scholarly journals Hydroxyl Group Separation Distances in Anti-Freeze Compounds and Their Effects on Ice Nucleation

2020 ◽  
Vol 21 (22) ◽  
pp. 8488
Author(s):  
Monika Bleszynski ◽  
Matt Reil ◽  
Maciej Kumosa
Keyword(s):  
Molecular Dynamics ◽  
Polyvinyl Alcohol ◽  
Synthetic Polymers ◽  
Separation Distance ◽  
Ice Nucleation ◽  
Hydroxyl Group ◽  
Group Separation ◽  
Antifreeze Glycoproteins ◽  
Key Factor ◽  
Dynamics Simulations

Since the discovery of biological antifreeze glycoproteins (AFGPs), which can inhibit ice nucleation, there has been considerable interest in understanding their mechanisms and mimicking them in synthetic polymers. In this study, we used molecular dynamics simulations of modified polyvinyl alcohol (PVA) compounds to show that the hydroxyl (OH) group distance is a key factor in whether certain compounds promote or inhibit ice nucleation. A hydroxyl distance smaller than ~2.8 Å but greater than ~7.1 Å in modified PVA (MPVA) compounds was associated with the promotion of ice nucleation, while a hydroxyl group separation distance of approximately ~5.0 Å was correlated with a delay in ice nucleation, owing to changes in the energy of the system. Thus, these results may help explain some of the mechanisms of current known anti-freeze compounds and may have implications for designing new anti-freeze compounds in the future.

scholarly journals Computational Assessment of Modified Antifreeze Glycoproteins on Ice Nucleation

Biophysica ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 168-178
Author(s):  
Monika Bleszynski ◽  
Matt Reil
Keyword(s):  
Separation Distance ◽  
Ice Nucleation ◽  
Hydroxyl Group ◽  
Hydroxyl Groups ◽  
Antifreeze Glycoproteins ◽  
Crystallization Inhibition ◽  
Nucleation Activity ◽  
Dynamics Simulations ◽  
Ice Nucleation Activity ◽  
Ice Crystallization

Antifreeze glycoproteins (AFGPs) found in various fish are used by the organisms to prevent freezing. While these compounds have been studied for their ability to bind to, and prevent the complete crystallization of water, the exact mechanisms by which AFGPs prevent freezing are still undetermined. Therefore, building upon our previous work, this study uses molecular dynamics simulations to assess the effects of hydroxyl group separation distance on AFGP ice nucleation activity. Water droplet crystallization simulations showed that modified AFGP structures containing hydroxyl distances smaller than ~3.0 Å lost their ability to prevent ice crystallization. Furthermore, modified AFGP containing hydroxyl distances of 7.327 Å and 6.160 Å was correlated with a promotion in ice nucleation, as demonstrated by the changes in the energy of the system. This supports the notion that the distance, and therefore, geometry characteristics between the hydroxyl groups located on the saccharide structures play a key role in the ice crystallization inhibition properties of AFGP compounds.

scholarly journals Icephobicity of Functionalized Graphene Surfaces

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Xiang-Xiong Zhang ◽  
Min Chen
Keyword(s):  
Molecular Dynamics ◽  
Freezing Temperature ◽  
Ice Nucleation ◽  
Chloride Ions ◽  
Water Molecules ◽  
Sodium Ions ◽  
Functionalized Graphene ◽  
Functionalized Surfaces ◽  
The Difference ◽  
Dynamics Simulations

Manipulating the ice nucleation ability of liquid water by solid surface is of fundamental importance, especially in the design of icephobic surfaces. In this paper, the icephobicity of graphene surfaces functionalized by sodium ions, chloride ions, or methane molecules is investigated using molecular dynamics simulations. The icephobicity of the surface is evaluated by the freezing temperature. The freezing temperature on surface functionalized by methane molecules decreases at first and then increases as a function of the number groups, while the freezing temperature increases monotonically as a function of the number groups upon surfaces functionalized by sodium ions or chloride ions. The difference can be partially explained by the potential morphologies near the surfaces. Additionally, the validity of indicating the ice nucleation ability of water molecules using the number of six rings in the system is examined. Current study shows that the ice nucleation upon functionalized surfaces is inhibited when compared with smooth graphene substrate, which proves the feasibility of changing the icephobicity of the surfaces by functionalizing with certain ions or molecules.

