Universität Stuttgart
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Item Open Access Machine learning-driven investigation of the structure and dynamics of the BMIM-BF4 room temperature ionic liquid(2024) Zills, Fabian; Schäfer, Moritz René; Tovey, Samuel; Kästner, Johannes; Holm, ChristianRoom-temperature ionic liquids are an exciting group of materials with the potential to revolutionize energy storage. Due to their chemical structure and means of interaction, they are challenging to study computationally. Classical descriptions of their inter- and intra-molecular interactions require time intensive parametrization of force-fields which is prone to assumptions. While ab initio molecular dynamics approaches can capture all necessary interactions, they are too slow to achieve the time and length scales required. In this work, we take a step towards addressing these challenges by applying state-of-the-art machine-learned potentials to the simulation of 1-butyl-3-methylimidazolium tetrafluoroborate. We demonstrate a learning-on-the-fly procedure to train machine-learned potentials from single-point density functional theory calculations before performing production molecular dynamics simulations. Obtained structural and dynamical properties are in good agreement with computational and experimental references. Furthermore, our results show that hybrid machine-learned potentials can contribute to an improved prediction accuracy by mitigating the inherent shortsightedness of the models. Given that room-temperature ionic liquids necessitate long simulations to address their slow dynamics, achieving an optimal balance between accuracy and computational cost becomes imperative. To facilitate further investigation of these materials, we have made our IPSuite-based training and simulation workflow publicly accessible, enabling easy replication or adaptation to similar systems.Item Open Access The presence of a wall enhances the probability for ring‐closing metathesis : insights from classical polymer theory and atomistic simulations(2020) Tischler, Ingo; Schlaich, Alexander; Holm, ChristianThe probability distribution of chain ends meeting when one end of the polymer is fixed to a certain distance to a reflecting wall is investigated. For an ideal polymer chain the probability distribution can be evaluated analytically via classic polymer theory. These analytical predictions are compared to atomistic MD simulations of one tethered alkane chain close to the wall. The results demonstrate that a confining wall can lead to a significant increase in the return probability for the chain ends, and thus, can increase the occurrence of ring‐closing reactions. It is further demonstrated that the excess return probability shows a maximum at a certain distance, thereby yielding an optimal catalyst position in the ring‐closing reaction.Item Open Access CO2-induced drastic decharging of dielectric surfaces in aqueous suspensions(2024) Vogel, Peter; Beyer, David; Holm, Christian; Palberg, ThomasWe study the influence of airborne CO2 on the charge state of carboxylate stabilized polymer latex particles suspended in aqueous electrolytes. We combine conductometric experiments interpreted in terms of Hessinger's conductivity model with Poisson-Boltzmann cell (PBC) model calculations with charge regulation boundary conditions. Without CO2, a minority of the weakly acidic surface groups are dissociated and only a fraction of the total number of counter-ions actually contribute to conductivity. The remaining counter-ions exchange freely with added other ions like Na+, K+ or Cs+. From the PBC-calculations we infer a corresponding pKa of 4.26 as well as a renormalized charge in reasonably good agreement with the number of freely mobile counter-ions. Equilibration of salt- and CO2-free suspensions against ambient air leads to a drastic de-charging, which exceeds by far the expected effects of to dissolved CO2 and its dissociation products. Further, no counter-ion-exchange is observed. To reproduce the experimental findings, we have to assume an effective pKa of 6.48. This direct influence of CO2 on the state of surface group dissociation explains our recent finding of a CO2-induced decrease of the ζ-potential and supports the suggestion of an additional charge regulation caused by molecular CO2. Given the importance of charged surfaces in contact with aqueous electrolytes, we anticipate that our observations bear substantial theoretical challenges and important implications for applications ranging from desalination to bio-membranes.Item Open Access A complementary experimental and theoretical approach for probing the surface functionalization of ZnO with molecular catalyst linkers(2023) Kousik, Shravan R.; Solodenko, Helena; YazdanYar, Azade; Kirchhof, Manuel; Schützendübe, Peter; Richter, Gunther; Laschat, Sabine; Fyta, Maria; Schmitz, Guido; Bill, Joachim; Atanasova, PetiaThe application of ZnO materials as solid-state supports for molecular heterogeneous catalysis is contingent on the functionalization of the ZnO surface with stable self-assembled monolayers (SAMs) of catalyst linker molecules. Herein, experimental and theoretical methods are used to study SAMs of azide-terminated molecular catalyst linkers with two different anchor groups (silane and thiol) on poly and monocrystalline (0001, ) ZnO surfaces. Angle-resolved and temperature-dependent X-ray photoelectron spectroscopy (XPS) is used to study SAM binding modes, thermal stabilities, and coverages. The binding strengths and atomistic ordering of the SAMs are determined via atom-probe tomography (APT). Density functional theory (DFT) and ab initio molecular dynamics (AIMD) calculations provide insights on the influence of the ZnO surface polarity on the interaction affinity and conformational behavior of the SAMs. The investigations show that SAMs based on 