Thorsten Koslowski

Aromatic amino acids as stepping stones in charge transfer in respiratory complex I: an unusual mechanism deduced from atomistic theory and bioinformatics.

With the help of a recent X-ray structure analysis of the hydrophilic part of the bacterial respiratory complex I, we present a theoretical and numerical study of the charge transfer properties of this protein. Our analysis is based upon an atomistic electronic structure model that accounts for the formation of chemical bonds, spin polarization on transition metal atoms, and solvent polarization effects. Solving this model at the Hartree-Fock mean-field level, we are able to access the energy parameters required to compute charge transfer rates, making use of Marcuss theory of nonadiabatic electron transfer. Besides iron-sulfur clusters, aromatic amino acids are identified as essential centers of localization that participate in the electron transfer process. This novel perspective of charge transfer in complex I is substantiated by a multiple sequence analysis of a broad spectrum of genomes, revealing that the amino acids identified as stepping stones in the electron transfer chain are conserved during the evolution of complex I.

Direct simulation of electron transfer reactions in DNA radical cations

The electron transfer properties of DNA radical cations are important in DNA damage and repair processes. Fast long-range charge transfer has been demonstrated experimentally, but the subtle influences that experimental conditions as well as DNA sequences and geometries have on the details of electron transfer parameters are still poorly understood. In this work, we employ an atomistic QM/MM approach, based on a one-electron tight binding Hamiltonian and a classical molecular mechanics forcefield, to conduct nanosecond length MD simulations of electron holes in DNA oligomers. Multiple spontaneous electron transfer events were observed in 100 ns simulations with neighboring adenine or guanine bases. Marcus parameters of charge transfer could be extracted directly from the simulations. The reorganization energy lambda for hopping between neighboring bases was found to be ca. 25 kcal/mol and charge transfer rates of 4.1 x 10(9) s(-1) for AA hopping and 1.3 x 10(9) s(-1) for GG hopping were obtained.

Unexpected Electron Transfer in Cryptochrome Identified by Time-Resolved EPR Spectroscopy†

Subtle differences in the local sequence and conformation of amino acids can result in diversity and specificity in electron transfer (ET) in proteins, despite structural conservation of the redox partners. For individual ET steps, distance is not necessarily the decisive parameter; orientation and solvent accessibility of the ET partners, and thus the stabilization of the charge-separated states, contribute substantially.

Size matters! On the way to ionic liquid systems without ion pairing.

Several, partly new, ionic liquids (ILs) containing imidazolium and ammonium cations as well as the medium-sized [NTf2 ](-) (0.230 nm(3) ; Tf=CF3 SO3 (-) ) and the large [Al(hfip)4 ](-) (0.581 nm(3) ; hfip=OC(H)(CF3 )2 ) anions were synthesized and characterized. Their temperature-dependent viscosities and conductivities between 25 and 80 °C showed typical Vogel-Fulcher-Tammann (VFT) behavior. Ion-specific self-diffusion constants were measured at room temperature by pulsed-gradient stimulated-echo (PGSTE) NMR experiments. In general, self-diffusion constants of both cations and anions in [Al(hfip)4 ](-) -based ILs were higher than in [NTf2 ](-) -based ILs. Ionicities were calculated from self-diffusion constants and measured bulk conductivities, and showed that [Al(hfip)4 ](-) -based ILs yield higher ionicities than their [NTf2 ](-) analogues, the former of which reach values of virtually 100 % in some cases.From these observations it was concluded that [Al(hfip)4 ](-) -based ILs come close to systems without any interactions, and this hypothesis is underlined with a Hirshfeld analysis. Additionally, a robust, modified Marcus theory quantitatively accounted for the differences between the two anions and yielded a minimum of the activation energy for ion movement at an anion diameter of slightly greater than 1 nm, which fits almost perfectly the size of [Al(hfip)4 ](-) . Shallow Coulomb potential wells are responsible for the high mobility of ILs with such anions.

