Dynamic hydrogen bonding and DNA flexibility in minor groove binders: molecular dynamics simulation of the polyamide f-ImPyIm bound to the Mlu1 (MCB) sequence 5′-ACGCGT-3′ in 2:1 motif

2015 ◽  
Vol 28 (5) ◽  
pp. 325-337 ◽  
Author(s):  
Chrystal D. Bruce ◽  
Maddi M. Ferrara ◽  
Julie L. Manka ◽  
Zachary S. Davis ◽  
Janna Register
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Dna Flexibility ◽  
Minor Groove Binders ◽  
Groove Binders

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.

Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study

2014 ◽  
Vol 16 (33) ◽  
pp. 17458-17465 ◽  
Author(s):  
Rajdeep Singh Payal ◽  
Sundaram Balasubramanian
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Simulation Study ◽  
Molecular Hydrogen ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Dissolution of cellulose in ionic liquids involves breaking of its inter- and intra-molecular hydrogen bonding network, as seen through ab initio molecular dynamics simulations.

scholarly journals First-principles molecular dynamics simulation of the Ca2UO2(CO3)3 complex in water

2016 ◽  
Vol 45 (24) ◽  
pp. 9812-9819 ◽  
Author(s):  
Chad Priest ◽  
Ziqi Tian ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
First Principles ◽  
Dynamics Simulation ◽  
Ca Ions ◽  
Hydrogen Bonding Network ◽  
First Principles Molecular Dynamics

First principles molecular dynamics simulation reveals the structure and solvation of the Ca2UO2(CO3)3 complex in water and the hydrogen bonding network that differentiates the two Ca ions.

Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

2015 ◽  
Vol 93 (3) ◽  
pp. 348-361 ◽  
Author(s):  
C. Izanloo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Double Helix ◽  
Melting Process ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Transition Curve ◽  
Water Molecules ◽  
Major Groove ◽  
Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

Hydrogen bonding energy determined by molecular dynamics simulation and correlation to properties of thermoplastic starch films

2017 ◽  
Vol 166 ◽  
pp. 256-263 ◽  
Author(s):  
Jinhui Yang ◽  
Kangkang Tang ◽  
Guoqiang Qin ◽  
Yanxue Chen ◽  
Ling Peng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
Thermoplastic Starch ◽  
Dynamics Simulation ◽  
Bonding Energy ◽  
Starch Films
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