3-azidopropyltriethoxysilane possess a higher binding strength and thermal stability than the corresponding thiol. SAM surface coverage is strongly influenced by the surface polarity of ZnO, and the highest coverage is observed on the polycrystalline surface. To demonstrate the applicability of linker-modified polycrystalline ZnO as a catalyst support, a chiral Rh diene complex is immobilized on the azide-terminal of the SAM and its coverage is evaluated via XPS.Item Open Access Confined Ru‐catalysts in a two‐phase heptane/ionic liquid solution : modeling aspects(2020) Kobayashi, Takeshi; Kraus, Hamzeh; Hansen, Niels; Fyta, MariaA modeling approach for atomic‐resolution studies of sup‐ ported ionic liquid phase (SILP) catalytic systems in silica mesoporous confinement with surface hydroxyl and functional groups is proposed. First, a force field for the Ru‐based catalyst is developed. Second, its solvation behavior within a bulk two‐phase system of heptane and an IL is studied. Third, static and dynamic properties of the confined system are investigated. Using classical molecular dynamics simulations, experimentally inaccessible properties can thus be studied that are important for an optimization of a SILP system for performing a ring‐closing metathesis reaction.Item Open Access Electronic transport properties of DNA sensing nanopores : insight from quantum mechanical simulations(2017) Sivaraman, Ganesh; Fyta, Maria (Jun.-Prof. Dr.)The translocation of DNA through nanopores is an intensively studied field as it can lead to a new perspective in DNA sequencing. During this process the DNA is electrophoretically driven through a nanoscale hole in a membrane, and use different sensing schemes to read out the sequence. Within the scope of nanopore sequencing two important sensing schemes relevant to this thesis are: 1.) Tunneling sequencers based on solid state nanopores embedded with gold electrodes 2.) 2D materials beyond graphene For scheme 1, an obvious improvement is to coat the gold electrode with molecules that have high conductance and can form instantaneous hydrogen bond bridges with the translocating polynucleotide thereby improving the transverse current signal. The molecule that we propose is the so called diamondoid which are diamond caged molecules with hydrogen termination. Before applying such a molecule to a nanopore electrode set up, one would like to understand their interaction with DNA and its nucleobases. For this purpose, hydrogen bonded complexes formed between nitrogen doped derivatives of smallest diamondoids (i.e. adamantane derivatives) and nucleobases were investigated using dispersion corrected density functional theory (DFT). Mutated and methylated nucleobases are also taken into consideration in these investigations. DFT calculations revealed that hydrogen bonds are of moderate strength. In addition, starting from the DFT predicted hydrogen bonding configuration for each complex, rotations, and translations along a reference axis was performed to capture variations in the interaction energies along the donor-acceptor groups of the hydrogen bonds. The electronic density of states analysis for the hydrogen bonded complexes revealed distinguishable signatures for each nucleobase, thereby showing the suitability for application in electrodes functionalised with such probe molecules. In the next step, an adamantane derivative is placed on one of the electrode and nucleotides are introduced in such a way that nucleobases form hydrogen bonds with the of the nitrogen group of the adamantane derivatives. Electronic transport calculations were performed for gold electrodes functionalised with 3 different adamantane derivatives. Four pristine nucleotides, one mutated, and one methylated nucleotides were considered. Analysis of the transmission spectra reveal that each of the nucleotides has a unique resonance peak far below the Fermi level. We have also proposed a gating voltage window to sample the resonance peaks of the nucleotide so that they can be distinguished from each other. An alternative to tunneling sequencers would be to use nanopores built in to ultra thin metallic nanoribbons such as graphene. The sequence can be read out from the in-plane current modulation resulting from the local field effect of the translocating nucleotides in the vicinity of the metallic pore edges. But the hydrophobicity of graphene makes it a difficult candidate in aqueous environment. Hence in scheme 2, the aim is to model an ultra thin material that can rectify the hydrophobicity of graphene and can be a very good candidate for current modulation sequencing. Ultra thin MoS2 (2H) monolayer exist as direct band gap semiconductor. Nanopores based on 2H phases have been reported in the literature and are not hydrophobic. By means of chemical exfoliation of the 2H phase, a meta stable 1T phase of MoS2 has also been synthesized by various experimental groups. The 1T phase of MoS2 is metallic. The aim of this thesis is to model a nano-biosensor template based on a hybrid MoS2 monolayer made up of a metallic (1T) phase sandwiched between semiconducting (2H) phase. The sensor that we propose, should have only metallic nanopore edges. As a first step, we have modeled the semiconductor-metal interface, and compared them with experiments. Then an investigation to understand the influence of the increase of the metallic unit on the electronic properties is performed. Since, point defects are highly relevant to electrochemical pore growth, a point sulfur defect analysis is provided to ascertain the weakest point in the sheet. Finally to understand the effect of the interface electronic transport calculations are performed. The transmission spectra reveals a clear asymmetry in the current flow across the interface by means of gating. In the end, the relevance of such a hybrid MoS2 material for nanopore sequencing is discussed.