT2) level with large active space and large basis set. Several possible channels responsible for the photo-induced reaction mechanism of the trans-nitrofurantoin were obtained, including the cleavage of the NO bond of the NO2 moiety, the photoisomerization at the central CN bond, and other internal conversion channels. Our findings give some preliminary explanations on available experimental observations. It is also demonstrates that the current theoretical approach is a powerful tool to explore the excited-state reactions in the photochemistry of media-sized or large-sized drug compounds.
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Affiliation(s)
- Kunni Lin
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry, South China Normal University, Guangzhou, 510006, PR China
| | - Deping Hu
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou, 510006, PR China
| | - Jiawei Peng
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou, 510006, PR China
| | - Chao Xu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry, South China Normal University, Guangzhou, 510006, PR China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry, South China Normal University, Guangzhou, 510006, PR China.
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou, 510006, PR China.
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10
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Titov E, Hummert J, Ikonnikov E, Mitrić R, Kornilov O. Electronic relaxation of aqueous aminoazobenzenes studied by time-resolved photoelectron spectroscopy and surface hopping TDDFT dynamics calculations. Faraday Discuss 2021; 228:226-241. [PMID: 33586720 DOI: 10.1039/d0fd00111b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Studies of ultrafast relaxation of molecular chromophores are complicated by the fact that most chromophores of biological and technological importance are rather large molecules and are strongly affected by their environment, either solvent or a protein cage. Here we present an approach which allows us to follow transient electronic structure of complex photoexcited molecules. We use the method of time-resolved photoelectron spectroscopy in solution to follow relaxation of two prototypical aqueous chromophores, Methyl Orange and Metanil Yellow, both of which are aminoazobenzene derivatives. Using excitation by 400 nm laser pulses and ionization by wavelength-selected 46.7 nm XUV pulses from high-order harmonic generation we follow relaxation of both molecules via the dark S1 state. The photoelectron spectra yield binding energies of both ground and excited states. We combine the experimental results with surface hopping time-dependent density functional theory (TDDFT) calculations employing B3LYP+D3 and ωB97X-D functionals. The results demonstrate that the method is generally suitable for description of ultrafast dynamics in these molecules and can recover absolute binding energies observed in the experiment. The B3LYP+D3 functional appears to be better suited for these systems, especially in the case of Metanil Yellow, where it indicates the importance of an intramolecular charge transfer state. Our results pave the way towards quantitative understanding of evolving electronic structure in photo-induced relaxation processes.
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Affiliation(s)
- Evgenii Titov
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany.
| | - Johan Hummert
- Max Born Institute, Max-Born-Straße 2A, 12489 Berlin, Germany.
| | | | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany.
| | - Oleg Kornilov
- Max Born Institute, Max-Born-Straße 2A, 12489 Berlin, Germany.
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11
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Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
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Affiliation(s)
- 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.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
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12
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Luo G, Zeng Z, Zhang L, Tao Z, Zhang Q. The fluorescence of a mercury probe based on osthol. Beilstein J Org Chem 2021; 17:22-27. [PMID: 33488828 PMCID: PMC7801779 DOI: 10.3762/bjoc.17.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
The ability of osthol (OST) to recognize mercury ions in aqueous solution was studied using fluorescence, UV–vis spectrophotometry, mass spectrometry, and 1H NMR spectroscopy, and the recognition mechanism is discussed. The results showed that OST and Hg2+ can form a complex with a stoichiometric ratio of 1:1. The binding constant was 1.552 × 105 L∙mol−1, having a highly efficient and specific selectivity for Hg2+. The fluorescence intensity of OST showed a good linear correlation with the Hg2+ concentration (6.0 × 10−5 to 24.0 × 10−5 mol∙L−1, R2 = 0.9954), and the detection limit of the probe was 5.04 × 10−8 mol∙L−1, which can be used for the determination of Hg2+ traces.
