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de Souza GLC, Peterson KA. A high level theory investigation on the lowest-lying ionization potentials of glycine (NH 2CH 2COOH). Phys Chem Chem Phys 2022; 24:17751-17758. [PMID: 35843227 DOI: 10.1039/d2cp02397k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, an investigation on the ionization potentials (IPs) of the glycine molecule (NH2CH2COOH) is presented. IPs ranging up to ∼20 eV were probed for each of the six conformations considered, with the referred threshold being chosen based on both: (i) the observations by recent photoelectron-photoion coincidence (PEPICO) experiments and (ii) the energy range of relevance to the modeling of other photo-induced processes (e.g., photoionization). For computing the IPs, the equation-of-motion ionization potential coupled-cluster with single and double excitations method (EOMIP-CCSD) was employed with large correlation consistent aug-cc-pVXZ and aug-cc-pCVXZ (X = D, T, and Q) basis sets. Extrapolation to the complete basis set limit and consideration of core electron correlation effects were also taken into account. Subsequently, the Feller-Peterson-Dixon (FPD) approach was used for considering all the contributions and to obtain accurate IPs. In addition, coupled-cluster with single and double excitations as well as perturbative triples, CCSD(T), was also used with the aug-cc-pVTZ basis set. When compared to each other, results obtained through the use of these approaches yielded excellent agreement. In general, the outcomes from the present work provide additional information to the insights gathered from the recent PEPICO experiments as well as accurate IPs for all 6 conformations of glycine using an approach based on high levels of theory. Hence, it is expected that other investigations focusing on photo-induced processes originating from NH2CH2COOH (for instance, the computational modeling of its photoionization) will be motivated for study in the future.
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Affiliation(s)
- Gabriel L C de Souza
- Departamento de Química, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, 78060-900, Brazil. .,Department of Chemistry, Washington State University, Pullman, Washington, 99164, USA
| | - Kirk A Peterson
- Department of Chemistry, Washington State University, Pullman, Washington, 99164, USA
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Khalili F, Vafaee M, Shokri B. Attosecond charge migration following oxygen K-shell ionization in DNA bases and base pairs. Phys Chem Chem Phys 2021; 23:23005-23013. [PMID: 34611693 DOI: 10.1039/d1cp02920g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Core ionization of DNA begins a cascade of events which could lead to cellular inactivation or death. The created core-hole following an impulse inner-shell ionization of molecules naturally decays in the auger timescale. We simulated charge migration (CM) phenomena following an impulsive core ionization of individual DNA bases at the oxygen K-edge which occurs before Auger decay of the oxygen. Our approach is based on real-time time dependent density functional theory (RT-TDDFT). It is shown that the pronounced hole fluctuation observed around bonds of the initial core-hole results in various valence orbital migrations. Also, the same photo-core-ionized dynamics is studied for the related base pairs. We investigate the role of base pairing and H-bonding interactions in the attosecond CM dynamics. In particular, the creation of a core-hole in the oxygen involved in H-bonding leads to an enhancement of charge migration relative to the respective single bases. Importantly, the hole oscillation of the adenine-thymine base pair upon creation of a core-hole at the oxygen, which does not contribute to the donor-acceptor interactions (not H-bonded), decreases compared to the single thymine base. Understanding the detailed dynamics of the localized core-hole initiating CM process would open the way for chemically controlling DNA damage/repair in the future.
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Affiliation(s)
- Fatemeh Khalili
- Department of Physics, Shahid Beheshti University, Velenjak, Tehran 19839, Iran.
| | - Mohsen Vafaee
- Department of Chemistry, Tarbiat Modares University, P. O. Box 14115-175, Tehran, Iran.
| | - Babak Shokri
- Department of Physics, Shahid Beheshti University, Velenjak, Tehran 19839, Iran. .,Laser-Plasma Research Institute, Shahid Beheshti University, Velenjak, Tehran 19839, Iran
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Karlsson D, van Leeuwen R, Pavlyukh Y, Perfetto E, Stefanucci G. Fast Green's Function Method for Ultrafast Electron-Boson Dynamics. PHYSICAL REVIEW LETTERS 2021; 127:036402. [PMID: 34328754 DOI: 10.1103/physrevlett.127.036402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 03/29/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
The interaction of electrons with quantized phonons and photons underlies the ultrafast dynamics of systems ranging from molecules to solids, and it gives rise to a plethora of physical phenomena experimentally accessible using time-resolved techniques. Green's function methods offer an invaluable interpretation tool since scattering mechanisms of growing complexity can be selectively incorporated in the theory. Currently, however, real-time Green's function simulations are either prohibitively expensive due to the cubic scaling with the propagation time or do neglect the feedback of electrons on the bosons, thus violating energy conservation. We put forward a computationally efficient Green's function scheme which overcomes both limitations. The numerical effort scales linearly with the propagation time while the simultaneous dressing of electrons and bosons guarantees the fulfillment of all fundamental conservation laws. We present a real-time study of the phonon-driven relaxation dynamics in an optically excited narrow band-gap insulator, highlighting the nonthermal behavior of the phononic degrees of freedom. Our formulation paves the way to first-principles simulations of electron-boson systems with unprecedented long propagation times.
