Publications

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2023 publications

Grimm, Volker, Tobias Kliesch, and G. R. W. Quispel.

Discrete Gradients in Short-Range Molecular Dynamics Simulations.

arXiv, 01, 2023. https://arxiv.org/pdf/2212.14344.pdf

2022 publications

Growth of Graphene on Cu(111) Surface.
Growth of Graphene on Cu(111) Surface.

Popov, I., Bügel. P., Kozlowska, M., Fink, K., Studt, F., Sharapa, D. I.:

Analytical Model of CVD Growth of Graphene on Cu (111) Surface,

Nanomaterials 202212 (17), 2963. https://doi.org/10.3390/nano12172963

 

Roozmeh, M.; Kondov, I.

Automating and Scaling Task-Level Parallelism of Tightly Coupled Models via Code Generation.

Computational Science – ICCS 2022. Groen, D., de Mulatier, C., Paszynski, M., Krzhizhanovskaya, V. V., Dongarra, J. J., Sloot, P. M. A., Eds.; Lecture Notes in Computer Science; Springer International Publishing: Cham, 2022; Vol. 13353, pp 69–82. https://doi.org/10.1007/978-3-031-08760-8_6.

Studying low-lying excited states in cluster molecules. Dalton Transactions

Bügel, P., Krummenacher, I., Weigend, F., Eichhöfer, A.:

Experimental and theoretical evidence for low-lying excited states in [Cr6E8(PEt3)6] (E = S, Se, Te) cluster molecules

Dalton Trans. 202251, 14568–14580. https://doi.org/10.1039/D2DT01690G

The formation of the hydrocarbon pool (HCP) in the ethanol-to-olefins (ETO) process catalyzed by H-SSZ-13 is studied in a kinetic model with ab initio computed reaction barriers. Catalysis Science & Technology
Studying the formation of the hydrocarbon pool (HCP) in the ethanol-to-olefins (ETO) process catalyzed by H-SSZ-13 in a kinetic model with ab initio computed reaction barriers.

Amsler, J.,Bernart, S., Plessow, P. N., Studt, F.:

Theoretical investigation of the olefin cycle in H-SSZ-13 for the ethanol-to-olefins process using ab initio calculations and kinetic modeling

Catal. Sci. Technol.202212, 3311-3321. https://doi.org/10.1039/D1CY02289J

The self-assembly of the graphene nanoribbon molecular precursor 10,10'-dibromo-9,9'-bianthryl (DBBA) on Au(111). Phys. Chem. Chem. Phys.
Molecular self-assembly of DBBA on Au(111).

Schneider, S.; Bytyqi, K.; Kohaut, S.; Bügel, P.; Weinschenk, B.; Marz, M.; Kimouche, A.; Fink, K.; Hoffmann-Vogel, R.

Molecular self-assembly of DBBA on Au(111) at room temperature.

Phys. Chem. Chem. Phys. 2022, 28371–28380. doi:10.1039/D2CP02268K

(a) Wild-type human dithiol HsGrx1 with two cysteines in the active site and monothiol HsGrx1 in which the C-terminal cysteine has been mutated to a serine.  (b)  The co-substrate GSH in its anionic form GS. (c) The protein substrate HMA4n.
(a) Wild-type human dithiol HsGrx1 with two cysteines in the active site and monothiol HsGrx1 in which the C-terminal cysteine has been mutated to a serine. (b) The co-substrate GSH in its anionic form GS. (c) The protein substrate HMA4n.

Böser, Julian; Kubař, Tomáš; Elstner, Marcus; Maag, Denis.

Reduction Pathway of Glutaredoxin 1 Investigated with QM/MM Molecular Dynamics Using a Neural Network Correction.

J. Chem. Phys. 2022, 157(15): 154104. https://doi.org/10.1063/5.0123089.

Representation of MOF materials of PCU topology. Front. Mater.
Representation of MOF materials of PCU topology.

Mostaghimi, Mersad; Rêgo, Celso R. C.; Haldar, Ritesh; Wöll, Christof; Wenzel, Wolfgang; Kozlowska, Mariana.

Automated Virtual Design of Organic Semiconductors Based on Metal-Organic Frameworks.

Front. Mater. 2022, 9. https://doi.org/10.3389/fmats.2022.840644

 

Graphical abstract of corresponding publication J. Colloid Interface Sci.

