1
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Aarabi M, Aranda D, Gholami S, Meena SK, Lerouge F, Bretonniere Y, Gürol I, Baldeck P, Parola S, Dumoulin F, Cerezo J, Garavelli M, Santoro F, Rivalta I. Quantum-Classical Protocol for Efficient Characterization of Absorption Lineshape and Fluorescence Quenching upon Aggregation: The Case of Zinc Phthalocyanine Dyes. J Chem Theory Comput 2023; 19:5938-5957. [PMID: 37641958 PMCID: PMC10500990 DOI: 10.1021/acs.jctc.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Indexed: 08/31/2023]
Abstract
A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.
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Affiliation(s)
- Mohammad Aarabi
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Daniel Aranda
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
- Instituto
de Ciencia Molecular (ICMol), Universidad
de Valencia, Catedrático
J. Beltrán 2, 46980 Paterna, Valencia, Spain
| | - Samira Gholami
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Santosh Kumar Meena
- Department
of Chemical Engineering, Indian Institute
of Technology Ropar, Rupnagar, 140001 Punjab, India
| | - Frederic Lerouge
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Yann Bretonniere
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Ilke Gürol
- TÜBITAK
Marmara Research Center, Materials Technologies, Gebze, 41470 Kocaeli, Türkiye
| | - Patrice Baldeck
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Stephane Parola
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Fabienne Dumoulin
- Department
of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Türkiye
| | - Javier Cerezo
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
- Departamento
de Química and Institute for Advanced Research in Chemical
Sciences (IAdChem), Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Fabrizio Santoro
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
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2
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Xu Y, Cheng Y, Song Y, Ma H. New Density Matrix Renormalization Group Approaches for Strongly Correlated Systems Coupled with Large Environments. J Chem Theory Comput 2023. [PMID: 37471519 DOI: 10.1021/acs.jctc.2c01316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Thanks to the high compression of the matrix product state (MPS) form of the wave function and the efficient site-by-site iterative sweeping optimization algorithm, the density matrix normalization group (DMRG) and its time-dependent variant (TD-DMRG) have been established as powerful computational tools in accurately simulating the electronic structure and quantum dynamics of strongly correlated molecules with a large number (101-2) of quantum degrees of freedom (active orbitals or vibrational modes). However, the quantitative characterization of the quantum many-body behaviors of realistic strongly correlated systems requires a further consideration of the interaction between the embedded active subsystem and the remaining correlated environment, e.g., a larger number (102-3) of external orbitals in electronic structure or infinite condensed-phase phononic modes in nucleus dynamics. To this end, we introduced three new post-DMRG and TD-DMRG approaches, namely (1) DMRG2sCI-MRCI and DMRG2sCI-ENPT by the reconstruction of selected configuration interaction (sCI) type of compact reference function from DMRG coefficients and the use of externally contracted MRCI (multireference configuration interaction) and Epstein-Nesbet perturbation theory (ENPT), without recourse to the expensive high order n-electron reduced density matrices (n-RDMs). (2) DMRG combined with RR-MRCI (renormalized residue-based MRCI), which improves the computational accuracy and efficiency of internally contracted (ic) MRCI by renormalizing the contracted bases with small-sized buffer environment(s) of a few external orbitals as probes based on quantum information theory. (3) HM (hierarchical mapping)-TD-DMRG in which a large environment is reduced to a small number of renormalized environmental modes (which accounts for the most vital system-environment interactions) through stepwise mapping transformation. These advances extend the efficacy of highly accurate DMRG/TD-DMRG computations to the quantitative characterization of the electronic structure and quantum dynamics in realistic strongly correlated systems coupled with large environments and are reviewed in this paper.
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Affiliation(s)
- Yihe Xu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yifan Cheng
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yinxuan Song
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haibo Ma
- Qingdao Institute for Theoretical and Computational Sciences, Qingdao Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
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3
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Pandey P, Prasad MD. Criteria for the Classification of System and Bath Variables in Nonadiabatic Dynamics: Application to Pyrazine. J Phys Chem A 2023; 127:3412-3426. [PMID: 37023395 DOI: 10.1021/acs.jpca.2c06155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
The present work deals with the system-bath separation of the vibrational modes involved in a nonadiabatic system. System modes are the strongly interacting modes which dominate the overall dynamics and, hence, need a near-exact treatment. Bath modes have relatively weaker couplings and can be approximately treated. Thus, the exponential bottleneck involved in computations is controlled by the size of the system-subspace. The aim of this work is to put forward a set of criteria that provides clear guidelines for choosing the system degrees of freedom. The extent of wave packet dephasing caused by repeated crossings across the surface of curve-crossing is the basis for distinction between system and bath modes. The mechanisms of the wave packet dephasing and the criteria are discussed in detail. Numerically converged results presented for the 24-mode pyrazine and 3-mode spin-boson model validate the efficiency of these criteria.
