Welcome to the Theoretical Chemical Biology

Schloss KA

Bachelor and Master Thesis

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

More information is available here

Contact us
Conferences and Workshops
Title Place Date

Recent Publications

Sara_Farhad_2022 F. Ghalami

Sara Roosta, Farhad Ghalami, Marcus Elstner, and Weiwei Xie

"Efficient Surface Hopping Approach for Modeling Charge Transport in Organic Semiconductors"

J. Chem. Theory Comput., Published online18 February 2022

Link to article

PCCP_2022 S. Inanlou
Influence of the applied methods on the computed vertical excitation energies

Samaneh Inanlou, Rodrigo Cortés-Mejia, Ali Deniz Özdemir, Sebastian Höfener, Wim Klopper, Wolfgang Wenzel, Weiwei Xie and Marcus Elstner

"Understanding excited state properties of host materials in OLEDs: simulation of absorption spectrum of amorphous 4,4-bis(carbazol-9-yl) -2,2-biphenyl (CBP)"

Phys. Chem. Chem. Phys., 2022, 24, 4576, accepted 1st February 2022

Link to article

Ziwei_Monja_2022 Monja Sokolov

Ziwei Pang, Monja Sokolov, Tomáš Kubař and Marcus Elstner

"Unravelling the mechanism of glucose binding in a protein-based fluorescence probe: molecular dynamics simulation with a tailor-made charge model"

Phys. Chem. Chem. Phys., 2022, 24, 2441-2453, First published on 4th January 2022

Link to article

LeticiaGomez2022 Leticia Goméz

Claudia L. Gómez-Flores, Denis Maag, Mayukh Kansari, Van-Quan Vuong, Stephan Irle, Frauke Gräter, Tomáš Kubař, and Marcus Elstner

"Accurate Free Energies for Complex Condensed-Phase Reactions Using an Artificial Neural Network Corrected DFTB/MM Methodology"

J. Chem. Theory Comput., Publication Date: January 3, 2022

Link to article

Toc_final_2021 Denis Maag
Thiol–disulfide exchange reactions in the protein

Denis Maag, Marina Putzu, Claudia L. Gómez-Flores, Frauke Gräter, Marcus Elstner and  Tomáš Kubař

"Electrostatic interactions contribute to the control of intramolecular thiol–disulfide isomerization in a protein"

Phys. Chem. Chem. Phys., 2021, Advance Article, first published 11 Nov 2021

Link to article

PNAS_2021 Denis Maag
Three-dimensional structure of the bR state and the photocycle at pH ≥ 6

Denis Maag, Thilo Mast, Marcus Elstner, Qiang Cui, and Tomáš Kubař

"O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism"

PNAS, published September 28, 2021, 118 (39) e2024803118

Link to article

Elstner_Höfener2021 Höfener2021

Nils Schieschke, Beatrix M. Bold, Philipp M. Dohmen, Daniel Wehl, Marvin Hoffmann, Andreas Dreuw, Marcus Elstner, Sebastian Höfener

„Geometry dependence of excitonic couplings and the consequences for configuration-space sampling“

J Comput Chem. 2021;1–17, First published: 16 May 2021

Link to article

JacobsUni_2021 U_Kleinekathoefer
Structure of the major LHCII trimer

Sayan Maity, Vangelis Daskalakis, Marcus Elstner and Ulrich Kleinekathöfer

„Multiscale QM/MM Molecular Dynamics Simulations of the Trimeric Major Light-harvesting Complex II“

Physical Chemistry Chemical Physics, 2021, 23, 7407 – 7417, first published on 18th March 2021

Link to article

Elstner_Nienhaus2021 T_Nienhaus

Monja Sokolov, Beatrix M. Bold, Julian J. Kranz, Sebastian Höfener, Thomas A. Niehaus, and Marcus Elstner

