Molecular Dynamic Simulation Analysis on the Inclusion Complexation of Plumbagin with β-Cyclodextrin Derivatives in Aqueous Solution

Stable encapsulation of medically active compounds can lead to longer storage life and facilitate the slow-release mechanism. In this work, the dynamic and molecular interactions between plumbagin molecule with β-cyclodextrin (BCD) and its two derivatives, which are dimethyl-β-cyclodextrin (MBCD), and 2-O-monohydroxypropyl-β-cyclodextrin (HPBCD) were investigated. Molecular dynamics simulations (MD) with GLYCAM-06 and AMBER force fields were used to simulate the inclusion complex systems under storage temperature (4 °C) in an aqueous solution. The simulation results suggested that HPBCD is the best encapsulation agent to produce stable host–guest binding with plumbagin. Moreover, the observation of the plumbagin dynamic inside the binding cavity revealed that it tends to orient the methyl group toward the wider rim of HPBCD. Therefore, HPBCD is a decent candidate for the preservation of plumbagin with a promising longer storage life and presents the opportunity to facilitate the slow-release mechanism.

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Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

10.26434/chemrxiv.9198770.v2 ◽

2019 ◽

Author(s):

Javier Oller ◽

David A. Sáez ◽

Esteban Vöhringer-Martinez

Keyword(s):

Carbon Dioxide ◽

Aqueous Solution ◽

Molecular System ◽

Chemical Reactivity ◽

Nucleophilic Attack ◽

Stable Conformation ◽

Fukui Functions ◽

Reactivity Descriptors ◽

Dynamics Simulations ◽

Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of changes in the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

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Molecular Dynamics Simulation Study of Lecithin Inhibiting Hydrate-Dissociation

Materials Science Forum ◽

10.4028/www.scientific.net/msf.890.252 ◽

2017 ◽

Vol 890 ◽

pp. 252-259

Author(s):

Le Wang ◽

Guan Cheng Jiang ◽

Xin Lin ◽

Xian Min Zhang ◽

Qi Hui Jiang

Keyword(s):

Molecular Dynamics ◽

Water Movement ◽

Simulation Analysis ◽

Mass Density ◽

Dynamics Simulation ◽

Dissociation Process ◽

Hydrate Dissociation ◽

Hydrocarbon Chains ◽

Dynamics Simulations ◽

Mass Density Profile

Molecular dynamics simulations are used to study the dissociation inhibiting mechanism of lecithin for structure I hydrates. Adsorption characteristics of lecithin and PVP (poly (N-vinylpyrrolidine)) on the hydrate surfaces were performed in the NVT ensemble at temperatures of 277K and the hydrate dissociation process were simulated in the NPT ensemble at same temperature. The results show that hydrate surfaces with lecithin is more stable than the ones with PVP for the lower potential energy. The conformation of lecithin changes constantly after the balanced state is reached while the PVP molecular dose not. Lecithin molecule has interaction with lecithin nearby and hydrocarbon-chains of lecithin molecules will form a network to prevent the diffusion of water and methane molecules, which will narrow the available space for hydrate methane and water movement. Compared with PVP-hydrate simulation, analysis results (snapshots and mass density profile) of the dissociation simulations show that lecithin-hydrate dissociates more slowly.

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Inclusion complexation of .BETA.-cyclodextrin with some sulfonamides in aqueous solution.

Chemical and Pharmaceutical Bulletin ◽

10.1248/cpb.26.1162 ◽

1978 ◽

Vol 26 (4) ◽

pp. 1162-1167 ◽

Cited By ~ 32

Author(s):

KANETO UEKAMA ◽

FUMITOSHI HIRAYAMA ◽

MASAKI OTAGIRI ◽

YOUKO OTAGIRI ◽

KEN IKEDA

Keyword(s):

Aqueous Solution ◽

Inclusion Complexation ◽

Beta Cyclodextrin

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Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/c6cp07284d ◽

2017 ◽

Vol 19 (10) ◽

pp. 6909-6920 ◽

Cited By ~ 24

Author(s):

Tatsuhiko Ohto ◽

Johannes Hunger ◽

Ellen H. G. Backus ◽

Wataru Mizukami ◽

Mischa Bonn ◽

...

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulations ◽

Surface Activity ◽

Vibrational Spectroscopy ◽

Biological Function ◽

Molecular Simulations ◽

Structure Surface ◽

Dynamics Simulations ◽

Hydrophilicity And Hydrophobicity

Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.

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Molecular-Dynamics Simulations of C- and N-Terminal Peptide Derivatives of GCN4-p1 in Aqueous Solution

Chemistry & Biodiversity ◽

10.1002/cbdv.200590078 ◽

2005 ◽

Vol 2 (8) ◽

pp. 1086-1104 ◽

Cited By ~ 13

Author(s):

John H. Missimer ◽

Michel O. Steinmetz ◽

Wolfgang Jahnke ◽

Fritz K. Winkler ◽

Wilfred F. van Gunsteren ◽

...

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulations ◽

Peptide Derivatives ◽

C And N ◽

Dynamics Simulations ◽

Derivatives Of

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The use of postharvest treatments to extend storage life and to control postharvest wastage of honeydew melons (Cucumis melo L. var. inodorus Naud.) in cool storage

Australian Journal of Experimental Agriculture ◽

10.1071/ea9900693 ◽

1990 ◽

Vol 30 (5) ◽

pp. 693 ◽

Cited By ~ 7

Author(s):

ME Edwards ◽

RM Blennerhassett

Keyword(s):

Water Loss ◽

Cucumis Melo ◽

Storage Temperature ◽

Chilling Injury ◽

Storage Period ◽

Storage Conditions ◽

Storage Life ◽

Storage Rots ◽

Wax Coating ◽

Cucumis Melo L

Three trials were undertaken to study storage conditions and handling procedures required to maximise the postharvest storage life of honeydew melons (Cucumis melo L. var. inodorus Naud.).Honeydew melons treated with chlorine (1000 mg/L), benomyl (250 mg/L) + guazatine (500 mg/L), shrink wrap (17 ym Cryovac XDR film), Semperfresh, wax, or combinations of these treatments were stored at 4 or 8�C, for 4 or 6 weeks. Benomyl plus guazatine reduced the development of storage rots associated with Alternaria and Fusarium spp. The use of shrink wrap and wax reduced water loss by melons but increased fungal infection in some cases. Shrink wrapping combined with the fungicide treatment effectively reduced the incidence of fungal breakdown in the storage period for up to 4 weeks. Wax coating with full strength Citruseal wax caused anaerobic tissue breakdown. Melons were affected by chilling injury at 4�C. Control of bacterial rots with benomyl + guazatine or with chlorine was variable. Semperfresh did not reduce the incidence of fungal breakdown or water loss from the melons. The results indicate that storage of honeydew melons for 4 weeks at 8�C by pretreating with fungicide is possible but the melons soften and rot after 6 weeks, making them unsaleable. Four weeks should be adequate to allow for sea freighting of honeydew melons to markets in South East Asia. Further research is required to determine the optimum storage temperature for honeydew melons.

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