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 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 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.