Welcome to the Theoretical Chemical Biology Group

Schloss KA

Bachelor and Master Thesis

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

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Recent Publications


Monja Sokolov, David S. Hoffmann, Philipp M. Dohmen, Mila Krämer, Sebastian Höfener, Ulrich Kleinekathöfer and Marcus Elstner

"Non-adiabatic molecular dynamics simulations provide new insights into the exciton transfer in the Fenna–Matthews–Olson complex"

Phys. Chem. Chem. Phys., 2024, 26, 19469

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Till Johann, Weiwei Xie, Sara Roosta, Marcus Elstner and  Martijn Kemerink

"Theory for nonlinear conductivity switching in semiconducting organic ferroelectrics"

Phys. Chem. Chem. Phys.,First published on 25 June 2024, DOI: 10.1039/d4cp01632g

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Xiaodi Hu, David S. Hoffmann, Mai Wang, Lars Schuhmacher, Maria C. Stroe , Birgit Schreckenberger, Marcus Elstner & Reinhard Fischer

"GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting"

Nat Microbiol (2024); doi.org/10.1038/s41564-024-01731-9, published online 14 June 2024

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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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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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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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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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