Suyetin, Mikhail; Bag, Saientan; Anand, Priya; Borkowska-Panek, Monika; Gußmann, Florian; Brieg, Martin; Fink, Karin; Wenzel, Wolfgang.

Modelling Peptide Adsorption Energies on Gold Surfaces with an Effective Implicit Solvent and Surface Model.

J. Colloid Interface Sci. 2022, 605, 493–99. https://doi.org/10.1016/j.jcis.2021.07.090.

Graphical abstract of corresponding publication. Org. Electron.
Steps in simulating the growth of organic thin film morphologies.

Degitz, C.; Konrad, M.; Kaiser, S.; Wenzel, W.

Simulating the Growth of Amorphous Organic Thin Films.

Org. Electron. 2022, 102, 106439. https://doi.org/10.1016/j.orgel.2022.106439.

Scale separation in a lubrication gap for multiscale simulations: macro problem (a), micro problem (b), and slip boundary conditions (c). Tribol. Lett.
Scale separation in a lubrication gap for multiscale simulations: macro problem (a), micro problem (b), and slip boundary conditions (c).

Holey, H.; Codrignani, A.; Gumbsch, P.; Pastewka, L.

Height-Averaged Navier–Stokes Solver for Hydrodynamic Lubrication.

Tribol. Lett. 2022, 70 (2), 36. https://doi.org/10.1007/s11249-022-01576-5.

Experimental measured mobilities versus FSSH-BC-IR mobilities obtained using input reorganization energies computed by (a) ωB97XD and (b) B3LYP, respectively. JCTC
Experimental measured mobilities versus FSSH-BC-IR mobilities obtained using input reorganization energies computed by (a) ωB97XD and (b) B3LYP, respectively.

Roosta, S.; Galami, F.; Elstner, M.; Xie, W.

Efficient Surface Hopping Approach for Modeling Charge Transport in Organic Semiconductors.

J. Chem. Theory Comput. 2022, acs.jctc.1c00944. https://doi.org/10.1021/acs.jctc.1c00944.

Two figures with a) Absorption spectra. b) Distribution of dihedral angles. PCCP
a) Absorption spectra. b) Distribution of dihedral angles.

Inanlou, S.; Cortés-Mejía, R.; Özdemir, A. D.; Höfener, S.; Klopper, W.; Wenzel, W.; Xie, W.; Elstner, M.

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, 10.1039.D1CP04293A. https://doi.org/10.1039/D1CP04293A.

Flattening of the energy-levels in the doped injection layer caused by doping activation. Front. Chem.
Flattening of the energy-levels in the doped injection layer caused by doping activation.

Özdemir, A. D.; Kaiser, S.; Neumann, T.; Symalla, F.; Wenzel, W.

Systematic kMC Study of Doped Hole Injection Layers in Organic Electronics.

Front. Chem. 2022, 9. https://doi.org/10.3389/fchem.2021.809415.

Thiol–disulfide exchange between a methylthiolate and a dimethyldisulfide with a transition state. JCTC
Thiol–disulfide exchange between a methylthiolate and a dimethyldisulfide. The trisulfide state is the global minimum in the gas phase and the transition state in aqueous solution.

Gómez-Flores, C. L.; Maag, D.; Kansari, M.; Vuong, V.-Q.; Irle, S.; Gräter, F.; Kubař, T.; Elstner, M.

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

J. Chem. Theory Comput. 2022, acs.jctc.1c00811. https://doi.org/10.1021/acs.jctc.1c00811.

2021 publications

Iron hydride nanoclusters Chemistry Open
Iron hydride nanocluster growth.

Chakraborty, U.; Bügel, P.; Fritsch, L.; Weigend, F.; Bauer, M.; Jacobi von Wangelin, A.

Planar Iron Hydride Nanoclusters: Combined Spectroscopic and Theoretical Insights into Structures and Building Principles.

 Chemistry Open 202110, 265–271. DOI doi:10.1002/open.202000307

Design strategies for receptors and synthetic binders for neurotransmitters. Adv. Mater.
Design strategies for receptors and synthetic binders for neurotransmitters.

Grimm, Laura M.; Sinn, Stephan; Krstić, Marjan; D’Este, Elisa; Sonntag, Ivo; Prasetyanto, Eko Adi; Kuner, Thomas; Wenzel, Wolfgang; De Cola, Luisa; Biedermann, Frank.

Fluorescent Nanozeolite Receptors for the Highly Selective and Sensitive Detection of Neurotransmitters in Water and Biofluids.