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Affiliation(s)
- Prachi Pandey
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - M Durga Prasad
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana 500046, India
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4
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Segatta F, Ruiz DA, Aleotti F, Yaghoubi M, Mukamel S, Garavelli M, Santoro F, Nenov A. Nonlinear Molecular Electronic Spectroscopy via MCTDH Quantum Dynamics: From Exact to Approximate Expressions. J Chem Theory Comput 2023; 19:2075-2091. [PMID: 36961952 PMCID: PMC10100531 DOI: 10.1021/acs.jctc.2c01059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
We present an accurate and efficient approach to computing the linear and nonlinear optical spectroscopy of a closed quantum system subject to impulsive interactions with an incident electromagnetic field. It incorporates the effect of ultrafast nonadiabatic dynamics by means of explicit numerical propagation of the nuclear wave packet. The fundamental expressions for the evaluation of first- and higher-order response functions are recast in a general form that can be used with any quantum dynamics code capable of computing the overlap of nuclear wave packets evolving in different states. Here we present the evaluation of these expressions with the multiconfiguration time-dependent Hartree (MCTDH) method. Application is made to pyrene, excited to its lowest bright excited state S2 which exhibits a sub-100-fs nonadiabatic decay to a dark state S1. The system is described by a linear vibronic coupling Hamiltonian, parametrized with multiconfiguration electronic structure methods. We show that the ultrafast nonadiabatic dynamics can have a remarkable effect on the spectral line shapes that goes beyond simple lifetime broadening. Furthermore, a widely employed approximate expression based on the time scale separation of dephasing and population relaxation is recast in the same theoretical framework. Application to pyrene shows the range of validity of such approximations.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Daniel Aranda Ruiz
- ICMol, Universidad de Valencia, Catedrático José Beltrán Martínez, 2, 46980 Paterna, Spain
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Martha Yaghoubi
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
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5
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Xu Y, Liu C, Ma H. Hierarchical Mapping for Efficient Simulation of Strong System-Environment Interactions. J Chem Theory Comput 2023; 19:426-435. [PMID: 36626721 DOI: 10.1021/acs.jctc.2c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Quantum dynamics (QD) simulation is a powerful tool for interpreting ultrafast spectroscopy experiments and unraveling their microscopic mechanism in out-of-equilibrium excited state behaviors in various chemical, biological, and material systems. Although state-of-the-art numerical QD approaches such as the time-dependent density matrix renormalization group (TD-DMRG) already greatly extended the solvable system size of general linearly coupled exciton-phonon models with up to a few hundred phonon modes, the accurate simulation of larger system sizes or strong system-environment interactions is still computationally highly challenging. Based on quantum information theory (QIT), in this work, we realize that only a small number of effective phonon modes couple to the excitonic system directly regardless of a large or even infinite number of modes in the condensed phase environment. On top of the identified small number of direct effective modes, we propose a hierarchical mapping (HM) approach through performing block Lanczos transformations on the remaining indirect modes, which transforms the Hamiltonian matrix to a nearly block-tridiagonal form and eliminates the long-range interactions. Numerical tests on model spin-boson systems and realistic singlet fission models in a rubrene crystal environment with up to 7000 modes and strong system-environment interactions indicate HM can reduce the system size by 1-2 orders of magnitude and accelerate the calculation by ∼80% without losing accuracy.
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Affiliation(s)
- Yihe Xu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haibo Ma
- Qingdao Institute for Theoretical and Computational Sciences, Qingdao Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
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6
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Picconi D. Quantum dynamics of the photoinduced charge separation in a symmetric donor–acceptor–donor triad: The role of vibronic couplings, symmetry and temperature. J Chem Phys 2022; 156:184105. [DOI: 10.1063/5.0089887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The photoinduced charge separation in a symmetric donor–acceptor–donor (D–A–D) triad is studied quantum mechanically using a realistic diabatic vibronic coupling model. The model includes a locally excited DA*D state and two charge-transfer states D+A−D and DA−D+ and is constructed according to a procedure generally applicable to semirigid D–A–D structures and based on energies, forces, and force constants obtained by quantum chemical calculations. In this case, the electronic structure is described by time-dependent density functional theory, and the corrected linear response is used in conjunction with the polarizable continuum model to account for state-specific solvent effects. The multimode dynamics following the photoexcitation to the locally excited state are simulated by the hybrid Gaussian-multiconfigurational time-dependent Hartree method, and temperature effects are included using thermo field theory. The dynamics are connected to the transient absorption spectrum obtained in recent experiments, which is simulated and fully assigned from first principles. It is found that the charge separation is mediated by symmetry-breaking vibrations of relatively low frequency, which implies that temperature should be accounted for to obtain reliable estimates of the charge transfer rate.
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Affiliation(s)
- David Picconi
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam-Golm, Germany and Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam-Golm, Germany
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Segalina A, Aranda D, Green JA, Cristino V, Caramori S, Prampolini G, Pastore M, Santoro F. How the Interplay among Conformational Disorder, Solvation, Local, and Charge-Transfer Excitations Affects the Absorption Spectrum and Photoinduced Dynamics of Perylene Diimide Dimers: A Molecular Dynamics/Quantum Vibronic Approach. J Chem Theory Comput 2022; 18:3718-3736. [PMID: 35377648 PMCID: PMC9202308 DOI: 10.1021/acs.jctc.2c00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
In this contribution
we present a mixed quantum-classical dynamical
approach for the computation of vibronic absorption spectra of molecular
aggregates and their nonadiabatic dynamics, taking into account the
coupling between local excitations (LE) and charge-transfer (CT) states.
The approach is based on an adiabatic (Ad) separation between the
soft degrees of freedom (DoFs) of the system and the stiff vibrations,
which are described by the quantum dynamics (QD) of wave packets (WPs)
moving on the coupled potential energy surfaces (PESs) of the LE and
CT states. These PESs are described with a linear vibronic coupling
(LVC) Hamiltonian, parameterized by an overlap-based diabatization
on the grounds of time-dependent density functional theory computations.
