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ABSTRACT: Aptamers, i.e. short sequences of RNA and single-stranded DNA, are capable of specificilly binding objects ranging from small molecules over proteins to entire cells. Here, we focus on the structure, stability, dynamics and electronic properties of oligonucleotides that interact with aromatic or heterocyclic targets. Large-scale molecular dynamics simulations indicate that aromatic rings such as dyes, metabolites or alkaloides form stable adducts with their oligonucleotide host molecules at least on the simulation time scale. From molecular dynamics snapshots, the energy parameters relevant to Marcus' theory of charge transfer are computed using a modified Su-Schrieffer-Heeger Hamiltonian, permitting an estimate of the charge transfer rates. In many cases, aptamer binding seriously influences the charge transfer kinetics and the charge carrier mobility within the complex, with conductivities up to the nanoampere range for a single complex. We discuss the conductivity properties with reference to potential applications as biosensors.
The Journal of Physical Chemistry B 12/2012; · 3.70 Impact Factor
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ABSTRACT: We approach the electronic conductivity of simple models of organic solar cells containing linear and branched αα(')-oligothiophenes and buckminsterfullerene. Close-packed model geometries are generated using a Monte Carlo method, this procedure is verified making use of an analogue model. The electronic structure is described by an extended Su-Schrieffer-Heeger Hamiltonian, the resulting potential energy surfaces relevant to charge transfer can be analyzed using Marcus' theory, leading to local and-via Kirchhoff's rule-global conductivities for uniform oligothiophene and fullerene systems and their mixtures. Dense fullerene systems or subsystems always exhibit a conductivity in excess of 100 S/cm. In contrast, oligothiophenes show a comparable conductivity only for uniform, well-ordered arrangements of layers. Branched oligomers show only a slight improvement over linear oligothiophenes. Our results support the bulk heterojunction approach as a design principle of organic solar cells from a theoretical perspective.
The Journal of chemical physics 09/2012; 137(9):094903. · 3.09 Impact Factor
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ABSTRACT: Motivated by recent progress in electron paramagnetic resonance spectroscopy, we describe hole transfer along a chain of tryptophan amino acids within the cryptochrome protein of Synechocystis sp.: surprisingly, despite a close sequential and structural similarity to E. coli DNA photolyase, the charge transfer paths and the final sites of charge localization are different for these two enzymes. We study this phenomenon using atomistic simulations and electronic structure computations as a theoretical basis, and we take a new look at the concepts of charge transfer and introduce a modification of Marcus' theory that incorporates dynamic polarization effects. Only this variant of theory describes the population of the correct branch on the subnanosecond time scale. Based on our numerical analysis, we further suggest that the Asp372-Arg374 salt bridge acts as a novel stepping stone in the charge transfer reaction.
Physical Chemistry Chemical Physics 07/2012; 14(32):11518-24. · 3.57 Impact Factor
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ABSTRACT: In this contribution, we discuss three recent developments in atomistic biological charge transfer theory. First, in the context of Marcus' classical theory of charge transfer, key quantities of the theory such as driving forces and reorganization enthalpies are now accessible by thermodynamic integration schemes within standard molecular dynamics simulations at high accuracy. Second, direct simulations of charge transfer enable the computation of fast charge transfer reaction rates without having to resort to Marcus' theory. Finally, exploring the electronic structure beyond that of hitherto presumed centers of localization helps to identify new stepping stones of charge transfer reactions. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
Biochimica et Biophysica Acta 02/2012; 1817(10):1955-7. · 4.66 Impact Factor
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ABSTRACT: 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.
Angewandte Chemie International Edition 11/2011; 50(52):12647-51. · 13.45 Impact Factor
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ABSTRACT: Motivated by recent progress in the mass spectroscopy of the elementary reaction of alkali metals and water dispersed in ultracold helium nanodroplets (S. Müller et al., Phys. Rev. Lett., 2009, 102, 183401.), we investigate the properties of pure and mixed Cs clusters and cluster ions, Cs(l)H(m)O(n)(0/+), from a quantum chemical perspective. The presence of Cs atoms requires a careful choice of the methodology, which we have tested for small molecules for which experimental results were available. With the thus selected density functional, pseudopotential and basis set, we compute the geometry, the ionization potentials and the atomization energy, enabling a proper estimate of the energetics of cluster fragmentation upon photoionization. Based upon these calculations, we are able to construct a fragmentation tree that rationalizes the origin of all peaks observed in the experimental mass spectrum. Infrared spectra are computed, and we introduce a simple mixed quantum-classical model that essentially reproduces the cluster geometries.