Advanced Materials 2021, 33, 49: 2104614. https://doi.org/10.1002/adma.202104614.

Basher, Abdulrahman H.; Krstić, Marjan; Fink, Karin; Ito, Tomoko; Karahashi, Kazuhiro;
Wenzel, Wolfgang; Hamaguchi, Satoshi.
 
Erratum: ‘Formation and Desorption of Nickel Hexafluoroacetylacetonate
Ni(Hfac)2 on a Nickel Oxide Surface in Atomic Layer Etching Processes’ [J.
Vac. Sci. Technol. A 38, 052602 (2020)].

 
J. Vac. Sci. Technol. A 2021, 39, 5: 057001. https://doi.org/10.1116/6.0001319.

Systematic steps to generate flexible, application-specific highly accurate force fields by training artificial neural networks. J. Chem. Theory Comput.
Systematic steps to generate flexible, application-specific highly accurate force fields by training artificial neural networks.

Bag, Saientan; Konrad, Manuel; Schlöder, Tobias; Friederich, Pascal; Wenzel, Wolfgang.

Fast Generation of Machine Learning-Based Force Fields for Adsorption Energies.

J. Chem. Theory Comput. 2021, 17, 11: 7195-7202. https://doi.org/10.1021/acs.jctc.1c00506.

Shape-based coarse-grained model of proteins, shown for lysozyme represented by 5 CG beads per a protein unit (a) and continuum model of ion–protein dispersion interactions (b) Phys. Chem. Chem. Phys.
Shape-based coarse-grained model of proteins, shown for lysozyme represented by 5 CG beads per a protein unit (a) and continuum model of ion–protein dispersion interactions (b).

Pusara, Srdjan; Yamin, Peyman; Wenzel, Wolfgang; Krstić, Marjan; Kozlowska, Mariana.

 

A Coarse-Grained xDLVO Model for Colloidal Protein–Protein Interactions.

 

Phys. Chem. Chem. Phys. 2021, 23: 12780–94. https://doi.org/10.1039/D1CP01573G.

Tight-binding scheme for the graphene self-energy calculation and the CNT-decoration. Commun. Phys.
Tight-binding scheme for the graphene self-energy calculation and the CNT-decoration.

Özdemir, A. D.; Barua, P.; Pyatkov, F.; Hennrich, F.; Chen, Y.; Wenzel, W.; Krupke, R.; Fediai, A.

Contact Spacing Controls the On-Current for All-Carbon Field Effect Transistors.

Commun. Phys. 20214 (1), 246. https://doi.org/10.1038/s42005-021-00747-5.

Electrostatic interaction in protein. PCCP
Electrostatic interactions in a protein.

Maag, D.; Putzu, M.; Gómez-Flores, C. L.; Gräter, F.; Elstner, M.; Kubař, T.

Electrostatic Interactions Contribute to the Control of Intramolecular Thiol–Disulfide Isomerization in a Protein.

Phys. Chem. Chem. Phys. 2021, 10.1039.D1CP03129E. https://doi.org/10.1039/D1CP03129E.

Three-dimensional structure of the bR state and the photocycle at pH ≥ 6. PNAS
Three-dimensional structure of the bR state and the photocycle at pH ≥ 6.

Maag, D.; Mast, T.; Elstner, M.; Cui, Q.; Kubař, T.

O to BR Transition in Bacteriorhodopsin Occurs through a Proton Hole Mechanism.

Proc. Natl. Acad. Sci. USA 2021, 118 (39). https://doi.org/10.1073/pnas.2024803118.

Interplay of Density Functional Theory and Machine Learning to analyze Charge Transport in Organic Semiconductors. J. Chem. Theory Comput.
Interplay of Density Functional Theory and Machine Learning to analyze Charge Transport in Organic Semiconductors.

Reiser, P.; Konrad, M.; Fediai, A.; Léon, S.; Wenzel, W.; Friederich, P.

Analyzing Dynamical Disorder for Charge Transport in Organic Semiconductors via Machine Learning.

J. Chem. Theory Comput. 2021, 17 (6), 3750–3759. https://doi.org/10.1021/acs.jctc.1c00191.

The component-separable noncovalent interaction network (CONI-Net) uses an alternative to the symmetry function descriptor designed for efficient large-scale simulations. J. Chem. Theory Comput.
The component-separable noncovalent interaction network (CONI-Net) uses an alternative to the symmetry function descriptor designed for efficient large-scale simulations.

Konrad, M.; Wenzel, W.