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Affiliation(s)
- Guangyan Luo
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Zhishu Zeng
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Lin Zhang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Zhu Tao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Qianjun Zhang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
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13
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Díaz Mirón G, González Lebrero MC. Fluorescence Quantum Yields in Complex Environments from QM-MM TDDFT Simulations: The Case of Indole in Different Solvents. J Phys Chem A 2020; 124:9503-9512. [PMID: 33166141 DOI: 10.1021/acs.jpca.0c06631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence is commonly exploited to probe microscopic properties. An important example is tryptophan in protein environments, where variations in fluorescence quantum yield, and in absorption and emission maxima, are used as indicators of changes in the environment. Modeling the fluorescence quantum yield requires the determination of both radiative and nonradiative decay constants, both on the potential energy surface of the excited fluorophore. Furthermore, the inclusion of complex environments implies their accurate representation as well as extensive configurational sampling. In this work, we present and test various methodologies based on time-dependent density functional theory (TDDFT) and quantum mechanics/molecular mechanics (QM/MM) dynamics that take all of these requirements into account to provide a quantitative prediction of the effect of the environment on the fluorescence quantum yield of indole, a tryptophan fluorophore. This investigation paves the way for applications to the realistic spectroscopic characterization of the local protein environment of tryptophan from computer simulations.
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Affiliation(s)
- Gonzalo Díaz Mirón
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina.,Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET Buenos Aires, C1428EHA Buenos Aires, Argentina
| | - Mariano C González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina.,Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET Buenos Aires, C1428EHA Buenos Aires, Argentina
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14
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Curchod BFE, Glover WJ, Martínez TJ. SSAIMS-Stochastic-Selection Ab Initio Multiple Spawning for Efficient Nonadiabatic Molecular Dynamics. J Phys Chem A 2020; 124:6133-6143. [PMID: 32580552 DOI: 10.1021/acs.jpca.0c04113] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Ab initio multiple spawning provides a powerful and accurate way of describing the excited-state dynamics of molecular systems, whose strength resides in the proper description of coherence effects during nonadiabatic processes thanks to the coupling of trajectory basis functions. However, the simultaneous propagation of a large number of trajectory basis functions can be numerically inconvenient. We propose here an elegant and simple solution to this issue, which consists of (i) detecting uncoupled groups of coupled trajectory basis functions and (ii) selecting stochastically one of these groups to continue the ab initio multiple spawning dynamics. We show that this procedure can reproduce the results of full ab initio multiple spawning dynamics in cases where the uncoupled groups of trajectory basis functions stay uncoupled throughout the dynamics (which is often the case in high-dimensional problems). We present and discuss the aforementioned idea in detail and provide simple numerical applications on indole, ethylene, and protonated formaldimine, highlighting the potential of stochastic-selection ab initio multiple spawning.
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Affiliation(s)
- Basile F E Curchod
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - William J Glover
- NYU Shanghai, 1555 Century Ave., Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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15
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Minezawa N, Nakajima T. Quantum mechanical/molecular mechanical trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory. J Chem Phys 2020; 152:024119. [DOI: 10.1063/1.5132879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Noriyuki Minezawa
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takahito Nakajima
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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16
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Paulikat M, Mata RA, Gelabert R. A high-throughput computational approach to UV-Vis spectra in protein mutants. Phys Chem Chem Phys 2019; 21:20678-20692. [PMID: 31508628 DOI: 10.1039/c9cp03908b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work we present a high-throughput approach to the computation of absorption UV-Vis spectra tailored to mutagenesis studies. The scheme makes use of a single molecular dynamics trajectory of a reference (non-mutated) species. The shifts in absorption energy caused by a residue mutation are evaluated by building an effective potential of the environment and computing a correction term based on perturbation theory. The sampling is only performed in the phase space of the initial protein. We analyze the robustness of the method by comparing different approximations for the effective potential, the sampling of mutant residue geometries and observing the impact in the prediction of both bathocromic and hypsochromic shifts. As a test subject, we consider a red fluorescent protein variant with potential biotechnological applications.
