scholarly journals Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

2019 ◽  
Vol 3 (4) ◽  
pp. 24
Author(s):  
Marie-Anne Hervé du Penhoat ◽  
Anis Hamila ◽  
Marie-Pierre Gaigeot ◽  
Rodolphe Vuilleumier ◽  
Kentaro Fujii ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
X Rays ◽  
Auger Decay ◽  
Hydration Layer ◽  
The Core ◽  
Dynamics Simulations

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

Energetics and diffusion of liquid water and hydrated ions through nanopores in graphene: ab initio molecular dynamics simulation

2017 ◽  
Vol 19 (31) ◽  
pp. 20551-20558 ◽  
Author(s):  
Raúl Guerrero-Avilés ◽  
Walter Orellana
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Functional Theory ◽  
Hydrated Ions ◽  
And Diffusion

The energetics and diffusion of water molecules and hydrated ions (Na+, Cl−) passing through nanopores in graphene are addressed by dispersion-corrected density functional theory calculations and ab initio molecular dynamics (MD) simulations.

scholarly journals Ab initio molecular dynamics studies of formic acid dimer colliding with liquid water

2018 ◽  
Vol 20 (36) ◽  
pp. 23717-23725 ◽  
Author(s):  
Vesa Hänninen ◽  
Garold Murdachaew ◽  
Gilbert M. Nathanson ◽  
R. Benny Gerber ◽  
Lauri Halonen
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Formic Acid ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid Water ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Functional Theory ◽  
Dynamics Simulations

Ab initio molecular dynamics simulations of formic acid (FA) dimer colliding with liquid water at 300 K have been performed using density functional theory.

scholarly journals Methanol Carbonylation over Acid Mordenite: Insights from Ab Initio Molecular Dynamics and Machine Learning Thermodynamic Perturbation Theory

2021 ◽  
Author(s):  
Monika Gešvandtnerová ◽  
Dario Rocca ◽  
Tomas Bucko
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Perturbation Theory ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Thermodynamic Perturbation Theory ◽  
Dynamics Simulations ◽  
Thermodynamic Perturbation

<div>In this work we present a detailed \textit{ab initio} study of the carbonylation reaction of methoxy groups in the zeolite mordenite, as it is the rate determining step in a series of elementary reactions leading to ethanol. </div><div>For the first time we employ full molecular dynamics simulations to evaluate free energies of activation for the reactions in side pockets and main channels. Results show that the reaction in the side pocket is preferred and, when dispersion interactions are taken into account, this preference becomes even stronger. This conclusion is confirmed using multiple levels of density functional theory approximations with (PBE-D2, PBE-MBD, and vdW-DF2-B86R) or without (PBE, HSE06) dispersion corrections. These calculations, that in principle would require several demanding molecular dynamics simulations, were made possible at a minimal computational cost by using a newly developed approach that combines thermodynamic perturbation theory with machine learning.</div>

scholarly journals The Effect of Hydrogen on the Stress-Strain Response in Fe3Al: An ab initio Molecular-Dynamics Study

Materials ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4155
Author(s):  
Petr Šesták ◽  
Martin Friák ◽  
Mojmír Šob
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Intrinsic Property ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Uniaxial Deformation ◽  
Ambient Conditions ◽  
Hydrogen Atoms ◽  
Octahedral Sites

We performed a quantum-mechanical molecular-dynamics (MD) study of Fe3Al with and without hydrogen atoms under conditions of uniaxial deformation up to the point of fracture. Addressing a long-lasting problem of hydrogen-induced brittleness of iron-aluminides under ambient conditions, we performed our density-functional-theory (DFT) MD simulations for T = 300 K (room temperature). Our MD calculations include a series of H concentrations ranging from 0.23 to 4 at. % of H and show a clear preference of H atoms for tetrahedral-like interstitial positions within the D03 lattice of Fe3Al. In order to shed more light on these findings, we performed a series of static lattice-simulations with the H atoms located in different interstitial sites. The H atoms in two different types of octahedral sites (coordinated by either one Al and five Fe atoms or two Al and four Fe atoms) represent energy maxima.Our structural relaxation of the H atoms in the octahedral sites lead to minimization of the energy when the H atom moved away from this interstitial site into a tetrahedral-like position with four nearest neighbors representing an energy minimum. Our ab initio MD simulations of uniaxial deformation along the ⟨001⟩ crystallographic direction up to the point of fracture reveal that the hydrogen atoms are located at the newly-formed surfaces of fracture planes even for the lowest computed H concentrations. The maximum strain associated with the fracture is then lower than that of H-free Fe3Al. We thus show that the hydrogen-related fracture initiation in Fe3Al in the case of an elastic type of deformation as an intrinsic property which is active even if all other plasticity mechanism are absent. The newly created fracture surfaces are partly non-planar (not atomically flat) due to thermal motion and, in particular, the H atoms creating locally different environments.

Dissociation mechanism from highly charged bromophenol: ab initio molecular dynamics simulations

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Satoshi Ohmura ◽  
Kiyonobu Nagaya ◽  
Fuyuki Shimojo ◽  
Makoto Yao
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Electronic State ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Electronic Temperature ◽  
Multi Stage ◽  
Dissociation Mechanisms ◽  
Dynamics Simulations

AbstractDissociation mechanisms are studied by ab initio molecular dynamics simulations based on density functional theory for the highly charged bromophenol (C6H4OHBr)n+ (n ≤ 10) in the ground electronic state and in an electronic state which has a high electronic temperature Te characterized by Fermi–Dirac distribution. In the case of the ground state, the dissociation occurs through a sequential multi-stage process. At times shorter than 20 fs after the molecule is charged, hydrogens are dissociated from the molecule and, subsequently, the carbon ring breaks at about 150 fs In the case of an electronic state with high Te, the mechanism changes from a sequential dissociation process to a simultaneous process occurring at Te > 5 eV. To estimate the charge transfer time in a molecular bromide parent ion with +6 charge, which is generated through Auger cascades, we also performed nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulations that include the effects of nonadiabatic electronic transition with a surface-hopping approach.

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