Ali Deniz Özdemir, Samaneh Inanlou, Franz Symalla, Weiwei Xie, Wolfgang Wenzel, and Marcus Elstner

"Dynamic Effects on HoleTransport in Amorphous Organic Semiconductors: a Combined QM/MM and kMC Study"

J. Chem.Theory Comput. 2023,19, 3849−3860

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N. J. Herrmann, N. von Coelln, R. M. Teichgreber, S. Höfener, C. Huck., F. Ghalami, S. Settele, M. Hertzog, M. Elstner, P. Tegeder, E. Herzig, J. Zaumseil

"Optical and electronic properties of different thin-film polymorphs of pdif-cn 2 controlled by zone-casting conditions"

 J. Mater. Chem. C, 2023,11, 10185-10197

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Mayukh Kansari, Lena Eichinger and Tomas Kubar

"Extended-sampling QM/MM simulation of biochemical reactions involving P–N bonds"

Phys. Chem. Chem. Phys., 2023, 10.1039.D2CP05890A, https://doi.org/10.1039/D2CP05890A

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Denis Maag, Josua Böser, Henryk A. Witek, Ben Hourahine, Marcus Elstner and Tomáš Kubař

"Mechanism of proton-coupled electron transfer described with QM/MM implementation of coupled-perturbed density-functional tight-binding"

J. Chem. Phys. 158, 124107 (2023); https://doi.org/10.1063/5.0137122

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Lisa Roß, Julius Reitemeier, Farhad Ghalami, Wen-Shan Zhang, Jürgen H. Gross, Frank Rominger, Sven M. Elbert, Rasmus Schröder, Marcus Elstner, Michael Mastalerz

"Two Dimensional Triptycene End-Capping and Its Influence on the Self-Assembly of Quinoxalinophenanthrophenazines"

Chin. J. Chem., 41, 2023: 1198—1208. https://doi.org/10.1002/cjoc.202200754

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T. Kubar, M. Elstner, and Q. Cui

"Hybrid QM/MM Methods For Studying Energy Transduction in Biomolecular Machines"

Annu. Rev. Biophys. 2023. AA: 1-27

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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

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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

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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

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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

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L. Ueberricke, F. Ghalami, W.-S. Zhang, W. Zhang, V. Rao, F. Rominger, R. Schröder, M. Elstner, M. Mastalerz

"Isostructural charge-transfer cocrystals based on triptycene end-capped quinoxalinophenanthrophenazine"

Crystal Growth & Design, vol. 21, no. 2, pp. 1329–1341, 2021

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L. Ueberricke, D. Mizioch, F. Ghalami, F. Mildner, F., T. Oeser, M. Elstner, M. Mastalerz

"Quinoxalinophenanthrophenazine based cruciforms"

European Journal of Organic Chemistry, vol. 2021, no. 34, pp. 4816–4823, 2021

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Orestis George Ziogos, Adam Kubas, Zdenek Futera, Weiwei Xie, Marcus Elstner, Jochen Blumberger

"HAB79: A new molecular dataset for benchmarking DFT and DFTB electronic couplings against high-level ab initio calculations"

J. Chem. Phys. 155, 234115 (2021), https://doi.org/10.1063/5.0076010

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Toc_final_2021 Denis Maag
Thiol–disulfide exchange reactions in the protein
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

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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

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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

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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

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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

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L. Ueberricke, J. Schwarz, F. Ghalami, M.  Matthiesen, F. Rominger, S.  Elbert, J. Zaumseil, M.  Elstner, M.  Mastalerz

"Triptycene End-Capped Benzothienobenzothiophene and Naphthothienobenzothiophene"

Chemistry–A European Journal, vol. 26, no. 55, pp. 12 596–12 605, 2020

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L. Ueberricke, I. Ciubotaru, F. Ghalami, F. Mildner, F. Rominger, M.  Elstner, M. Mastalerz

"Di-and tetracyano-substituted pyrene- fused pyrazaacenes: Aggregation in the solid state"

Chemistry-A European Journal, vol. 26, no. 50, pp. 11 634–11 642, 2020

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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

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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

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ChemistryEurope_2020 A_Masterlaz
Hole Transfer Integral
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

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Graphical_Abstract_BeaBold2020 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

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phra_NatachaG2019 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

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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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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

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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

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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

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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

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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

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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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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

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1.5027100.figures.online.f3_Natacha_Tomas 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)

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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

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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

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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

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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

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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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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

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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

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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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