The WPs time evolution is computed with the multiconfiguration time-dependent
Hartree method, using effective modes defined through a hierarchical
representation of the LVC Hamiltonian. The soft DoFs are sampled with
classical molecular dynamics (MD), and the coupling between the slow
and fast DoFs is included by recomputing the key parameters of the
LVC Hamiltonians, specifically for each MD configuration. This method,
named Ad-MD|gLVC, is applied to a perylene diimide (PDI) dimer in
acetonitrile and water solutions, and it is shown to accurately reproduce
the change in the vibronic features of the absorption spectrum upon
aggregation. Moreover, the microscopic insight offered by the MD trajectories
allows for a detailed understanding of the role played by the fluctuation
of the aggregate structure on the shape of the vibronic spectrum and
on the population of LE and CT states. The nonadiabatic QD predicts
an extremely fast (∼50 fs) energy transfer between the two
LEs. CT states have only a moderate effect on the absorption spectrum,
despite the fact that after photoexcitation they are shown to acquire
a fast and non-negligible population, highlighting their relevance
in dictating the charge separation and transport in PDI-based optical
devices.
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Affiliation(s)
- Alekos Segalina
- Université de Lorraine and CNRS, LPCT, UMR 7019, F-54000 Nancy, France
| | - Daniel Aranda
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, Catedrático J. Beltrán 2, 46980 Paterna, Valencia, Spain
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Vito Cristino
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Stefano Caramori
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche, (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | | | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche, (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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Abstract
Chemical systems normally possess strong nonlinear vibronic couplings at both zero and finite temperature. For the lowest-order quadratic couplings, here, we introduce a squeezing operator into a variational coherent-state-based method, Davydov ansatz, to simulate the quantum dynamics and the respective spectroscopy. Two molecular systems, pyrazine and the 2-pyridone dimer, are taken as calculated model systems, both of which involve nontrivial quadratic vibronic couplings in high- and low-frequency regions, respectively. Upon a comparison with the benchmarks, the method manifests its advantage for nonlinear couplings. The squeezed bases are also proven to be applicable for the finite temperature by adapting with the thermofield dynamics.
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Affiliation(s)
- Jiarui Zeng
- Department of Physics, South China University of Technology, Guangzhou 510640, China
| | - Yao Yao
- Department of Physics, South China University of Technology, Guangzhou 510640, China.,State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
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Picconi D. Nonadiabatic quantum dynamics of the coherent excited state intramolecular proton transfer of 10-hydroxybenzo[h]quinoline. Photochem Photobiol Sci 2021; 20:1455-1473. [PMID: 34657277 DOI: 10.1007/s43630-021-00112-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022]
Abstract
The photoinduced nonadiabatic dynamics of the enol-keto isomerization of 10-hydroxybenzo[h]quinoline (HBQ) are studied computationally using high-dimensional quantum dynamics. The simulations are based on a diabatic vibronic coupling Hamiltonian, which includes the two lowest [Formula: see text] excited states and a [Formula: see text] state, which has high energy in the Franck-Condon zone, but significantly stabilizes upon excited state intramolecular proton transfer. A procedure, applicable to large classes of excited state proton transfer reactions, is presented to parametrize this model using potential energies, forces and force constants, which, in this case, are obtained by time-dependent density functional theory. The wave packet calculations predict a time scale of 10-15 fs for the photoreaction, and reproduce the time constants and the coherent oscillations observed in time-resolved spectroscopic studies performed on HBQ. In contrast to the interpretation given to the most recent experiments, it is found that the reaction initiated by [Formula: see text] photoexcitation proceeds essentially on a single potential energy surface, and the observed coherences bear signatures of Duschinsky mode-mixing along the reaction path. The dynamics after the [Formula: see text] excitation are instead nonadiabatic, and the [Formula: see text] state plays a major role in the relaxation process. The simulations suggest a mainly active role of the proton in the isomerization, rather than a passive migration assisted by the vibrations of the benzoquinoline backbone.
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Affiliation(s)
- David Picconi
- Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany.
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Jouybari MY, Green JA, Improta R, Santoro F. The Ultrafast Quantum Dynamics of Photoexcited Adenine-Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model. J Phys Chem A 2021; 125:8912-8924. [PMID: 34609880 PMCID: PMC9281421 DOI: 10.1021/acs.jpca.1c08132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
this contribution we present a quantum dynamical study of the
photoexcited hydrogen bonded base pair adenine–thymine (AT)
in a Watson–Crick arrangement. To that end, we parametrize
Linear Vibronic Coupling (LVC) models with Time-Dependent Density
Functional Theory (TD-DFT) calculations, exploiting a fragment diabatization
scheme (FrD) we have developed to define diabatic states on the basis
of individual chromophores in a multichromophoric system. Wavepacket
propagations were run with the multilayer extension of the Multiconfiguration
Time-Dependent Hartree method. We considered excitations to the three
lowest bright states, a ππ* state of
thymine and two ππ* states (La and Lb) of adenine, and we found that on the 100 fs time
scale the main decay pathways involve intramonomer population transfers
toward nπ* states of the same nucleobase. In AT this transfer
is less effective than in the isolated nucleobases, because hydrogen
bonding destabilizes the nπ* states. The population transfer
to the A → T charge transfer state is negligible, making the
ultrafast (femtosecond) decay through the proton coupled electron
transfer mechanism unlikely, in line with experimental results in
apolar solvents. The excitation energy transfer is also very small.
We carefully compare the predictions of LVC Hamiltonians obtained
with different sets of diabatic states, defined so to match either
local states of the two separated monomers or the base pair adiabatic
states in the Franck–Condon region. To that end we also extend
the flexibility of the FrD-LVC approach, introducing a new strategy
to define fragments diabatic states that account for the effect of
the rest of the multichromohoric system through a Molecular Mechanics
potential.
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Affiliation(s)
- Martha Yaghoubi Jouybari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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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: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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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Green JA, Jouybari MY, Aranda D, Improta R, Santoro F. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules 2021; 26:1743. [PMID: 33804640 PMCID: PMC8003674 DOI: 10.3390/molecules26061743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.