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Affiliation(s)
- Daniel Karlsson
- Department of Physics, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Robert van Leeuwen
- Department of Physics, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Yaroslav Pavlyukh
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle, Germany
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Enrico Perfetto
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Gianluca Stefanucci
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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Williams JR, Tancogne-Dejean N, Ullrich CA. Time-Resolved Exciton Wave Functions from Time-Dependent Density-Functional Theory. J Chem Theory Comput 2021; 17:1795-1805. [PMID: 33577734 DOI: 10.1021/acs.jctc.0c01334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-dependent density-functional theory (TDDFT) is a computationally efficient first-principles approach for calculating optical spectra in insulators and semiconductors including excitonic effects. We show how exciton wave functions can be obtained from TDDFT via the Kohn-Sham transition density matrix, both in the frequency-dependent linear-response regime and in real-time propagation. The method is illustrated using one-dimensional model solids. In particular, we show that our approach provides insight into the formation and dissociation of excitons in real time. This opens the door to time-resolved studies of exciton dynamics in materials by means of real-time TDDFT.
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Affiliation(s)
- Jared R Williams
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | | | - Carsten A Ullrich
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
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Tuovinen R, van Leeuwen R, Perfetto E, Stefanucci G. Electronic transport in molecular junctions: The generalized Kadanoff-Baym ansatz with initial contact and correlations. J Chem Phys 2021; 154:094104. [PMID: 33685185 DOI: 10.1063/5.0040685] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The generalized Kadanoff-Baym ansatz (GKBA) offers a computationally inexpensive approach to simulate out-of-equilibrium quantum systems within the framework of nonequilibrium Green's functions. For finite systems, the limitation of neglecting initial correlations in the conventional GKBA approach has recently been overcome [Karlsson et al., Phys. Rev. B 98, 115148 (2018)]. However, in the context of quantum transport, the contacted nature of the initial state, i.e., a junction connected to bulk leads, requires a further extension of the GKBA approach. In this work, we lay down a GKBA scheme that includes initial correlations in a partition-free setting. In practice, this means that the equilibration of the initially correlated and contacted molecular junction can be separated from the real-time evolution. The information about the contacted initial state is included in the out-of-equilibrium calculation via explicit evaluation of the memory integral for the embedding self-energy, which can be performed without affecting the computational scaling with the simulation time and system size. We demonstrate the developed method in carbon-based molecular junctions, where we study the role of electron correlations in transient current signatures.
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Affiliation(s)
- Riku Tuovinen
- QTF Centre of Excellence, Turku Centre for Quantum Physics, Department of Physics and Astronomy, University of Turku, 20014 Turku, Finland
| | - Robert van Leeuwen
- Department of Physics, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Enrico Perfetto
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Gianluca Stefanucci
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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Perfetto E, Trabattoni A, Calegari F, Nisoli M, Marini A, Stefanucci G. Ultrafast Quantum Interference in the Charge Migration of Tryptophan. J Phys Chem Lett 2020; 11:891-899. [PMID: 31944766 DOI: 10.1021/acs.jpclett.9b03517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Extreme-ultraviolet-induced charge migration in biorelevant molecules is a fundamental step in the complex path leading to photodamage. In this work we propose a simple interpretation of the charge migration recently observed in an attosecond pump-probe experiment on the amino acid tryptophan. We find that the decay of the prominent low-frequency spectral structure with increasing pump-probe delay is due to a quantum beating between two geometrically distinct, almost degenerate charge oscillations. Quantum beating is ubiquitous in these systems, and at least on the few-to-tens of femtosecond time scales, it may dominate over decoherence the line intensities of time-resolved spectra. We also address the experimentally observed phase shift in the charge oscillations of two different amino acids, tryptophan and phenylalanine. Our results indicate that a beyond mean-field treatment of the electron dynamics is necessary to reproduce the correct behavior.
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Affiliation(s)
- E Perfetto
- Dipartimento di Fisica , Università di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
- CNR-ISM , Division of Ultrafast Processes in Materials (FLASHit) , Area della Ricerca di Roma 1, Via Salaria Km 29.3 , I-00016 Monterotondo Scalo , Italy
| | - A Trabattoni
- Center for Free-Electron Laser Science (CFEL) , DESY , 22607 Hamburg , Germany
| | - F Calegari
- Center for Free-Electron Laser Science (CFEL) , DESY , 22607 Hamburg , Germany
- Institute for Photonics and Nanotechnologies , IFN-CNR , 20133 Milano , Italy
- Institut fur Experimentalphysik , Universität Hamburg , D-22761 Hamburg , Germany
| | - M Nisoli
- Institute for Photonics and Nanotechnologies , IFN-CNR , 20133 Milano , Italy
- Dipartimento di Fisica , Politecnico di Milano , 20133 Milano , Italy
| | - A Marini
- CNR-ISM , Division of Ultrafast Processes in Materials (FLASHit) , Area della Ricerca di Roma 1, Via Salaria Km 29.3 , I-00016 Monterotondo Scalo , Italy
| | - G Stefanucci
- Dipartimento di Fisica , Università di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
- INFN , Sezione di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
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