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Affiliation(s)
- Mirko Paulikat
- Institute of Physical Chemistry, University of Goettingen, Tammannstraße 6, D-37077 Göttingen, Germany.
| | - Ricardo A Mata
- Institute of Physical Chemistry, University of Goettingen, Tammannstraße 6, D-37077 Göttingen, Germany.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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17
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Minezawa N, Nakajima T. Trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory. J Chem Phys 2019; 150:204120. [DOI: 10.1063/1.5096217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Noriyuki Minezawa
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takahito Nakajima
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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18
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Montero R, Lamas I, León I, Fernández JA, Longarte A. Excited state dynamics of aniline homoclusters. Phys Chem Chem Phys 2019; 21:3098-3105. [PMID: 30672912 DOI: 10.1039/c8cp06416d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the relaxation, following excitation in the 290-235 nm region, of neutral aniline homoclusters (An)n formed in a supersonic expansion by femtosecond time resolved ionization. The applied method permits isolation of the dynamics of the dimer from that originated in bigger species of the generated distribution. Interestingly, and differently from the monomer and (An)n≥3 clusters, the dimer does not present a N-H dissociative 1πσ* channel. This fact can be explained in terms of the symmetric structure adopted, in which each molecule establishes two N-Hπ interactions, destabilizing the H dissociation channel. The observations permit relating the photophysics to the interactions established by the aniline units and confirming previous observations and theoretical predictions on the structure of aniline aggregates.
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Affiliation(s)
- Raúl Montero
- SGIker Laser Facility, UPV/EHU, Sarriena, s/n, Leioa 48940, Spain
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19
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Parker SM, Roy S, Furche F. Multistate hybrid time-dependent density functional theory with surface hopping accurately captures ultrafast thymine photodeactivation. Phys Chem Chem Phys 2019; 21:18999-19010. [DOI: 10.1039/c9cp03127h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an efficient analytical implementation of first-order nonadiabatic derivative couplings between arbitrary Born–Oppenheimer states in the hybrid time-dependent density functional theory (TDDFT) framework using atom-centered basis functions.
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Affiliation(s)
- Shane M. Parker
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
| | - Saswata Roy
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
| | - Filipp Furche
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
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20
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Abstract
A cavity or excluded-volume structure best explains the experimental properties of the aqueous or “hydrated” electron.
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Affiliation(s)
- John M. Herbert
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
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21
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Falahati K, Hamerla C, Huix-Rotllant M, Burghardt I. Ultrafast photochemistry of free-base porphyrin: a theoretical investigation of B → Q internal conversion mediated by dark states. Phys Chem Chem Phys 2018; 20:12483-12492. [PMID: 29700539 DOI: 10.1039/c8cp00657a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We examine the mechanism of ultrafast internal conversion between the B band (Soret band) and the Q band in porphine (H2P), the prototypical free-base porphyrin, using electronic structure studies and on-the-fly surface-hopping nonadiabatic dynamics. Our study highlights the crucial role of dark states within the N band which are found to mediate B/Q state transfer, necessitating a treatment beyond Gouterman's classic four-orbital model. The sequential B → N → Q pathway dominates largely over the direct B → Q pathway which is found to be energetically unfavorable. Potential energy surface cuts and conical intersections between excited states are determined by TDDFT and validated by CASSCF/CASPT2 and XMCQDPT2 calculations. Both the static analysis and on-the-fly surface-hopping calculations suggest a pathway which involves minor structural deformations via in-plane vibrations. The B → N conversion is a barrierless adiabatic process occurring within ∼20 fs, while the subsequent N → Q conversion occurs via a conical intersection within ∼100 fs, in agreement with time-resolved experiments for porphine and related free base porphyrins. Furthermore, evidence for both sequential and direct transfer to the Qx and Qy states is obtained.
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Affiliation(s)
- Konstantin Falahati
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany.
