The electronic structure of amorphous silica: A numerical study

We present a computational study of the electronic properties of amorphous SiO2. The ionic configurations used are the ones generated by an earlier molecular dynamics simulations in which the system was cooled with different cooling rates from the liquid state to a glass, thus giving access to glass-like configurations with different degrees of disorder [Phys. Rev. B 54, 15808 (1996)]. The electronic structure is described by a tight-binding Hamiltonian. We study the influence of the degree of disorder on the density of states, the localization properties, the optical absorption, the nature of defects within the mobility gap, and on the fluctuations of the Madelung potential, where the disorder manifests itself most prominently. The experimentally observed mismatch between a photoconductivity threshold of 9 eV and the onset of the optical absorption around 7 eV is interpreted by the picture of eigenstates localized by potential energy fluctuations in a mobility gap of approximately 9 eV and a density of states that exhibits valence and conduction band tails which are, even in the absence of defects, deeply located within the former band gap.Comment: 21 pages of Latex, 5 eps figure

The simulation of interquinone charge transfer in a bacterial photoreaction center highlights the central role of a hydrogen-bonded non-heme iron complex

AbstractWe consider electron transfer between the quinones QA and QB, one of the final steps in the photoinduced charge separation in the photoreaction center of Rhodobacter sphaeroides. The system is described by a model with atomic resolution using classical force fields and a carefully parameterized tight-binding Hamiltonian. The rates estimated for direct interquinone charge transfer hopping involving a non-heme iron complex bridging the quinones and superexchange based on the geometry of the photochemically inactive dark state are orders of magnitude smaller than those obtained experimentally. Only if the iron complex is attached to both quinones via hydrogen bonds – as characteristic of the charge transfer active light state – the computed rate for superexchange involving the histidine ligands of the complex will become comparable to the experimental value of kCT=105 s−1

The electronic structure of amorphous silica: A numerical study

We present a computational study of the electronic properties of amorphous SiO2. The ionic configurations used are the ones generated by an earlier molecular dynamics simulations in which the system was cooled with different cooling rates from the liquid state to a glass, thus giving access to glass-like configurations with different degrees of disorder [Phys. Rev. B 54, 15808 (1996)]. The electronic structure is described by a tight-binding Hamiltonian. We study the influence of the degree of disorder on the density of states, the localization properties, the optical absorption, the nature of defects within the mobility gap, and on the fluctuations of the Madelung potential, where the disorder manifests itself most prominently. The experimentally observed mismatch between a photoconductivity threshold of 9 eV and the onset of the optical absorption around 7 eV is interpreted by the picture of eigenstates localized by potential energy fluctuations in a mobility gap of approximately 9 eV and a density of states that exhibits valence and conduction band tails which are, even in the absence of defects, deeply located within the former band gap.Comment: 21 pages of Latex, 5 eps figure

Atomistic Models of DNA Charge Transfer

In Chap. 4, Koslowski and Cramer address the phenomenon of charge transport in DNA using a simple, but chemically specific approach intimately related to the Su-Schrieffer-Heeger model. In that model, the Hamiltonian is carefully parameterized using the ab-initio density-functional calculations. In the presence of an excess positive charge, the emerging potential energy surfaces for hole transfer are found to correspond to the formation of small polarons localized mainly on the individual bases. Thermally activated hopping between these states is analyzed using the Marcus theory of charge transfer. Their results are fully compatible with the conjecture of long-range charge transfer in DNA via two competing mechanisms, and the computations provide the corresponding charge-transfer rates both in the short-range superexchange and in the long-range hopping regime as the output of a single atomistic theory. Furthermore, it reproduces the order of magnitude of the current flow in DNA-gold nanojunctions, the over all shape of the current-voltage curves and their dependence upon the DNA sequence

Charge transfer through a cytochrome multiheme chain: Theory and simulation

We study sequential charge transfer within a chain of four heme cofactors located in the c-type cytochrome subunit of the photoreaction center of Rhodopseudomonas viridis from a theoretical perspective. Molecular dynamics simulations of the thermodynamic integration type are used to compute two key energies of Marcus' theory of charge transfer, the driving force ΔG and the reorganization energy λ. Due to the small exposure of the cofactors to the solvent and to charged amino acids, the outer sphere contribution to the reorganization energy almost vanishes. Interheme effective electronic couplings are estimated using ab initio wave functions and a well-parameterized semiempirical scheme for long-range interactions. From the resulting charge transfer rates, we conclude that at most the two heme molecules closest to themembrane participate in a fast recharging of the photoreaction center, whereas the remaining hemes are likely to have a different function, such as intermediate electron storage. Finally, we suggest means to verify or falsify this hypothesis

DNA charge transfer: An atomistic model

In this work, we address the phenomenon of charge transport in DNA using a simple, but chemically specific, approach that is intimately related to the Su-Schrieffer-Heeger (SSH) model. The emerging potential energy surface for hole transport is analyzed using Marcus' theory of charge transfer. Our results are fully compatible with the conjecture of charge transfer in DNA via two competing mechanisms, and the computations provide the corresponding charge-transfer rates both in the short-range superexchange and in the long-range hopping regime as the output of a single atomistic theory. Finally, the model allows the computation of the transport properties of systems containing modified bases and of more complex arrangements of base pairs as an additional element of verification

Charge transfer through the nucleosome: A theoretical approach

In this work, we approach the problem of charge transfer in deoxyribonucleic acid (DNA) from a theoretical and numerical perspective. We focus on a DNA geometry characteristic of the eukaryotic genome and study transport along a superhelix that contains 292 nucleobases. The electronic structure is described within the Su-Schrieffer-Heeger model in an atomistic parameterization, which has been extended by a nonretarded reaction field to take dielectric polarization effects into account. The emerging potential energy surface is analyzed using the Marcus theory of electron transfer. The computed reaction coefficients are compared to their counterparts originating from idealized geometries and to experimental findings. This comparison and the palindromic nature of the DNA sequence used here permit the assessment of fluctuations in the local orientation of the bases and their impact upon transport properties