Helical Parameters, Fluctuations, Alternative Hydrogen Bonding, and Bending in Oligonucleotides Containing a Mistmatched Base-pair by NOESY Distance Restrained and Distance Free Molecular Dynamics

1995 ◽  
Vol 246 (1) ◽  
pp. 209-226 ◽  
Author(s):  
J.A.H. Cognet ◽  
Y. Boulard ◽  
G.V. Fazakerley
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Base Pair ◽  
Helical Parameters

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

2018 ◽  
Author(s):  
Rakesh K. Tiwari ◽  
Rajendra P. Ojha ◽  
Gargi Tiwari ◽  
Vishnudatt Pandey ◽  
Vijaysree Mall
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Base Pair ◽  
Dna Strands

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 Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

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