CONI-Net: Machine Learning of Separable Intermolecular Force Fields.

J. Chem. Theory Comput. 2021, acs.jctc.1c00328. https://doi.org/10.1021/acs.jctc.1c00328.

Combination of 'Winged termites swarming' by T. R. Shankar Raman and some protein structures. Marie Weiel-Potyagaylo and T. R. Shankar Raman (CC BY-SA 4.0)
Illustration of dynamic particle swarm optimization of biomolecular simulation parameters.

Weiel, M.; Götz, M.; Klein, A.; Coquelin, D.; Floca, R.; Schug, A.

Dynamic particle swarm optimization of biomolecular simulation parameters with flexible objective functions.

Nat. Mach. Intell. 2021. https://doi.org/10.1038/s42256-021-00366-3.

Structure and interactions at the Mavirus capsomer's base. J. Mol. Biol.
Structure and interactions at the Mavirus capsomer's base.

Christiansen, A.; Weiel, M.; Winkler, A.; Schug, A.; Reinstein, J.

The Trimeric Major Capsid Protein of Mavirus Is Stabilized by Its Interlocked N-Termini Enabling Core Flexibility for Capsid Assembly.

J. Mol. Biol. 2021, 166859. https://doi.org/10.1016/j.jmb.2021.166859.

Thermodynamic integration from harmonic approximation to fully interacting system yields anharmonic correction to adsorption free energy. JCTC
Thermodynamic integration from the harmonic approximation to the fully interacting system yields anharmonic correction.

Amsler, J.; Plessow, P. N.; Studt, F.; Bučko, T.

Anharmonic Correction to Adsorption Free Energy from DFT-Based MD Using Thermodynamic Integration.

J. Chem. Theory Comput. 2021,17 (2), 1155–1169. https://doi.org/10.1021/acs.jctc.0c01022.

Boltzmann-average weighted CBP absorption spectra (FWHM 0.1 eV) with varying temperatures 0, 100, 200, 300, 400 and 500 K. Mol. Phys.
Boltzmann-average weighted CBP absorption spectra (FWHM 0.1 eV) with varying temperatures.

Cortés-Mejía, R.; Höfener, S.; Klopper, W.

Effects of Rotational Conformation on Electronic Properties of 4,4′-Bis(Carbazol-9-Yl)Biphenyl (CBP): The Single-Molecule Picture and Beyond.

Mol. Phys. 2021, e1876936. https://doi.org/10.1080/00268976.2021.1876936.

Effect of Impurities on the Initiation of the Methanol-to-Olefins Process: Kinetic Modeling Based on Ab Initio Rate Constants. Catal. Lett.
Entry points of organic impurities into the Methanol-to-Olefins initiation pathway.

Amsler, J.; Plessow, P. N.; Studt, F.

Effect of Impurities on the Initiation of the Methanol-to-Olefins Process: Kinetic Modeling Based on Ab Initio Rate Constants.

Catal. Lett. 2021. https://doi.org/10.1007/s10562-020-03492-6.

2020 publications

Workflow description, wfGenes process stages and subsequent WMS specific validation. IEEE
Workflow description, wfGenes process stages and subsequent WMS specific validation.

Roozmeh, M.; Kondov, I.

Workflow Generation with WfGenes.

IEEE/ACM workflows in support of large-scale science (WORKS). IEEE, 2020; pp 9–16. https://doi.org/10.1109/WORKS51914.2020.00007.

 

Examination of the potential of oxide-supported rhodium single atom catalysts (SACs) for heterogeneous hydroformylation J. Am. Chem. Soc.
Examination of potential of oxide-supported rhodium single atom catalysts (SACs) for heterogeneous hydroformylation.

Amsler J., Sarma, B. B., Agostini, G., Prieto, G., Plessow, P. N., & Studt, F.:

Prospects of heterogeneous hydroformylation with supported single atom catalysts

J. Am. Chem. Soc., 2020,142 (11), 5087-5096. https://doi.org/10.1021/jacs.9b12171

 

Symalla, Franz; Heidrich, Shahriar; Friederich, Pascal; Strunk, Timo; Neumann, Tobias; Minami, Daiki; Jeong, Daun; Wenzel, Wolfgang.

Multiscale Simulation of Photoluminescence Quenching in Phosphorescent OLED Materials.

Adv. Theory Simul. 2020, 3, 4: 1900222. https://doi.org/10.1002/adts.201900222.