„Analytical Time-Dependent Long-Range Corrected Density Functional Tight Binding (TD-LC-DFTB) Gradients in DFTB+: Implementation and Benchmark for Excited-State Geometries and Transition Energies“

J. Chem. Theory Comput. 2021, 17, 4, 2266–2282, Publication Date: March 9, 2021

Link to article

ChemicalScience_2021 ChristofWöll
Surface-anchored crystalline thin film

Ritesh Haldar, Mariana Kozlowska, Michael Ganschow, Samrat Ghosh, Marius Jakoby, Hongye Chen, Farhad Ghalami, Weiwei Xie, Shahriar Heidrich, Yusuke Tsutsui, Jan Freudenberg, Shu Seki, Ian A. Howard, Bryce S. Richards, Uwe H. F. Bunz, Marcus Elstner, Wolfgang Wenzel and Christof Wöll

"Interplay of structural dynamics and electronic effects in an engineered assembly of pentacene in a metal–organic framework"

Chem. Sci., 2021,12, 4477-4483, First published 08 Feb 2021

Link to article

BeaBold2020 BeatrixBold
DFTB/MM Molecular Dynamics Simulations

Sayan Maity, Beatrix M. Bold, Jigneshkumar Dahyabhai Prajapati, Monja Sokolov, Tomáš Kubař, Marcus Elstner, and Ulrich Kleinekathöfer

"DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex"

J. Phys. Chem. Lett. 2020, 11, XXX, 8660–8667, September 29, 2020

Link to article

MilaK MilaKraemer
Charge and exciton propagation in organic semiconductors.

Mila Krämer, Philipp M. Dohmen, Weiwei Xie, Daniel Holub, Anders S. Christensen, and Marcus Elstner

"Charge and Exciton Transfer Simulations Using Machine-Learned Hamiltonians"

J. Chem. Theory Comput, https://dx.doi.org/10.1021/acs.jctc.0c00246, published: June 3, 2020

Link to article

ChemEurope_2020 A_Masterlaz
Hole Transfer Integral

Michael Mastalerz, Lucas Ueberricke, Ioana Ciubotaru, Farhad Ghalami, Felix Mildner, Frank Rominger, Marcus Elstner

"Di‐ and Tetracyano Substituted Pyrene‐Fused Pyrazaacenes –Aggregation in the Solid State"

Chemistry Europe, First published: 27 May 2020, https://doi.org/10.1002/chem.202002382

Link to article

WeiweiXie_2020 Weiwei Xie 2020
Hopping Transport

Weiwei Xie, Daniel Holub, Tomáš Kubař, and Marcus Elstner

"Performance of Mixed Quantum-Classical Approaches on Modeling the Crossover from Hopping to Bandlike Charge Transport in Organic Semiconductors"

J. Chem. Theory Comput. 2020, 16, 4, 2071–2084, Publication Date: March 16, 2020

Link to article

Graphical_Abstract_2020 BeatrixBold
Graphical Abstract

Beatrix M. Bold, Monja Sokolov, Sayan Maity, Marius Wanko, Philipp M. Dohmen, Julian J. Kranz,   Ulrich Kleinekathöfer, Sebastian Höfener and Marcus Elstner

"Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes"

Phys. Chem. Chem. Phys., first published on 13 Jan 2020

Link to article

Natacha_Daniel_2019 Natacha Gillet

Daniel Holub, Tilman Lamparter, Marcus Elstner and Natacha Gillet 

"Biological Relevance of Charge Transfer Branching Pathways in Photolyases"

Phys. Chem. Chem. Phys., first published on 10 Jul 2019

Link to article

VioSchneider2018 VioSchneider

Violetta Schneider, Parvesh Wadhwani, Johannes Reichert, Jochen Bürck, Marcus Elstner, Anne S. Ulrich and Tomáš Kubař

"Tetrameric Charge-Zipper Assembly of the TisB Peptide in Membranes - Computer Simulation and Experiment"

