Large-ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26-derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

2007 ◽  
Vol 107 (8) ◽  
pp. 1657-1672 ◽  
Author(s):  
Martin G. Gotsev ◽  
Petko M. Ivanov
Keyword(s):  
Molecular Dynamics ◽  
Water Solution ◽  
Large Ring

Encapsulation of α-Tocopherol in Large-ring Cyclodextrin Containing 26 α-D-Glucopyranose Units: A Molecular Dynamics Study

2021 ◽  
pp. 116802
Author(s):  
Khanittha Kerdpol ◽  
Bodee Nutho ◽  
Kuakarun Krusong ◽  
Rungtiva P. Poo-arporn ◽  
Thanyada Rungrotmongkol ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Ring

scholarly journals Insight into Cellulose Dissolution with the Tetrabutylphosphonium Chloride–Water Mixture using Molecular Dynamics Simulations

Polymers ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 627 ◽  
Author(s):  
Brad Crawford ◽  
Ahmed E. Ismail
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Water Solution ◽  
Water Concentration ◽  
High Water ◽  
Water Mixture ◽  
Cellulose Dissolution ◽  
Working Together ◽  
Dynamics Simulations

All-atom molecular dynamics simulations are utilized to determine the properties and mechanisms of cellulose dissolution using the ionic liquid tetrabutylphosphonium chloride (TBPCl)–water mixture, from 63.1 to 100 mol % water. The hydrogen bonding between small and large cellulose bundles with 18 and 88 strands, respectively, is compared for all concentrations. The Cl, TBP, and water enable cellulose dissolution by working together to form a cooperative mechanism capable of separating the cellulose strands from the bundle. The chloride anions initiate the cellulose breakup, and water assists in delaying the cellulose strand reformation; the TBP cation then more permanently separates the cellulose strands from the bundle. The chloride anion provides a net negative pairwise energy, offsetting the net positive pairwise energy of the peeling cellulose strand. The TBP–peeling cellulose strand has a uniquely favorable and potentially net negative pairwise energy contribution in the TBPCl–water solution, which may partially explain why it is capable of dissolving cellulose at moderate temperatures and high water concentrations. The cellulose dissolution declines rapidly with increasing water concentration as hydrogen bond lifetimes of the chloride–cellulose hydroxyl hydrogens fall below the cellulose’s largest intra-strand hydrogen bonding lifetime.

Molecular dynamics study of solvation in urea water solution

1984 ◽  
Vol 106 (20) ◽  
pp. 5786-5793 ◽  
Author(s):  
Robert A. Kuharski ◽  
Peter J. Rossky
Keyword(s):  
Molecular Dynamics ◽  
Water Solution

Molecular Dynamics Simulation of Diffusion of Vitamin C in Water Solution

2012 ◽  
Vol 30 (1) ◽  
pp. 115-120 ◽  
Author(s):  
Jianping Zeng ◽  
Aimin Wang ◽  
Xuedong Gong ◽  
Jingwen Chen ◽  
Song Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Vitamin C ◽  
Water Solution ◽  
Dynamics Simulation

scholarly journals Self-Association of Antimicrobial Peptides: A Molecular Dynamics Simulation Study on Bombinin

2019 ◽  
Vol 20 (21) ◽  
pp. 5450 ◽  
Author(s):  
Peicho Petkov ◽  
Elena Lilkova ◽  
Nevena Ilieva ◽  
Leandar Litov
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptides ◽  
Lipid Membrane ◽  
Water Solution ◽  
Dynamics Simulation ◽  
Primary Host ◽  
Helix Loop Helix ◽  
Microbial Invasion ◽  
Self Association ◽  
Dynamics Simulations

Antimicrobial peptides (AMPs) are a diverse group of membrane-active peptides which play a crucial role as mediators of the primary host defense against microbial invasion. Many AMPs are found to be fully or partially disordered in solution and to acquire secondary structure upon interaction with a lipid membrane. Here, we report molecular dynamics simulations studies on the solution behaviour of a specific AMP, bombinin H2. We show that in monomeric form in water solution the peptide is somewhat disordered and preferably adopts a helix-loop-helix conformation. However, when more than a single monomer is placed in the solution, the peptides self-associate in aggregates. Within the aggregate, the peptides provide each other with an amphipathic environment that mimics the water–membrane interface, which allows them to adopt a single-helix structure. We hypothesise that this is the mechanism by which bombinin H2 and, possibly, other small linear AMPs reach the target membrane in a functional folded state and are able to effectively exert their antimicrobial action on it.

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