1,721,011 research outputs found
Computational approach to study electron-transfer proteins: Azurin for bio-molecular devices
No full textA DFT Study of Cysteine Adsorption on Au(111)
No full textThe adsorption of the cysteine amino acid (H-SCbetaH2-CalphaH-NH2-COOH) on the (111) surface of gold is studied by means of periodic density functional calculations. Results for different adsorption sites and molecular configurations show that chemisorption involving S(thiolate)-Au bonds on Au(111) is favored by starting with either cysteine or cystine gas-phase molecular precursors. In the most stable adsorption configuration, the sulfur headgroup sits at the bridge site between two surface An atoms, and the S-C-beta bond is tilted by 57degrees with respect to the surface normal, whereas the in-plane orientation of the molecular backbone plays a secondary role. The analysis of the electronic properties shows that the hybridization of the p-like S states with the d-like Au states produces both bonding and antibonding occupied orbitals, and the process is well described by a model for the interaction of localized orbitals with narrow-band dispersive electron states. The bonding orbitals well below the Fermi level contribute to the strong chemisorption of cysteine on gold. The calculated sulfur-projected density of states allows us to locate the cysteine molecular orbitals with respect to the system Fermi level, which gives a measure of the injection barrier at the molecule/electrode junction
Electronic properties of guanine-based nanowires
No full textWe present a first-principles study of the electronic and conduction properties of a few classes of nanowires composed of guanine (G) molecules, self-assembled in different geometries. We first analyze the effect of the vertical pi-pi interaction in model G-stack columns. Then, we exploit the results obtained from those models to interpret the features of realistically stacked and hydrogen-bonded aggregates, namely the guanine quadruple helices and the planar ribbons. With respect to natural DNA, the different structures drastically affect the bonding pattern among the bases, introducing novel features in the electronic properties of the systems. These supramolecular G-aggregates, alternative to DNA, are expected to show interesting properties for molecular electronics applications
Reactivity of the ZnS(101̄0) surface to small organic ligands by density functional theory
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Ab initio study of model guanine assemblies: The role of pi-pi coupling and band transport
No full textSeveral assemblies of guanine molecules are investigated by means of first-principles calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the pi orbitals in adjacent guanine molecules. pi-pi coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The band structure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible.Several assemblies of guanine molecules are investigated by means of first-principles calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the (formula presented) orbitals in adjacent guanine molecules. (formula presented) coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The band structure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible. © 2001 The American Physical Society
First-principles DFT calculations of Electron Transfer rates in Azurin Dimers
No full textWe have conceived and implemented a new method to calculate transfer integrals between molecular sites, which exploits few quantities derived from density-functional theory electronic structure computations and does not require the knowledge of the exact transition state coordinate. The method uses a complete multielectron scheme, thus including electronic relaxation effects. Moreover, it makes no use of empirical parameters. The computed electronic couplings can then be combined with estimates of the reorganization energy to evaluate electron-transfer rates that are measured in kinetic experiments: the latter are the basis to interpret electron-transfer mechanisms. We have applied our approach to the study of the electron self-exchange reaction of azurin, an electron-transfer protein belonging to the family of cupredoxins. The transfer integral estimates provided by the proposed method have been compared with those resulting from other computational techniques, from empirical models, and with available experimental data
Electron channels in biomolecular nanowires
No full textWe report a first-principle study of the electronic and conduction properties of a quadruple-helix guanine wire (G4 wire), a DNA derivative, with inner potassium ions. The analysis of the electronic structure highlights the presence of energy manifolds that are equivalent to the bands of (semi)conducting materials and reveals the formation of extended electron channels available for charge transport along the wire. The specific metal-nucleobase interactions affect the electronic properties at the Fermi level, leading the wire to behave as an intrinsically p-doped system
Ab-Initio Study of Model Guanosine Assemblies: the Role of pi-pi Coupling and Band Transport
No full textSeveral assemblies of guanine molecules are investigated by means of first-principles calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the pi orbitals in adjacent guanine molecules. pi-pi coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The band structure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible
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