Universität Stuttgart
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Item Open Access On the use of side‐chain NMR relaxation data to derive structural and dynamical information on proteins : a case study using hen lysozyme(2020) Smith, Lorna J.; Gunsteren, Wilfred F. van; Hansen, NielsValues of S2CH and S2NH order parameters derived from NMR relaxation measurements on proteins cannot be used straightforwardly to determine protein structure because they cannot be related to a single protein structure, but are defined in terms of an average over a conformational ensemble. Molecular dynamics simulation can generate a conformational ensemble and thus can be used to restrain S2CH and S2NH order parameters towards experimentally derived target values S2CH(exp) and S2NH(exp). Application of S2CH and S2NH order‐parameter restraining MD simulation to bond vectors in 63 side chains of the protein hen egg white lysozyme using 51 S2CH(exp) target values and 28 S2NH(exp) target values shows that a conformational ensemble compatible with the experimentally derived data can be obtained by using this technique. It is observed that S2CH order‐parameter restraining of C-H bonds in methyl groups is less reliable than S2NH order‐parameter restraining because of the possibly less valid assumptions and approximations used to derive experimental S2CH(exp) values from NMR relaxation measurements and the necessity to adopt the assumption of uniform rotational motion of methyl C-H bonds around their symmetry axis and of the independence of these motions from each other. The restrained simulations demonstrate that side chains on the protein surface are highly dynamic. Any hydrogen bonds they form and that appear in any of four different crystal structures, are fluctuating with short lifetimes in solution.Item Open Access Calculation of pure substance and mixture viscosities using PCP-SAFT and entropy scaling(Stuttgart : Universität Stuttgart, Institut für Technische Thermodynamik und Thermische Verfahrenstechnik, 2020) Lötgering-Lin, Oliver; Gross, Joachim (Prof. Dr.-Ing.)Item Open Access Probing self-diffusion of guest molecules in a covalent organic framework : simulation and experiment(2024) Grunenberg, Lars; Keßler, Christopher; Teh, Tiong Wei; Schuldt, Robin; Heck, Fabian; Kästner, Johannes; Groß, Joachim; Hansen, Niels; Lotsch, Bettina V.Covalent organic frameworks (COFs) are a class of porous materials whose sorption properties have so far been studied primarily by physisorption. Quantifying the self-diffusion of guest molecules inside their nanometer-sized pores allows for a better understanding of confinement effects or transport limitations and is thus essential for various applications ranging from molecular separation to catalysis. Using a combination of pulsed field gradient nuclear magnetic resonance measurements and molecular dynamics simulations, we have studied the self-diffusion of acetonitrile and chloroform in the 1D pore channels of two imine-linked COFs (PI-3-COF) with different levels of crystallinity and porosity. The higher crystallinity and porosity sample exhibited anisotropic diffusion for MeCN parallel to the pore direction, with a diffusion coefficient of Dpar = 6.1(3) × 10-10 m2 s-1 at 300 K, indicating 1D transport and a 7.4-fold reduction in self-diffusion compared to the bulk liquid. This finding aligns with molecular dynamics simulations predicting 5.4-fold reduction, assuming an offset-stacked COF layer arrangement. In the low-porosity sample, more frequent diffusion barriers result in isotropic, yet significantly reduced diffusivities (DB = 1.4(1) × 10-11 m2 s-1). Diffusion coefficients for chloroform at 300 K in the pores of the high- (Dpar = 1.1(2) × 10-10 m2 s-1) and low-porosity (DB = 4.5(1) × 10-12 m2 s-1) samples reproduce these trends. Our multimodal study thus highlights the significant influence of real structure effects such as stacking faults and grain boundaries on the long-range diffusivity of molecular guest species while suggesting efficient intracrystalline transport at short diffusion times.