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Karlsruher Institut für Technologie
Institut für Physikalische Chemie
Abteilung für Theoretische Chemische Biologie
Gebäude 30.44
Kaiserstr. 12
D-76131 Karlsruhe
Tel. +49 (0) 721 608-45700
Fax +49 (0) 721 608-45710

Welcome to the Theoretical Chemical Biology



Bachelor and Master Thesis

We are always looking for students interested in research projects or bachelor/master theses.

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Upcoming Conferences
Title Location Date


November 6-13, 2016.

Sample trajectory of an exciton from a run with no relaxation forces. The exciton delocalizes almost immediately

Julian J. Kranz and Marcus Elstner

"Simulation of singlet exciton diffusion in bulk organic materials"

J. Chem. Theory Comput., Just Accepted Manuscript • DOI: 10.1021/acs.jctc.6b00235 • Publication Date (Web):

19 Jul 2016

Link to article

Exemplary time evolution of the excess charge in anthracene

Alexander Heck, Julian J. Kranz and Marcus Elstner

"Simulation of Temperature-Dependent Charge Transport in Organic Semiconductors with Various Degrees of Disorder"

J. Chem. Theory Comput., Article ASAP, DOI: 10.1021/acs.jctc.6b00215, Publication Date (Web): May 25, 2016

Link to article


Anders S. Christensen, Tomáš Kubař, Qiang Cui and Marcus Elstner

"Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications"

Chem. Rev., Article ASAP, DOI: 10.1021/acs.chemrev.5b00584, Publication Date (Web): April 13, 2016

Link to article


Maria Ilaria Mallus, Mortaza Aghtar, Suryanarayanan Chandrasekaran, Gesa Lüdemann, Marcus Elstner and Ulrich Kleinekathöfer

"Relation between Dephasing Time and Energy Gap Fluctuations in Biomolecular Systems"

J. Phys. Chem. Lett., 2016, 7 (7), pp 1102–1108, DOI: 10.1021/acs.jpclett.6b00134, Publication Date (Web): March 07, 2016

Link to article


Yanan Guo, Franziska E. Beyle, Beatrix M. Bold, Hiroshi C. Watanabe, Axel Koslowski, Walter Thiel, Peter Hegemann, Marco Marazzi, Marcus Elstner

"Active site structure and absorption spectrum of channelrhodopsin-2 wild-type and C128T mutant"

Chemical Science, Received 29th January 2016, Accepted 24th February 2016,

DOI: 10.1039/c6sc00468g

Link to article


Cristina García-Iriepa, Moussa Gueye, Jérémie Léonard, David Martínez-López, Pedro J. Campos, Luis Manuel Frutos, Diego Sampedro and Marco Marazzi

"A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement"

Phys. Chem. Chem. Phys., 2016, Advance Article, DOI: 10.1039/C5CP07599H, Received 09 Dec 2015, Accepted 03 Feb 2016, First published online 03 Feb 2016

Link to article

Molecular dynamics simulation

A. Vogt, Y. Guo, S. P. Tsunoda, S. Kateriya, M. Elstner & P. Hegemann

"Conversion of a light-driven proton pump into a light-gated ion channel"

Scientific Reports 5, Article number: 16450 (2015), doi:10.1038/srep16450

Received: 20 April 2015, Accepted: 14 October 2015, Published online: 24 November 2015

Link to article


Alexander Heck, Julian J. Kranz, Tomáš Kubař  and Marcus Elstner

"Multi-Scale Approach to Non-Adiabatic Charge Transport in High-Mobility Organic Semiconductors"

J. Chem. Theory Comput., 2015, 11 (11), pp 5068–5082, DOI: 10.1021/acs.jctc.5b00719, Publication Date (Web): September 30, 2015

Link to article

HOMO-Complex 193L

Van Ngo, Mauricio C. da Silva, Maximilian Kubillus, Hui Li, Benoît Roux, Marcus Elstner, Qiang Cui, Dennis R. Salahub and Sergei Yu. Noskov

"Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins"

J. Chem. Theory Comput., 2015, 11 (10), pp 4992–5001, DOI: 10.1021/acs.jctc.5b00524, Publication Date (Web): September 22, 2015

Link to article

The RMSD interaction energy relative to CCSD(T) for 9 data sets using five different methods

Anders S. Christensen, Marcus Elstner and Qiang Cui

"Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization"

J. Chem. Phys. 143, 084123 (2015); http://dx.doi.org/10.1063/1.4929335, Received 30 June 2015; accepted 10 August 2015; published online 28 August 2015

Link to article

The photo-isomerization of zwitterionic gluazo

Yanan Guo, Tino Wolter, Tomáš Kubař, Martin Sumser, Dirk Trauner, Marcus Elstner

"Molecular Dynamics Investigation of gluazo, a Photo-Switchable Ligand for the Glutamate Receptor GluK2"

Published: August 26, 2015, DOI: 10.1371/journal.pone.0135399

Link to article

DFTB3 Parametrization for Copper

Michael Gaus, Haiyun Jin, Darren Demapan, Anders S. Christensen, Puja Goyal, Marcus Elstner and Qiang Cui

"DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters"

J. Chem. Theory Comput., 2015, 11 (9), pp 4205–4219, DOI: 10.1021/acs.jctc.5b00600, Publication Date (Web): August 11, 2015

Link to article

QM/MM Implementation

Tomáš Kubař,  Kai Welke and Gerrit Groenhof

"New QM/MM implementation of the DFTB3 method in the gromacs package"

Article first published online: 4 AUG 2015, DOI: 10.1002/jcc.24029

Link to article


Asif Bashir, Alexander Heck,  Akimitsu Narita, Xinliang Feng, Alexei Nefedov, Michael Rohwerder, Klaus Müllen, Marcus Elstner and Christof Wöll

"Charge carrier mobilities in organic semiconductors: crystal engineering and the importance of molecular contacts"

Phys. Chem. Chem. Phys., 2015,17, 21988-21996, DOI: 10.1039/C5CP03171K, Received 02 Jun 2015, Accepted 27 Jul 2015, First published online 27 Jul 2015

Link to article


Gesa Lüdemann , Ilia A. Solov’yov, Tomáš Kubař  and Marcus Elstner

"Solvent Driving Force Ensures Fast Formation of a Persistent and Well-Separated Radical Pair in Plant Cryptochrome"

J. Am. Chem. Soc., 2015, 137 (3), pp 1147–1156, DOI: 10.1021/ja510550g

Link to article


Pascal Friederich,  Velimir Meded,  Franz Symalla,  Marcus Elstner and Wolfgang Wenzel

"QM/QM Approach to Model Energy Disorder in Amorphous Organic Semiconductors"

J. Chem. Theory Comput., 2015, 11 (2), pp 560–567, DOI: 10.1021/ct501023n, Publication Date (Web): January 7, 2015

Link to article


Xiya Lu, Michael Gaus, Marcus Elstner and Qiang Cui

"Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications"

dx.doi.org/10.1021/jp506557r | J. Phys. Chem. B 2015, 119, 1062−1082

Link to article

DFTB3/3OB Periodic Table

Maximilian Kubillus , Tomáš Kubař , Michael Gaus , Jan Řezáč , and Marcus Elstner

Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems

J. Chem. Theory Comput., 2015, 11 (1), pp 332–342, DOI: 10.1021/ct5009137, Publication Date (Web): December 9, 2014

Link to article


Adam Kubas, Fruzsina Gajdos, Alexander Heck, Harald Oberhofer, Marcus Elstner and Jochen Blumberger

"Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations"

Royal Society of Chemistry, Published 22 December 2014 DOI: 10.1039/c4cp04749d

Link to article


Puja Goyal , Hu-Jun Qian, Stephan Irle, Xiya Lu, Daniel Roston , Toshifumi Mori, Marcus Elstner and Qiang Cui

"Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models"