J. Phys. Chem. B 2019, 123, 1770−1779

Link to article

FranziWolf2019 FranziWolf

Franziska E. Wolff,  Sebastian Höfener, Marcus Elstner and Tomasz A. Wesołowski

"Origin of the Solvatochromism in Organic Fluorophores with Flexible Side Chains: A Case Study of Flugi2"

J. Phys. Chem. A 2019, 123, 4581−4587

Link to article

Chemistry Europe Daniel Holub
Chemistry Europe

Lucas Ueberricke, Daniel Holub, Julian Kranz, Frank Rominger, Marcus Elstner and Michael Masta

"Triptycene End-capped Quinoxalinophenanthrophenazines (QPPs) –Influence of Substituents and Conditions on Aggregationin the Solid State"

Chem. Eur. J. 10.1002/chem.201902002, 18 June 2019

Link to article

Marco Marazzi 2019 Marco Marazzi

Victor Moron, Marco Marazzi, Marius Wanko

"Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore?"

J. Chem. Theory Comput. 2019, 15, 7, 4228-4240, May 30, 2019

Link to article

DanielH Daniel Holub

Daniel Holub, Tomáš Kubař, Thilo Mast, Marcus Elstner and Natacha Gillet

"What accounts for the different functions in photolyases and cryptochromes: a computational study of proton transfers to FAD"

Phys. Chem. Chem. Phys., 2019, 21, 11956-11966

Link to article

Natacha_Daniel_2019 febs
Comparison between PhrB (cyan, MD snapshot) and Drosophila melanogaster photolyase (orange PDB 3CVU)

Hongju Ma, Daniel Holub, Natacha Gillet, Gero Kaeser, Katharina Thoulass, Marcus Elstner, Norbert Krauß, Tilman Lamparter

"Two aspartate residues close to the lesion binding site of Agrobacterium (6‐4) photolyase are required for Mg2+ stimulation of DNA repair"

FEBS Press, first published: 31 January 2019, https://doi.org/10.1111/febs.14770

Link to article

Channel_2018 Phys. Chem. Chem. Phys.,
A monomer of the ChR2-WT studied here.

Yanan Guo, Franziska E. Wolff, Igor Schapiro, Marcus Elstner and  Marco Marazzi

"Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2"

Phys.Chem.Chem.Phys.,  20, 27501, first published on 11th October 2018

Link to article

SabineReisser2018 Sabine Reisser

Sabine Reißer, Erik Strandberg, Thomas Steinbrecher, Marcus Elstner and Anne S. Ulrich

"Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid- State NMR"

J. Chem. Theory Comput. 2018, 14, 6002−6014

Link to article

Maja_Marcus_2018 WileyOnlineLibrary
Examples for structures in the standard test set (with water, ammonia, and hydrogen sulfide as the ligands)

Milena Vujović, Mioy Huynh, Sebastian Steiner, Pablo Garcia‐Fernandez, Marcus Elstner, Qiang Cui, Maja Gruden

"Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin‐polarized DFTB3 model"

Journal of Computational Chemistry 2018, 09 October 2018, doi.org/10.1002/jcc.25614

Link to article

Natacha_Tomas2018 Tomas Kubar
Free energies of Tyr−2 in the gas phase from one-dimensional metadynamics simulations with the PT reaction coordinate biased

Natacha Gillet, Marcus Elstner and Tomáš Kubař

"Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer"

The Journal of Chemical Physics 149, 072328 (2018)

Link to article

Julian Kranz 2018 Julian Kranz
Example of a potential bond descriptor

Julian J. Kranz,  Maximilian Kubillus, Raghunathan Ramakrishnan, O. Anatole von Lilienfeld, and Marcus Elstner

"Generalized Density-Functional Tight-Binding Repulsive Potentials from Unsupervised Machine Learning"

J. Chem. Theory Comput. 2018, 14, 2341−2352

Link to article

MarcusElstner2018 Marcus Elstner
Structural model of the X. laevis cryptochrome DASH