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 Influence of ionic liquid film thickness and flow rate on macrocyclization efficiency and selectivity in supported ionic liquid‐liquid phase catalysis(2024) Högler, Marc; Kobayashi, Takeshi; Kraus, Hamzeh; Atwi, Boshra; Buchmeiser, Michael R.; Fyta, Maria; Hansen, NielsSupported ionic‐liquid phase (SILP) technology in a biphasic setting with n ‐heptane as the transport phase was applied to the Ru‐alkylidene‐N‐heterocyclic carbene (NHC) catalyzed macrocyclization of α , ω ‐dienes to elucidate the effect of ionic liquid (IL)‐film thickness, flow rate as well as substrate and product concentration on macrocyclization efficiency, and Z ‐selectivity. To understand the molecular‐level behavior of the substrates and products at the n ‐heptane/IL interphase, atomistic molecular dynamics simulations were conducted and correlated with experimental observations. The thickness of the IL layer strongly influences the Z/E ratio of the products in that a thin IL layer favors higher Z/E ratios by confining the catalyst between the pore wall and the liquid‐liquid interphase whereas a thick IL layer favors formation of the E ‐product and Ru‐hydride catalyzed isomerization reactions. Also, macrocyclization efficiency, expressed by the ratio of oligomers/macromonocycle (O/MMC), is influenced both by the flow rate and the thickness of the IL layer.Item Open Access On the use of 3J-coupling NMR data to derive structural information on proteins(2021) Smith, Lorna J.; Gunsteren, Wilfred F. van; Stankiewicz, Bartosz; Hansen, NielsValues of 3J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate 3J-coupling values (4-8 Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the 3J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and 3J-coupling. Both problems can be solved by using 3J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain 3J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of 3J-coupling data in protein structure determination.Item Open Access Biocatalytic stereocontrolled head-to-tail cyclizations of unbiased terpenes as a tool in chemoenzymatic synthesis(2024) Schneider, Andreas; Lystbæk, Thomas B.; Markthaler, Daniel; Hansen, Niels; Hauer, BernhardTerpene synthesis stands at the forefront of modern synthetic chemistry and represents the state-of-the-art in the chemist’s toolbox. Notwithstanding, these endeavors are inherently tied to the current availability of natural cyclic building blocks. Addressing this limitation, the stereocontrolled cyclization of abundant unbiased linear terpenes emerges as a valuable tool, which is still difficult to achieve with chemical catalysts. In this study, we showcase the remarkable capabilities of squalene-hopene cyclases (SHCs) in the chemoenzymatic synthesis of head-to-tail-fused terpenes. By combining engineered SHCs and a practical reaction setup, we generate ten chiral scaffolds with >99% ee and de , at up to decagram scale. Our mechanistic insights suggest how cyclodextrin encapsulation of terpenes may influence the performance of the membrane-bound enzyme. Moreover, we transform the chiral templates to valuable (mero)-terpenes using interdisciplinary synthetic methods, including a catalytic ring-contraction of enol-ethers facilitated by cooperative iodine/lipase catalysis.Item Open Access Palladium hydride catalysts confined in silica mesopores : effects on catalytic enyne cyclization(2026) Wimmer, Erik J.; Beydeda, Zeki; Högler, Marc; Wendland, Nikolaj; Hansen, Niels; Dyballa, Michael; Estes, Deven P.Confinement of molecular catalysts in the pores of solid supports is a common method for heterogenizing molecular catalysts. However, such heterogenization leads to confinement effects that often change the catalytic properties in poorly understood ways. We investigate the effect(s) of confinement on Pd-H catalyzed enyne cycloisomerization in porous SBA-15-type materials. COOH-functionalized SBA-15 samples of varying pore sizes were tested for their reactivity with Pd(0) complexes. Pd-H formation in the pores is reversible, and the equilibrium constants could be measured by 31 P MAS NMR of solid samples wetted with Pd(0) stock solutions. While less favorable than in solution, Pd-H can form via protonation of Pd(0) complexes by surface COOH groups, with smaller pores favoring Pd-H. Confined Pd-H demonstrated higher selectivity and, in certain cases, better activity than homogeneous analogues. Overall, higher activity for confined catalysts was achieved in cases