The journal of physical chemistry. B Volume: 118 Issue: 38 Pages: 11007-27 Published: 2014-Sep-25 DOI: 10.1021/jp503372v

Link to article

Multipartitioning QM/MM

Hiroshi C. Watanabe , Tomáš Kubař  and Marcus Elstner

"Size-Consistent Multipartitioning QM/MM: A Stable and Efficient Adaptive QM/MM Method"

J. Chem. Theory Comput., Article ASAP, DOI: 10.1021/ct5005593 Publication Date (Web): September 10, 2014

Link to article


Tino Wolter, Marcus Elstner, Stefan Fischer, Jeremy C. Smith and Ana-Nicoleta Bondar

“Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States”

J. Phys. Chem. B, 2015, 119 (6), pp 2229–2240, DOI: 10.1021/jp505818r, Publication Date (Web): September 7, 2014

Link to article

3D Hydrophobic Moment Vectors

Sabine Reißer, Erik Strandberg, Thomas Steinbrecher,  Anne S. Ulrich

"3D Hydrophobic Moment Vectors as a Tool to Characterize the Surface Polarity of Amphiphilic Peptides"

DOI: http://dx.doi.org/10.1016/j.bpj.2014.04.020

Link to article

Excited-state pathways

Tomče Runčevski, Dr. Marina Blanco-Lomas, Dr. Marco Marazzi, Marcos Cejuela, Dr. Diego Sampedro and Prof. Robert E. Dinnebier

"Following a Photoinduced Reconstructive Phase Transformation and its Influence on the Crystal Integrity: Powder Diffraction and Theoretical Study"

Angew. Chem. Int. Ed., Article first published online: 21 MAY 2014, DOI: 10.1002/anie.201402515

Link to article


Qiang Cui and Marcus Elstner

"Density functional tight binding: values of semi-empirical methods in an ab initio era"

Phys. Chem. Chem. Phys., 2014, Advance Article, DOI: 10.1039/C4CP00908H,  First published online 13 May 2014

Link to article


Marcus Elstner and Gotthard Seifert

"Density functional tight binding"

Phil.Trans.R.Soc. A 372:20120483, 2014


Link to article



Chemical structure of cis-ATA-3

Tino Wolter, Thomas Steinbrecher, Dirk Trauner, Marcus Elstner

"Ligand Photo-Isomerization Triggers Conformational Changes in iGluR2 Ligand Binding Domain"

PLOS one, Published: April 08, 2014, DOI: 10.1371/journal.pone.0092716

Link to article

Peptide fragments
Peptide Fragments

Alexander Heck, P. Benjamin Woiczikowski, Tomáš Kubař, Kai Welke, Thomas Niehaus, Bernd Giese, Spiros Skourtis, Marcus Elstner and Thomas B. Steinbrecher

"Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals"

 J. Phys. Chem. B, Article ASAP, DOI: 10.1021/jp408907g, Publication Date (Web): March 21, 2014

Link to article

Structural models
Structural models obtained from MD simulation

Jonas Wietek, J. Simon Wiegert, Nona Adeishvili, Franziska Schneider, Hiroshi Watanabe, Satoshi P. Tsunoda, Arend Vogt, Marcus Elstner, Thomas G. Oertner, Peter Hegemann

Conversion of Channelrhodopsin into a Light-Gated Chloride Channel

ScienceVol. 344 no. 6182 pp. 409-412 DOI: 10.1126/science.1249375

Link to article


Michael Gaus , Xiya Lu , Marcus Elstner , and Qiang Cui

"Parameterization of DFTB3/3OB for Sulfur and Phosphorus for chemical and biological applications"

J. Chem. Theory  Comput., 2014, 10 (4), pp 1518–1537 DOI: 10.1021/ct401002w, Publication Date (Web): March 12, 2014

Link to article


Oleg Babii, Dr. Sergii Afonin, Dr. Marina Berditsch, Sabine Reiβer, Dr. Pavel K. Mykhailiuk, Dr. Vladimir S. Kubyshkin, Dr. Thomas Steinbrecher, Prof. Anne S. Ulrich and Prof. Igor V. Komarov

