scholarly journals Molecular Dynamics Simulations of Hydrogen Bonding in Clathrate Hydrates with Ammonia and Methanol Guest Molecules

2014 ◽  
Vol 60 (2) ◽  
pp. 389-397 ◽  
Author(s):  
Saman Alavi ◽  
Kyuchul Shin ◽  
John A. Ripmeester
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Clathrate Hydrates ◽  
Guest Molecules ◽  
Dynamics Simulations

scholarly journals A molecular dynamics study of guest–host hydrogen bonding in alcohol clathrate hydrates

2015 ◽  
Vol 17 (19) ◽  
pp. 12639-12647 ◽  
Author(s):  
Masaki Hiratsuka ◽  
Ryo Ohmura ◽  
Amadeu K. Sum ◽  
Saman Alavi ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Vibrational Spectra ◽  
Clathrate Hydrates ◽  
Dynamics Simulations

Molecular dynamics simulations showed the significant impacts of the guest–host hydrogen bonding on the cage stability and vibrational spectra of the clathrate hydrates.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

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 Simulations ofp-tert-Butylcalix[4]arene with Small Guest Molecules

2006 ◽  
Vol 12 (20) ◽  
pp. 5231-5237 ◽  
Author(s):  
Saman Alavi ◽  
Nicholas A. Afagh ◽  
John A. Ripmeester ◽  
Donald L. Thompson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Guest Molecules ◽  
Dynamics Simulations

scholarly journals A Theoretical Study on Trehalose + Water Mixtures for Dry Preservation Purposes

Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1435
Author(s):  
Amit Kumar ◽  
Alberto Cincotti ◽  
Santiago Aparicio
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Theoretical Study ◽  
Mixture Composition ◽  
Detailed Characterization ◽  
Local Dynamics ◽  
Water Structuring ◽  
Dynamics Simulations

The properties of trehalose + water mixtures are studied as a function of mixture composition and temperature using molecular dynamics simulations. As trehalose disaccharide has been proposed for dry preservation purposes, the objective of this work is to analyse the nanoscopic properties of the considered mixtures, in terms of aggregation, clustering, interactions energies, and local dynamics, and their relationships with hydrogen bonding. The reported results allow a detailed characterization of hydrogen bonding and its evolution with mixture composition and thus inferring the effects of trehalose on water structuring providing results to justify the mechanisms of trehalose acting as preservation agent.

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