Optimized structure of an hfacH molecule placed near a metallic Ni model surface; (a) front view and (b) side view J. Vac. Sci. Technol.
Optimized structure of an hfacH molecule placed near a metallic Ni model surface; (a) front view and (b) side view.

Basher, Abdulrahman H.; Krstić, Marjan; Takeuchi, Takae; Isobe, Michiro; Ito, Tomoko; Kiuchi, Masato; Karahashi, Kazuhiro; Wenzel, Wolfgang; Hamaguchi, Satoshi.

Stability of Hexafluoroacetylacetone Molecules on Metallic and Oxidized Nickel Surfaces in Atomic-Layer-Etching Processes.

J. Vac. Sci. Technol. A 2020, 38, 2: 022610. https://doi.org/10.1116/1.5127532.

Tertiary structure of VHP. PLoS ONE
Tertiary structure observed in VHP REMD simulation.

Voronin, A.; Weiel, M.; Schug, A.

Including Residual Contact Information into Replica-Exchange MD Simulations Significantly Enriches Native-like Conformations.

PLoS ONE 202015 (11), e0242072. https://doi.org/10.1371/journal.pone.0242072.

Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations of Bond Scissions in Proteins. J. Chem. Theory Comput.
Hybrid kinetic Monte Carlo/Molecular Dynamics simulations of bond scissions in proteins.

Rennekamp, B.; Kutzki, F.; Obarska-Kosinska, A.; Zapp, C.; Gräter, F.

Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations of Bond Scissions in Proteins.

J. Chem. Theory Comput. 202016 (1), 553–563. https://doi.org/10.1021/acs.jctc.9b00786.

Tenth type III domain of fibronectin with Alexa Fluor dyes attached. Isr. J. Chem.
Tenth type III domain of fibronectin with Alexa Fluor dyes attached.

Reinartz, I.; Weiel, M.; Schug, A.

FRET Dyes Significantly Affect SAXS Intensities of Proteins.

Isr. J. Chem. 202060 (7), 725–734. https://doi.org/10.1002/ijch.202000007.

Charge and Exciton Transfer Simulations Using Machine-Learned Hamiltonians. J. Chem. Theory Comput.
Charge and Exciton transfer simulations using Machine-Learned Hamiltonians.

Krämer, M.; Dohmen, P. M.; Xie, W.; Holub, D.; Christensen, A. S.; Elstner, M.

Charge and Exciton Transfer Simulations Using Machine-Learned Hamiltonians.

J. Chem. Theory Comput. 202016 (7), 4061–4070. https://doi.org/10.1021/acs.jctc.0c00246.

One‐Pot Cooperation of Single‐Atom Rh and Ru Solid Catalysts for a Selective Tandem Olefin Isomerization‐Hydrosilylation Process. Angew. Chem. Int. Ed.
One‐Pot cooperation of Single-Atom Rh and Ru solid catalysts for selective Tandem Olefin Isomerization‐Hydrosilylation.

Sarma, B. B.; Kim, J.; Amsler, J.; Agostini, G.; Weidenthaler, C.; Pfänder, N.; Arenal, R.; Concepción, P.; Plessow, P.; Studt, F.; Prieto, G.

One‐Pot Cooperation of Single‐Atom Rh and Ru Solid Catalysts for a Selective Tandem Olefin Isomerization‐Hydrosilylation Process.

Angew. Chem. Int. Ed. 202059 (14), 5806–5815. https://doi.org/10.1002/anie.201915255.

Prospects of Heterogeneous Hydroformylation with Supported Single Atom Catalysts. J. Am. Chem. Soc.
Activity and stability of Single Atom Catalysts investigated with hierarchical computational approach and experiments.

Amsler, J.; Sarma, B. B.; Agostini, G.; Prieto, G.; Plessow, P. N.; Studt, F.

Prospects of Heterogeneous Hydroformylation with Supported Single Atom Catalysts.

J. Am. Chem. Soc. 2020142 (11), 5087–5096. https://doi.org/10.1021/jacs.9b12171.

2019 publications

Bias potential versus target RMSD for elongated-to-bent transition. PLoS Comput. Biol.
Bias potential versus target RMSD for elongated-to-bent transition.

Weiel, M.; Reinartz, I.; Schug, A.

Rapid Interpretation of Small-Angle X-Ray Scattering Data.

PLoS Comput. Biol. 201915 (3), e1006900. https://doi.org/10.1371/journal.pcbi.1006900.