Simulation of structural and electronic properties of amorphous tungsten oxycarbides

Electron beam induced deposition with tungsten hexacarbonyl W(CO)6 as precursors leads to granular deposits with varying compositions of tungsten, carbon and oxygen. Depending on the deposition conditions, the deposits are insulating or metallic. We employ an evolutionary algorithm to predict the crystal structures starting from a series of chemical compositions that were determined experimentally. We show that this method leads to better structures than structural relaxation based on guessed initial structures. We approximate the expected amorphous structures by reasonably large unit cells that can accommodate local structural environments that resemble the true amorphous structure. Our predicted structures show an insulator to metal transition close to the experimental composition at which this transition is actually observed. Our predicted structures also allow comparison to experimental electron diffraction patterns.Comment: 17 Pages, 11 figure

Spontaneous Dissociation of Co2(CO)8 and Autocatalytic growth of Co on SiO2 : A Combined Experimental and Theoretical Investigation

We present experimental results and theoretical simulations of the adsorption behavior of the metal-organic precursor Co2(CO)8 on SiO2 surfaces after application of two different pre-treatment steps, namely by air plasma cleaning or a focused electron beam pre-irradiation. We observe a spontaneous dissociation of the precursor molecules as well as auto-deposition of cobalt on the pre-treated SiO2 surfaces. We also find that the differences in metal content and relative stability of these deposits depend on the pre-treatment conditions of the substrate. Transport measurements of these deposits are also presented. We are led to assume that the degree of passivation of the SiO2 surface by hydroxyl groups is an important controlling factor in the dissociation process. Our calculations of various slab settings using dispersion corrected density functional theory support this assumption. We observe physisorption of the precursor molecule on a fully hydroxylated SiO2 surface (untreated surface) and chemisorption on a partially hydroxylated SiO2 surface (pre-treated surface) with a spontaneous dissociation of the precursor molecule. In view of these calculations, we discuss the origin of this dissociation and the subsequent autocatalysis.Comment: 22 pages, 8 Figures, In Press Article, Beilstein Journal of Nanotechnology, 201

Modification of the conductance of single fullerene molecules by endohedral doping

We use scanning tunneling microscopy to establish controlled contacts to single molecules of endohedrally doped Ce(2)@C(80) fullerenes with C(60) as a reference. The stability of the experimental setup allows for the determination of the conductance of Ce(2)@C(80) relative to the conductance of C(60). The endohedral doping reduces the conductance of Ce(2)@C(80) by a factor of about five with respect to C(60). Ab initio calculations show that the reason for this reduced conductance is the absence of electron orbitals delocalized over the cage of Ce(2)@C(80) in the energy window of the conductance measurement. (C) 2009 American Institute of Physics. (doi:10.1063/1.3236529

Molecular dynamics simulation approach to explore atomistic molecular mechanism of peroxidase activity of apoptotic cytochrome c mutants

Mutations in cytochrome c (Cyt c) have been reported in tuning peroxidase activity, which in-turn cause Cyt c release from mitochondria and early apoptosis. However, the molecular tuning mechanism underlying this activity remains elusive. Herein, multiple 20 ns molecular dynamics (MD) simulations of wild type (WT), Y67F and K72W mutated Cyt c in aqueous solutions have been carried out to study how the changes in structural features alters the peroxidase activity of the protein. MD simulation results indicate that Y67F mutation caused, (i) increased distances between critical electron-transfer residues, (ii) higher fluctuations in omega loops, and (iii) weakening of intraprotein hydrogen bonds result in open conformation at heme crevice loop in Cyt c leading to an enhanced peroxidase activity. Interestingly, the aforementioned structural features are strengthened in K72W compared to WT and Y67F, which triggers K72W mutated Cyt c into a poor peroxidase. Essential dynamics results unveil that first two eigenvectors are responsible for overall motions of WT, Y67F and K72W mutated Cyt c. This study thus provides atomic level insight into molecular mechanism of peroxidase activity of Cyt c, which will help in designing novel Cyt c structures that is more desirable than natural Cyt c for biomedical and industrial processes. Keywords: Peroxidase activity, Cytochrome c, Mutations, Apoptosis, Molecular dynamic