Reactive Molecular Dynamics study on the first steps of DNA-damage by free hydroxyl radicals

We employ a large scale molecular simulation based on bond-order ReaxFF to simulate the chemical reaction and study the damage to a large fragment of DNA-molecule in the solution by ionizing radiation. We illustrate that the randomly distributed clusters of diatomic OH-radicals that are primary products of megavoltage ionizing radiation in water-based systems are the main source of hydrogen-abstraction as well as formation of carbonyl- and hydroxyl-groups in the sugar-moiety that create holes in the sugar-rings. These holes grow up slowly between DNA-bases and DNA-backbone and the damage collectively propagate to DNA single and double strand break.Comment: 6 pages and 8 figures. movies and simulations are available at: http://qmsimulator.wordpress.com

Development of a ReaxFF potential for Ag/Zn/O and application to Ag deposition on ZnO

This paper was accepted for publication in the journal Surface Science and the definitive published version is available at http://dx.doi.org/10.1016/j.susc.2015.11.009.A new empirical potential has been derived to model an Ag–Zn–O system. Additional parameters have been included into the reactive force field (ReaxFF) parameter set established for ZnO to describe the interaction between Ag and ZnO for use in molecular dynamics (MD) simulations. The reactive force field parameters have been fitted to density functional theory (DFT) calculations performed on both bulk crystal and surface structures. ReaxFF accurately reproduces the equations of state determined for silver, silver zinc alloy and silver oxide crystals via DFT. It also compares well to DFT binding energies and works of separation for Ag on a ZnO surface. The potential was then used to model single point Ag deposition on polar (000View the MathML source1¯) and non-polar (10View the MathML source1¯0) orientations of a ZnO wurtzite substrate, at different energies. Simulation results then predict that maximum Ag adsorption on a ZnO surface requires deposition energies of ≤ 10 eV

Hydroxylation Structure and Proton Transfer Reactivity at the Zinc Oxide−Water Interface

The hydroxylation structural features of the first adsorption layer and its connection to proton transfer reactivity has been studied for the ZnO–liquid water interface at room temperature. Molecular Dynamics simulations employing the ReaxFF forcefield were performed for water on seven ZnO surfaces with varying step concentration. At higher water coverage a higher level of hydroxylation was found, in agreement with previous experimental results. We have also calculated the free energy barrier for transferring a proton to the surface, showing that stepped surfaces stabilizes the hydroxylated state and decreases the water dissociation barrier. On highly stepped surfaces the barrier is only 2 kJ/mol or smaller. Outside the first adsorption layer no dissociation events were observed during almost 100 ns of simulation time; this indicates that these reactions are much more likely if catalysed by the metal oxide surface. Also, when exposed to a vacuum, the less stepped surfaces stabilizes adsorption beyond monolayer coverage.</p

An SCC-DFTB Repulsive Potential for Various ZnO Polymorphs and the ZnO–Water System

[Image: see text] We have developed an efficient scheme for the generation of accurate repulsive potentials for self-consistent charge density-functional-based tight-binding calculations, which involves energy-volume scans of bulk polymorphs with different coordination numbers. The scheme was used to generate an optimized parameter set for various ZnO polymorphs. The new potential was subsequently tested for ZnO bulk, surface, and nanowire systems as well as for water adsorption on the low-index wurtzite (101̅0) and (112̅0) surfaces. By comparison to results obtained at the density functional level of theory, we show that the newly generated repulsive potential is highly transferable and capable of capturing most of the relevant chemistry of ZnO and the ZnO/water interface

New ab initio based pair potential for accurate simulation of phase transitions in ZnO

A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model (8), a wide range of physical properties is accurately reproduced using the new potential model. The calculated lattice parameters and elastic constants of ZnO in the wurtzite (WZ) phase, as well as the lattice parameters and stabilities of ZnO in other high-pressure and metastable phases, agree well with experiments and with density functional theory (DFT) calculations. The calculated transition pressure of the wurtzite-to-rocksalt (WZ-to-RS) transition is 12.3 GPa. A wurtzite-to-honeycomb (WZ-to-HC) phase transition induced by uniaxial pressure along the c-axis is simulated by means of molecular dynamics (MD) simulations. The WZ-to-HC transition takes place at an uniaxial pressure of 8.8 GPa while the reverse transition takes place at 2.9 GPa, which is consistent with DFT calculations. Other physical properties, including phonon dispersion, phonon density of states, and melting point calculated using our ZnO potential model are in good agreement with experimental and DFT data. Limitations of the novel ZnO potential model are also discussed