Thorsten Koslowski

Name:

Organization: Universit?t Freiburg , Germany

Department: Institut für Physikalische Chemie

Title: (PhD)

Chemicals
References

Thermodynamic Integration Networks and Their Application to Charge Transfer Reactions within the AauDyPI Fungal Peroxidase

Co-reporter:Anna Bauß, Michael Langenmaier, Eric Strittmatter, Dietmar A. Plattner, and Thorsten Koslowski

The Journal of Physical Chemistry B 2016 Volume 120(Issue 22) pp:4937-4944

Publication Date(Web):May 16, 2016

DOI:10.1021/acs.jpcb.6b03327

We present a computer simulation study of the thermodynamics and kinetics of charge transfer reactions within the fungal peroxidase AauDyPI from Auricularia auriculae-judae. Driving forces and reorganization energies are obtained from a thermodynamic integration scheme based upon molecular dynamics simulations. To enhance the numerical accuracy, the free energies are analyzed within a least-squares scheme of a closely knit thermodynamic network. We identify Tyr147, Tyr229, and Trp105 as oxidative agents, and find Trp377 to be a long-lived reaction intermediate. The results are compared to recent experimental findings.

Storage, transport, release: heme versatility in nitrite reductase electron transfer studied by molecular dynamics simulations

Co-reporter:Anna Bauß and Thorsten Koslowski

Physical Chemistry Chemical Physics 2015 vol. 17(Issue 6) pp:4483-4491

Publication Date(Web):2015/01/02

DOI:10.1039/C4CP04383A

Using molecular dynamics simulations of the thermodynamic integration type, we study the energetics and kinetics of electron transfer through the nitrite reductase enzyme of Sulfurospirillum deleyianum, Wolinella succinogenes and Campylobacter jejuni. In all of these five-heme proteins, the storage of an even number of electrons within a monomeric chain is thermodynamically favoured. Kinetically, two of these electrons are usually transferred almost simultaneously towards the active site. Although the free energy landscape for charge transfer varies significantly from organism to organism, the heme cofactor closest to the interface of a protein dimer always exhibits a particularly low free energy, suggesting that protein dimerization is functional. Interheme electron interaction effects do not play a significant role.

Sensing Organic Molecules by Charge Transfer through Aptamer-Target Complexes: Theory and Simulation

Co-reporter:Maria Schill and Thorsten Koslowski

The Journal of Physical Chemistry B 2013 Volume 117(Issue 2) pp:475-483

Publication Date(Web):December 10, 2012

DOI:10.1021/jp308042n

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 road not taken: a theoretical view of an unexpected cryptochrome charge transfer path

Co-reporter:Sebastian Krapf, Stefan Weber and Thorsten Koslowski

Physical Chemistry Chemical Physics 2012 vol. 14(Issue 32) pp:11518-11524

Publication Date(Web):27 Jun 2012

DOI:10.1039/C2CP40793K

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.

A theoretical study of pure and mixed caesium clusters and cluster ions, CslHmO0/+n, l ≤ 5: geometry, energetics and photofragmentation

Co-reporter:Sebastian Krapf, Maria Schill, Sebastian Krötz and Thorsten Koslowski

Physical Chemistry Chemical Physics 2011 vol. 13(Issue 33) pp:14973-14983

Publication Date(Web):14 Jul 2011

DOI:10.1039/C1CP21274E

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, CslHmO0/+n, 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.

Semiempirical configuration interaction calculations in biochemical environments: Parametrization and application to γD-crystallin, an eye-lense protein

Co-reporter:Sandra Kruse, Sebastian Krapf, Benjamin Lampe, Thorsten Koslowski

Biophysical Chemistry 2011 Volume 153(2–3) pp:173-178

Publication Date(Web):January 2011

DOI:10.1016/j.bpc.2010.11.005

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.Research Highlights►Protein optical excitations are computed using π electron models. ►A system-specific reparametrization is imperative. ►Aromatic amino acid aggregates show a charge transfer absorption edge. ►Excitations can be traced following dielectric relaxation.

A combined Kirchhoff–Master equation approach to electronic transport in one-dimensional molecular conductors

Co-reporter:Thorsten Koslowski, Anke Wilkening

Chemical Physics 2010 Volume 369(Issue 1) pp:22-26

Publication Date(Web):24 March 2010

DOI:10.1016/j.chemphys.2010.02.001

Theory and simulation of charge transfer through DNA – nanotube contacts

Co-reporter:Gunda Rink, Yong Kong, Thorsten Koslowski

Chemical Physics 2006 Volume 327(Issue 1) pp:98-104

Publication Date(Web):21 August 2006

DOI:10.1016/j.chemphys.2006.03.041

Abstract

We address the problem of charge transfer between a single-stranded adenine oligomer and semiconducting boron nitride nanotubes from a theoretical and numerical perspective. The model structures have been motivated by computer simulations; sample geometries are used as the input of an electronic structure theory that is based upon an extended Su-Schrieffer-Heeger Hamiltonian. By analyzing the emerging potential energy surfaces, we obtain hole transfer rates via Marcus’ theory of charge transfer. In the presence of nanotubes, these rates exceed those of isolated DNA single strands by a factor of up to 10⁴. This enhancement can be rationalized and quantified as a combination of a template effect and the participation of the tube within a superexchange mechanism.

Models of Irregular Hyperbranched Polymers: Topological Disorder and Mechanical Response

Co-reporter:Thorsten Koslowski;Aurel Jurjiu;Alexer Blumen

Macromolecular Theory and Simulations 2006 Volume 15(Issue 7) pp:538-545

Publication Date(Web):15 AUG 2006

DOI:10.1002/mats.200600004

Summary: We study the impact of topological disorder on the mechanical response of hyperbranched macromolecules from a theoretical and numerical perspective. The polymer models are generated using a bond switching algorithm, and the emerging systems are described within the Zimm and Rouse pictures of macromolecular dynamics. The topological disorder is manifest in the frequency-dependent dynamic moduli, . These are clearly distinct from that of regular hyperbranched fractals of the same size, and they do not obey simple scaling rules. The dynamic moduli reflect the short-range order inherent in the model, and we thus suggest that the extent of disorder in branched tree-like polymers may be well-estimated experimentally using .

Charge transfer through the nucleosome: a theoretical approach

Co-reporter:Tobias Cramer, Sebastian Krapf and Thorsten Koslowski

Physical Chemistry Chemical Physics 2004 vol. 6(Issue 12) pp:3160-3166

Publication Date(Web):27 May 2004

DOI:10.1039/B402410A

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.

Recent progress in biological charge transfer: Theory and simulation

Co-reporter:Thorsten Koslowski, Fabian Burggraf, Sebastian Krapf, Thomas Steinbrecher, Christian Wittekindt

Biochimica et Biophysica Acta (BBA) - Bioenergetics (October 2012) Volume 1817(Issue 10) pp:1955-1957

Publication Date(Web):October 2012

DOI:10.1016/j.bbabio.2012.02.025

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

Co-reporter:Fabian Burggraf, Thorsten Koslowski

Biochimica et Biophysica Acta (BBA) - Bioenergetics (January 2011) Volume 1807(Issue 1) pp:53-58

Publication Date(Web):January 2011

DOI:10.1016/j.bbabio.2010.08.001

A theoretical study of pure and mixed caesium clusters and cluster ions, CslHmO0/+n, l ≤ 5: geometry, energetics and photofragmentation

Co-reporter:Sebastian Krapf, Maria Schill, Sebastian Krötz and Thorsten Koslowski