Unrestrained Molecular Dynamics Simulations of [d(AT)5]2Duplex in Aqueous Solution:  Hydration and Binding of Sodium Ions in the Minor Groove

2000 ◽  
Vol 122 (21) ◽  
pp. 5025-5033 ◽  
Author(s):  
Richard Štefl ◽  
Jaroslav Koča
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Minor Groove ◽  
Sodium Ions ◽  
Dynamics Simulations

scholarly journals Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations

2017 ◽  
Vol 19 (10) ◽  
pp. 6909-6920 ◽  
Author(s):  
Tatsuhiko Ohto ◽  
Johannes Hunger ◽  
Ellen H. G. Backus ◽  
Wataru Mizukami ◽  
Mischa Bonn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Surface Activity ◽  
Vibrational Spectroscopy ◽  
Biological Function ◽  
Molecular Simulations ◽  
Structure Surface ◽  
Dynamics Simulations ◽  
Hydrophilicity And Hydrophobicity

Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.

scholarly journals Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations

2001 ◽  
Vol 1510 (1-2) ◽  
pp. 1-9 ◽  
Author(s):  
P.C. Biggin ◽  
G.R. Smith ◽  
I. Shrivastava ◽  
S. Choe ◽  
M.S.P. Sansom
Keyword(s):  
Molecular Dynamics ◽  
Potassium Channel ◽  
Molecular Dynamics Simulations ◽  
Sodium Ions ◽  
Dynamics Simulations

scholarly journals Molecular-Dynamics Simulations of C- and N-Terminal Peptide Derivatives of GCN4-p1 in Aqueous Solution

2005 ◽  
Vol 2 (8) ◽  
pp. 1086-1104 ◽  
Author(s):  
John H. Missimer ◽  
Michel O. Steinmetz ◽  
Wolfgang Jahnke ◽  
Fritz K. Winkler ◽  
Wilfred F. van Gunsteren ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Peptide Derivatives ◽  
C And N ◽  
Dynamics Simulations ◽  
Derivatives Of

Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin

2011 ◽  
Vol 17 (11) ◽  
pp. 2805-2816 ◽  
Author(s):  
Mathew Varghese Koonammackal ◽  
Unnikrishnan Viswambharan Nair Nellipparambil ◽  
Chellappanpillai Sudarsanakumar
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Analysis ◽  
Binding Free Energy ◽  
Minor Groove ◽  
Dna Minor Groove ◽  
Dynamics Simulations ◽  
Free Energy Analysis

scholarly journals Positively and Negatively Hydrated Counterions in Molecular Dynamics Simulations of DNA Double Helix

2020 ◽  
Vol 65 (6) ◽  
pp. 510
Author(s):  
S. Perepelytsya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Double Helix ◽  
Dipole Moments ◽  
Hydration Shell ◽  
Minor Groove ◽  
Water Molecules ◽  
Negative Hydration ◽  
Dynamics Simulations ◽  
Dna Double Helix

The DNA double helix is a polyanionic macromolecule that is neutralized in water solutions by metal ions (counterions). The property of counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na+ counterions and negative hydration of K+ and Cs+ counterions incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations. The results have shown that the dynamics of the hydration shell of counterions depends on the region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions localized in the minor groove of the double helix (about 50 ps for Na+ and lower than 10 ps for K+ and Cs+). The estimated potentials of the mean force for the hydration shells of counterions show that the water molecules are constrained too strongly, and the effect of negative hydration for K+ and Cs+ counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.

Salt Crystallization from an Evaporating Aqueous Solution by Molecular Dynamics Simulations

2003 ◽  
Vol 107 (33) ◽  
pp. 8271-8274 ◽  
Author(s):  
Martin Mucha ◽  
Pavel Jungwirth
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Salt Crystallization ◽  
Dynamics Simulations
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