Emil Sjulstok, Gesa Lüdemann, Tomas Kubar, Marcus Elstner, and Ilia A. Solov’yov

"Molecular Insights into Variable Electron Transfer in Amphibian Cryptochrome"

Biophysical Journal 114, 2563–2572, June 5, 2018

Link to article

Tomas_Marina2018 Tomas Kubar
The disulfide exchange reaction

Marina Putzu, Frauke Gräter, Marcus Elstner and Tomáš Kubar

"On the mechanism of spontaneous thiol–disulfide exchange in proteins"

Phys. Chem. Chem. Phys., 2018, Advance Article, first published on 24 May 2018,

DOI: 10.1039/C8CP01325J

Link to article

TKubar2018 Tomas Kubar
Representative structures of DNA and binding cations from three MD simulation repeats

Z. Meng, T. Kubař, Y. Mu, F. Shao

"A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids"

J Chem Theory Comput 14(5):2733–2742, 2018

Link to article

Elghobashi-Meinhard2018 Elghobashi-Meinhard2018

Nadia ElghobashiMeinhardt, Prasad Phatak, Ana-Nicoleta Bondar, Marcus Elstner, Jeremy C. Smith

"Catalysis of Ground State cis→ trans Isomerization of Bacteriorhodopsin’s Retinal Chromophore by a HydrogenBond Network"

The Journal of Membrane Biology (2018) 251:315–327, Published online: 8 March 2018

Link to article

Kubar_Wagenknecht Tomas Kubar
Fluorescence decay curves

J. Steinmeyer, H.-K. Walter, M.A. Bichelberger, V. Schneider, T. Kubař, F. Rönicke, B. Olshausen, K. Nienhaus, G.U. Nienhaus, U. Schepers, M. Elstner, H.-A. Wagenknecht

"siRNA traffic lights: Arabino-configured 2'-anchors for fluorescent dyes are key for dual color readout in cell imaging"

Org Biomol Chem 16(20):3726–3731, 2018

Link to article

TKubar_Ulrich2018 Tomas Kubar
Amino acid sequence of HZ, illustrating the employed labeling scheme

S.L. Grage, S. Kara, A. Bordessa, V. Doan, F. Rizzolo, M. Putzu, T. Kubař, A.M. Papini, G. Chaume, T. Brigaud, S. Afonin, A.S. Ulrich

"Orthogonal 19F-labeling for solid-state NMR reveals the conformation and orientation of short peptaibols in membranes"

Chem Eur J 24(17):4328–4335, 2018

Link to article

Repulsive potential for C−C interaction

Van Quan Vuong, Jissy Akkarapattiakal Kuriappan, Maximilian Kubillus, Julian J. Kranz, Thilo Mast, Thomas A. Niehaus, Stephan Irle and Marcus Elstner

"Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules"

J. Chem. Theory Comput. 2018, 14, 115−125

Link to article

FAD photoreduction mechanism by different aromatic residues in a phylogenetically ancient photolyase

Daniel Holub, Hongju Ma, Norbert Krauß, Tilman Lamparter, Marcus Elstner and  Natacha Gillet

"Functional role of an unusual tyrosine residue in the electron transfer chain of a prokaryotic (6–4) photolyase"

Chemical Science, Accepted on 09 Dec 2017 and first published on 11 Dec 2017

Link to article


H.C. Watanabe, M. Kubillus, T. Kubař, R. Stach, B. Mizaikoff, H. Ishikita

"Cation solvation with quantum chemical effects modeled by size-consistent multi-partitioning quantum mechanics/molecular mechanics method"

Phys Chem Chem Phys 19(27):17985–17997, 2017

Link to article


Yusaku Hontani, Marco Marazzi, Katja Stehfest, Tilo Mathes, Ivo H. M. van Stokkum, Marcus Elstner, Peter Hegemann & John T. M. Kennis

"Reaction dynamics of the chimeric channelrhodopsin C1C2"

