Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations

2022 ◽  
pp. 106758
Author(s):  
Pradeep Pant ◽  
Leena Aggarwal
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Structural Integrity ◽  
Dynamics Simulations

scholarly journals Towards understanding of delignification of grassy and woody biomass in cholinium-based ionic liquids

2021 ◽  
Author(s):  
Mood Mohan ◽  
Hemant Choudhary ◽  
Anthe George ◽  
Blake A. Simmons ◽  
Kenneth Sale ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Woody Biomass ◽  
Dissolution Mechanism ◽  
Dynamics Simulations ◽  
Multiple Hydrogen Bonds

Herein we report the dissolution mechanism of lignin in cholinium-based ionic liquids by molecular dynamics simulations. Multiple hydrogen bonds, longer HB lifetimes, and higher pKa of [Ch][Lys] makes it a better solvent for lignin than acidic ILs.

How strong are hydrogen bonds in the peptide model?

2020 ◽  
Vol 22 (3) ◽  
pp. 1392-1399
Author(s):  
Jakub Dąbrowski ◽  
Wiesław Nowak ◽  
Arkadiusz Ptak
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Force Spectroscopy ◽  
Steered Molecular Dynamics ◽  
Dynamic Force ◽  
Dynamic Force Spectroscopy ◽  
Dynamics Simulations

We provide a methodology based on the steered molecular dynamics simulations and dynamic force spectroscopy calculations to determine the kinetic and energetic characteristics of hydrogen bonds.

Molecular-level insights into the structures, dynamics, and hydrogen bonds of ethylammonium nitrate protic ionic liquid at the liquid–vacuum interface

2020 ◽  
Vol 22 (24) ◽  
pp. 13780-13789
Author(s):  
Qin Huang ◽  
Yiping Huang ◽  
Yi Luo ◽  
Li Li ◽  
Guobing Zhou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Molecular Level ◽  
Mutual Relationship ◽  
Protic Ionic Liquid ◽  
Vacuum Interface ◽  
Ethylammonium Nitrate ◽  
Dynamics Simulations

Molecular dynamics simulations have been used to systematically explore the structures, dynamics, and hydrogen bonds of ethylammonium nitrate (EAN) protic ionic liquid and their mutual relationship at the liquid–vacuum interface.

Solvation of diclofenac in water from atomistic molecular dynamics simulations – interplay between solute–solute and solute–solvent interactions

2018 ◽  
Vol 20 (13) ◽  
pp. 8629-8639 ◽  
Author(s):  
Mariana Kozlowska ◽  
Pawel Rodziewicz ◽  
Tillmann Utesch ◽  
Maria Andrea Mroginski ◽  
Anna Kaczmarek-Kedziera
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Aqueous Solubility ◽  
Solvent Interactions ◽  
Π Interactions ◽  
Self Association ◽  
Dynamics Simulations

Self-association of diclofenac in water via π–π interactions and C–H⋯π hydrogen bonds as a reason for its low aqueous solubility.

Resolving the anomalous infrared spectrum of the MeCN–HCl molecular cluster using ab Initio molecular dynamics

2014 ◽  
Vol 16 (45) ◽  
pp. 24685-24690 ◽  
Author(s):  
Nicolai Bork ◽  
Ville Loukonen ◽  
Henrik G. Kjaergaard ◽  
Hanna Vehkamäki
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Infrared Spectrum ◽  
Ir Spectra ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Molecular Complexes ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Cluster ◽  
Dynamics Simulations

Molecular dynamics simulations reveal that the asymmetric peak seen in IR spectra of acetonitrile–HCl molecular complexes are due to high population of complexes with partially broken hydrogen bonds.

Molecular dynamics simulations of ubiquinone; a survey over torsional potentials and hydrogen bonds

2001 ◽  
Vol 99 (21) ◽  
pp. 1795-1804 ◽  
Author(s):  
J. ARVID NILSSON ◽  
ALEXANDER LYUBARTSEV ◽  
LEIF A. ERIKSSON ◽  
AATTO LAAKSONEN
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Torsional Potentials

scholarly journals The geometry of intercalation complex of antitumor mitoxantrone and ametantrone with DNA: molecular dynamics simulations.

1998 ◽  
Vol 45 (1) ◽  
pp. 1-11 ◽  
Author(s):  
J Mazerski ◽  
S Martelli ◽  
E Borowski
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Antitumor Drugs ◽  
Intercalation Complex ◽  
Intercalation Complexes ◽  
Dynamics Simulations ◽  
Binding Orientations ◽  
Molecular Nature

Intercalative binding of the antitumor drugs ametantrone and mitoxantrone to the dodecamer duplex d(CGCGAGCTCGCG)2 was studied by applying molecular dynamics in water with the GROMOS 87 force field. A number of reasonable binding orientations were tested by short pre-simulations. It was shown that in energetically favourable orientation the anthraquinone chromophore is perpendicular to the direction of inter-base hydrogen bonds. Helically shaped side-chains of the drugs fit to the minor groove. The best orientation obtained in pre-simulations was applied in the main simulations. Small but significant differences were found between structures of intercalation complexes of the two drugs with the dodecamer duplex, the mitoxantrone complex possessing more favourable energy. The molecular nature of interactions responsible for those differences has been discussed.

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