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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

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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

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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

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Chemistry Europe
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

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Marco Marazzi 2019

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

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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

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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

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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

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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

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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

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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)

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Julian Kranz 2018
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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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QM/MM Implementation

Tomáš Kubar,  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

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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

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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

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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

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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

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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

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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

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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

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Multipartitioning QM/MM

Hiroshi C. Watanabe , Tomáš Kubar  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

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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

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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

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Excited-state pathways

Tomce Runcevski, 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

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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

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Marcus Elstner and Gotthard Seifert

"Density functional tight binding"

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


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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

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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

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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

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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

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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

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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)

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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

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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

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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

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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)

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Charge Transfer in E. coli DNA Photolyase

Gesa Lüdemann, P. Benjamin Woiczikowski, Tomáš Kubar, 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

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

Tomáš Kubar, 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

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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. Kubar, S. P. Patil, H. Grubmüller, G. Groenhof, F. Gräter

"Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene"

ChemPhysChem 2013, 14 (12), 2687–2697

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

T. Kubar and M. Elstner


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


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


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


T. Kubar , 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

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Transfer of an electron hole in double-stranded DNA

T. Kubar 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

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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

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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

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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

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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

Extended Polarization in Third-Order SCC-DFTB
Extended Polarization in Third-Order SCC-DFTB

S. Kaminski, T. J. Giese, M. Gaus, D. M. York and M. Elstner

"Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization"

J. Phys. Chem. A, 2012, 116 (36), pp 9131–9141, Link to article

Free Energy Calculations
Free Energy Calculations

T. Steinbrecher, D. A. Case, A. Labahn

"Free Energy Calculations on the Binding of Novel Thiolactomycin Derivatives to E. Coli Fatty Acid Synthase I"

Bioorg. Med. Chem., 2012, 20, 3446-3453

Snake Venom Metalloproteinase BaP1
Snake Venom Metalloproteinase BaP1

T. Lingott, I. Merfort, T. Steinbrecher

"Free Energy Calculations on Snake Venom Metalloproteinase BaP1"

Chem. Biol. & Drug Des., 2012, 79, 990-1000

 Protein-Ligand Interactions
Protein-Ligand Interactions

T. Steinbrecher

"Free energy calculations in drug lead optimization in Protein-Ligand Interactions"

Methods and Principles in Medicinal Chemistry

2012, Eds. Gohlke, H., Wiley-VCH

Model of the Blue Cone Pigment
Model of the Blue Cone Pigment

J. S. Frähmcke, M. Wanko and M. Elstner

"Building a Model of the Blue Cone Pigment Based on the Wild Type Rhodopsin Structure with QM/MM Methods"

J. Phys. Chem. B, 2012, 116 (10), pp 3313–3321, Link to article

Transition from helix to ladder
CT in stretched DNA

M.Wolter, P. B. Woiczikowski, M. Elstner and T. Kubar

"Response of the electric conductivity of double-stranded DNA on moderate mechanical stretching stresses"

Phys. Rev. B, 2012, Link to article

CT in Model Peptides
CT in Model Peptides

A. Heck, P. B. Woiczikowski, T. Kubar, B. Giese, M. Elstner, and T. B. Steinbrecher

"Charge Transfer in Model Peptides: Obtaining Marcus Parameters from Molecular Simulation"

J. Phys. Chem. B, 2012, 116 (7), pp 2284–2293, Link to article

Structural model of channelrhodopsin
Structural Model of Channelrhodopsin

H. C. Watanabe, K. Welke, F. Schneider, S. Tsunoda, F. Zhang, K. Deisseroth, P. Hegemann and M. Elstner

"Structural model of channelrhodopsin"

J. Biol. Chem., 2012, Link to article

Drug binding site "Sudlow I" in human serum albumin
Drug binding site "Sudlow I" in human serum albumin

