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Rapacioli M, Buey MY, Spiegelman F. Addressing electronic and dynamical evolution of molecules and molecular clusters: DFTB simulations of energy relaxation in polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2024; 26:1499-1515. [PMID: 37933901 PMCID: PMC10793726 DOI: 10.1039/d3cp02852f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
We present a review of the capabilities of the density functional based Tight Binding (DFTB) scheme to address the electronic relaxation and dynamical evolution of molecules and molecular clusters following energy deposition via either collision or photoabsorption. The basics and extensions of DFTB for addressing these systems and in particular their electronic states and their dynamical evolution are reviewed. Applications to PAH molecules and clusters, carbonaceous systems of major interest in astrochemical/astrophysical context, are reported. A variety of processes are examined and discussed such as collisional hydrogenation, fast collisional processes and induced electronic and charge dynamics, collision-induced fragmentation, photo-induced fragmentation, relaxation in high electronic states, electronic-to-vibrational energy conversion and statistical versus non-statistical fragmentation. This review illustrates how simulations may help to unravel different relaxation mechanisms depending on various factors such as the system size, specific electronic structure or excitation conditions, in close connection with experiments.
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Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Maysa Yusef Buey
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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Tolu D, Guillaumont D, de la Lande A. Irradiation of Plutonium Tributyl Phosphate Complexes by Ionizing Alpha Particles: A Computational Study. J Phys Chem A 2023; 127:7045-7057. [PMID: 37606197 DOI: 10.1021/acs.jpca.3c02117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The PUREX solvent extraction process, widely used for recovering uranium and plutonium from spent nuclear fuel, utilizes an organic solvent composed of tributyl phosphate (TBP). The emission of ionizing particles such as alpha particles, resulting from the decay of plutonium, makes the organic solvent vulnerable to degradation. Here, we study the ultrashort time alpha irradiation of tributylphosphate (TBP) and Pu(NO3)4(TBP)2 complex formed in the PUREX process. Electron dynamics is propagated by Real-Time-Dependent Auxiliary Density Functional Theory (RT-TD-ADFT). We investigate the use of previously proposed absorption boundary conditions (ABC) in the molecular orbital space to treat secondary electron emission. Basis set and exchange correlation functional effects with ABC are reported as well as a detailed analysis of the ABC parametrization. Preliminary results on the water molecule and then on TBP show that the phenomenological nature of the ABC parameters necessitates selecting appropriate values for each system under study. Irradiation of free and complexed TBP shows an influence of the ligands on the variation of atomic charges on the femtosecond time scale. An accumulation of atomic charges in the alkyl chains of TBP is observed in the case where the nitrate groups are predominantly irradiated. In addition, we find that the Pu atom regains its electric charge very rapidly after being hit by the projectile, with the coordination sphere serving as an electron reservoir to preserve its formal redox state. This study paves the road toward a full understanding of the degradation of organic extracants employed in the nuclear industry.
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Affiliation(s)
- Damien Tolu
- CEA, DES, ISEC, DMRC, Université Montpellier, Marcoule, 30207 Bagnols sur Cèze, France
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, Paris, 91405, France
| | - Dominique Guillaumont
- CEA, DES, ISEC, DMRC, Université Montpellier, Marcoule, 30207 Bagnols sur Cèze, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, Paris, 91405, France
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Narayanan S J J, Tripathi D, Verma P, Adhikary A, Dutta AK. Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials. ACS OMEGA 2023; 8:10669-10689. [PMID: 37008102 PMCID: PMC10061531 DOI: 10.1021/acsomega.2c06776] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.