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22
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Abstract
We show that the importance sampling technique can effectively augment the range of problems where the nuclear ensemble approach can be applied. A sampling probability distribution function initially determines the collection of initial conditions for which calculations are performed, as usual. Then, results for a distinct target distribution are computed by introducing compensating importance sampling weights for each sampled point. This mapping between the two probability distributions can be performed whenever they are both explicitly constructed. Perhaps most notably, this procedure allows for the computation of temperature dependent observables. As a test case, we investigated the UV absorption spectra of phenol, which has been shown to have a marked temperature dependence. Application of the proposed technique to a range that covers 500 K provides results that converge to those obtained with conventional sampling. We further show that an overall improved rate of convergence is obtained when sampling is performed at intermediate temperatures. The comparison between calculated and the available measured cross sections is very satisfactory, as the main features of the spectra are correctly reproduced. As a second test case, one of Tully's classical models was revisited, and we show that the computation of dynamical observables also profits from the importance sampling technique. In summary, the strategy developed here can be employed to assess the role of temperature for any property calculated within the nuclear ensemble method, with the same computational cost as doing so for a single temperature.
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Affiliation(s)
- Fábris Kossoski
- Instituto de Fı́sica "Gleb Wataghin" , Universidade Estadual de Campinas , 13083-859 Campinas , São Paulo , Brazil.,Aix Marseille Univ , CNRS, ICR , Marseille , France
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23
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Kananenka AA, Sun X, Schubert A, Dunietz BD, Geva E. A comparative study of different methods for calculating electronic transition rates. J Chem Phys 2018; 148:102304. [DOI: 10.1063/1.4989509] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alexei A. Kananenka
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiang Sun
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alexander Schubert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, USA
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, USA
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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24
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Affiliation(s)
- Basile F. E. Curchod
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Todd J. Martínez
- Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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25
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Avanzini F, Moro GJ. Quantum stochastic trajectories: the Smoluchowski-Bohm equation. Phys Chem Chem Phys 2018; 20:165-179. [PMID: 29181466 DOI: 10.1039/c7cp06071h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular systems are quantum systems, but the complete characterization of molecular motions within a fully quantum framework might appear to be an unfeasible task because it would require that the actual nuclear positions are established at any time. One would like to use a quantum molecular trajectory that defines the instantaneous nuclear positions and satisfies the predictions of quantum mechanics in terms of its statistical properties. Even though it can be proven that the single Bohm trajectory provides a representation of the quantum molecular trajectory, this solves the issue only on a theoretical ground: exact solutions of the Schrödinger-Bohm dynamical system are extremely computationally demanding. Therefore, we derive a stochastic equation of Smoluchowski type from the Schrödinger-Bohm dynamics, through projection operator techniques, in order to characterize the molecular motions of open quantum systems. The main quantum features of the motions emerge from the equilibrium distribution, i.e., the wave function's squared modulus integrated on the environment degrees of freedom. Furthermore, we verify the accuracy of the stochastic equation by comparing its predictions with those of the deterministic dynamics for a model system of six interacting harmonic oscillators. The indisputable advantage of this full quantum mechanical approach is that of representing the molecular dynamics, which controls important phenomena like vibrational relaxation, conformational transitions and activated processes, in a self consistent way and at the low computational cost of solving simple stochastic equations.
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Affiliation(s)
- Francesco Avanzini
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova, Italy.
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26
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Affiliation(s)
- Francesco Avanzini
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Giorgio J. Moro
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova, Italy
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27
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Novak J, Prlj A, Basarić N, Corminboeuf C, Došlić N. Photochemistry of 1- and 2-Naphthols and Their Water Clusters: The Role of1ππ*(La) Mediated Hydrogen Transfer to Carbon Atoms. Chemistry 2017; 23:8244-8251. [DOI: 10.1002/chem.201700691] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jurica Novak
- Department of Physical Chemistry; Ruđer Bošković Institute; Bijenička cesta 54 10000 Zagreb Croatia
| | - Antonio Prlj
- Institut des Sciences et Ingénierie Chimiques; Ecole Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry; Ruđer Bošković Institute; Bijenička cesta 54 10000 Zagreb Croatia
| | - Clémence Corminboeuf
- Institut des Sciences et Ingénierie Chimiques; Ecole Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Nađa Došlić
- Department of Physical Chemistry; Ruđer Bošković Institute; Bijenička cesta 54 10000 Zagreb Croatia
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28
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Mališ M, Novak J, Zgrablić G, Parmigiani F, Došlić N. Mechanism of ultrafast non-reactive deactivation of the retinal chromophore in non-polar solvents. Phys Chem Chem Phys 2017; 19:25970-25978. [DOI: 10.1039/c7cp03293e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Counterion sensitive photodynamics of the retinal chromophore in solution.
