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Acocella A, Marforio TD, Calvaresi M, Bottoni A, Zerbetto F. Electron Dynamics with Explicit-Time Density Functional Theory of the [4+2] Diels–Alder Reaction. J Chem Theory Comput 2020; 16:2172-2180. [PMID: 32091885 PMCID: PMC7997368 DOI: 10.1021/acs.jctc.9b00690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The prototype Diels–Alder
(DA) reaction between butadiene
and ethene (system 1) and the DA reaction involving 1-methoxy-butadiene
and cyano-ethylene (system 2) are investigated with an
explicit-time-dependent Density Functional Theory approach. Bond orders
and atomic net charges obtained in the dynamics at the transition
state geometry and along the reaction coordinate toward reactants
are used to provide a picture of the process in terms of VB/Lewis
resonance structures that contribute to a resonance hybrid. The entire
dynamics can be divided into different domains (reactant-like, product-like,
and transition state domains) where different Lewis resonance structures
contribute with different weights. The relative importance of these
three domains varies along the reaction coordinate. In addition to
the usual reactant-like and product-like covalent Lewis structures,
ionic Lewis structures have non-negligible weights. In system 2, the electron-donor OCH3 on the diene and the
electron-acceptor CN on the dienophile make more important the contributions
of ionic Lewis structures that stabilize the transition state and
determine the decrease of the reaction barrier with respect to system 1.
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Affiliation(s)
- Angela Acocella
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
| | - Tainah D. Marforio
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
| | - Matteo Calvaresi
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
| | - Andrea Bottoni
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
| | - Francesco Zerbetto
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
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2
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Fadanni J, Acocella A, Zerbetto F. White and Colored Noises as Driving Forces of Electron Transfer: The Photolyase Repair Mechanism as a Test Case. J Phys Chem Lett 2019; 10:4511-4516. [PMID: 31343886 DOI: 10.1021/acs.jpclett.9b01763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We introduce a model to investigate electron transfer where the explicit temporal propagation of the electronic wave function is modified by white and colored noises. Atomic energies are perturbed randomly to determine an electron transfer where the periodic electronic oscillations are greatly smothered and the transfer rates can reach up to the experimental time scale. Application to the photolyase enzyme that repairs the DNA lesions shows that the optimal conditions to reproduce the experimental lifetime are equivalent to a red or Brownian noise acting every 80 fs, that is, of ∼400 cm-1. Two-state model calculations show that the results of the quantum dynamics are robust and intrinsic to the use of noise in the simulations.
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Affiliation(s)
- Jacopo Fadanni
- Dipartimento di Chimica "G. Ciamician" , Università di Bologna , V. F. Selmi 2 , 40126 Bologna , Italy
| | - Angela Acocella
- Dipartimento di Chimica "G. Ciamician" , Università di Bologna , V. F. Selmi 2 , 40126 Bologna , Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica "G. Ciamician" , Università di Bologna , V. F. Selmi 2 , 40126 Bologna , Italy
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3
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Matsuda S, Yamazaki M, Harata A, Yabushita A. CO 2 Formation Yields from Different States of CO Adsorbed on Amorphous Solid Water under 157 nm Photoirradiation. CHEM LETT 2018. [DOI: 10.1246/cl.171121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shohei Matsuda
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Motoki Yamazaki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Akira Harata
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Akihiro Yabushita
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
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Baldini E, Mann A, Benfatto L, Cappelluti E, Acocella A, Silkin VM, Eremeev SV, Kuzmenko AB, Borroni S, Tan T, Xi XX, Zerbetto F, Merlin R, Carbone F. Real-Time Observation of Phonon-Mediated σ-π Interband Scattering in MgB_{2}. PHYSICAL REVIEW LETTERS 2017; 119:097002. [PMID: 28949564 DOI: 10.1103/physrevlett.119.097002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Indexed: 06/07/2023]
Abstract
In systems having an anisotropic electronic structure, such as the layered materials graphite, graphene, and cuprates, impulsive light excitation can coherently stimulate specific bosonic modes, with exotic consequences for the emergent electronic properties. Here we show that the population of E_{2g} phonons in the multiband superconductor MgB_{2} can be selectively enhanced by femtosecond laser pulses, leading to a transient control of the number of carriers in the σ-electronic subsystem. The nonequilibrium evolution of the material optical constants is followed in the spectral region sensitive to both the a- and c-axis plasma frequencies and modeled theoretically, revealing the details of the σ-π interband scattering mechanism in MgB_{2}.
