Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

López‐Tarifa, Pablo; Penhoat, Marie‐Anne Hervé du; Vuilleumier, Rodolphe; Gaigeot, Marie‐Pierre; Röthlisberger, Ursula; Tavernelli, Ivano; Padellec, A. Le; Champeaux, Jean-Philippe; Alcamı́, Manuel; Moretto-Capelle, P; Martı́n, Fernando; Politis, M. F.

doi:10.2478/s11534-014-0428-0

Cited by 6 publications

(7 citation statements)

References 36 publications

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“…(13) and the two-step propagation of Eqs. (18) and (19), we compare their performance versus the P-TDDFT implementation 88 of the CPMD code 89 in the case of a double ionization of a uracil molecule in the gas phase 90,91 . Simulations of this type provide access to the ultrafast electronic dynamics that occurs at the atto and femto time-scales in the ionized genetic material (DNA and RNA) as a consequence of collisions with proton or carbon beams 92 .…”

Section: Improved Real-time Propagatorsmentioning

confidence: 99%

Siesta: Recent developments and applications

Garcı́a

Papior

Akhtar

et al. 2020

The Journal of Chemical Physics

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346

210

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A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-nineties, SIESTA's flexibility, efficiency and free distribution has given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudoatomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here we describe the more recent implementations on top of that core scheme, which include: full spin-orbit interaction, non-repeated and multiple-contact ballistic electron transport, DFT+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, densityfunctional perturbation theory, efficient Van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as WANNIER90 and the second-principles modelling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various postprocessing utilities. SIESTA has also been a) Electronic mail:

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Section: Improved Real-time Propagatorsmentioning

confidence: 99%

Siesta: Recent developments and applications

Garcı́a

Papior

Akhtar

et al. 2020

The Journal of Chemical Physics

Self Cite

346

210

View full text Add to dashboard Cite

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“…Many theoretical approaches have been used to model excited-state dynamics, including time-dependent Hartree–Fock, TDDFT, coupled cluster, and multiconfigurational self-consistent field calculations, in conjunction with nuclear dynamics methods such as Born–Oppenheimer molecular dynamics, Ehrenfest dynamics, and surface hopping. , A time domain approach that explicitly propagates the electron dynamics in an external field is a natural for describing ultrafast spectroscopy. RT-TDDFT ,− has been successfully applied to compute absorption spectra of large molecules, core excitation, polaron pair formation, charge transfer, , light absorption of a photocatalyst, and molecular conductance …”

Section: Theoretical Frameworkmentioning

confidence: 99%

“…Extensive Green’s function theoretical studies on the mechanism of charge migration and the role of electron correlations were performed by Cederbaum. , Subfemtosecond charge migration simulations in Tyr-terminated tetrapeptides were reported by Levine . The molecular dynamics of doubly charged uracil in the gas phase has recently been simulated by time-dependent density functional theory (TDDFT) . The calculations become rapidly intractable with molecular size because of the prohibitively large number of relevant eigenstates in the ionized states.…”

Section: Introductionmentioning

confidence: 99%

“…14 The molecular dynamics of doubly charged uracil in the gas phase has recently been simulated by time-dependent density functional theory (TDDFT). 15 The calculations become rapidly intractable with molecular size because of the prohibitively large number of relevant eigenstates in the ionized states. This is especially true for core ionized states, where many valence states can participate in the dynamics.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Attosecond X-ray Diffraction Triggered by Core or Valence Ionization of a Dipeptide

Cho

Rouxel

Kowalewski

et al. 2017

J. Chem. Theory Comput.

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With the advancement of intense ultrafast X-ray sources, it is now possible to create a molecular movie by following the electronic dynamics in real time and real space through time-resolved X-ray diffraction. Here we employ real-time time-dependent density functional theory (RT-TDDFT) to simulate the electronic dynamics after an impulse core or valence ionization in the glycine-phenylalanine (GF) dipeptide. The time-evolving dipole moment, the charge density, and the time-resolved X-ray diffraction signals are calculated. The charge oscillation is calculated for 7 fs for valence ionization and 500 as for core ionization. The charge oscillation time scale is comparable to that found in a phenylalanine monomer (4 fs) [ Science 2014 , 346 , 336 ] and is slightly longer because of the elongated glycine chain. Following valence ionization, the charge migration across the GF is mediated by the delocalized lone-pair orbitals of oxygen and nitrogen of the electron-rich amide group. The temporal Fourier transform of the dipole moment provides detailed information on the charge migration dynamics and the molecular orbitals involved. Heterodyne-detected attosecond X-ray diffraction signals provide the magnitude and phase of the scattering amplitude in momentum space and can thus be inverted to yield the charge density in real space.

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“…Instead, they stretched bonds up to break and determined the involved dissociation energies and possible fragments. Loṕez-Tarifa et al 16 have recently used the TDDFT approach to study the fragmentation of doubly ionized uracil in the gas phase. They did not account for the explicit incidence of any projectile.…”

Section: ■ Introductionmentioning

confidence: 99%

TDDFT-Based Study on the Proton–DNA Collision

et al. 2017

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The interaction of heavy charged particles with DNA is of interest for hadrontherapy and the aerospace industry. Here, a time-dependent density functional theory study on the interaction of a 4 keV proton with an isolated DNA base pair (bp) was carried out. Ehrenfest dynamics was used to study the evolution of the system up to about 193 fs. It was observed that the dissociation of the target occurs between 80 and 100 fs. The effect of bp linking to the DNA double helix was emulated by fixing the four O3' atoms responsible for the attachment. The bp tends to dissociate into its main components, namely, the phosphate groups, sugars, and nitrogenous bases. A central impact with an energy transfer of 17.9 eV only produces a base damage while keeping the backbone intact. An impact on a phosphate group with an energy transfer of about 60 eV leads to a backbone break at that site together with a base damage, and the opposite backbone site integrity is kept. As the whole system is perturbed during this collision, no atom remains passive. These results suggest that base damage accompanies all backbone breaks as the hydrogen bonds that keep bases together are much weaker that those between the other components of the DNA.

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Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

Cited by 6 publications

References 36 publications

Siesta: Recent developments and applications

Siesta: Recent developments and applications

Attosecond X-ray Diffraction Triggered by Core or Valence Ionization of a Dipeptide

TDDFT-Based Study on the Proton–DNA Collision

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