scholarly journals Tumbling with a limp: local asymmetry in water's hydrogen bond network and its consequences

2020 ◽  
Vol 22 (19) ◽  
pp. 10397-10411 ◽  
Author(s):  
Hossam Elgabarty ◽  
Thomas D. Kühne
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Liquid Water ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Energy Decomposition ◽  
Bond Network ◽  
Dynamics Simulations

Ab initio molecular dynamics simulations of ambient liquid water and energy decomposition analysis have recently shown that water molecules exhibit significant asymmetry between the strengths of the two donor and/or the two acceptor interactions.

Temperature-dependence of the dielectric relaxation of water using non-polarizable water models

2020 ◽  
Vol 22 (3) ◽  
pp. 1011-1018 ◽  
Author(s):  
Piotr Zarzycki ◽  
Benjamin Gilbert
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Dielectric Relaxation ◽  
Liquid Water ◽  
Bulk Liquid ◽  
Hydrogen Bond Network ◽  
Debye Relaxation ◽  
Bond Network ◽  
Water Models ◽  
Dynamics Simulations

Testing the ability of molecular dynamics simulations using non-polarizable water models to reproduce dielectric spectra of bulk liquid water we show that the Debye relaxation is determined by the dynamics of the hydrogen-bond network.

Reversible Hydrogen Bond Network Dynamics: Molecular Dynamics Simulations of Calix[4]arene-Catenanes

2011 ◽  
Vol 115 (20) ◽  
pp. 6445-6454 ◽  
Author(s):  
Thomas Schlesier ◽  
Thorsten Metzroth ◽  
Andreas Janshoff ◽  
Jürgen Gauss ◽  
Gregor Diezemann
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Network Dynamics ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Dynamics Simulations

scholarly journals Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

2021 ◽  
Vol 8 ◽  
Author(s):  
Lorenzo Di Rienzo ◽  
Mattia Miotto ◽  
Leonardo Bò ◽  
Giancarlo Ruocco ◽  
Domenico Raimondo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Computational Method ◽  
Side Chain ◽  
Water Molecules ◽  
Amino Acid Side Chain ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Protein Environment

Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.

How does hydrogen bond network analysis reveal the golden ratio of water–glycerol mixtures?

2020 ◽  
Vol 22 (5) ◽  
pp. 2887-2907
Author(s):  
Trevor R. Fisher ◽  
Guobing Zhou ◽  
Yijun Shi ◽  
Liangliang Huang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Network Analysis ◽  
Molecular Dynamics Simulations ◽  
Golden Ratio ◽  
Hydrogen Bond Network ◽  
Maximum Contribution ◽  
Water Glycerol ◽  
Bond Network ◽  
Dynamics Simulations

Molecular dynamics simulations reveal that the maximum contribution of H-bonds between water and glycerol occurs around 30 mol% glycerol. Such a concentration is also where several of the mixture's properties have an observed maxima or minima.

scholarly journals Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network

2014 ◽  
Vol 189 ◽  
pp. 20-29 ◽  
Author(s):  
Alexander Kaiser ◽  
Oksana Ismailova ◽  
Antti Koskela ◽  
Stefan E. Huber ◽  
Marcel Ritter ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Ethylene Glycol ◽  
Molecular Dynamics Simulations ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Dynamics Simulations
Sign in / Sign up

Export Citation Format

Share Document