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Affiliation(s)
- E Baldini
- Institute of Physics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - A Mann
- Institute of Physics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - L Benfatto
- Institute for Complex Systems-CNR, and Physics Department, University of Rome "La Sapienza", I-00185 Rome, Italy
| | - E Cappelluti
- Institute for Complex Systems-CNR, and Physics Department, University of Rome "La Sapienza", I-00185 Rome, Italy
| | - A Acocella
- Department of Chemistry "G. Ciamician," Università di Bologna, I-40126 Bologna, Italy
| | - V M Silkin
- Departamento de Física de Materiales, Universidad del País Vasco, 20080 San Sebastián/Donostia, Spain
- Donostia International Physics Center, 20018 San Sebastián/Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - S V Eremeev
- Institute of Strength Physics and Materials Science, 634055 Tomsk, Russia
- Tomsk State University, 634050 , Tomsk, Russia
| | - A B Kuzmenko
- Department of Quantum Matter Physics, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - S Borroni
- Institute of Physics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - T Tan
- Department of Material Science and Engineering, The Pennsylvania State University, Pennsylvania 16802, USA
| | - X X Xi
- Department of Material Science and Engineering, The Pennsylvania State University, Pennsylvania 16802, USA
| | - F Zerbetto
- Department of Chemistry "G. Ciamician," Università di Bologna, I-40126 Bologna, Italy
| | - R Merlin
- Department of Physics, Center for Photonics and Multiscale Nanomaterials, University of Michigan, Ann Arbor, Michigan 48109-1040, USA
| | - F Carbone
- Institute of Physics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Acocella A, de Simone M, Evangelista F, Coreno M, Rudolf P, Zerbetto F. Time-dependent quantum simulation of coronene photoemission spectra. Phys Chem Chem Phys 2016; 18:13604-15. [PMID: 27141554 DOI: 10.1039/c5cp06455d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoelectron spectroscopy is usually described by a simple equation that relates the binding energy of the photoemitted electron, Ebinding, its kinetic energy, Ekinetic, the energy of the ionizing photon, Ephoton, and the work function of the spectrometer, ϕ, Ebinding = Ephoton - Ekinetic - ϕ. Behind this equation there is an extremely rich physics, which we describe here using as an example a relatively simple conjugated molecule, namely coronene. The theoretical analysis of valence band and C1s core level photoemission spectra showed that multiple excitations play an important role in determining the intensities of the final spectrum. An explicit, time-evolving model is applied, which is able to count all possible photo-excitations occurring during the photoemission process, showing that they evolve on a short time-scale, of about 10 fs. The method reveals itself to be a valid approach to reproduce photoemission spectra of polycyclic aromatic hydrocarbons (PAHs).
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Affiliation(s)
- Angela Acocella
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, V. F. Selmi 2, I-40126 Bologna, Italy.
| | - Monica de Simone
- CNR-IOM Lab TASC, ss. 14 km 163,5, Basovizza, I-34149 Trieste, Italy
| | - Fabrizio Evangelista
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, NL-9747AG Groningen, The Netherlands
| | - Marcello Coreno
- CNR-ISM, uos Trieste, ss.14 km 163,5 Basovizza, I-34139 Trieste, Italy
| | - Petra Rudolf
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, NL-9747AG Groningen, The Netherlands
| | - Francesco Zerbetto
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, V. F. Selmi 2, I-40126 Bologna, Italy.
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DeSimone AJ, Orlando TM. O(3PJ) formation and desorption by 157-nm photoirradiation of amorphous solid water. J Chem Phys 2014; 140:094702. [DOI: 10.1063/1.4867194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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7
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DeSimone AJ, Crowell VD, Sherrill CD, Orlando TM. Mechanisms of H2O desorption from amorphous solid water by 157-nm irradiation: An experimental and theoretical study. J Chem Phys 2013; 139:164702. [DOI: 10.1063/1.4825239] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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