Browsing by Author "Kraus, Hamzeh"

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Open Access
Atomistic simulation of fluid structure and diffusion in functionalized mesoporous silica
(Stuttgart : Universität Stuttgart, Institut für Technische Thermodynamik und Thermische Verfahrenstechnik, 2023) Kraus, Hamzeh; Hansen, Niels (Prof. Dr.-Ing.)
Despite the importance of supported catalysts in industrial applications a rational design based on an understanding of molecular-level processes is still a challenging endeavor, in particular for liquid phase reactions. Ordered mesoporous silicas are common support materials for hosting organometallic catalysts and provide a tailored microenvironment that may lead to enhanced selectivities, productivities and activities. In the present work a computational tool box was developed that facilitates rapid model building of functionalized silica pores and, together with pre- and post-analysis tools, allows for systematic molecular simulation studies of confinement effects in various applications. The tool box was subsequently applied to different research questions including modelling of the uptake of aromatic compounds from the aqueous phase on cyclodextrin-functionalized silica and a detailed investigation of diffusion in cylindrical mesopores allowing to assess the discrepancy among recent experimental diffusion measurements.
Open Access
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.
Open Access
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.
Open Access
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.