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List of works by Marcus Elstner

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis

scientific article published on December 2006

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

scientific article published on 01 May 2018

11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore

scientific article

A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions

scientific article

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

scientific article published on 03 January 2022

Active site structure and absorption spectrum of channelrhodopsin-2 wild-type and C128T mutant

Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

scholarly article

An approximate DFT method for QM/MM simulations of biological structures and processes

scientific article published in August 2003

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

scientific article published on 09 March 2021

Anomalous conductance response of DNA wires under stretching

scientific article published on 30 August 2008

Application of the Computationally Efficient Self-Consistent-Charge Density-Functional Tight-Binding Method to Magnesium-Containing Molecules†

scientific article published in July 2007

Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water

scientific article

Atomistic simulations of complex materials: ground-state and excited-state properties

scientific article published on 8 March 2002

Automatized parametrization of SCC-DFTB repulsive potentials: application to hydrocarbons

scientific article published on 01 October 2009

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

scientific article published on 17 January 2020

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

scientific article published on 7 July 2005

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

scientific article published on 24 July 2017

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

Binding of hydroxyquinoline probes to human serum albumin: combining molecular modeling and Förster's resonance energy transfer spectroscopy to understand flexible ligand binding

scientific article

Biological relevance of charge transfer branching pathways in photolyases

scientific article published on 17 July 2019

Building a model of the blue cone pigment based on the wild type rhodopsin structure with QM/MM methods

scientific article published on 6 March 2012

Catalysis of Ground State cis[Formula: see text] trans Isomerization of Bacteriorhodopsin's Retinal Chromophore by a Hydrogen-Bond Network.

scientific article published on 8 March 2018

Charge and Exciton Transfer Simulations using Machine-Learned Hamiltonians

scientific article published on 03 June 2020

Charge carrier mobilities in organic semiconductors: crystal engineering and the importance of molecular contacts

scientific article

Charge transfer in E. coli DNA photolyase: understanding polarization and stabilization effects via QM/MM simulations

scientific article published on 4 September 2013

Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation

scientific article published on 09 February 2012

Charge transport in desolvated DNA

scientific article published on 01 September 2013

Coarse-grained time-dependent density functional simulation of charge transfer in complex systems: application to hole transfer in DNA.

scientific article published on September 2010

Color Tuning in Rhodopsins:  The Mechanism for the Spectral Shift between Bacteriorhodopsin and Sensory Rhodopsin II

scientific article

Color tuning in binding pocket models of the chlamydomonas-type channelrhodopsins

scientific article published on 28 November 2011

Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories

scientific article published on 01 June 2009

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

scientific article

Computational photochemistry of retinal proteins

scientific article published on July 2006

Computational study of synthetic agonist ligands of ionotropic glutamate receptors

scientific article

Conversion of channelrhodopsin into a light-gated chloride channel.

scientific article

Correction: Computational Study of Synthetic Agonist Ligands of Ionotropic Glutamate Receptors.

scientific article published on 17 January 2014

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

scientific article published on 01 May 2019

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

scientific article published on 01 August 2018

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

scientific article published on 29 September 2020

DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters

scientific article published on 24 August 2015

DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

scientific article

Decomposition of HMX at Extreme Conditions: A Molecular Dynamics Simulation

scientific article published in October 2002

Density functional tight binding

scientific article published on 10 February 2014

Density functional tight binding: values of semi-empirical methods in an ab initio era.

scientific article published on July 2014

Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization

scientific article published on January 2008

Determination of a Density Functional Tight Binding Model with an Extended Basis Set and Three-Body Repulsion for Carbon Under Extreme Pressures and Temperatures

scientific article published on 8 April 2013

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes

scientific article published in April 2006

Di- and Tetracyano Substituted Pyrene-Fused Pyrazaacenes -Aggregation in the Solid State

scientific article published on 27 May 2020

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

Dynamic regulation of CD24 expression and release of CD24-containing microvesicles in immature B cells in response to CD24 engagement.

scientific article published on 9 June 2015

Effect of nitrogen adsorption on the mid-infrared spectrum of water clusters

scientific article published on 13 April 2011

Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II.

