@unpublished{64071, abstract = {{Stimulated by the renewed interest and recent developments in semi-empirical quantum chemical (SQC) methods for noncovalent interactions, we examine the properties of liquid water at ambient conditions by means of molecular dynamics (MD) simulations, both with the conventional NDDO-type (neglect of diatomic differential overlap) methods, e.g. AM1 and PM6, and with DFTB-type (density-functional tight-binding) methods, e.g. DFTB2 and GFN-xTB. Besides the original parameter sets, some specifically reparametrized SQC methods (denoted as AM1-W, PM6-fm, and DFTB2-iBi) targeting various smaller water systems ranging from molecular clusters to bulk are considered as well. The quality of these different SQC methods for describing liquid water properties at ambient conditions are assessed by comparison to well-established experimental data and also to BLYP-D3 density functional theory-based ab initio MD simulations. Our analyses reveal that static and dynamics properties of bulk water are poorly described by all considered SQC methods with the original parameters, regardless of the underlying theoretical models, with most of the methods suffering from too weak hydrogen bonds and hence predicting a far too fluid water with highly distorted hydrogen bond kinetics. On the other hand, the reparametrized force-matchcd PM6-fm method is shown to be able to quantitatively reproduce the static and dynamic features of liquid water, and thus can be used as a computationally efficient alternative to electronic structure-based MD simulations for liquid water that requires extended length and time scales. DFTB2-iBi predicts a slightly overstructured water with reduced fluidity, whereas AM1-W gives an amorphous ice-like structure for water at ambient conditions.}}, author = {{Wu, Xin and Elgabarty, Hossam and Alizadeh, Vahideh and Henao Aristizabal, Andres and Zysk, Frederik and Plessl, Christian and Ehlert, Sebastian and Hutter, Jürg and Kühne, Thomas D.}}, title = {{{Benchmarking semi-empirical quantum chemical methods on liquid water}}}, year = {{2025}}, } @article{56080, abstract = {{CPO‐27 is a metal‐organic framework (MOF) with coordinatively unsaturated metal centers (open metal sites). It is therefore an ideal host material for small guest molecules, including water. This opens up numerous possible applications, such as proton conduction, humidity sensing, water harvesting, or adsorption‐driven heat pumps. For all of these applications, profound knowledge of the adsorption and desorption of water in the micropores is mandatory. The hydration and water structure in CPO‐27‐M (M = Zn or Cu) is investigated using water vapor sorption, Fourier transform infrared (FTIR) spectroscopy, density functional theory (DFT) calculations, and molecular dynamics simulation. In the pores of CPO‐27‐Zn, water binds as a ligand to the Zn center. Additional water molecules are stepwise incorporated at defined positions, forming a network of H‐bonds with the framework and with each other. In CPO‐27‐Cu, hydration proceeds by an entirely different mechanism. Here, water does not coordinate to the metal center, but only forms H‐bonds with the framework; pore filling occurs mostly in a single step, with the open metal site remaining unoccupied. Water in the pores forms clusters with extensive intra‐cluster H‐bonding.}}, author = {{Kloß, Marvin and Beerbaum, Michael and Baier, Dominik and Weinberger, Christian and Zysk, Frederik and Elgabarty, Hossam and Kühne, Thomas D. and Tiemann, Michael}}, issn = {{2196-7350}}, journal = {{Advanced Materials Interfaces}}, number = {{35}}, pages = {{2400476}}, publisher = {{Wiley}}, title = {{{Understanding Hydration in CPO‐27 Metal‐Organic Frameworks: Strong Impact of the Chemical Nature of the Metal (Cu, Zn)}}}, doi = {{10.1002/admi.202400476}}, volume = {{11}}, year = {{2024}}, } @article{56075, abstract = {{An isostructural series of FeII, FeIII, and Fe(IV)complexes [Fe(ImP)2]0/+/2+ utilizing the ImP 1,1′-(1,3-phenylene)-bis(3-methyl-1-imidazol-2-ylidene) ligand, combining N-heterocy-clic carbenes and cyclometalating functions, is presented. The strong donor motif stabilizes the high-valent Fe(IV) oxidation state yet keeps the FeII oxidation state accessible from the parent Fe(III)compound. Chemical oxidation