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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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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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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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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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

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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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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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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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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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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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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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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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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

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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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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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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 Flugi‑2"

J. Phys. Chem. A 2019, 123, 4581−4587

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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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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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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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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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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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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 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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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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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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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 Elghobashi‑Meinhardt, Prasad Phatak, Ana-Nicoleta Bondar, Marcus Elstner, Jeremy C. Smith

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

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

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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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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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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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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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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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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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