"Controlling Biological Activity with Light: Diarylethene-Containing Cyclic Peptidomimetics"

Article first published online: 19 FEB 2014, DOI: 10.1002/anie.201310019

Link to article


Adam Kubas, Felix Hoffmann, Alexander Heck, Harald Oberhofer, Marcus Elstner and Jochen Blumberger

"Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations"

J. Chem. Phys. 140, 104105 (2014)

Link to article


Michael Gaus, Qiang Cui, Marcus Elstner

"Density functional tight binding: application to organic and biological molecules"

WIREs Comput Mol Sci 2014, 4:49–61. doi: 10.1002/wcms.1156

Link to article



Microbial and Animal Rhodopsins

Oliver P. Ernst, David T. Lodowski, Marcus Elstner, Peter Hegemann, Leonid S. Brown and Hideki Kandori

"Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms"

Chem. Rev., 2014, 114 (1), pp 126–163, DOI: 10.1021/cr4003769

Link to article


Structural influence on the excitation energy within the binding pocket of bR.

Tino Wolter, Kai Welke, Prasad Phatak, Ana-Nicoleta Bondar and Marcus Elstner

"Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation"

Phys. Chem. Chem. Phys., 2013,15, 12582-12590

Link to article

The conductivity of microhydrated DNA is similar to that of DNA in bulk aqueous solution, and the effect of the closest hydration shell on the conductivity is identified

Mario Wolter, Marcus Elstner, and Tomáš Kubař

"Charge transport in desolvated DNA"

J. Chem. Phys. 139, 125102 (2013)

Link to article

Charge Transfer in E. coli DNA Photolyase

Gesa Lüdemann, P. Benjamin Woiczikowski, Tomáš Kubař, Marcus Elstner, and Thomas B. Steinbrecher

"Charge Transfer in E. coli DNA Photolyase: Understanding Polarization and Stabilization Effects via QM/MM Simulations"

Journal of Physical Chemistry B (2013) DOI: 10.1021/ jp406319b

Link to article

We review the application of our recently developed multi-scale methodology to the description of coherent charge transport in DNA

Tomáš Kubař, Rafael Gutiérrez, Ulrich Kleinekathöfer, Gianaurelio Cuniberti, Marcus Elstner

"Modeling charge transport in DNA using multi-scale methods"

physica status solidi (b) (2013) DOI: 10.1002/pssb.201349148

Link to article



Quantum-chemical calculations aimed at the decomposition of intramolecular forces contribute to the understanding of reaction mechanisms

W. Li, S. A. Edwards,  L. Lu, T. Kubař, S. P. Patil, H. Grubmüller, G. Groenhof, F. Gräter

"Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene"

ChemPhysChem 2013, 14 (12), 2687–2697

Link to article

We review our methodology for electron transfer simulations as well as the recent applications

T. Kubař and M. Elstner


"A hybrid approach to simulation of electron transfer in complex molecular systems"


J. R. Soc. Interface 2013, 10, 20130415


Link to article



SCC-DFTB calculations can be performed for organic and inorganic molecules containing halogen atoms


T. Kubař , Z. Bodrog , M. Gaus , Chr. Köhler , B. Aradi , Th. Frauenheim , and M. Elstner

"Parametrization of the SCC-DFTB Method for Halogens"

J. Chem. Theory Comput., 2013, 9 (7), pp 2939–2949

Link to article


Transfer of an electron hole in double-stranded DNA

T. Kubař and M. Elstner

"Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA"

Phys. Chem. Chem. Phys., 2013, 15, 5794-5813

Link to article



Human serum albumin (HSA)

Osama K. Abou-Zied, Najla Al-Lawatia, Marcus Elstner and Thomas B. Steinbrecher

"Binding of Hydroxyquinoline Probes to Human Serum Albumin: Combining Molecular Modeling and Forster’s Resonance Energy Transfer Spectroscopy to Understand Flexible Ligand Binding"

J. Phys. Chem. B 2013, 117, 1062 - 1074

Link to article

Bild Tino
Rearrangement of the AMPA-LBD hydrogen bonding network.

