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Publication Type: search.filters.UBSTyp.ZeitschriftenartikelAuthor: search.filters.author.Kraus, Hamzeh

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    Confined Ru‐catalysts in a two‐phase heptane/ionic liquid solution : modeling aspects
    (2020) Kobayashi, Takeshi; Kraus, Hamzeh; Hansen, Niels; Fyta, Maria
    A 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.
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    Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange
    (2022) Markthaler, Daniel; Kraus, Hamzeh; Hansen, Niels
    Umbrella sampling along a one-dimensional order parameter in combination with Hamiltonian replica exchange was employed to calculate the binding free energy of five guest molecules with known affinity to cucurbit[8]uril. A simple empirical approach correcting for the overestimation of the affinity by the GAFF force field was proposed and subsequently applied to the seven guest molecules of the “Drugs of Abuse” SAMPL8 challenge. Compared to the uncorrected binding free energies, the systematic error decreased but quantitative agreement with experiment was only reached for a few compounds. From a retrospective analysis a weak point of the correction term was identified.
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    An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica
    (2022) Kraus, Hamzeh; Hansen, Niels
    The effect of immobilized β-cyclodextrin (bCD) molecules inside a mesoporous silica support on the uptake of benzene and p -nitrophenol from aqueous solution was investigated using all-atom molecular dynamics (MD) simulations. The calculated adsorption isotherms are discussed with respect to the free energies of binding for a 1:1 complex of bCD and the aromatic guest molecule. The adsorption capacity of the bCD-containing material significantly exceeds the amount corresponding to a 1:1 binding scenario, in agreement with experimental observations. Beside the formation of 1:2 and, to a lesser extent, 1:3 host:guest complexes, also host-host interactions on the surface as well as more unspecific host-guest interactions govern the adsorption process. The demonstrated feasibility of classical all-atom MD simulations to calculate liquid phase adsorption isotherms paves the way to a molecular interpretation of experimental data that are too complex to be described by empirical models.