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Affiliation(s)
- M. Mališ
- Department of Physical Chemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
- Centre Européen de Calcul Atomique et Moléculaire
| | - J. Novak
- Department of Physical Chemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - G. Zgrablić
- Elettra-Sincrotrone Treste
- T-ReX Laboratory
- Trieste
- Italy
- Politehnika Pula
| | - F. Parmigiani
- Elettra-Sincrotrone Treste
- T-ReX Laboratory
- Trieste
- Italy
- Department of Physics
| | - N. Došlić
- Department of Physical Chemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
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29
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Schubert A, Falvo C, Meier C. Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein. J Chem Phys 2016; 145:054108. [DOI: 10.1063/1.4959859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alexander Schubert
- Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse, France
| | - Cyril Falvo
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Christoph Meier
- Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse, France
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30
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Montero R, León I, Fernández JA, Longarte A. Femtosecond Excited State Dynamics of Size Selected Neutral Molecular Clusters. J Phys Chem Lett 2016; 7:2797-2802. [PMID: 27388417 DOI: 10.1021/acs.jpclett.6b00997] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The work describes a novel experimental approach to track the relaxation dynamics of an electronically excited distribution of neutral molecular clusters formed in a supersonic expansion, by pump-probe femtosecond ionization. The introduced method overcomes fragmentation issues and makes possible to retrieve the dynamical signature of a particular cluster from each mass channel, by associating it to an IR transition of the targeted structure. We have applied the technique to study the nonadiabatic relaxation of pyrrole homoclusters. The results obtained exciting at 243 nm, near the origin of the bare pyrrole electronic absorption, allow us to identify the dynamical signature of the dimer (Py)2, which exhibits a distinctive lifetime of τ1 ∼ 270 fs, considerably longer than the decays recorded for the monomer and bigger size clusters (Py)n>2. A possible relationship between the measured lifetime and the clusters geometries is tentatively discussed.
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Affiliation(s)
- Raúl Montero
- SGIker Laser Facility, UPV/EHU , Sarriena, s/n, 48940 Leioa, Spain
| | - Iker León
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU) , Apartment 644, 48080 Bilbao, Spain
| | - José A Fernández
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU) , Apartment 644, 48080 Bilbao, Spain
| | - Asier Longarte
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU) , Apartment 644, 48080 Bilbao, Spain
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31
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Aschi M, Barone V, Carlotti B, Daidone I, Elisei F, Amadei A. Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico model. Phys Chem Chem Phys 2016; 18:28919-28931. [PMID: 27725986 DOI: 10.1039/c6cp06167b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical–computational method is proposed for modelling the complete kinetics – from photo-excitation to relaxation – of a chromophore in solution.
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Affiliation(s)
| | | | - Benedetta Carlotti
- Department of Chemistry
- Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN)
- University of Perugia
- 06123 Perugia
- Italy
| | - Isabella Daidone
- Dipartimento di Scienze Fisiche e Chimiche
- University of l'Aquila
- Italy
| | - Fausto Elisei
- Department of Chemistry
- Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN)
- University of Perugia
- 06123 Perugia
- Italy
| | - Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche
- Universiy of Roma Tor Vergata
- 00100 Roma
- Italy
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32
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Du L, Lan Z. Correction to An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications. J Chem Theory Comput 2015; 11:4522-3. [PMID: 26575942 DOI: 10.1021/acs.jctc.5b00654] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Wang J, Huang J, Du L, Lan Z. Photoinduced Ultrafast Intramolecular Excited-State Energy Transfer in the Silylene-Bridged Biphenyl and Stilbene (SBS) System: A Nonadiabatic Dynamics Point of View. J Phys Chem A 2015; 119:6937-48. [DOI: 10.1021/acs.jpca.5b00354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun Wang
- Key
Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jing Huang
- Key
Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Likai Du
- Key
Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhenggang Lan
- Key
Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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34
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Zobač V, Lewis JP, Abad E, Mendieta-Moreno JI, Hapala P, Jelínek P, Ortega J. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:175002. [PMID: 25791682 DOI: 10.1088/0953-8984/27/17/175002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.