scientific article published on 12 August 2008

Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins

scientific article published on 26 August 2008

Efficient Surface Hopping Approach for Modeling Charge Transport in Organic Semiconductors

scientific article published on 18 February 2022

Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA.

scientific article published on 15 March 2013

Efficient calculation of charge-transfer matrix elements for hole transfer in DNA.

scientific article published on 11 June 2008

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

scientific article published on 9 September 2016

Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations. II.

scientific article published on June 2015

Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

scientific article published on 01 March 2014

Electronic structure of overstretched DNA

scholarly article in Physical Review B, vol. 66 no. 24, December 2002

Electronic structure of solid nitromethane: Effects of high pressure and molecular vacancies

scientific article published on 8 July 2002

Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations

scientific article published in January 2001

Erratum: "Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations" [J. Chem. Phys. 140, 104105 (2014)]

scientific article published on 01 March 2015

Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation

scientific article published in August 2013

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

scientific article published on 09 October 2018

Extended polarization in third-order SCC-DFTB from chemical-potential equalization

scientific article published on 4 September 2012

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction

scientific article published on 3 October 2007

Formation of Fullerene Molecules from Carbon Nanotubes: A Quantum Chemical Molecular Dynamics Study

Fragment orbital based description of charge transfer in peptides including backbone orbitals

scientific article published on 11 April 2014

From C2Molecules to Self-Assembled Fullerenes in Quantum Chemical Molecular Dynamics

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

scientific article published on 11 December 2017

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

scientific article published on 26 March 2018

Geometry dependence of excitonic couplings and the consequences for configuration‐space sampling

scientific article published on 16 May 2021

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

article published in 2010

Host-Guest Chemistry of Truncated Tetrahedral Imine Cages with Ammonium Ions

scientific article published on 03 February 2020

Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment

article

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package

scientific article published on 24 May 2007

Improved Electronic Properties from Third-Order SCC-DFTB with Cost Efficient Post-SCF Extensions

scientific article published on 20 November 2012

Improvement of d-d interactions in density functional tight binding for transition metal ions with a ligand field model: assessment of a DFTB3+U model on nickel coordination compounds

scientific article published on 21 November 2020

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization ⬇️

scientific article published on August 2015

Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6‘-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study

scientific article published in 2003

Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study

scientific article published in April 2002

Key role of electrostatic interactions in bacteriorhodopsin proton transfer

scientific article published in November 2004

Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain

scientific article

Long-distance proton transfer with a break in the bacteriorhodopsin active site.

scientific article published on May 2009

Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States

scientific article published on 07 September 2014

Mechanism of a proton pump analyzed with computer simulations

Mechanism of primary proton transfer in bacteriorhodopsin

scientific article published in July 2004

Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.

scientific article published on 23 December 2013

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

scientific article published on 3 January 2017

Modeling charge transport in DNA using multi-scale methods

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis

scientific article published in April 2003

Molecular Dynamics Investigation of gluazo, a Photo-Switchable Ligand for the Glutamate Receptor GluK2.

scientific article published on 26 August 2015

Molecular Insights into Variable Electron Transfer in Amphibian Cryptochrome

scientific article published on 01 June 2018

Molecular origin of differences in hole and electron mobility in amorphous Alq3--a multiscale simulation study

scientific article published on 15 February 2012

Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models

scientific article

Multi-Scale Approach to Non-Adiabatic Charge Transport in High-Mobility Organic Semiconductors

scientific article published on 16 October 2015

Nonadiabatic QM/MM simulations of fast charge transfer in Escherichia coli DNA photolyase

scientific article published on 27 July 2011

On the mechanism of spontaneous thiol-disulfide exchange in proteins

scientific article published on 01 June 2018

On the structure and stretching of microhydrated DNA

scientific article published on 07 September 2011

Origin of the Solvatochromism in Organic Fluorophores with Flexible Side Chains: A Case Study of Flugi-2

scientific article published on 15 May 2019

Parameter Calibration of Transition-Metal Elements for the Spin-Polarized Self-Consistent-Charge Density-Functional Tight-Binding (DFTB) Method:  Sc, Ti, Fe, Co, and Ni.