of [Fe(ImP)2]+ yields stable [FeIV(ImP)2]2+. In contrast, [FeII(ImP)2]0, obtained by reduction,is highly sensitive toward oxygen. Exhaustive ground state characterization by single-crystal X-ray diffraction, 1H NMR,Mössbauer spectroscopy, temperature-dependent magnetic measurements, a combination of X-ray absorption near edge structureand valence-to-core, as well as core-to-core X-ray emission spectroscopy, complemented by detailed density functional theory (DFT) analysis, reveals that the three complexes[Fe(ImP)2]0/+/2+ can be unequivocally attributed to low-spin d6, d5, and d4 complexes. The excited state landscape of the Fe(II) and Fe(IV) complexes is characterized by short-lived 3MLCT and 3LMCT states, with lifetimes of 5.1 and 1.4 ps, respectively. In the FeII-compound, an energetically low-lying MC state leads to fast deactivation of the MLCT state. The distorted square-pyramidal state, where one carbene is dissociated, can not only relax into the ground state, but also into a singlet dissociated state. Its formation was investigated with time-dependent optical spectroscopy, while insights into its structure were gained by NMR spectroscopy.}}, author = {{Steube, Jakob and Fritsch, Lorena and Kruse, Ayla and Bokareva, Olga S. and Demeshko, Serhiy and Elgabarty, Hossam and Schoch, Roland and Alaraby, Mohammad and Egold, Hans and Bracht, Bastian Johannes and Schmitz, Lennart and Hohloch, Stephan and Kühne, Thomas D. and Meyer, Franc and Kühn, Oliver and Lochbrunner, Stefan and Bauer, Matthias}}, issn = {{0020-1669}}, journal = {{Inorganic Chemistry}}, keywords = {{Photo}}, publisher = {{American Chemical Society (ACS)}}, title = {{{Isostructural Series of a Cyclometalated Iron Complex in Three Oxidation States}}}, doi = {{10.1021/acs.inorgchem.4c02576}}, year = {{2024}}, } @article{56074, abstract = {{Effective photoinduced charge transfer makes molecular bimetallic assemblies attractive for applications as active light‐induced proton reduction systems. Developing competitive base metal dyads is mandatory for a more sustainable future. However, the electron transfer mechanisms from the photosensitizer to the proton reduction catalyst in base metal dyads remain so far unexplored. A Fe─Co dyad that exhibits photocatalytic H2 production activity is studied using femtosecond X‐ray emission spectroscopy, complemented by ultrafast optical spectroscopy and theoretical time‐dependent DFT calculations, to understand the electronic and structural dynamics after photoexcitation and during the subsequent charge transfer process from the Fe(II) photosensitizer to the cobaloxime catalyst. This novel approach enables the simultaneous measurement of the transient X‐ray emission at the iron and cobalt K‐edges in a two‐color experiment. With this methodology, the excited state dynamics are correlated to the electron transfer processes, and evidence of the Fe→Co electron transfer as an initial step of proton reduction activity is unraveled.}}, author = {{Nowakowski, Michał and Huber‐Gedert, Marina and Elgabarty, Hossam and Kalinko, Aleksandr and Kubicki, Jacek and Kertmen, Ahmet and Lindner, Natalia and Khakhulin, Dmitry and Lima, Frederico A. and Choi, Tae‐Kyu and Biednov, Mykola and Schmitz, Lennart and Piergies, Natalia and Zalden, Peter and Kubicek, Katerina and Rodriguez‐Fernandez, Angel and Salem, Mohammad Alaraby and Canton, Sophie E. and Bressler, Christian and Kühne, Thomas D. and Gawelda, Wojciech and Bauer, Matthias}}, issn = {{2198-3844}}, journal = {{Advanced Science}}, keywords = {{Photo, Xray}}, publisher = {{Wiley}}, title = {{{Ultrafast Two‐Color X‐Ray Emission Spectroscopy Reveals Excited State Landscape in a Base Metal Dyad}}}, doi = {{10.1002/advs.202404348}}, year = {{2024}}, } @article{45361, abstract = {{ The non-orthogonal local submatrix method applied to electronic structure–based molecular dynamics simulations is shown to exceed 1.1 EFLOP/s in FP16/FP32-mixed floating-point arithmetic when using 4400 NVIDIA A100 GPUs of the Perlmutter system. This is enabled by a modification of the original method that pushes the sustained fraction of the peak performance to about 80%. Example calculations are performed for SARS-CoV-2 spike proteins with up to 83 million atoms. }}, author = {{Schade, Robert and Kenter, Tobias and Elgabarty, Hossam