in which the substrates adsorb strongly in the pores, leading to high local reactant concentrations as demonstrated by MD simulations. However, in some cases, higher [COOH] inhibited the catalyst, leading to lower conversions in confinement. This work highlights the potential of confinement effects to improve catalytic properties but also underscores the complex interplay of factors that influence confined catalytic reactions.Item Open Access Ethylene oligomerization under confinement using supported Cr(II) and Cr(III) catalysts(2026) Bhattacharya, Somnath; Högler, Marc; Bruckner, Johanna R.; Atwi, Boshra; Bauer, Matthias; Hansen, Niels; Fischer, Felix R.; Buchmeiser, Michael R.Supported Cr(II) and Cr(III) catalysts have emerged as versatile systems for the selective oligomerization of ethylene, offering advantages such as easy separation, catalyst recyclability, and reduced polymer formation. However, their performance can be significantly influenced by factors such as pore confinement, active site accessibility, and metal-support interactions, which leads to an altered selectivity as compared to their homogeneous counterparts. Herein, to better understand and potentially overcome these limitations, we investigated how support morphology and confinement influence the behavior of immobilized Cr catalysts during ethylene oligomerization. Supported catalysts were prepared by selective immobilization of the Cr(III) complexes [1-methyl-3-(2-amido-N-(2,6-diisopropylpheny-1-yl)phen-1-ylimidazol-2-ylidene)2Cr2-(μ-Cl)4] (Cr1), [1-methyl-3-(2-amido-N-(2,6-diisopropylpheny-1-yl)phen-1-ylimidazol-2-ylidene)Cr(benzyl)2(THF)] (Cr2), and the Cr(II) complex [(CAAC)2CrCl2] (Cr3, CAAC = 1-(2,6-diisopropylpheny-1-yl)-3,3,5,5-tetramethyltetrahydropyrrol-2-ylidene), which are all non-selective for ethylene oligomerization in solution, inside the mesopores of ordered mesoporous silica (OMS) materials with varying pore sizes (OMS66Å, OMS57Å, OMS28Å), as well as amorphous silica (Si60). The activity and selectivity of the supported catalysts were assessed in comparison to the parent homogenous catalysts. In the presence of methylalumoxane (MAO) as cocatalyst, the immobilized catalysts exhibited lower catalytic activity (0.1-3.1 kg mol Cr-1 h-1 bar-1) compared to the homogeneous catalysts (6.9-8.3 kg mol Cr-1 h-1 bar-1), yet with significant reduction in polyethylene (PE) byproduct formation. Upon activation with MAO, particularly the OMS-immobilized catalyst Cr1@OMS28Å as well as Cr2@OMS28Å allowed for the selective synthesis of linear α-olefins (LAOs) ≤ C12.Item Open Access Understanding the language of molecules : predicting pure component parameters for the PC-SAFT equation of state from SMILES(2025) Winter, Benedikt; Rehner, Philipp; Esper, Timm; Schilling, Johannes; Bardow, AndréA major bottleneck in developing sustainable processes and materials is a lack of property data. Recently, machine learning approaches have vastly improved previous methods for predicting molecular properties. However, these machine learning models are often not able to handle thermodynamic constraints adequately. In this work, we present a machine learning model based on natural language processing to predict pure-component parameters for the perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state. The model is based on our previously proposed SMILES-to-Properties-Transformer (SPT). By incorporating PC-SAFT into the neural network architecture, the machine learning model is trained directly on experimental vapor pressure and liquid density data. Combining established physical modeling approaches with state-of-the-art machine learning methods enables high-accuracy predictions across a wide range of pressures and temperatures, while keeping the thermodynamic consistency of an equation of state like PC-SAFT. SPTPC-SAFT demonstrates exceptional prediction accuracy even for complex molecules with various functional groups, outperforming traditional group contribution methods by a factor of four in the mean average percentage deviation. Moreover, SPTPC-SAFT captures the behavior of stereoisomers without any special consideration. To facilitate the application of our model, we provide predicted PC-SAFT parameters of 13 279 components, making PC-SAFT accessible to all researchers.