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Affiliation(s)
- Vladimír Zobač
- Institute of Physic, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-16200 Prague, Czech Republic. Department of Physical Electronics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Czech Republic
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35
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Mennucci B. QM/MM Approaches for the Modeling of Photoinduced Processes in Biological Systems. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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36
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Petrone A, Donati G, Caruso P, Rega N. Understanding THz and IR Signals beneath Time-Resolved Fluorescence from Excited-State Ab Initio Dynamics. J Am Chem Soc 2014; 136:14866-74. [DOI: 10.1021/ja507518k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Alessio Petrone
- Dipartimento
di Scienze Chimiche, Università di Napoli ‘Federico
II’, Complesso Universitario di M.S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Greta Donati
- Dipartimento
di Scienze Chimiche, Università di Napoli ‘Federico
II’, Complesso Universitario di M.S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Pasquale Caruso
- Italian Institute of Technology, IIT@CRIB Center for Advanced Biomaterials for Healthcare, Largo
Barsanti e Matteucci, I-80125 Napoli, Italy
| | - Nadia Rega
- Dipartimento
di Scienze Chimiche, Università di Napoli ‘Federico
II’, Complesso Universitario di M.S. Angelo, via Cintia, I-80126 Napoli, Italy
- Italian Institute of Technology, IIT@CRIB Center for Advanced Biomaterials for Healthcare, Largo
Barsanti e Matteucci, I-80125 Napoli, Italy
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37
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Riahi S, Rowley CN. The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties. J Comput Chem 2014; 35:2076-86. [PMID: 25178266 DOI: 10.1002/jcc.23716] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 01/05/2023]
Abstract
The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.
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Affiliation(s)
- Saleh Riahi
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, A1B 3X7, Canada
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38
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Liu X, Sobolewski AL, Domcke W. Photoinduced Oxidation of Water in the Pyridine–Water Complex: Comparison of the Singlet and Triplet Photochemistries. J Phys Chem A 2014; 118:7788-95. [DOI: 10.1021/jp505188y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xiaojun Liu
- Department
of Chemistry, Technische Universität München, D-85747 Garching, Germany
- Key
Laboratory of Luminescence and Optical Information, Institute of Optoelectronic
Technology, Beijing Jiaotong University, Beijing 100044, People’s Republic of China
| | | | - Wolfgang Domcke
- Department
of Chemistry, Technische Universität München, D-85747 Garching, Germany
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39
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An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1526-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Li X, Chung LW, Morokuma K, Li G. Theoretical Study on the UVR8 Photoreceptor: Sensing Ultraviolet-B by Tryptophan and Dissociation of Homodimer. J Chem Theory Comput 2014; 10:3319-30. [DOI: 10.1021/ct5003362] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xin Li
- State
Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Lung Wa Chung
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
- Department
of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Guohui Li
- State
Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian 116023, China
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41
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Giegerich J, Petersen J, Mitrić R, Fischer I. Photodissociation dynamics of propargylene, HCCCH. Phys Chem Chem Phys 2014; 16:6294-302. [DOI: 10.1039/c3cp53213e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a joint theoretical and experimental study on the photodissociation of the C3H2 isomer propargylene, HCCCH, combining velocity map imaging with nonadiabatic surface hopping calculations.
