The difference between cholesterol-and glycyrrhizin-γ-cyclodextrin complexes— an analysis by MD simulations in vacuo and in aquo and the calculation of solvation free energies with AMSOL

Köhler, Jutta; Hohla, Manfred; Söllner, Reinhard; Amann, Manfred

doi:10.1016/s0968-5677(97)00066-7

Cited by 9 publications

(3 citation statements)

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“…Molecular dynamics simulations displayed different hydrogen bond patterns of cyclodextrins in crystal and in solution and confirmed the experimental findings of soluble cyclodextrin complexes of cholesterol type versus precipitates of cis / trans -cyclohexadecenone//CDs [10–12]. MD with λ-dynamics and calculation of the solvation-free-energy differences was used to distinguish amylose helices from cellulose sheets by analysing the different reactivity of oxygen atoms O2, O3 and O6 of the sugar units with and without methylation, in line with experimental data [13].…”

Section: Introductionsupporting

confidence: 65%

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

Köhler¹,

Grczelschak-Mick²

2013

Beilstein J. Org. Chem.

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SummaryFour highly ordered hydrogen-bonded models of β-cyclodextrin (β-CD) and its inclusion complex with benzene were investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β-CDs prefer the right-hand orientation, e.g., O3-H…O2-H in the same glucose unit and bifurcated towards …O4 and O3 of the next glucose unit on the right side. On AM1 level the complex energy was −2.75 kcal mol−1 when the benzene molecule was located parallel inside the β-CD cavity and −2.46 kcal mol−1 when it was positioned vertically. The AM1 HOMO/LUMO gap of the empty β-CD with about 12 eV is lowered to about 10 eV in the complex, in agreement with data from the literature. AM1 IR spectra displayed a splitting of the O–H frequencies of cyclodextrin upon complex formation. At the BP/TZVP-DISP3 level the parallel and vertical positions from the starting structures converged to a structure where benzene assumes a more oblique position (−20.16 kcal mol−1 and −20.22 kcal mol−1, resp.) as was reported in the literature. The character of the COSMO-RS σ-surface of β-CD was much more hydrophobic on its O6 rim than on its O2/O3 side when all hydrogen bonds were arranged in a concerted mode.This static QM picture of the β-CD/benzene complex at 0 K was extended by MD simulations. At 120 K benzene was mobile but always stayed inside the cavity of β-CD. The trajectories at 273, 280, 290 and 300 K certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side.

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Section: Introductionsupporting

confidence: 65%

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

Köhler¹,

Grczelschak-Mick²

2013

Beilstein J. Org. Chem.

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“…First, the molecules from benzene to phenanthrene were constructed by the graphical interface program INSIGHT and their geometries were optimized by the standard energy minimization routines including all intramolecular degrees of freedom (bonds, angles, torsions etc.). The structures of cholesterol and glycyrrhetinic acid stem from the Cambridge Data Base 21 and were modeled as described in our previous paper, 22,23 which means that they have optimized hydrogen atoms but all heavy atoms remained in their experimentally-defined positions. Second, each of these single molecules was kept rigid and was placed with its center of mass into the origin of a coordinate system and in an orientation as displayed in Fig.…”

Section: Methods and Computational Detailsmentioning

confidence: 99%

Liquid Crystal Modeling: Electrostatic and Van Der Waals Interaction Energies for Molecular Building Blocks From Benzene to Cholesterol

Braun

Hohla

Köhler

1999

Int. J. Mod. Phys. C

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Intermolecular interaction energies for molecular dimers of benzene, indene, naphthalene, phenanthrene, cholesterol and glycyrrhetinic acid have been calculated according to the CVFF empirical force field of the DISCOVER program. The parallel orientations (side by-side) turned out to be the energetically most favourable ones, in agreement with the parametrization of Gay-Berne potentials. The energies of the T-shape and in-plane (endto-end) orientations of the entirely asymmetric molecules cholesterol and glycyrrhetinic acid depend strongly on the actual atomic positions. This shows the extent to which the shape and charges of molecules determine all possible orientations and interaction energies in molecular ensembles.

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“…However, this may be lipid specific [47] as lipids with unsaturated acyl chains have a lower affinity for CDs than their saturated counterparts-due to steric limitations introduced by double bonds (Figure 4C) [43]. Additionally, in the case of α-, β-, and γ-CD, studies have suggested the formation of cholesterol-CD complexes, where 1-2 CDs bind a single cholesterol molecule (Figure 4A,B) [48,49]. 1 Cd-cholesterol complexes.…”

Section: Using Cyclodextrins To Generate Asymmetric Vesiclesmentioning

confidence: 99%

Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry

et al. 2021

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It is well known that the lipid distribution in the bilayer leaflets of mammalian plasma membranes (PMs) is not symmetric. Despite this, model membrane studies have largely relied on chemically symmetric model membranes for the study of lipid–lipid and lipid–protein interactions. This is primarily due to the difficulty in preparing stable, asymmetric model membranes that are amenable to biophysical studies. However, in the last 20 years, efforts have been made in producing more biologically faithful model membranes. Here, we review several recently developed experimental and computational techniques for the robust generation of asymmetric model membranes and highlight a new and particularly promising technique to study membrane asymmetry.

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The difference between cholesterol-and glycyrrhizin-γ-cyclodextrin complexes— an analysis by MD simulations in vacuo and in aquo and the calculation of solvation free energies with AMSOL

Cited by 9 publications

References 0 publications

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

Liquid Crystal Modeling: Electrostatic and Van Der Waals Interaction Energies for Molecular Building Blocks From Benzene to Cholesterol

Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry

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