Molecular Dynamics Simulations of Initial Decomposition Process on the Unique N−N Bond in Nitramines in the Crystalline State

1996 ◽  
Vol 100 (12) ◽  
pp. 4701-4712 ◽  
Author(s):  
Yuji Kohno ◽  
Kazuyoshi Ueda ◽  
Akira Imamura
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystalline State ◽  
Decomposition Process ◽  
Dynamics Simulations

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 Molecular Dynamics Simulations of hydrophobic peptides that form β-hairpin structures in solution

2021 ◽  
Author(s):  
Tushar Ranjan Moharana ◽  
Ramakrishnan Nagaraj
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystalline State ◽  
Experimental Methods ◽  
Extended Conformation ◽  
Hydrophobic Peptides ◽  
High Propensity ◽  
Hairpin Structures ◽  
Dynamics Simulations ◽  
Hairpin Conformation

Peptides designed with residues that have high propensity to occur in β-turns, form β-hairpin structures in apolar solvents as well in polar organic solvents such as dimethyl sulfoxide (DMSO), methanol and varying percentages of DMSO in chloroform (CHCl3). Presumably due to limited solubility, their conformations have not been investigated by experimental methods in water. We have examined the conformations of such designed peptides that fold into well-defined β-hairpin structures facilitated by β-turns, in the crystalline state and in solution, by Molecular Dynamics Simulations (MDS). The peptides fold into β-hairpin structures in water, starting from extended conformation. In DMSO, folding into β-hairpin structures was not observed, starting from extended conformation. However, when the starting structure is in β-hairpin conformation, unfolding is not observed during MDS in DMSO. Water clearly favours folding of short, hydrophobic peptides into β-turn and β-hairpin conformations from extended structures. DMSO does not have a denaturing effect on short, hydrophobic peptides.

Molecular Dynamics of Side Chain Liquid Crystalline Polysiloxanes

1996 ◽  
Vol 425 ◽  
Author(s):  
G. M. Podojil ◽  
B. L. Farmer ◽  
T. J. Bunning ◽  
R. Pachter ◽  
W. W. Adams
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystalline State ◽  
Liquid Crystalline ◽  
Side Chain ◽  
Flexible Spacer ◽  
Siloxane Oligomers ◽  
Dynamics Simulations ◽  
The Individual ◽  
Insight Into

AbstractMolecular dynamics simulations have been used to characterize the development and longevity of associations between cholesterol and biphenyl mesogens when attached to linear siloxane oligomers by flexible spacer groups. Single substituents, alternating substituents, and diblock and triblock arrangements of the substituents were considered. The backbone and spacer groups allow sufficient flexibility that long-lived associations between cholesterol mesogens form quite rapidly, as do more fluid associations between biphenyl and cholesterol mesogens. The study of the individual mesogen interactions and how these lead to larger scale aligned structures has provided insight into the nature of the liquid crystalline state in these materials.

Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

2000 ◽  
Vol 98 (11) ◽  
pp. 701-707
Author(s):  
Alessandro Sergi, Mauro Ferrario, Francesco Bu
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

ERRATUM Molecular dynamics simulations of liquid crystal phases using atomistic potentials

1998 ◽  
Vol 95 (1) ◽  
pp. 121-121
Author(s):  
CARL MCBRIDE MARK R. WILSON JUDITH A. K.
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystal ◽  
Molecular Dynamics Simulations ◽  
Crystal Phases ◽  
Dynamics Simulations ◽  
Liquid Crystal Phases
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