and Lass, Michael and Kühne, Thomas and Plessl, Christian}}, issn = {{1094-3420}}, journal = {{The International Journal of High Performance Computing Applications}}, keywords = {{Hardware and Architecture, Theoretical Computer Science, Software}}, publisher = {{SAGE Publications}}, title = {{{Breaking the exascale barrier for the electronic structure problem in ab-initio molecular dynamics}}}, doi = {{10.1177/10943420231177631}}, year = {{2023}}, } @unpublished{40982, abstract = {{Effective photoinduced charge transfer makes molecular bimetallic assemblies attractive for applications as active light induced proton reduction systems. For a more sustainable future, development of competitive base metal dyads is mandatory. However, the electron transfer mechanisms from the photosensitizer to the proton reduction catalyst in base metal dyads remain so far unexplored. We study a Fe-Co dyad that exhibits photocatalytic H2 production activity using femtosecond X-ray emission spectroscopy, complemented by ultrafast optical spectroscopy and theoretical time-dependent DFT calculations, to understand the electronic and structural dynamics after photoexcitation and during the subsequent charge transfer process from the FeII photosensitizer to the cobaloxime catalyst. Using this novel approach, the simultaneous measurement of the transient Kalpha X-ray emission at the iron and cobalt K-edges in a two-colour experiment is enabled making it possible to correlate the excited state dynamics to the electron transfer processes. The methodology, therefore, provides a clear and direct spectroscopic evidence of the Fe->Co electron transfer responsible for the proton reduction activity.}}, author = {{Nowakowski, Michał and Huber-Gedert, Marina and Elgabarty, Hossam and Kubicki, Jacek and Kertem, Ahmet and Lindner, Natalia and Khakhulin, Dimitry and Lima, Frederico Alves and Choi, Tae-Kyu and Biednov, Mykola and Piergies, Natalia and Zalden, Peter and Kubicek, Katerina and Rodriguez-Fernandez, Angel and Salem, Mohammad Alaraby and Kühne, Thomas and Gawelda, Wojciech and Bauer, Matthias}}, booktitle = {{arxiv}}, title = {{{Ultrafast two-colour X-ray emission spectroscopy reveals excited state landscape in a base metal dyad}}}, year = {{2023}}, } @article{34300, abstract = {{AbstractThe solvation of ions changes the physical, chemical and thermodynamic properties of water, and the microscopic origin of this behaviour is believed to be ion-induced perturbation of water’s hydrogen-bonding network. Here we provide microscopic insights into this process by monitoring the dissipation of energy in salt solutions using time-resolved terahertz–Raman spectroscopy. We resonantly drive the low-frequency rotational dynamics of water molecules using intense terahertz pulses and probe the Raman response of their intermolecular translational motions. We find that the intermolecular rotational-to-translational energy transfer is enhanced by highly charged cations and is drastically reduced by highly charged anions, scaling with the ion surface charge density and ion concentration. Our molecular dynamics simulations reveal that the water–water hydrogen-bond strength between the first and second solvation shells of cations increases, while it decreases around anions. The opposite effects of cations and anions on the intermolecular interactions of water resemble the effects of ions on the stabilization and denaturation of proteins.}}, author = {{Balos, Vasileios and Kaliannan, Naveen Kumar and Elgabarty, Hossam and Wolf, Martin and Kühne, Thomas and Sajadi, Mohsen}}, issn = {{1755-4330}}, journal = {{Nature Chemistry}}, keywords = {{General Chemical Engineering, General Chemistry}}, number = {{9}}, pages = {{1031--1037}}, publisher = {{Springer Science and Business Media LLC}}, title = {{{Time-resolved terahertz–Raman spectroscopy reveals that cations and anions distinctly modify intermolecular interactions of water}}}, doi = {{10.1038/s41557-022-00977-2}}, volume = {{14}}, year = {{2022}}, } @article{33684, author = {{Schade, Robert and Kenter, Tobias and Elgabarty, Hossam and Lass, Michael and Schütt, Ole and Lazzaro, Alfio and Pabst, Hans and Mohr, Stephan and Hutter, Jürg and Kühne, Thomas and Plessl, Christian}}, issn = {{0167-8191}}, journal = {{Parallel Computing}}, keywords = {{Artificial Intelligence, Computer Graphics and Computer-Aided Design, Computer Networks and Communications, Hardware and Architecture, Theoretical Computer Science, Software}}, publisher = {{Elsevier BV}}, title = {{{Towards electronic structure-based ab-initio molecular dynamics simulations with hundreds of millions of atoms}}}, doi = {{10.1016/j.parco.2022.102920}}, volume = {{111}}, year = {{2022}}, } @article{33653, author = {{Gurinov, Andrei and Sieland, Benedikt and Kuzhelev, Andrey and Elgabarty, Hossam and Kühne, Thomas and Prisner, Thomas and Paradies, Jan and Baldus, Marc and Ivanov, Konstantin L. and Pylaeva, Svetlana}}, issn = {{1433-7851}}, journal = {{Angewandte Chemie International Edition}}, keywords = {{General Chemistry, Catalysis}}, number = {{28}}, pages = {{15371--15375}}, publisher = {{Wiley}}, title = {{{Mixed‐Valence Compounds as Polarizing Agents for Overhauser Dynamic Nuclear Polarization in Solids}}}, doi = {{10.1002/anie.202103215}}, volume = {{60}}, year = {{2021}}, } @article{33644, author = {{Pylaeva, Svetlana and Marx, Patrick and Singh, Gurjot and Kühne, Thomas and Roemelt, Michael and Elgabarty, Hossam}}, issn = {{1089-5639}}, journal = {{The Journal of Physical Chemistry A}}, keywords = {{Physical and Theoretical Chemistry}}, number = {{3}}, pages = {{867--874}}, publisher = {{American Chemical Society (ACS)}}, title = {{{Organic Mixed-Valence Compounds and the Overhauser Effect in Insulating Solids}}}, doi = {{10.1021/acs.jpca.0c11296}}, volume = {{125}}, year = {{2021}}, } @inproceedings{33654, author = {{Balos, Vasileios and Elgabarty, Hossam and Wolf, Martin and Kühne, Thomas and Netz, Roland and Bonthuis, Douwe Jan and Kaliannan, Naveen and Loche, Philip and Kampfrath, Tobias and Sajadi, Mohsen}}, booktitle = {{Terahertz Emitters, Receivers, and Applications XII}}, editor = {{Razeghi, Manijeh and Baranov, Alexei N.}}, publisher = {{SPIE}}, title = {{{Ultrafast solvent-to-solvent and solvent-to-solute energy transfer driven by single-cycle THz electric fields}}}, doi = {{10.1117/12.2594143}}, year = {{2021}}, } @article{34302, abstract = {{Energy flow in the hydrogen bonding network of water is traced by resonant terahertz excitation and off-resonant optical probing.}}, author = {{Elgabarty, Hossam and Kampfrath, Tobias and Bonthuis, Douwe Jan and Balos, Vasileios and Kaliannan, Naveen Kumar and Loche, Philip and Netz, Roland R. and Wolf, Martin and Kühne, Thomas and Sajadi, Mohsen}}, issn = {{2375-2548}}, journal = {{Science Advances}}, keywords = {{Multidisciplinary}}, number = {{17}}, publisher = {{American Association for the Advancement of Science (AAAS)}}, title = {{{Energy transfer within the hydrogen bonding network of water following resonant terahertz excitation}}}, doi = {{10.1126/sciadv.aay7074}}, volume = {{6}}, year = {{2020}}, } @article{34301, abstract = {{

Ab initio molecular dynamics simulations of ambient liquid water and energy decomposition analysis have recently shown that water molecules exhibit significant asymmetry between the strengths of the two donor and/or the two acceptor interactions.

}}, author = {{Elgabarty, Hossam and Kühne, Thomas}}, issn = {{1463-9076}}, journal = {{Physical Chemistry Chemical Physics}}, keywords = {{Physical and Theoretical Chemistry, General Physics and Astronomy}}, number = {{19}}, pages = {{10397--10411}}, publisher = {{Royal Society of Chemistry (RSC)}}, title = {{{Tumbling with a limp: local asymmetry in water's hydrogen bond network and its consequences}}}, doi = {{10.1039/c9cp06960g}}, volume = {{22}}, year = {{2020}}, } @article{34303, author = {{Elgabarty, Hossam and Kaliannan, Naveen Kaliannan and Kühne, Thomas}}, issn = {{2045-2322}}, journal = {{Scientific Reports}}, keywords = {{Multidisciplinary}}, number = {{1}}, publisher = {{Springer Science and Business Media LLC}}, title = {{{Enhancement of the local asymmetry in the hydrogen bond network of liquid water by an ultrafast electric field pulse}}}, doi = {{10.1038/s41598-019-46449-5}}, volume = {{9}}, year = {{2019}}, } @article{34304, abstract = {{

Extensive molecular dynamics simulations reveal two distinct isoforms of the cyanobacteriochrome AnPixJg2 (in its Pr state) with different chromophore conformations, yielding implications for spectroscopic properties.