N. Al-Lawatia, T. Steinbrecher, O. K. Abou-Zied

"Water participation in molecular recognition and protein-ligand association: Probing the drug binding site "Sudlow I" in human serum albumin"

Proc. SPIE, 2012, 8233, 82331D

Path through the amorphous solid (Alq3)

A. Fuchs, T. Steinbrecher, M. S. Mommer, Y. Nagata, M. Elstner and C. Lennartz

"Molecular Origin of Differences in Hole and Electron Mobility in Amorphous Alq3 - A Multiscale Simulation Study"

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

Binding Pocket Models of Channelrhodopsin
Binding Pocket of the Channelrhodopsin

K. Welke, J. S. Frähmcke, H. C. Watanabe, P. Hegemann and M. Elstner

"Color Tuning in Binding Pocket Models of the Chlamydomonas-Type Channelrhodopsins"

J. Phys. Chem. B, 2011, Link to article

On the Structure and Stretching of Microhydrated DNA
Structure and Stretching of Microhydrated DNA

M. Wolter, M. Elstner and T. Kubar

"On the Structure and Stretching of Microhydrated DNA"


J. Phys. Chem. A, 2011 Link to article


T. Steinbrecher, I. Joung, D. A. Case

Soft-Core Potentials in Thermodynamic Integration - Comparing One- and Two-Step Transformations

J. Comp. Chem., 2011, 32, 3253–3263

Three Tryptophane resideues involved in the photoactivation in E. coli DNA photolyase
Photoactivation of DNA phtotolyase

P. B. Woiczikowski, T. Steinbrecher, T. Kubar and M. Elstner

"Nonadiabatic QM/MM Simulations of Fast Charge Transfer in Escherichia coli DNA Photolyase"

J. Phys. Chem. B, 2011, 115 (32), pp 9846–9863 Link to article

Proton Storage Site in Bacteriorhodopsin
Proton Storage Site in Bacteriorhodopsin

P. Goyal, N. Ghosh, P. Phatak, M. Clemens, M. Gaus, M. Elstner, and Q. Cui

"Proton Storage Site in Bacteriorhodopsin: New Insights from Quantum Mechanics/Molecular Mechanics Simulations of Microscopic pKa and Infrared Spectra"


J. Am. Chem. Soc., 2011, 133 (38), pp 14981–14997 Link to article

Role of London Dispersion Forces
London Dispersion Forces in Biomolecular Structure Determination

M. Kolar, T. Kubar, and Pavel Hobza 

"On the Role of London Dispersion Forces in Biomolecular Structure Determination"

J. Phys. Chem. B, 2011, 115 (24), pp 8038–8046 Link to article

Early Steps of the Bacteriorhodopsin Proton-Pumping Cycle

M. Clemens, P. Phatak, Q. Cui, A.-N. Bondar, and M. Elstner

"Role of Arg82 in the Early Steps of the Bacteriorhodopsin Proton-Pumping Cycle"

J. Phys. Chem. B. Link to article

Neutral and Protonated Water Clusters

P. Goyal, M. Elstner, and Q. Cui

"Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water"

J. Phys. Chem. B. Link to article


N. Al-Lawatia, J. Husband, T. Steinbrecher, O. K. Abou-Zied

"Tautomerism in 7-Hydroxyquinoline: A Combined Experimental and Theoretical Study in Water"

J. Phys. Chem. A, 2011, 115, 4195-4201

Effect of Nitrogen Adsorption

W. Hujo, M. Gaus, M. Schultze, T. Kubar, J. Grunenberg, M. Elstner, and S. Bauerecker

"Effect of Nitrogen Adsorption on the Mid-Infrared Spectrum of Water Clusters"

J. Phys. Chem. A. Link to article

DFTB3: γ function for hydrogen−hydrogen interaction

Michael Gaus, Qiang Cui, and Marcus Elstner

"DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)"

 J. Chem. Theory Comput.; Link to article

Configurational Entropy Change of DNA upon Intercalation
Configurational Entropy Change of DNA upon Intercalation

