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Green JA, Gómez S, Worth G, Santoro F, Improta R. Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine-Cytosine in Chloroform. Chemistry 2022; 28:e202201731. [PMID: 35950519 PMCID: PMC9828530 DOI: 10.1002/chem.202201731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Indexed: 01/12/2023]
Abstract
We study the ultrafast photoactivated dynamics of the hydrogen bonded dimer Guanine-Cytosine in chloroform solution, focusing on the population of the Guanine→Cytosine charge transfer state (GC-CT), an important elementary process for the photophysics and photochemistry of nucleic acids. We integrate a quantum dynamics propagation scheme, based on a linear vibronic model parameterized through time dependent density functional theory calculations, with four different solvation models, either implicit or explicit. On average, after 50 fs, 30∼40 % of the bright excited state population has been transferred to GC-CT. This process is thus fast and effective, especially when transferring from the Guanine bright excited states, in line with the available experimental studies. Independent of the adopted solvation model, the population of GC-CT is however disfavoured in solution with respect to the gas phase. We show that dynamical solvation effects are responsible for this puzzling result and assess the different chemical-physical effects modulating the population of CT states on the ultrafast time-scale. We also propose some simple analyses to predict how solvent can affect the population transfer between bright and CT states, showing that the effect of the solute/solvent electrostatic interactions on the energy of the CT state can provide a rather reliable indication of its possible population.
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Affiliation(s)
- James A. Green
- Istituto di Biostrutture e Bioimmagini-CNRVia De Amicis 95I-80145Napoli
| | - Sandra Gómez
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUnited Kingdom
- Departamento de Química FísicaUniversity of SalamancaSalamanca37008Spain
| | - Graham Worth
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUnited Kingdom
| | - Fabrizio Santoro
- Istituto di Chimica die Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNRVia Moruzzi 1I-56124Pisa
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNRVia De Amicis 95I-80145Napoli
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2
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Zobel JP, González L. The Quest to Simulate Excited-State Dynamics of Transition Metal Complexes. JACS AU 2021; 1:1116-1140. [PMID: 34467353 PMCID: PMC8397362 DOI: 10.1021/jacsau.1c00252] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Indexed: 05/15/2023]
Abstract
This Perspective describes current computational efforts in the field of simulating photodynamics of transition metal complexes. We present the typical workflows and feature the strengths and limitations of the different contemporary approaches. From electronic structure methods suitable to describe transition metal complexes to approaches able to simulate their nuclear dynamics under the effect of light, we give particular attention to build a bridge between theory and experiment by critically discussing the different models commonly adopted in the interpretation of spectroscopic experiments and the simulation of particular observables. Thereby, we review all the studies of excited-state dynamics on transition metal complexes, both in gas phase and in solution from reduced to full dimensionality.
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Affiliation(s)
- J. Patrick Zobel
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währingerstr. 19, 1090 Vienna Austria
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3
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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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4
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Conti I, Cerullo G, Nenov A, Garavelli M. Ultrafast Spectroscopy of Photoactive Molecular Systems from First Principles: Where We Stand Today and Where We Are Going. J Am Chem Soc 2020; 142:16117-16139. [PMID: 32841559 PMCID: PMC7901644 DOI: 10.1021/jacs.0c04952] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Computational spectroscopy is becoming a mandatory tool for the interpretation of the
complex, and often congested, spectral maps delivered by modern non-linear multi-pulse
techniques. The fields of Electronic Structure Methods,
Non-Adiabatic Molecular Dynamics, and Theoretical
Spectroscopy represent the three pillars of the virtual ultrafast
optical spectrometer, able to deliver transient spectra in
silico from first principles. A successful simulation strategy requires a
synergistic approach that balances between the three fields, each one having its very
own challenges and bottlenecks. The aim of this Perspective is to demonstrate that,
despite these challenges, an impressive agreement between theory and experiment is
achievable now regarding the modeling of ultrafast photoinduced processes in complex
molecular architectures. Beyond that, some key recent developments in the three fields
are presented that we believe will have major impacts on spectroscopic simulations in
the very near future. Potential directions of development, pending challenges, and
rising opportunities are illustrated.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
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Keefer D, Reiter S, de Vivie-Riedle R. Ultrafast Photorelaxation of Uracil Embedded in an RNA Strand. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920510002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ultrafast photorelaxation of uracil can be hindered by its natural RNA environment. Multiscale quantum dynamical simulations show that the wave packet can be trapped in the photoexcited electronic state, which could potentially lead to photodamage.