Physical Chemistry Chemical Physics 09/2011; 13(33):14973-83. · 3.57 Impact Factor
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ABSTRACT: We approach the electronic properties of a simple model of organic solar cells, a binary mixture of αα'-oligothiophenes and buckminsterfullerene, from a theoretical and numerical perspective. Close-packed model geometries are generated using a Monte Carlo method, the electronic structure is described by a reparametrized semiempirical Pariser-Parr-Pople Hamiltonian. All electronic properties, such as optical absorption spectra, tightly-bound charge transfer states and exciton bands, arise from the same atomistic Hamiltonian using a configuration interaction method involving single excitations. The absorption spectra are dominated by intramolecular contributions, whereas in the optical gap low-lying charge transfer states are predicted. The efficiency of the solar cell crucially depends on the structure of the charge-transfer exciton bands and on the relaxation mechanism. We discuss how these findings may help improve the design of organic solar cells from an excitonic view.
Physical Chemistry Chemical Physics 08/2011; 13(36):16247-53. · 3.57 Impact Factor
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ABSTRACT: We present the full enthalpic phase transition cycle for ionic liquids (ILs) as examples of non-classical salts. The cycle was closed for the lattice, solvation, dissociation, and vaporization enthalpies of 30 different ILs, relying on as much experimental data as was available. High-quality dissociation enthalpies were calculated at the G3 MP2 level. From the cycle, we could establish, for the first time, the lattice and solvation enthalpies of ILs with imidazolium ions. For vaporization, lattice, and dissociation enthalpies, we also developed new prediction methods in the course of our investigations. Here, as only single-ion values need to be calculated and the tedious optimization of an ion pair can be circumvented, the computational time is short. For the vaporization enthalpy, a very simple approach was found, using a surface term and the calculated enthalpic correction to the total gas-phase energy. For the lattice enthalpy, the most important constituent proved to be the calculated conductor-like screening model (COSMO) solvation enthalpy in the ideal electric conductor. A similar model was developed for the dissociation enthalpy. According to our assessment, the typical error of the lattice enthalpy would be 9.4 kJ mol(-1), which is less than half the deviation we get when using the (optimized) Kapustinskii equation or the recent volume-based thermodynamics (VBT) theory. In contrast, the non-optimized VBT formula gives lattice enthalpies 20 to 140 kJ mol(-1) lower than the ones we assessed in the cycle, because of the insufficient description of dispersive interactions. Our findings show that quantum-chemical calculations can greatly improve the VBT approaches, which were parameterized for simple, inorganic salts with ideally point-shaped charges. In conclusion, we suggest the term "augmented VBT", or "aVBT", to describe this kind of theoretical approach.
Chemistry 05/2011; 17(23):6508-17. · 5.93 Impact Factor
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ABSTRACT: We approach the problem of optical excitations in molecular aggregates in complex biochemical environments from a computational, all-atom perspective. The system is divided into a π orbital part described by a Pariser-Parr-Pople model with configuration interaction using singly excited Slater determinants (PPP-CIS). It is coupled to the protein and water charges of a classical force field. Strategies for a high-accuracy reparameterization and an efficient computational solution are presented. For γD-crystallin, a band edge consisting of charge-transfer states emerges for a coupled molecular aggregate compared to the uncoupled residues. The energies of some charge-transfer states strongly depend on the dielectric properties of the model, giving a first insight into the potential temporal evolution of these excitations. Possible biochemical implications are discussed.
Biophysical chemistry 01/2011; 153(2-3):173-8. · 2.28 Impact Factor
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ABSTRACT: DNA Photolyases are light sensitive oxidoreductases present in many organisms that participate in the repair of photodamaged DNA. They are capable of electron transfer between a bound cofactor and a chain of tryptophan amino acid residues. Due to their unique mechanism and important function, photolyases have been subject to intense study in recent times, with both experimental and computational efforts. In this work, we present a novel application of classical molecular dynamics based free energy calculations, combined with quantum mechanical computations, to biomolecular charge transfer. Our approach allows for the determination of all reaction parameters in Marcus' theory of charge transport. We were able to calculate the free energy profile for the movement of a positive charge along protein sidechains involved in the biomolecule's function as well as charge-transfer rates that are in good agreement with experimental results. Our approach to simulate charge-transfer reactions explicitly includes the influence of protein flexibility and solvent dynamics on charge-transfer energetics. As applied here to a biomolecular system of considerable scientific interest, we believe the method to be easily adaptable to the study of charge-transfer phenomena in biochemistry and other fields.
