Molecular dynamics simulations of a guaiacyl ?-O-4 lignin model compound: Examination of intramolecular hydrogen bonding and conformational flexibility

Biopolymers ◽  
2004 ◽  
Vol 73 (3) ◽  
pp. 301-315 ◽  
Author(s):  
St�phane Besombes ◽  
Karim Mazeau
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Model Compound ◽  
Intramolecular Hydrogen Bonding ◽  
Conformational Flexibility ◽  
Lignin Model Compound ◽  
Lignin Model ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

scholarly journals Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

2019 ◽  
Vol 58 (12) ◽  
pp. 3759-3763 ◽  
Author(s):  
Francesco Colizzi ◽  
Adam Hospital ◽  
Sanja Zivanovic ◽  
Modesto Orozco
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Intramolecular Hydrogen Bonding ◽  
Classical Molecular Dynamics ◽  
Intramolecular Hydrogen

scholarly journals Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

2019 ◽  
Vol 131 (12) ◽  
pp. 3799-3803 ◽  
Author(s):  
Francesco Colizzi ◽  
Adam Hospital ◽  
Sanja Zivanovic ◽  
Modesto Orozco
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Intramolecular Hydrogen Bonding ◽  
Classical Molecular Dynamics ◽  
Intramolecular Hydrogen

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.

Normal and abnormal heme biosynthesis Part 4: Molecular dynamics simulations of coproporphyrinogen-III and related di- and tricarboxylic acids

2005 ◽  
Vol 09 (03) ◽  
pp. 170-185 ◽  
Author(s):  
Jingyuan He ◽  
Todd A. Kaprak ◽  
Marjorie A. Jones ◽  
Timothy D. Lash
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biosynthetic Pathway ◽  
Local Environment ◽  
Md Simulations ◽  
Structural Requirement ◽  
Coproporphyrinogen Oxidase ◽  
Flat Structures ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

The first cyclic tetrapyrrolic intermediates in the heme biosynthetic pathway are generated as porphyrinogens (hexahydroporphyrins), but unlike the aromatic porphyrin nucleus these structures must take on highly distorted conformations. Although this structural requirement is self-evident, these intermediates are often represented as flat structures. In order to gain a better understanding of the enzyme coproporphyrinogen oxidase, which is responsible for the conversion of coproporphyrinogen-III to protoporphyrinogen-IX, conformational studies were performed using molecular dynamics simulations. These studies were carried out on the natural substrate and six synthetic analogues using a Silicon Graphics workstation and the BIOGRAF 3.1 program (Molecular Simulations Inc.). The dynamics were run for 50 ps using the Verlet algorithm and Dreiding force field for each porphyrinogen with 500 quenching steps at 300 and 500 K. The five lowest energy conformations were then used as starting structures for simulations of 200 ps. The data show that the propionic acid side chains critically affect the conformations by hydrogen bonding interactions, and the chair and saddle forms are the most stable conformations. In many cases the B ring propionate moiety, which is known to be crucial for substrate recognition for coproporphyrinogen oxidase, is found to be free of intramolecular hydrogen bonds. However, simulations in the presence of water molecules gave chaise longe conformations and intermolecular interactions overwhelmed other effects for solvated porphyrinogens. Although the local environment will influence the preferred conformations, these MD simulations provide insights into how natural porphyrinogens can behave under physiological conditions.

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