Scientific Reports, Received: 8 February 2017, Accepted: 28 June 2017, Published online: 3 August 2017

Link to article

Journal of Computational Chemistry

Maja, Gruden, Ljubica Andjelkovic, Jissy Akkarapattiakal Kuriappan, Stepan Stepanovic, Matija Zlatar, Qiang Cui, Marcus Elstner

"Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules"

Journal of Computational Chemistry, Volume 38, Issue 25, September 30, 2017, Pages 2171–2185

First published: 24 July 2017,  DOI: 10.1002/jcc.24866

Link to article

HZ molecule in a lipid bilayer

Marina Putzu, Sezgin Kara, Sergii Afonin, Stephan L. Grage, Andrea Bordessa, Grégory Chaume, Thierry Brigaud, Anne S. Ulrich, Tomáš Kubař

"Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations"

Biophysical Journal, Volume 112, Issue 12, 20 June 2017, Pages 2602-2614

Link to article

Julian J. Kranz, Marcus Elstner, Bálint Aradi, Thomas Frauenheim, Vitalij Lutsker, Adriel Dominguez Garcia and Thomas A. Niehaus

"Time-Dependent Extension of the Long-Range Corrected Density Functional Based Tight-Binding Method"

J. Chem. Theory Comput., 2017, 13 (4), pp 1737–1747, DOI: 10.1021/acs.jctc.6b01243, Publication Date (Web): March 8, 2017

Link to article

Michal H. Kolář and Tomáš Kubař

"Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer"

J. Phys. Chem. B, Article ASAP, DOI: 10.1021/acs.jpcb.6b12109, Publication Date (Web): January 25, 2017

Link to article

Mario Wolter, Marcus Elstner, Ulrich Kleinekathöfer, and Tomáš Kubař

"Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details"

J. Phys. Chem. B, 2017, 121 (3), pp 529–549, DOI: 10.1021/acs.jpcb.6b11384, Publication Date (Web): January 3, 2017

Link to article


Tomáš Kubař, Marcus Elstner, Bogdan Popescu, and Ulrich Kleinekathöfer

"Polaron Effects on Charge Transport through Molecular Wires: A Multiscale Approach"

J. Chem. Theory Comput., 2017, 13 (1), pp 286–296, DOI: 10.1021/acs.jctc.6b00879, Publication Date (Web): December 1, 2016

Link to article

Matías Berdakin, Martín Taccone, Kranz J. Julian, Gustavo Pino, and Cristián G. Sánchez

"Disentangling the Photophysics of DNA-Stabilized Silver Nanocluster Emitters"

J. Phys. Chem. C, 2016, 120 (42), pp 24409–24416, DOI: 10.1021/acs.jpcc.6b05363, Publication Date (Web): September 28, 2016

Link to article

Electronic coupling

Natacha Gillet, Laura Berstis, Xiaojing Wu, Fruzsina Gajdos, Alexander Heck, Aurélien de la Lande, Jochen Blumberger and Marcus Elstner

"Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level"

J. Chem. Theory Comput., 2016, 12 (10), pp 4793–4805, DOI: 10.1021/acs.jctc.6b00564, Publication Date (Web): September 9, 2016

Link to article

Potential energy along the intrinsic reaction coordinate for the methyl-transfer reaction between trimethylsulfonium and phenolate

David Adrian Saez, Stefan Vogt-Geisse, Ricardo Inostroza-Rivera, Tomáš Kubař, Marcus Elstner, Alejandro Toro-Labbée and Esteban Vöhringer-Martinez

"The effect of the environment on the methyl transfer reaction mechanism between trimethylsulfonium and phenolate"

Phys. Chem. Chem. Phys., 2016,18, 24033-24042, DOI: 10.1039/C6CP02821G, Received 27 Apr 2016, Accepted 26 Jul 2016, First published online 27 Jul 2016

Link to article

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

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 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

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

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

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

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

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

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

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

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

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