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Parrinello Molecular Dynamics (parrinello + molecular_dynamics)

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Chemistry80%

Terms modified by Parrinello Molecular Dynamics

  • parrinello molecular dynamics simulation
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    Selected Abstracts

    Short-Range Structure of Yttrium Alumino-Silicate Glass for Cancer Radiotherapy: Car,Parrinello Molecular Dynamics Simulations,

    ADVANCED ENGINEERING MATERIALS, Issue 7 2010
    Jamieson K. Christie
    We present Car,Parrinello molecular dynamics (CPMD) simulations of yttrium alumino-silicate (YAS) glass. Alumino-silicate glass microspheres are used as vectors of yttrium radioisotopes in cancer radiotherapy; understanding in detail how yttrium is bound within the glass network is important to control the unwanted release of radioactive yttrium in the bloodstream. Our simulations, focused on a specific composition relevant to practical applications, show that silicon and aluminum form a disordered glass network, where Si is mainly four-coordinated, whereas, Al is mainly four- and five-coordinated. Yttrium cations have a network-modifying role, disrupting the alumino-silicate network by breaking Si(Al)O bonds and coordinating the resulting non-bridging oxygens (NBO). The local environment of yttrium in the glass turns out to be rather flexible: between five and eight oxygen atoms, with a marked predominance of NBO, are found coordinated to a central Y cation, leading to a corresponding broad and multimodal distribution of OYO angles. [source]

    Extended Car,Parrinello molecular dynamics and electronic g -tensors study of benzosemiquinone radical anion,

    MAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2005
    James R. Asher
    Abstract Car-Parrinello molecular dynamics simulations of benzoquinone and benzosemiquinone radical anion in both aqueous solution and the gas phase have been carried out at ambient conditions. Hydrogen bonding is considerably more extensive to the anionic than to the neutral aqueous system. In addition to the conventional hydrogen bonding to the carbonyl oxygen atoms, T-stacked hydrogen bonding to the , -system is statistically and energetically significant for the semiquinone anion but not for the neutral quinone. EPR g -tensors have been calculated at DFT level for snapshots taken at regular intervals from the gas-phase and solution semiquinone anion trajectories. Different criteria for extraction of semiquinone/water clusters from the solution trajectory give insight into the effects of different interactions on the g -tensor, as does correlation of the g -tensor with statistically significant hydrogen-bond configurations identified along the trajectories. Comparison of gas-phase and solution results indicates opposite directions of direct electronic and indirect structural influences of hydrogen bonding on g -tensors. Short-time oscillations in gx along the trajectory are due mainly to CO bond vibrations. Copyright © 2005 John Wiley & Sons, Ltd. [source]

    Proton-transfer dynamics in the (HCO3,)2 dimer of KHCO3 from Car,Parrinello and path-integrals molecular dynamics calculations

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010
    Przemyslaw D. Dopieralski
    The proton motion in the (HCO)2 dimer of KHCO3 at 298,K has been studied with Car,Parrinello molecular dynamics (CPMD) and path-integrals molecular dynamics (PIMD) simulations. According to earlier neutron diffraction studies at 298,K hydrogen is disordered and occupies two positions with an occupancy ratio of 0.804/0.196. A simulation with only one unit cell is not sufficient to reproduce the disorder of the protons found in the experiments. The CPMD results with four cells, 0.783/0.217, are in close agreement with experiment. The motion of the two protons along the O...O bridge is highly correlated inside one dimer, but strongly uncoupled between different dimers. The present results support a mechanism for the disorder which involves proton transfer from donor to acceptor and not orientational disordering of the entire dimer. The question of simultaneous or successive proton transfer in the two hydrogen bonds in the dimer remains unanswered. During the simulation situations with almost simultaneous proton transfer with a time gap of around 1,fs were observed, as well as successive processes where first one proton is transferred and then the second one with a time gap of around 20,fs. The calculated vibrational spectrum is in good agreement with the experimental IR spectrum, but a slightly different assignment of the bands is indicated by the present simulations. [source]

    Transport Processes at ,-Quartz,Water Interfaces: Insights from First-Principles Molecular Dynamics Simulations

    CHEMPHYSCHEM, Issue 7 2008
    Waheed A. Adeagbo Dr.
    Abstract Car,Parrinello molecular dynamics (CP,MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the ,-quartz,water interface. The model system initially consists of a periodically repeated quartz slab with O-terminated and Si-terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H2O molecules into H+ and OH, is observed at the Si-terminated surface. The OH, fragments immediately bind chemically to the Si-terminated surface while Grotthus-type proton diffusion through the water film leads to protonation of the O-terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO2 present as Si(OH)4 in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)4 molecule as would have been indicated by a substantial lowering of the Si(OH)4 diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP,MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two SiO bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new SiO bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz SiO bond. The final solute species is Si(OH)4. [source]

    Ab Initio Molecular Dynamics Simulation of a Water,Hydrogen Fluoride Equimolar Mixture

    CHEMPHYSCHEM, Issue 1 2005
    Christian Simon
    Abstract Hydrogen fluoride and water can be mixed in any proportion. The resulting solutions have unique acidic properties. In particular, hydrogen fluoride undergoes a weak-to-strong acidity transition with increasing concentration of HF. To supplement the knowledge already obtained on dilute or moderately concentrated solutions and gas-phase aggregates, an equimolar mixture is studied here by Car,Parrinello molecular dynamics. The natures of the ions and of the complexes formed in the equimolar liquid were determined. Specifically, H3O+, H5O2+, FHOH2, and HF2,were spontaneously obtained while only hydronium and fluoride ions pre-exist in the equimolar crystal. The behaviour of the proton in the equimolar liquid was compared with mixtures of other proportions simulated previously in an attempt to relate proton dynamics to acidity. In the same way, the behaviour of HF2,was also examined. In this case, proton localization and transfer appeared to be driven by the fluctuating environment of the solvated ion. [source]