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Affiliation(s)
- James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Martha Yaghoubi Jouybari
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Daniel Aranda
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Fabrizio Santoro
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
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13
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Aleotti F, Aranda D, Yaghoubi Jouybari M, Garavelli M, Nenov A, Santoro F. Parameterization of a linear vibronic coupling model with multiconfigurational electronic structure methods to study the quantum dynamics of photoexcited pyrene. J Chem Phys 2021; 154:104106. [PMID: 33722019 DOI: 10.1063/5.0044693] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
With this work, we present a protocol for the parameterization of a Linear Vibronic Coupling (LVC) Hamiltonian for quantum dynamics using highly accurate multiconfigurational electronic structure methods such as RASPT2/RASSCF, combined with a maximum-overlap diabatization technique. Our approach is fully portable and can be applied to many medium-size rigid molecules whose excited state dynamics requires a quantum description. We present our model and discuss the details of the electronic structure calculations needed for the parameterization, analyzing critical situations that could arise in the case of strongly interacting excited states. The protocol was applied to the simulation of the excited state dynamics of the pyrene molecule, starting from either the first or the second bright state (S2 or S5). The LVC model was benchmarked against state-of-the-art quantum mechanical calculations with optimizations and energy scans and turned out to be very accurate. The dynamics simulations, performed including all active normal coordinates with the multilayer multiconfigurational time-dependent Hartree method, show good agreement with the available experimental data, endorsing prediction of the excited state mechanism, especially for S5, whose ultrafast deactivation mechanism was not yet clearly understood.
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Affiliation(s)
- Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Daniel Aranda
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Martha Yaghoubi Jouybari
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
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14
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Fedotov DA, Paul AC, Posocco P, Santoro F, Garavelli M, Koch H, Coriani S, Improta R. Excited-State Absorption of Uracil in the Gas Phase: Mapping the Main Decay Paths by Different Electronic Structure Methods. J Chem Theory Comput 2021; 17:1638-1652. [PMID: 33529532 DOI: 10.1021/acs.jctc.0c01150] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present a computational study of the one-photon and excited-state absorption (ESA) from the two lowest energy excited states of uracil in the gas phase: an nπ* dark state (1n) and the lowest energy bright ππ* state (1π). The predictions of six different linear response electronic structure methods, namely, TD-CAM-B3LYP, EOM-CCSD, EOM-CC3, ADC(2), ADC(2)-x, and ADC(3) are critically compared. In general, the spectral shapes predicted by TD-CAM-B3LYP, EOM-CCSD, EOM-CC3, and ADC(3) are fairly similar, though the quality of TD-CAM-B3LYP slightly deteriorates in the high-energy region. By computing the spectra at some key structures on different potential energy surfaces (PES), that is, the Franck-Condon point, the 1n minimum, and structures representative of different regions of the 1π PES, we obtain important insights into the shift of the ESA spectra, following the motion of the wavepacket on the excited-state PES. Though 1π has larger ESA than 1n, some spectral regions are dominated by these latter signals. Aside from its methodological interest, we thus obtain interesting indications to interpret transient absorption spectra to disentangle the photoactivated dynamics of nucleobases.
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Affiliation(s)
- Daniil A Fedotov
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark
| | - Alexander C Paul
- Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Paolo Posocco
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Marco Garavelli
- Department of Industrial Chemistry "Toso Montanari", Università degli Studi di Bologna, I-40126 Bologna, Italy
| | - Henrik Koch
- Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56100 Pisa, Italy
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark.,Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 6, I-80134 Napoli, Italy
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15
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Picconi D, Burghardt I. Time-resolved spectra of I2 in a krypton crystal by G-MCTDH simulations: nonadiabatic dynamics, dissipation and environment driven decoherence. Faraday Discuss 2020; 221:30-58. [DOI: 10.1039/c9fd00065h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time- and frequency-resolved pump-probe spectra of I2 in a krypton crystal are calculated and analyzed using high-dimensional multi-state quantum dynamics by the Gaussian-based multi-configuration time-dependent Hartree (G-MCTDH) method.
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Affiliation(s)
- David Picconi
- Institute of Physical and Theoretical Chemistry
- Goethe University Frankfurt
- D-60438 Frankfurt am Main
- Germany
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry
- Goethe University Frankfurt
- D-60438 Frankfurt am Main
- Germany
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16
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Erickson BA, Heim ZN, Pieri E, Liu E, Martinez TJ, Neumark DM. Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy. J Phys Chem A 2019; 123:10676-10684. [PMID: 31756106 DOI: 10.1021/acs.jpca.9b08258] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relaxation dynamics of thymine and its derivatives thymidine and thymidine monophosphate are studied using time-resolved photoelectron spectroscopy applied to a water microjet. Two absorption bands are studied; the first is a bright ππ* state which is populated using tunable-ultraviolet light in the range 4.74-5.17 eV and probed using a 6.20 eV probe pulse. By reversing the order of these pulses, a band containing multiple ππ* states is populated by the 6.20 eV pulse and the lower energy pulse serves as the probe. The lower lying ππ* state is found to decay in ∼400 fs in both thymine and thymidine independent of pump photon energy, while thymidine monophosphate decays vary from 670 to 840 fs with some pump energy dependence. The application of a computational quantum mechanical/molecular mechanical scheme at the XMS-CASPT2//CASSCF/AMBER level of theory suggests that conformational differences existing between thymidine and thymidine monophosphate in solution account for this difference. The higher lying ππ* band is found to decay in ∼600 fs in all three cases, but it is only able to be characterized when the 5.17 eV probe pulse is used. Notably, no long-lived signal from an nπ* state can be identified in either experiment on any of the three molecules.