Tino Wolter, Thomas Steinbrecher, Marcus Elstner

"Computational Study of Synthetic Agonist Ligands of Ionotropic Glutamate Receptors"

PLoS ONE 8(3): e58774. doi:10.1371/journal.pone.0058774, Published: March 25, 2013

Link to article



Three-Body Repulsion for Carbon under Extreme Pressures and Temperatures

Nir Goldman, Sriram Goverapet Srinivasan, Sebastian Hamel, Laurence E. Fried, Michael Gaus and Marcus Elstner

"Determination of a Density Functional Tight Binding Model with an Extended Basis Set and Three-Body Repulsion for Carbon under Extreme Pressures and Temperatures"

J. Phys. Chem. C, 2013, 117 (15), pp 7885–7894

Link to article

QM/MM Simulations of Vibrational Spectra
QM/MM Simulations of Vibrational Spectra

K. Welke, H. C. Watanabe, T. Wolter, M. Gaus and M. Elstner

"QM/MM Simulations of Vibrational Spectra in Bacteriorhodopsin and Channelrhodopsin-2"

Phys. Chem. Chem. Phys., 2013, DOI: 10.1039/C3CP44181D, Link to article

Channelrhodopsin function

H.C. Watanabe, K. Welke, D.J. Sindhikara, P. Hegemann and M. Elstner

"Towards an understanding of channelrhodopsin function: Simulations lead to novel insights of channel mechanism"  

J. Mol. Biol. (2013), 425, 1795-1814, Link to article

Rotamer decomposition and protein dynamics
Rotamer decomposition and protein dynamics

H. C. Watanabe, M. Elstner and T. Steinbrecher

"Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics"

J. Comp. Chem., 2013, 34, 3, 198-205, Link to article

QM and QM/MM Simulations of Proteins
QM and QM/MM Simulations of Proteins

T. Steinbrecher and M. Elstner

"QM and QM/MM Simulations of Proteins"

Biomolecular Simulations : Methods and Protocols; Methods in Molecular Biology, 924, 2012, Link

DFTB3 for Organic Molecules
DFTB3 for Organic Molecules

M. Gaus , A. Goez , and M. Elstner

"Parametrization and Benchmark of DFTB3 for Organic Molecules"

J. Chem. Theory Comput., 2012, Link to article

Improved Electronic Properties from 3rd Order SCC-DFTB
Improved Electronic Properties from 3rd Order SCC-DFTB

S. Kaminski, M. Gaus and M. Elstner

"Improved Electronic Properties from 3rd Order SCC-DFTB with Cost Efficient Post-SCF Extensions"

J. Phys. Chem. A, 2012, Link to article

Sequential Transport through Molecules
Sequential Transport through Molecules

B. Popescu, P. B. Woiczikowski, M. Elstner, and U. Kleinekathöfer

"Time-Dependent View of Sequential Transport through Molecules with Rapidly Fluctuating Bridges"

Phys. Rev. Lett. 109, 176802 (2012), Link to article

Peptide-Lipid Interactions of the Stress-Response Peptide TisB
Peptide-Lipid Interactions of the Stress-Response Peptide TisB

T. Steinbrecher, S. Prock, J. Reichert, P. Wadhwani, B. Zimpfer, J. Bürck, M. Berditsch, M. Elstner and A. S. Ulrich

"Peptide-Lipid Interactions of the Stress-Response Peptide TisB That Induces Bacterial Persistence"

Biophys. J., 2012, 103, 7, 1460-1469, Link to article

Highly Charged QM Regions
Highly Charged QM Regions

G. Hou, X. Zhu, M. Elstner and Q. Cui

"A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions"

J. Chem. Theory Comput., 2012, 8 (11), pp 4293–4304, Link to article