scientific article published in July 2007

Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

scientific article published on 12 March 2014

Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems

article

Parametrization and Benchmark of DFTB3 for Organic Molecules

scientific article published on 26 November 2012

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

scientific article published on 12 December 2017

Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications

scientific article

Parametrization of the SCC-DFTB Method for Halogens

scientific article published on 12 June 2013

Peptide-lipid interactions of the stress-response peptide TisB that induces bacterial persistence

scientific article

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

scientific article published on 26 March 2020

Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules

article

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

scientific article

Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra

scientific article

QM and QM/MM Simulations of Proteins ⬇️

scientific article published on January 1, 2013

QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2

scientific article published on 06 February 2013

QM/QM approach to model energy disorder in amorphous organic semiconductors

scientific article published on 22 January 2015

Quantum Chemical Molecular Dynamics Model Study of Fullerene Formation from Open-Ended Carbon Nanotubes†

article

Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins

scientific article published on 5 October 2015

Reaction dynamics of the chimeric channelrhodopsin C1C2.

scientific article

Relation between Dephasing Time and Energy Gap Fluctuations in Biomolecular Systems

scientific article published on 7 March 2016

Relativistic Parametrization of the Self-Consistent-Charge Density-Functional Tight-Binding Method. 1. Atomic Wave Functions and Energies†

scientific article published in July 2007

Role of Arg82 in the early steps of the bacteriorhodopsin proton-pumping cycle.

scientific article

Rotamer decomposition and protein dynamics: efficiently analyzing dihedral populations from molecular dynamics.

scientific article

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

scientific article published on 13 April 2016

Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state

scientific article published on 3 May 2007

Simulation of Singlet Exciton Diffusion in Bulk Organic Materials

scientific article published in August 2016

Simulation of Temperature-Dependent Charge Transport in Organic Semiconductors with Various Degrees of Disorder

scientific article published on 08 June 2016

Size-Consistent Multipartitioning QM/MM: A Stable and Efficient Adaptive QM/MM Method.

scientific article published in October 2014

Solvent driving force ensures fast formation of a persistent and well-separated radical pair in plant cryptochrome.

scientific article published on 15 January 2015

Solvent fluctuations drive the hole transfer in DNA: a mixed quantum-classical study

scientific article published in October 2009

Solvent reorganization energy of hole transfer in DNA

scientific article published on 01 April 2009

Structural model of channelrhodopsin

scientific article published on 11 January 2012

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

scientific article published on 01 July 2010

Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements

scientific article published on 20 October 2006

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

scientific article published on 14 February 2019

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

scientific article published on 15 August 2016

The protonation state of Glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations

scientific article

The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure

scientific article

Theoretical Study of AqueousN-Acetyl-l-alanineN‘-Methylamide: Structures and Raman, VCD, and ROA Spectra

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

scientific article

Time-Dependent View of Sequential Transport through Molecules with Rapidly Fluctuating Bridges

scientific article published in Physical Review Letters

Torsional potentials and full-dimensional simulation of electronic absorption and fluorescence spectra of para-phenylene oligomers using the semiempirical self-consistent charge density-functional tight binding approach.

scientific article

Toward a reversible isolation of a C20 fullerene inside a tetraureacalix[4]arene dimer. A theoretical study

scientific article published on 01 August 2006

Towards an understanding of channelrhodopsin function: simulations lead to novel insights of the channel mechanism.

scientific article published on 30 January 2013

Triptycene End-Capped Benzothienobenzothiophene and Napthothienobenzothiophene

scientific article published on 05 May 2020

Triptycene End-Capped Quinoxalinophenanthrophenazines (QPPs): Influence of Substituents and Conditions on Aggregation in the Solid State

scientific article published on 01 August 2019

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

scientific article published on 14 February 2019

Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data

scientific article

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

article

What Accounts for the Different Function in Photolyases and Cryptochromes: A Computational Study of Critical Events in the Protein Active Site

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

scientific article published on 01 June 2019

What governs the charge transfer in DNA? The role of DNA conformation and environment

scientific article published on 27 June 2008

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