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Affiliation(s)
- Jishnu Narayanan S J
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Pooja Verma
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Amitava Adhikary
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Achintya Kumar Dutta
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
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Self-assembly for hybrid biomaterial of uridine monophosphate to enhance the optical phenomena. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Salahub DR. Multiscale molecular modelling: from electronic structure to dynamics of nanosystems and beyond. Phys Chem Chem Phys 2022; 24:9051-9081. [PMID: 35389399 DOI: 10.1039/d1cp05928a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Important contemporary biological and materials problems often depend on interactions that span orders of magnitude differences in spatial and temporal dimensions. This Tutorial Review attempts to provide an introduction to such fascinating problems through a series of case studies, aimed at beginning researchers, graduate students, postdocs and more senior colleagues who are changing direction to focus on multiscale aspects of their research. The choice of specific examples is highly personal, with examples either chosen from our own work or outstanding multiscale efforts from the literature. I start with various embedding schemes, as exemplified by polarizable continuum models, 3-D RISM, molecular DFT and frozen-density embedding. Next, QM/MM (quantum mechanical/molecular mechanical) techniques are the workhorse of pm-to-nm/ps-to-ns simulations; examples are drawn from enzymes and from nanocatalysis for oil-sands upgrading. Using polarizable force-fields in the QM/MM framework represents a burgeoning subfield; with examples from ion channels and electron dynamics in molecules subject to strong external fields, probing the atto-second dynamics of the electrons with RT-TDDFT (real-time - time-dependent density functional theory) eventually coupled with nuclear motion through the Ehrenfest approximation. This is followed by a section on coarse graining, bridging dimensions from atoms to cells. The penultimate chapter gives a quick overview of multiscale approaches that extend into the meso- and macro-scales, building on atomistic and coarse-grained techniques to enter the world of materials engineering, on the one hand, and cell biology, on the other. A final chapter gives just a glimpse of the burgeoning impact of machine learning on the structure-dynamics front. I aim to capture the excitement of contemporary leading-edge breakthroughs in the description of physico-chemical systems and processes in complex environments, with only enough historical content to provide context and aid the next generation of methodological development. While I aim also for a clear description of the essence of methodological breakthroughs, equations are kept to a minimum and detailed formalism and implementation details are left to the references. My approach is very selective (case studies) rather than exhaustive. I think that these case studies should provide fodder to build as complete a reference tree on multiscale modelling as the reader may wish, through forward and backward citation analysis. I hope that my choices of cases will excite interest in newcomers and help to fuel the growth of multiscale modelling in general.
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Affiliation(s)
- Dennis R Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
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Denisov SA, Ward S, Shcherbakov V, Stark AD, Kaczmarek R, Radzikowska-Cieciura E, Debnath D, Jacobs T, Kumar A, Sevilla MD, Pernot P, Dembinski R, Mostafavi M, Adhikary A. Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group. J Phys Chem B 2022; 126:430-442. [PMID: 34990129 PMCID: PMC8776618 DOI: 10.1021/acs.jpcb.1c09068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This work shows that S atom substitution in phosphate controls the directionality of hole transfer processes between the base and sugar-phosphate backbone in DNA systems. The investigation combines synthesis, electron spin resonance (ESR) studies in supercooled homogeneous solution, pulse radiolysis in aqueous solution at ambient temperature, and density functional theory (DFT) calculations of in-house synthesized model compound dimethylphosphorothioate (DMTP(O-)═S) and nucleotide (5'-O-methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O-)═S)). ESR investigations show that DMTP(O-)═S reacts with Cl2•- to form the σ2σ*1 adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O-)═S to produce [-P-S[Formula: see text]S-P-]-. -P-S[Formula: see text]Cl in G-P(O-)═S undergoes hole transfer to Gua, forming the cation radical (G•+) via thermally activated hopping. However, pulse radiolysis measurements show that DMTP(O-)═S forms the thiyl radical (-P-S•) by one-electron oxidation, which did not produce [-P-S[Formula: see text]S-P-]-. Gua in G-P(O-)═S is oxidized unimolecularly by the -P-S• intermediate in the sub-picosecond range. DFT thermochemical calculations explain the differences in ESR and pulse radiolysis results obtained at different temperatures.
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Affiliation(s)
- Sergey A. Denisov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Viacheslav Shcherbakov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Alexander D. Stark
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Ewa Radzikowska-Cieciura
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Dipra Debnath
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Taisiya Jacobs
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Michael D. Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Pascal Pernot
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Roman Dembinski
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA,Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
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Reliability and performances of real-time time-dependent auxiliary density functional theory. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02819-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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