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6
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Amadei A, Aschi M. Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems. RSC Adv 2018; 8:27900-27918. [PMID: 35542751 PMCID: PMC9083445 DOI: 10.1039/c8ra03900c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/23/2018] [Indexed: 11/21/2022] Open
Abstract
In this paper we present a theoretical-computational methodology specifically aimed at describing processes involving internal conversion or intersystem crossing, from atomistic (semiclassical) simulations and, hence, very suitable for treating complex atomic-molecular systems. The core of the presented approach is the evaluation of the diabatic perturbed energy surfaces of a portion of the whole system, treated at the quantum level and therefore preventively selected, in semi-classical interaction with the atomic-molecular environment. Subsequently, the estimation of the coupling between the diabatic surfaces and the inclusion of the obtained observables within a properly designed kinetic model allows the reconstruction of the whole phenomenology directly comparable to the experimental (typically kinetic) data. Application to two systems has demonstrated that the proposed approach can represent a valuable tool, somewhat complementary to other methods based on explicit quantum-dynamical approaches, for the theoretical-computational investigations of large and complex atomic-molecular systems.
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Affiliation(s)
- Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche, Universita' di Roma 'Tor Vergata' Roma Italy +390672594905
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Universita' di L'Aquila L'Aquila Italy +390862433775
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Reiter S, Keefer D, de Vivie-Riedle R. RNA Environment Is Responsible for Decreased Photostability of Uracil. J Am Chem Soc 2018; 140:8714-8720. [DOI: 10.1021/jacs.8b02962] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sebastian Reiter
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Daniel Keefer
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
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Zauleck JPP, Peschel MT, Rott F, Thallmair S, de Vivie-Riedle R. Ultrafast Reactive Quantum Dynamics Coupled to Classical Solvent Dynamics Using an Ehrenfest Approach. J Phys Chem A 2018; 122:2849-2857. [PMID: 29498853 DOI: 10.1021/acs.jpca.7b10372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The inclusion of solvent effects in the theoretical analysis of molecular processes becomes increasingly important. Currently, it is not feasible to directly include the solvent on the quantum level. We use an Ehrenfest approach to study the coupled time evolution of quantum dynamically treated solutes and classical solvents system. The classical dynamics of the solvent is coupled to the wavepacket dynamics of the solute and rotational and translational degrees of freedom of the solute are included classically. This allows quantum dynamics simulations for ultrafast processes that are decided by environment interactions without explicit separation of time scales. We show the application to the dissociation of ICN in liquid Ar as a proof of principal system and to the more applied example of uracil in water.
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Affiliation(s)
- Julius P P Zauleck
- Department of Chemistry , Ludwig-Maximilians-Universität München , D-81377 München , Germany
| | - Martin T Peschel
- Department of Chemistry , Ludwig-Maximilians-Universität München , D-81377 München , Germany
| | - Florian Rott
- Department of Chemistry , Ludwig-Maximilians-Universität München , D-81377 München , Germany
| | - Sebastian Thallmair
- Department of Chemistry , Ludwig-Maximilians-Universität München , D-81377 München , Germany
| | - Regina de Vivie-Riedle
- Department of Chemistry , Ludwig-Maximilians-Universität München , D-81377 München , Germany
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9
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Cerezo J, Liu Y, Lin N, Zhao X, Improta R, Santoro F. Mixed Quantum/Classical Method for Nonadiabatic Quantum Dynamics in Explicit Solvent Models: The ππ*/nπ* Decay of Thymine in Water as a Test Case. J Chem Theory Comput 2018; 14:820-832. [PMID: 29207245 DOI: 10.1021/acs.jctc.7b01015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mutual coupling of the solute and solvent dynamics is included within a mean-field framework and the quantum and classical equations of motions are solved simultaneously. As a test case we apply our method to the ultrafast ππ* → nπ* decay of thymine in water. Solvent dynamical response modifies IC yield already on the 50 fs time scale. This effect is due to water librational motions that stabilize the most populated state. Pure static disorder, that is, the existence of different solvent configurations when photoexcitation takes place, also has a remarkable impact on the dynamics.