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Affiliation(s)
- Jens Giegerich
- Institute of Physical and Theoretical Chemistry
- University of Würzburg
- D-97074 Würzburg, Germany
| | - Jens Petersen
- Institute of Physical and Theoretical Chemistry
- University of Würzburg
- D-97074 Würzburg, Germany
| | - Roland Mitrić
- Institute of Physical and Theoretical Chemistry
- University of Würzburg
- D-97074 Würzburg, Germany
| | - Ingo Fischer
- Institute of Physical and Theoretical Chemistry
- University of Würzburg
- D-97074 Würzburg, Germany
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42
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Barbatti M, Crespo-Otero R. Surface Hopping Dynamics with DFT Excited States. DENSITY-FUNCTIONAL METHODS FOR EXCITED STATES 2014; 368:415-44. [DOI: 10.1007/128_2014_605] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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43
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Isborn CM, Mar BD, Curchod BFE, Tavernelli I, Martínez TJ. The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules. J Phys Chem B 2013; 117:12189-201. [DOI: 10.1021/jp4058274] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christine M. Isborn
- Chemistry
and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Brendan D. Mar
- PULSE
Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Basile F. E. Curchod
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Todd J. Martínez
- PULSE
Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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44
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Abedi A, Agostini F, Suzuki Y, Gross EKU. Dynamical steps that bridge piecewise adiabatic shapes in the exact time-dependent potential energy surface. PHYSICAL REVIEW LETTERS 2013; 110:263001. [PMID: 23848868 DOI: 10.1103/physrevlett.110.263001] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Indexed: 06/02/2023]
Abstract
We study the exact time-dependent potential energy surface (TDPES) in the presence of strong nonadiabatic coupling between the electronic and nuclear motion. The concept of the TDPES emerges from the exact factorization of the full electron-nuclear wave function [A. Abedi, N. T. Maitra, and E. K. U. Gross, Phys. Rev. Lett. 105, 123002 (2010)]. Employing a one-dimensional model system, we show that the TDPES exhibits a dynamical step that bridges between piecewise adiabatic shapes. We analytically investigate the position of the steps and the nature of the switching between the adiabatic pieces of the TDPES.
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Affiliation(s)
- Ali Abedi
- Max-Planck Institut für Mikrostrukturphysik, Weinberg 2, D-06120 Halle, Germany
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45
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Curchod BFE, Rothlisberger U, Tavernelli I. Trajectory-Based Nonadiabatic Dynamics with Time-Dependent Density Functional Theory. Chemphyschem 2013; 14:1314-40. [DOI: 10.1002/cphc.201200941] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 11/11/2022]
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46
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Abad E, Lewis JP, Zobač V, Hapala P, Jelínek P, Ortega J. Calculation of non-adiabatic coupling vectors in a local-orbital basis set. J Chem Phys 2013; 138:154106. [DOI: 10.1063/1.4801511] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Röhr MIS, Petersen J, Wohlgemuth M, Bonačić-Koutecký V, Mitrić R. Nonlinear Absorption Dynamics Using Field-Induced Surface Hopping: Zinc Porphyrin in Water. Chemphyschem 2013; 14:1377-86. [DOI: 10.1002/cphc.201300053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/13/2013] [Indexed: 11/11/2022]
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48
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Allolio C, Sajadi M, Ernsting NP, Sebastiani D. An Ab Initio Microscope: Molecular Contributions to the Femtosecond Time-Dependent Fluorescence Shift of a Reichardt-Type Dye. Angew Chem Int Ed Engl 2013; 52:1813-6. [DOI: 10.1002/anie.201204532] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/30/2012] [Indexed: 11/08/2022]
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49
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Unter dem Ab-initio-Mikroskop: molekulare Beiträge in der Femtosekunden-Stokes-Verschiebung eines Reichardt-Farbstoffs. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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50
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Minezawa N, Gordon MS. Optimizing conical intersections of solvated molecules: The combined spin-flip density functional theory/effective fragment potential method. J Chem Phys 2012; 137:034116. [DOI: 10.1063/1.4734314] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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