M. Kolár, T. Kubar and Pavel Hobza

"Sequence-Dependent Configurational Entropy Change of DNA upon Intercalation"

J. Phys. Chem. B, 114, 11446 (2010); Link to article

Protonation State of Glu181 in Rhodopsin
Protonation State of Glu181 in Rhodopsin

J. S. Frähmcke, M. Wanko, P. Phatak, M. A. Mroginski, and Marcus Elstner

"The Protonation State of Glu181 in Rhodopsin Revisited: Interpretation of Experimental Data on the Basis of QM/MM Calculations."

J. Phys. Chem. B, 114, 11338 (2010); Link to article

Time-Dependent Density Functional Simulation of Charge Transfer in DNA
Time-Dependent Density Functional Simulation of Charge Transfer in DNA

T. Kubar and M. Elstner.

"Coarse-Grained Time-Dependent Density Functional Simulation of Charge Transfer in Complex Systems: Application to Hole Transfer in DNA."

J. Phys. Chem. B, 114, 11221 (2010); Link to article

Charge Transfer in Photolyase

S. Krapf, T. Koslowski, and T. Steinbrecher.

"The thermodynamics of charge transfer in DNA photolyase - using thermodynamic integration calculations to analyze the kinetics of electron transfer reactions."

PCCP, 12, 9516 (2010); Link to article

CT in G4 - Scheme
Electrical Conductance of G-quadruplex DNA

P. B. Woiczikowski, T. Kubar, R. Gutiérrez, G. Cuniberti, and M. Elstner.

"Structural stability versus conformational sampling in biomolecular systems: Why is the charge transfer efficiency in G4-DNA better than in double-stranded DNA?"

J. Chem. Phys. 133, 035103 (2010); Link to article


S. Krapf, T. Koslowski, T. Steinbrecher

"The Thermodynamics of Charge Transfer in DNA Photolyase"

Phys. Chem. Chem. Phys., 2010, 12, 9516-9525


T. Steinbrecher, A. Labahn

"Towards Accurate Free Energy Calculations in Ligand Protein Binding Studies"

Curr. Med. Chem. (invited Review), 2010, 17, 767-785

Raman spectrum of Phenylalanine
Vibrational Raman spectrum of phenylalanine in solution, calculated with SCC-DFTB

S. Kaminski, M. Gaus, P. Phatak, D. von Stetten, M. Elstner and M. A. Mroginski.

"Vibrational Raman Spectra from the Self-Consistent Charge Density Functional Tight Binding Method via Classical Time-Correlation Functions."

J. Chem. Theory and Comp. 6, 1240 (2010); Link to article

Proton transfer steps in bacteriorhodopsin

A.-N. Bondar, J. C. Smith, and M. Elstner.

"Mechanism of a proton pump analyzed with computer simulations."

Theoretical Chemical Accounts 125, 353 (2010); Link to article

A New Synthetic Approach to Thiophene-Nickel(II)porphyrin
A New Synthetic Approach to Thiophene-Nickel(II)porphyrin

M. J. Zöllner, J. S. Frähmcke, M. Elstner, U. Jahn, P. G. Jones, E. Becker, W. Kowalsky, and H.-H. Johannes.

"A New Synthetic Approach to Thiophene-Nickel(II)porphyrin Hybrid Molecules and their Electrochemical and Computational Investigation."

Macromol. Chem. Phys., 211, 359 (2010); Link to article

Graphene on Au(111): High-Resolution Bio/ Nanodetection and Identification
Graphene on Au(111): High-Resolution Bio/ Nanodetection and Identification

B. Song, D. Li, W. Qi, M. Elstner, C. Fan, and H. Fang

"Graphene on Au(111): A Highly Conductive Material with Excellent Adsorption Properties for High-Resolution Bio/Nanodetection and Identification."

ChemPhysChem, 11, 585 (2010); Link to article