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Affiliation(s)
- Blake A Erickson
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Zachary N Heim
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Elisa Pieri
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Erica Liu
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Todd J Martinez
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Daniel M Neumark
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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17
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Abstract
Multichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment-protein complexes to nucleic acids. The former are designed to capture, harvest, efficiently transport, and transform energy from sunlight for photosynthesis, while the latter should dissipate the absorbed radiation as quickly as possible to prevent photodamages and corruption of the carried genetic information. Because of the unique electronic and structural characteristics, the modeling of their photoinduced activity is a real challenge. Numerous approaches have been devised building on the theoretical development achieved for single chromophores and on model Hamiltonians that capture the essential features of the system. Still, a question remains: is a general strategy for the accurate modeling of multichromophoric systems possible? By using a quantum chemical point of view, here we review the advancements developed so far highlighting differences and similarities with the single chromophore treatment. Finally, we outline the important limitations and challenges that still need to be tackled to reach a complete and accurate picture of their photoinduced properties and dynamics.
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Affiliation(s)
- Francesco Segatta
- Dipartimento
di Chimica Industriale “Toso Montanari” University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, University
of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari” University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University
of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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18
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Frati F, de Groot F, Cerezo J, Santoro F, Cheng L, Faber R, Coriani S. Coupled cluster study of the x-ray absorption spectra of formaldehyde derivatives at the oxygen, carbon, and fluorine K-edges. J Chem Phys 2019. [DOI: 10.1063/1.5097650] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Federica Frati
- Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 GC Utrecht, The Netherlands
| | - Frank de Groot
- Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 GC Utrecht, The Netherlands
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM–CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Lan Cheng
- Department of Chemistry, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rasmus Faber
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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19
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Aranda D, Cerezo J, Pescitelli G, Avila Ferrer FJ, Soto J, Santoro F. A computational study of the vibrationally-resolved electronic circular dichroism spectra of single-chain transoid and cisoid oligothiophenes in chiral conformations. Phys Chem Chem Phys 2018; 20:21864-21880. [PMID: 30105334 DOI: 10.1039/c8cp03482f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We simulate the vibronic profile of the electronic circular dichroism (ECD) spectra of oligothiophenes in cisoid and transoid chiral arrangements. We consider oligomers of different lengths, from two to fifteen units, and investigate extensively how the ECD spectral shapes depend on the inter-ring torsions. In general, the molecular structures we consider are not stationary points of the ground state potential energy surface. Therefore, in order to perform vibronic calculations, we present a new computational protocol able to define reduced-dimensionality models where the effect of the off-equilibrium modes is removed. This is done adopting a description of the vibrational motions in curvilinear internal coordinates, and vertical harmonic models coupled with an iterative application of projectors to define energy Hessians, and therefore effective normal modes, in the space complementary to the one of the off-equilibrium coordinates. Although we consider both Franck-Condon and Herzberg-Teller contributions, the results show that transoid twisted ribbons always give rise to monosignated ECD spectra, while bi-signated and multi-signated spectra are expected for cisoid helices. These findings are explained on the basis of the different transition strengths of the lowest electronic states imparted by the different spatial arrangement, that is almost linear for transoid structures and more globular for cisoid ones. We predicted the chiroptical response of a large number of possible molecular arrangements. These data are employed to critically discuss the experimental ECD of polythiophenes in different experimental conditions, forming either aggregates or host-guest complexes. The method here proposed to perform vibronic calculations in reduced-dimensionality models is of general applicability and its potential interest goes beyond the practical application presented here.
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Affiliation(s)
- Daniel Aranda
- Department of Physical Chemistry, Faculty of Science, University of Málaga, E-29071-Málaga, Spain
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20
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Abstract
Resonance energy transfer (RET) is a complex phenomenon where energy is transferred between two nonequivalent molecules. In the Förster picture, that applies to the weak coupling regime, RET occurs from the energy donor molecule in the relaxed excited state toward the acceptor, in an energy-conserving process. However, energy dissipation is crucial for a more general picture of RET that also applies to the strong coupling regime. Here we present a dynamical, nonadiabatic model for RET also accounting for energy relaxation. We exploit the essential state formalism to set up a model for the RET pair that yields an accurate picture of the relevant physics, accounting for just a few electronic states and a single coupled vibrational coordinate per molecule. Molecular vibrations are treated in a nonadiabatic approach, and energy dissipation is dealt within the Redfield formalism. The approach is first validated on an isolated dye, demonstrating that a very simple relaxation model, defined in terms of a single relaxation parameter, properly describes the different regimes of energy dissipation expected for a molecule, with a fast (fs time window) internal conversion to the lowest excited state and a slow relaxation toward the ground state (ns time window). The same approach is then applied to follow the real time dynamics of a RET pair. In line with the Förster model, in the weak coupling regime the internal conversion of the donor molecule is completed before energy transfer takes place. Our approach also applies to the strong coupling regime, where we observe ultrafast energy transfer occurring well before the internal relaxation of the energy donor is completed.
