Glycerol condensed phases Part II.A molecular dynamics study of the conformational structure and hydrogen bonding

1999 ◽  
Vol 1 (5) ◽  
pp. 879-885 ◽  
Author(s):  
Riccardo Chelli ◽  
Piero Procacci ◽  
Gianni Cardini ◽  
Salvatore Califano
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Condensed Phases ◽  
Conformational Structure

scholarly journals Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

2009 ◽  
Vol 62 (9) ◽  
pp. 1054 ◽  
Author(s):  
Defang Ouyang ◽  
Hong Zhang ◽  
Dirk-Peter Herten ◽  
Harendra S. Parekh ◽  
Sean C. Smith
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Structural Information ◽  
Structural Parameters ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Viral Gene ◽  
Conformational Structure ◽  
Crystal Forms ◽  
Gene Delivery Vectors

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A′-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA – namely major groove width, inclination and the number of base pairs in a helical twist – over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A′-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).

scholarly journals Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study

2013 ◽  
Vol 117 (17) ◽  
pp. 4860-4869 ◽  
Author(s):  
Marcos D. Battistel ◽  
Robert Pendrill ◽  
Göran Widmalm ◽  
Darón I. Freedberg
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Direct Evidence

Correlation between mobility and the hydrogen bonding network of water at an electrified-graphite electrode using molecular dynamics simulation

2020 ◽  
Vol 22 (3) ◽  
pp. 1767-1773
Author(s):  
Masaya Imai ◽  
Yasuyuki Yokota ◽  
Ichiro Tanabe ◽  
Kouji Inagaki ◽  
Yoshitada Morikawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
Graphite Electrode ◽  
Dynamics Simulation ◽  
Applied Potential ◽  
Dissolved Ions ◽  
Hydrogen Bonding Network

Mobility and hydrogen bonding network of water at a graphite electrode: effects of dissolved ions and applied potential.

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
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