Physical Chemistry Chemical Physics 08/2010; 12(32):9516-25. · 3.57 Impact Factor
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ABSTRACT: 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 Marcus's 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.
Journal of the American Chemical Society 07/2009; 131(23):8134-40. · 9.91 Impact Factor
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ABSTRACT: We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.
The Journal of chemical physics 03/2009; 130(8):085104. · 3.09 Impact Factor
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ABSTRACT: 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.
The Journal of Physical Chemistry B 01/2009; 112(51):16935-44. · 3.70 Impact Factor
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ABSTRACT: 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.
08/2007: pages 63-75;
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ABSTRACT: We address the problem of charge transfer through DNA−gold junctions from a theoretical and numerical perspective. The geometry and the electronic structure of the DNA fragment is described on an atomistic level making use of an extended Su−Schrieffer−Heeger Hamiltonian. The emerging potential energy surfaces exhibit the characteristics of small polaron formation and can be analyzed to obtain the energy parameters relevant to Marcus' theory of charge transfer and the corresponding interbase hopping rates. At stationarity, the resulting master equations lead to a maximum current of 5 nA per A−DNA double strand upon the application of a potential of ±2 V, a value comparable to recent experimental findings. In addition, the overall shape of the I−V curves and their pronounced dependence upon the DNA sequence is reproduced.
05/2007;
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Macromolecular Theory and Simulations 08/2006; 15(7):538 - 545. · 1.71 Impact Factor
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ABSTRACT: Based upon Monte Carlo simulations of amorphous molecular glasses, we have computed the electronic structure of five prototypical polyaromatic hydrocarbons using an extended Su-Schrieffer-Heeger model [J. R. Schrieffer, W. P. Su, and A. J. Heeger, Phys. Rev. Lett. 42, 1698 (1979)]. In the presence of excess charges, the resulting potential energy surfaces have been analyzed using Marcus' [Annu. Rev. Phys. Chem. 15, 155 (1964)] theory of charge transfer to yield reaction coefficients and--via the application of linear response theory--local conductivities. Applying Kirchhoff's rules, the emerging random resistor network problem leads to global conductivities of the order of 10(-1)-1 Scm, which correlate with the structural characteristics of the underlying geometry.
The Journal of Chemical Physics 08/2006; 125(1):014707. · 3.33 Impact Factor
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ABSTRACT: We address the problem of charge transfer (CT) between a nanosized inorganic system and a protein from a theoretical and numerical perspective. The CT process is described on an atomistic level by applying an electronic Hamiltonian that takes into account the chemical bond, vibronic coupling effects, and polarization degrees of freedom. As a structurally well-characterized example, we consider a complex of C60 and its antibody. For this system, we find a novel efficient protein CT mechanism; through-space superexchange is mediated by stacked pi orbital systems. The predicted rates are comparable to those obtained for short-range electron tunneling through covalent bonds, the fastest ground-state CT process known for proteins.
The Journal of Physical Chemistry B 06/2006; 110(18):9333-8. · 3.70 Impact Factor
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ABSTRACT: 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.
Journal of Biological Chemistry 06/2006; 281(21):14756-63. · 4.77 Impact Factor
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ABSTRACT: In this work, we approach the impact of dynamic and static disorder on DNA charge transfer from a theoretical and numerical perspective. Disordered or defect geometries are either realized via molecular dynamics simulations using a classical force field or by experimentally determined DNA bulge structures. We apply a chemically specific, atomically resolved extended Su-Schrieffer-Heeger model to compute the energy parameters relevant to DNA charge transfer. For both models studied here, the effective donor-acceptor couplings--and hence the charge transfer rates--significantly depend upon the geometry. Dynamic disorder leads to a correlation time in this quantity of the order of 30 fs, and the transfer rates universally exhibit a broad, yet well-defined, exponential distribution. For DNA bulges, the angle characterizing the defect controls the charge transfer efficiency. The results are discussed and extensively compared to experimental findings and other calculations.
Physical Chemistry Chemical Physics 01/2006; 7(24):4039-50. · 3.57 Impact Factor