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Affiliation(s)
- Javier Cerezo
- 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.,Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Yanli Liu
- 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.,School of Physics and Optoelectronics Engineering, Ludong University , 264025 Yantai, P. R. China
| | - Na Lin
- State Key Laboratory of Crystal Materials, Shandong University , 250100 Jinan, Shandong, P. R. China
| | - Xian Zhao
- State Key Laboratory of Crystal Materials, Shandong University , 250100 Jinan, Shandong, P. R. China
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR) , via Mezzocannone 16, I-80136 Napoli, Italy.,LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - 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
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10
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Riedle E, Roos MK, Thallmair S, Sailer CF, Krebs N, Fingerhut BP, de Vivie-Riedle R. Ultrafast photochemistry with two product channels: Wavepacket motion through two distinct conical intersections. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Hedegård ED, Bast R, Kongsted J, Olsen JMH, Jensen HJA. Relativistic Polarizable Embedding. J Chem Theory Comput 2017; 13:2870-2880. [DOI: 10.1021/acs.jctc.7b00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Radovan Bast
- High
Performance Computing Group, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | - Hans Jørgen Aagaard Jensen
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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12
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Thallmair S, Roos MK, de Vivie-Riedle R. Molecular features in complex environment: Cooperative team players during excited state bond cleavage. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:043205. [PMID: 26958588 PMCID: PMC4752547 DOI: 10.1063/1.4941600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
Photoinduced bond cleavage is often employed for the generation of highly reactive carbocations in solution and to study their reactivity. Diphenylmethyl derivatives are prominent precursors in polar and moderately polar solvents like acetonitrile or dichloromethane. Depending on the leaving group, the photoinduced bond cleavage occurs on a femtosecond to picosecond time scale and typically leads to two distinguishable products, the desired diphenylmethyl cations (Ph2CH(+)) and as competing by-product the diphenylmethyl radicals ([Formula: see text]). Conical intersections are the chief suspects for such ultrafast branching processes. We show for two typical examples, the neutral diphenylmethylchloride (Ph2CH-Cl) and the charged diphenylmethyltriphenylphosphonium ions ([Formula: see text]) that the role of the conical intersections depends not only on the molecular features but also on the interplay with the environment. It turns out to differ significantly for both precursors. Our analysis is based on quantum chemical and quantum dynamical calculations. For comparison, we use ultrafast transient absorption measurements. In case of Ph2CH-Cl, we can directly connect the observed signals to two early three-state and two-state conical intersections, both close to the Franck-Condon region. In case of the [Formula: see text], dynamic solvent effects are needed to activate a two-state conical intersection at larger distances along the reaction coordinate.
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Affiliation(s)
| | - Matthias K Roos
- Department Chemie, Ludwig-Maximilians-Universität München , D-81377 München, Germany
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Thallmair S, Roos MK, de Vivie-Riedle R. Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation. J Chem Phys 2016; 144:234104. [DOI: 10.1063/1.4953667] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Sebastian Thallmair
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 München, Germany
| | - Matthias K. Roos
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
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Cruz GN, Lima FS, Dias LG, El Seoud OA, Horinek D, Chaimovich H, Cuccovia IM. Molecular Dynamics Simulations of the Initial-State Predict Product Distributions of Dediazoniation of Aryldiazonium in Binary Solvents. J Org Chem 2015; 80:8637-42. [PMID: 26263052 DOI: 10.1021/acs.joc.5b01289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dediazoniation of aryldiazonium salts in mixed solvents proceeds by a borderline SN1 and SN2 pathway, and product distribution should be proportional to the composition of the solvation shell of the carbon attached to the -N2 group (ipso carbon). The rates of dediazoniation of 2,4,6-trimethylbenzenediazonium in water, methanol, ethanol, propanol, and acetonitrile were similar, but measured product distributions were noticeably dependent on the nature of the water/cosolvent mixture. Here we demonstrated that solvent distribution in the first solvation shell of the ipso carbon, calculated from classical molecular dynamics simulations, is equal to the measured product distribution. Furthermore, we showed that regardless of the charge distribution of the initial state, i.e., whether the positive charge is smeared over the molecule or localized on phenyl moiety, the solvent distribution around the reaction center is nearly the same.
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Affiliation(s)
| | | | | | | | - Dominik Horinek
- Institute für Physikalische und Theoretischen Chemie, University of Regensburg , 93053 Regensburg, Germany
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