Variational approach to charge transfer reactions in bridged triarylamine cations

Abstract In this work, we apply a recently proposed nonperturbative approach to the energetics of charge localization and charge transfer within molecules. The electronic structure of bridged organic donor–acceptor systems is described by a tight-binding Hamiltonian, which is extended by a nonretarded reaction field to account for the dielectric polarizability of the environment. The resulting Hamiltonian is solved self-consistently, and approximations to the potential energy curves for adiabatic self-exchange in the electronic ground state are obtained. The crossover from the localized (Day–Robin class I and II) to the delocalized (Day–Robin class IIIa) regime with decreasing bridge length is described. Kinetic parameters are computed by analyzing the potential energy curve of the charge transfer reaction. The limitations of the concept are discussed, and we give an outlook to its implementation for more elaborate electronic structure computations and advanced reaction fields.

The active conformation of avilamycin A is conferred by AviX12, a radical AdoMet enzyme.

The antibiotic avilamycin A is produced by Streptomyces viridochromogenes Tü57. Avilamycin belongs to the family of orthosomycins with a linear heptasaccharide chain linked to a terminal dichloroisoeverninic acid as aglycone. The gene cluster for avilamycin biosynthesis contains 54 open reading frames. Inactivation of one of these genes, namely aviX12, led to the formation of a novel avilamycin derivative named gavibamycin N1. The structure of the new metabolite was confirmed by mass spectrometry (MS) and NMR analysis. It harbors glucose as a component of the heptasaccharide chain instead of a mannose moiety in avilamycin A. Antibacterial activity tests against a spectrum of Gram-positive organisms showed that the new derivative possesses drastically decreased biological activity in comparison to avilamycin A. Thus, AviX12 seems to be implicated in converting avilamycin to its bioactive conformation by catalyzing an unusual epimerization reaction. Sequence comparisons grouped AviX12 in the radical S-adenosylmethionine protein family. AviX12 engineered with a His tag was overexpressed in Escherichia coli and purified by affinity chromatography. The iron sulfur cluster [Fe-S] present in radical AdoMet enzymes was detected in purified AviX12 by means of electron paramagnetic resonance spectroscopy.

Linear combination of Lanczos vectors: a storage-efficient algorithm for sparse matrix eigenvector computations

We present a storage‐efficient and robust algorithm for the computation of eigenvectors of large sparse symmetrical matrices using a Lanczos scheme. The algorithm is based upon a linear combination of Lanczos vectors (LCLV) with a variable iteration depth. A simple method is given to determine the iteration depth before the eigenvector computation is performed. Test calculations are reported for tight‐binding models of ordered and disordered 2‐D systems. The algorithm turns out to be reliable if an eigenvector residual less than 10−4 is required. We report benchmarks for various computers. Possible fields of application are discussed.

NUMERICAL STUDY OF THE ELECTRONIC STRUCTURE OF AMORPHOUS SILICA

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 ∼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.

Mean-field approach to extended Su–Schrieffer–Heeger models

Abstract In this work, we present a new approach to the numerical solution of the Su–Schrieffer–Heeger model. It is based on a polaron transformation that decouples nuclear and electronic degrees of freedom and a mean-field approach to the resulting electronic Hamiltonian. The emerging self consistent field procedure allows the simultaneous computation of the microscopic and electronic structure of Su–Schrieffer–Heeger models that are extended by explicitly taking electron–electron interactions into account. As an example, we apply the scheme to models of carbon nanotubes.

Refractory metals in molten salts: Theory and simulation of geometry, electronic structure, and electron transport

In this work, we present a theoretical and numerical study of the microscopic and electronic structure of solutions of refractory metal halides in alkali halide melts, [NbCl5]x[KCl]1−x and [TaCl5]x[KCl]1−x with 0⩽x⩽0.5. The geometry of the melts is described by ensembles of charged hard spheres, the electronic structure is modeled by a tight-binding Hamiltonian, which is extended by a reaction field to describe the diabatic energy profile of the electronic self-exchange in many-orbital mixed-valence systems. Despite its simplicity, the model leads to the formation of distorted octahedral [NbCl6]− and [TaCl6]− clusters, as evident both from the inspection of the simulation geometries and from the analysis of the partial pair distribution functions. Even in the presence of the strong potential energy fluctuations characteristic of ionic liquids, the octahedral structure is manifest in the density of states in a t2g–eg splitting of the conduction band. The Hamiltonian that describes mixed-valence systems is ...