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Affiliation(s)
- Francesco Di Maiolo
- Department of Chemistry, Life Science and Environmental Sustainability , Università di Parma , 43124 Parma , Italy
| | - Anna Painelli
- Department of Chemistry, Life Science and Environmental Sustainability , Università di Parma , 43124 Parma , Italy
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21
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Liu Y, Cerezo J, Lin N, Zhao X, Improta R, Santoro F. Comparison of the results of a mean-field mixed quantum/classical method with full quantum predictions for nonadiabatic dynamics: application to the $$\pi \pi ^*/n\pi ^*$$ π π ∗ / n π ∗ decay of thymine. Theor Chem Acc 2018; 137. [DOI: 10.1007/s00214-018-2218-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Baiardi A, Paoloni L, Barone V, Zakrzewski VG, Ortiz JV. Assessment of Electron Propagator Methods for the Simulation of Vibrationally Resolved Valence and Core Photoionization Spectra. J Chem Theory Comput 2017; 13:3120-3135. [PMID: 28521087 PMCID: PMC5732571 DOI: 10.1021/acs.jctc.6b00958] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The analysis of photoelectron spectra is usually facilitated by quantum mechanical simulations. Because of the recent improvement of experimental techniques, the resolution of experimental spectra is rapidly increasing, and the inclusion of vibrational effects is usually mandatory to obtain a reliable reproduction of the spectra. With the aim of defining a robust computational protocol, a general time-independent formulation to compute different kinds of vibrationally resolved electronic spectra has been generalized to also support photoelectron spectroscopy. The electronic structure data underlying the simulation are computed using different electron propagator approaches. In addition to the more standard approaches, a new and robust implementation of the second-order self-energy approximation of the electron propagator based on a transition operator reference (TOEP2) is presented. To validate our implementation, a series of molecules has been used as test cases. The result of the simulations shows that, for ultraviolet photoionization spectra, the more accurate nondiagonal approaches are needed to obtain a reliable reproduction of vertical ionization energies but that diagonal approaches are sufficient for energy gradients and pole strengths. For X-ray photoelectron spectroscopy, the TOEP2 approach, besides being more efficient, is also the most accurate in the reproduction of both vertical ionization energies and vibrationally resolved bandshapes.
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Affiliation(s)
- A Baiardi
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - L Paoloni
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - V Barone
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - V G Zakrzewski
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849-5312, United States
| | - J V Ortiz
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849-5312, United States
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24
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Keefer D, Thallmair S, Matsika S, de Vivie-Riedle R. Controlling Photorelaxation in Uracil with Shaped Laser Pulses: A Theoretical Assessment. J Am Chem Soc 2017; 139:5061-5066. [DOI: 10.1021/jacs.6b12033] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Keefer
- Department
Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Sebastian Thallmair
- Department
Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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25
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Abstract
In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.
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26
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Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche; Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR); Pisa Italy
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230; Université de Nantes; Nantes France
- Institut Universitaire de France; Paris France
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27
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Affiliation(s)
- Raffaele Borrelli
- Department of Agricultural, Forestry and Food Science, Università di Torino, I-10095 Grugliasco, TO, Italy
| | - Andrea Peluso
- Department of Chemistry and Biology, Università di Salerno, I-84081 Fisciano, SA, Italy
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28
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Segarra-Martí J, Garavelli M, Aquilante F. Multiconfigurational Second-Order Perturbation Theory with Frozen Natural Orbitals Extended to the Treatment of Photochemical Problems. J Chem Theory Comput 2016; 11:3772-84. [PMID: 26574459 DOI: 10.1021/acs.jctc.5b00479] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new flavor of the frozen natural orbital complete active space second-order perturbation theory method (FNO-CASPT2, Aquilante et al., J. Chem. Phys. 131, 034113) is proposed herein. In this new implementation, the virtual space in Cholesky decomposition-based CASPT2 computations (CD-CASPT2) is truncated by excluding those orbitals that contribute the least toward preserving a predefined value of the trace of an approximate density matrix, as that represents a measure of the amount of dynamic correlation retained in the model. In this way, the amount of correlation included is practically constant at all nuclear arrangements, thus allowing for the computation of smooth electronic states surfaces and energy gradients-essential requirements for theoretical studies in photochemistry. The method has been benchmarked for a series of relevant biochromophores for which large speed-ups have been recorded while retaining the accuracy achieved in the corresponding CD-CASPT2 calculations. Both vertical excitation energies and gradient calculations have been carried out to establish general guidelines as to how much correlation needs to be retained in the calculation for the results to be consistent with the CD-CASPT2 findings. Our results feature errors within a tenth of an eV for the most difficult cases and have been validated to be used for gradient computations where an up to 3-fold speed-up is observed depending on the size of the system and the basis set employed.
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Affiliation(s)
- Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy.,Université de Lyon, CNRS , Institut de Chimie de Lyon, École Normale Supérieure de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France
| | - Francesco Aquilante
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy
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29
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 321] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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30
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Liu Y, Cerezo J, Santoro F, Rizzo A, Lin N, Zhao X. Theoretical investigation of the broad one-photon absorption line-shape of a flexible symmetric carbazole derivative. Phys Chem Chem Phys 2016; 18:22889-905. [DOI: 10.1039/c6cp04162k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The one-photon absorption spectrum of a carbazole derivative has been studied by employing density functional response theory combined with a mixed quantum/classical approach to simulate the spectral shape.
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Affiliation(s)
- Yanli Liu
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
- CNR – Consiglio Nazionale delle Ricerche
| | - Javier Cerezo
- CNR – Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- CNR – Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- I-56124 Pisa
- Italy
| | - Antonio Rizzo
- CNR – Consiglio Nazionale delle Ricerche
- Istituto per i Processi Chimico Fisici (IPCF-CNR)
- I-56124 Pisa
- Italy
| | - Na Lin
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
| | - Xian Zhao
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
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31
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Padula D, Santoro F, Pescitelli G. A simple dimeric model accounts for the vibronic ECD spectra of chiral polythiophenes in their aggregated states. RSC Adv 2016. [DOI: 10.1039/c6ra05500a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aggregates of chiral polythiophenes (PTs) show exciton-coupled electronic circular dichroism (ECD) spectra with a unique vibronic structure, which can be reproduced by quantum dynamical simulations on the coupled states of small dimeric models.
