Combined Molecular Dynamics, Atoms in Molecules, and IR Studies of the Bulk Monofluoroethanol and Bulk Ethanol To Understand the Role of Organic Fluorine in the Hydrogen Bond Network

2017 ◽  
Vol 121 (6) ◽  
pp. 1250-1260 ◽  
Author(s):  
Biswajit Biswas ◽  
Saptarsi Mondal ◽  
Prashant Chandra Singh
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Atoms In Molecules ◽  
Hydrogen Bond Network ◽  
Ir Studies ◽  
Bond Network ◽  
Organic Fluorine

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.

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