}}, author = {{Scarbath-Evers, Laura Katharina and Jähnigen, Sascha and Elgabarty, Hossam and Song, Chen and Narikawa, Rei and Matysik, Jörg and Sebastiani, Daniel}}, issn = {{1463-9076}}, journal = {{Physical Chemistry Chemical Physics}}, keywords = {{Physical and Theoretical Chemistry, General Physics and Astronomy}}, number = {{21}}, pages = {{13882--13894}}, publisher = {{Royal Society of Chemistry (RSC)}}, title = {{{Structural heterogeneity in a parent ground-state structure of AnPixJg2 revealed by theory and spectroscopy}}}, doi = {{10.1039/c7cp01218g}}, volume = {{19}}, year = {{2017}}, } @article{34306, abstract = {{

The tautomeric equilibrium of 1-lithium-1,2,3-triazolate (1Li-TR) and 2-lithium-1,2,3-triazolate (2Li-TR) is studied by X-ray diffraction, NMR spectroscopy and molecular dynamics simulations.

}}, author = {{Pulst, Martin and Elgabarty, Hossam and Sebastiani, Daniel and Kressler, Jörg}}, issn = {{1144-0546}}, journal = {{New Journal of Chemistry}}, keywords = {{Materials Chemistry, General Chemistry, Catalysis}}, number = {{4}}, pages = {{1430--1435}}, publisher = {{Royal Society of Chemistry (RSC)}}, title = {{{The annular tautomerism of lithium 1,2,3-triazolate}}}, doi = {{10.1039/c6nj03732a}}, volume = {{41}}, year = {{2017}}, } @article{34305, author = {{Pylaeva, Svetlana and Ivanov, Konstantin L. and Baldus, Marc and Sebastiani, Daniel and Elgabarty, Hossam}}, issn = {{1948-7185}}, journal = {{The Journal of Physical Chemistry Letters}}, keywords = {{General Materials Science, Physical and Theoretical Chemistry}}, number = {{10}}, pages = {{2137--2142}}, publisher = {{American Chemical Society (ACS)}}, title = {{{Molecular Mechanism of Overhauser Dynamic Nuclear Polarization in Insulating Solids}}}, doi = {{10.1021/acs.jpclett.7b00561}}, volume = {{8}}, year = {{2017}}, } @article{34307, abstract = {{

“On-the-fly” coupled cluster-based path-integral molecular dynamics simulations predict that the effective potential of the protonated water–dimer has a single-well only.

}}, author = {{Spura, Thomas and Elgabarty, Hossam and Kühne, Thomas}}, issn = {{1463-9076}}, journal = {{Physical Chemistry Chemical Physics}}, keywords = {{Physical and Theoretical Chemistry, General Physics and Astronomy}}, number = {{22}}, pages = {{14355--14359}}, publisher = {{Royal Society of Chemistry (RSC)}}, title = {{{“On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer}}}, doi = {{10.1039/c4cp05192k}}, volume = {{17}}, year = {{2015}}, } @article{34309, author = {{Kessler, Jan and Elgabarty, Hossam and Spura, Thomas and Karhan, Kristof and Partovi-Azar, Pouya and Hassanali, Ali A. and Kühne, Thomas}}, issn = {{1520-6106}}, journal = {{The Journal of Physical Chemistry B}}, keywords = {{Materials Chemistry, Surfaces, Coatings and Films, Physical and Theoretical Chemistry}}, number = {{31}}, pages = {{10079--10086}}, publisher = {{American Chemical Society (ACS)}}, title = {{{Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations}}}, doi = {{10.1021/acs.jpcb.5b04185}}, volume = {{119}}, year = {{2015}}, } @article{34308, author = {{Kühne, Thomas and Partovi-Azar, P. and Elgabarty, Hossam}}, issn = {{1439-9598}}, journal = {{Nachrichten aus der Chemie}}, keywords = {{General Chemical Engineering, General Chemistry}}, number = {{3}}, pages = {{327--335}}, publisher = {{Wiley}}, title = {{{Ab-initio-Moleküldynamik}}}, doi = {{10.1002/nadc.201590095}}, volume = {{63}}, year = {{2015}}, }