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Affiliation(s)
- Daniele Padula
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale Via G. Moruzzi 13
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche – CNR
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- UOS di Pisa
- I-56124 Pisa
- Italy
| | - Gennaro Pescitelli
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale Via G. Moruzzi 13
- I-56124 Pisa
- Italy
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32
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Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal VK, Altavilla SF, Mukamel S, Garavelli M. Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations. Faraday Discuss 2015; 177:345-62. [PMID: 25607949 DOI: 10.1039/c4fd00175c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The SOS//QM/MM [Rivalta et al., Int. J. Quant. Chem., 2014, 114, 85] method consists of an arsenal of computational tools allowing accurate simulation of one-dimensional (1D) and bi-dimensional (2D) electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy. Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as charge-transfer states arise naturally through the fully quantum-mechanical description of the aggregates. In this contribution the SOS//QM/MM approach is extended to simulate time-resolved 2D spectra that can be used to characterize ultrafast excited state relaxation dynamics with atomistic details. We demonstrate how critical structures on the excited state potential energy surface, obtained through state-of-the-art quantum chemical computations, can be used as snapshots of the excited state relaxation dynamics to generate spectral fingerprints for different de-excitation channels. The approach is based on high-level multi-configurational wavefunction methods combined with non-linear response theory and incorporates the effects of the solvent/environment through hybrid quantum mechanics/molecular mechanics (QM/MM) techniques. Specifically, the protocol makes use of the second-order Perturbation Theory (CASPT2) on top of Complete Active Space Self Consistent Field (CASSCF) strategy to compute the high-lying excited states that can be accessed in different 2D experimental setups. As an example, the photophysics of the stacked adenine-adenine dimer in a double-stranded DNA is modeled through 2D near-ultraviolet (NUV) spectroscopy.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
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33
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Padula D, Lahoz IR, Díaz C, Hernández FE, Di Bari L, Rizzo A, Santoro F, Cid MM. A Combined Experimental-Computational Investigation to Uncover the Puzzling (Chiro-)optical Response of Pyridocyclophanes: One- and Two-Photon Spectra. Chemistry 2015; 21:12136-47. [DOI: 10.1002/chem.201500557] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/26/2015] [Indexed: 11/09/2022]
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34
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Endicott JS, Joubert-Doriol L, Izmaylov AF. A perturbative formalism for electronic transitions through conical intersections in a fully quadratic vibronic model. J Chem Phys 2014; 141:034104. [DOI: 10.1063/1.4887258] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Julia S. Endicott
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Loïc Joubert-Doriol
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Artur F. Izmaylov
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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35
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Avila Ferrer FJ, Cerezo J, Soto J, Improta R, Santoro F. First-principle computation of absorption and fluorescence spectra in solution accounting for vibronic structure, temperature effects and solvent inhomogenous broadening. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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36
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Narth C, Gillet N, Lévy B, Demachy I, de la Lande A. Investigation of the molecular mechanisms of electronic decoherence within a quinone cofactor. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The notion of decoherence is particularly adapted to discuss the quantum-to-classical transition in the context of chemical reactions. Decoherence can be modeled by computing the time evolution of nuclear wave packets evolving on distinct potential energy surfaces, here using density functional theory (DFT) and Born–Oppenheimer molecular dynamics simulations. We investigate a redox cofactor of biological interest (tryptophan tryptophylquinone, TTQ) found in the enzyme methylamine dehydrogenase. We also report the first systematic comparison of semi-empirical DFT (tight-binding DFT) and classical force field approaches for estimating decoherence in molecular systems. In the TTQ cofactor, we find that decoherence combines structural and dynamical aspects: it is initiated by the divergent motions of few atoms and then propagates dynamically to the remaining atoms. It is the mass effect of all the atoms that leads to decoherence within a few femtosecond.
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Affiliation(s)
- Christophe Narth
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
- Laboratoire de Chimie Théorique, CNRS UMR 7616, Université Pierre et Marie Curie, case courrier 137, 4, Place Jussieu, 75 252 Paris Cedex 05, France
| | - Natacha Gillet
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
| | - Bernard Lévy
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
| | - Isabelle Demachy
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
| | - Aurélien de la Lande
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
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37
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Lin N, Barone V, Cappelli C, Zhao X, Ruud K, Santoro F. Effective time-independent studies on resonance Raman spectroscopy of trans-stilbene including the Duschinsky effect. Mol Phys 2013. [DOI: 10.1080/00268976.2013.809490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Na Lin
- a State Key Laboratory of Crystal Materials , Shandong University , Shandong , China
- b Centre for Theoretical and Computational Chemistry, Department of Chemistry , University of Tromsø , Tromsø , Norway
| | - Vincenzo Barone
- c Scuola Normale Superiore, Piazza dei Cavalieri 7 , Pisa , Italy
| | - Chiara Cappelli
- c Scuola Normale Superiore, Piazza dei Cavalieri 7 , Pisa , Italy
- d Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Pisa , Italy
| | - Xian Zhao
- a State Key Laboratory of Crystal Materials , Shandong University , Shandong , China
| | - Kenneth Ruud
- b Centre for Theoretical and Computational Chemistry, Department of Chemistry , University of Tromsø , Tromsø , Norway
| | - Fabrizio Santoro
- e Consiglio Nazionale delle Ricerche – CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , Pisa , Italy
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38
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Padula D, Picconi D, Lami A, Pescitelli G, Santoro F. Electronic Circular Dichroism in Exciton-Coupled Dimers: Vibronic Spectra from a General All-Coordinates Quantum-Dynamical Approach. J Phys Chem A 2013; 117:3355-68. [DOI: 10.1021/jp400894v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica
Industriale, Università degli Studi di Pisa, via Risorgimento 35, I-56126 Pisa, Italy
| | - David Picconi
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa,
Italy
- Department of Chemistry, Technische Universität München, Lichtenbergstr.
4, D-85747 Garching, Germany
| | - Alessandro Lami
- Consiglio Nazionale delle Ricerche
− CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca
del CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica
Industriale, Università degli Studi di Pisa, via Risorgimento 35, I-56126 Pisa, Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche
− CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca
del CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
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39
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Avila Ferrer FJ, Cerezo J, Stendardo E, Improta R, Santoro F. Insights for an Accurate Comparison of Computational Data to Experimental Absorption and Emission Spectra: Beyond the Vertical Transition Approximation. J Chem Theory Comput 2013; 9:2072-82. [PMID: 26583553 DOI: 10.1021/ct301107m] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work we carefully investigate the relationship between computed data and experimental electronic spectra. To that end, we compare both vertical transition energies, EV, and characteristic frequencies of the spectrum like the maximum, ν(max), and the center of gravity, M(1), taking advantage of an analytical expression of M(1) in terms of the parameters of the initial- and final-state potential energy surfaces. After pointing out that, for an accurate comparison, experimental spectra should be preliminarily mapped from wavelength to frequency domain and transformed to normalized lineshapes, we simulate the absorption and emission spectra of several prototypical chromophores, obtaining lineshapes in very good agreement with experimental data. Our results indicate that the customary comparison of experimental ν(max) and computational EV, without taking into account vibrational effects, is not an adequate measure of the performance of an electronic method. In fact, it introduces systematic errors that, in the investigated systems, are on the order of 0.1-0.3 eV, i.e., values comparable to the expected accuracy of the most accurate computational methods. On the contrary, a comparison of experimental and computed M(1) and/or 0-0 transition frequencies provides more robust results. Some rules of thumbs are proposed to help rationalize which kind of correction one should expect when comparing EV, M(1), and ν(max).
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Affiliation(s)
- Francisco J Avila Ferrer
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.,University of Málaga, Physical Chemistry, Faculty of Science, Málaga, 29071, Spain
| | - Javier Cerezo
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.,Departamento de Quı́mica Fı́sica, Universidad de Murcia, 30100 Murcia, Spain
| | - Emiliano Stendardo
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture Biommagini (IBB-CNR) Via Mezzocannone 16, I-80136, Napoli, Italy
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture Biommagini (IBB-CNR) Via Mezzocannone 16, I-80136, Napoli, Italy
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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40
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Avila Ferrer FJ, Santoro F. Comparison of vertical and adiabatic harmonic approaches for the calculation of the vibrational structure of electronic spectra. Phys Chem Chem Phys 2013; 14:13549-63. [PMID: 22847219 DOI: 10.1039/c2cp41169e] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The calculation of the vibrational structure associated to electronic spectra in large molecules requires a Taylor expansion of the initial and final state potential energy surface (PES) around some reference nuclear structure. Vertical (V) and adiabatic (A) approaches expand the final state PES around the initial-state (V) or final-state (A) equilibrium structure. Simplest models only take into account displacements of initial- and final-state minima, intermediate ones also allow for difference in frequencies and more accurate models introduce the Dushinsky effect through the computation of the Hessians of both the initial and final state. In this contribution we summarize and compare the mathematical expressions of the complete hierarchy of V and A harmonic models and we implement them in a numerical code, presenting a detailed comparison of their performance on a number of prototypical systems. We also address non-Condon effects through linear expansions of the transition dipole as a function of nuclear coordinates (Herzberg-Teller effect) and compare the results of expansions around initial and final state equilibrium geometries. By a throughout analysis of our results we highlight a number of general trends in the relative performance of the models that can provide hints for their proper choice. Moreover we show that A and V models including final state PES Hessian outperform the simpler ones and that discrepancies in their predictions are diagnostic for failure of harmonic approximation and/or of Born-Oppenheimer approximation (existence of remarkable geometry-dependent mixing of electronic states).
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Affiliation(s)
- Francisco José Avila Ferrer
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Pisa, Italy
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41
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Santoro F, Improta R, Avila F, Segado M, Lami A. The interplay between neutral exciton and charge transfer states in single-strand polyadenine: a quantum dynamical investigation. Photochem Photobiol Sci 2013; 12:1527-43. [DOI: 10.1039/c3pp50111f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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42
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Picconi D, Avila Ferrer FJ, Improta R, Lami A, Santoro F. Quantum-classical effective-modes dynamics of the ππ* → nπ* decay in 9H-adenine. A quadratic vibronic coupling model. Faraday Discuss 2013; 163:223-42; discussion 243-75. [DOI: 10.1039/c3fd20147c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Stendardo E, Avila Ferrer F, Santoro F, Improta R. Vibrationally Resolved Absorption and Emission Spectra of Dithiophene in the Gas Phase and in Solution by First-Principle Quantum Mechanical Calculations. J Chem Theory Comput 2012; 8:4483-93. [DOI: 10.1021/ct300664d] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- E. Stendardo
- CNR−Consiglio Nazionale
delle Ricerche, Istituto di Biostrutture e Biommagini (IBB-CNR), Via Mezzocannone 16, I-80136, Napoli, Italy
| | - F. Avila Ferrer
- CNR−Consiglio Nazionale
delle Ricerche, Istituto di Chimica dei Composti Organo-Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G.
Moruzzi 1, I-56124 Pisa, Italy
| | - F. Santoro
- CNR−Consiglio Nazionale
delle Ricerche, Istituto di Chimica dei Composti Organo-Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G.
Moruzzi 1, I-56124 Pisa, Italy
| | - R. Improta
- CNR−Consiglio Nazionale
delle Ricerche, Istituto di Biostrutture e Biommagini (IBB-CNR), Via Mezzocannone 16, I-80136, Napoli, Italy
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