scholarly journals Molecular-Dynamics Simulations of the Emergence of Surface Roughness in a Polymer under Compression

Materials ◽  
2021 ◽  
Vol 14 (23) ◽  
pp. 7327
Author(s):  
Robin Vacher ◽  
Astrid S. de Wijn
Keyword(s):  
Molecular Dynamics ◽  
Surface Roughness ◽  
Plastic Deformation ◽  
Polyvinyl Alcohol ◽  
Molecular Dynamics Simulations ◽  
Complex Materials ◽  
Multi Scale ◽  
Dynamics Simulations ◽  
Scale Roughness ◽  
Mechanisms Of Plasticity

Roughness of surfaces is both surprisingly ubiquitous on all length scales and extremely relevant practically. The appearance of multi-scale roughness has been linked to avalanches and plastic deformation in metals. However, other, more-complex materials have mechanisms of plasticity that are significantly different from those of metals. We investigated the emergence of roughness in a polymer under compression. We performed molecular-dynamics simulations of a slab of solid polyvinyl alcohol that was compressed bi-axially, and we characterised the evolution of the surface roughness. We found significantly different behaviour than what was previously observed in similar simulations of metals. We investigated the differences and argue that the visco-elasticity of the material plays a crucial role.

Molecular Dynamics Study of Diffusion Behavior in Amorphous Silica with Hydroxyl Group

2008 ◽  
Vol 368-372 ◽  
pp. 1677-1679
Author(s):  
Fan Wei Zhang ◽  
Qui Ang Zhu ◽  
Yuan Fa Ding ◽  
Yue Zhang ◽  
Da Hai Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amorphous Silica ◽  
Hydroxyl Group ◽  
Theoretical Interpretation ◽  
Hydroxyl Groups ◽  
Diffusion Behavior ◽  
Self Diffusion ◽  
Initial Charge ◽  
Dynamics Simulations

Molecular dynamics simulations are performed to research the diffusion behavior of amorphous silica with hydroxyl group. Muliken analysis is employed for the determination of initial charge status of simulated systems with various hydroxyl contents. Modified BKS potentials for the interactions between introduced hydroxyl groups and other atoms, are adopted in the present molecular dynamics simulations. Short-range atomic arrangement and self diffusion coefficients of hydroxyl-doped amorphous silica systems are calculated and hereafter compared with those of pure amorphous silica. The calculation results suggest that the doped hydroxyl groups play an important role for the mobility of atoms within the system, which can be employed to the theoretical interpretation of the oxidation process of the ceramics such as silicon nitride.

Effects of surface roughness on the self-diffusion dynamics of a single polymer

Soft Matter ◽  
2018 ◽  
Vol 14 (18) ◽  
pp. 3550-3556 ◽  
Author(s):  
Jiaxiang Li ◽  
Mingming Ding ◽  
Ran Zhang ◽  
Tongfei Shi
Keyword(s):  
Molecular Dynamics ◽  
Surface Roughness ◽  
Molecular Dynamics Simulations ◽  
Separation Distance ◽  
The Self ◽  
Self Diffusion ◽  
Diffusion Dynamics ◽  
Dynamics Simulations

We employ molecular dynamics simulations to simulate the diffusion dynamics of a single polymer adsorbed on surfaces with different roughnesses, which are characterized by the separation distance between obstacles and the height of obstacles.

Molecular Dynamics Simulation of Quasi-Two-Dimensional Water Network on Ice Nucleation Protein

2011 ◽  
Author(s):  
Daisuke Murakami ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Water Clusters ◽  
Ice Nucleation ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Two Dimensional ◽  
Threshold Density ◽  
Ice Nucleation Protein ◽  
Network Of Hydrogen Bonds ◽  
Dynamics Simulations

An ice nucleation protein induces a phase transition from liquid water to ice in air. A specific hydrophilic surface of the protein may have an influence on the network of hydrogen bonds touching on the protein. However, microscopic characteristics of the ice nucleation protein and behavior of water molecules on it have not been clarified. So we carried out molecular dynamics simulations in various quasi-two-dimensional densities of water molecules on the ice nucleation protein. The percolation threshold of water clusters was confirmed. Comparing another hydrophilic protein, the threshold density in both cases had nearly the same value. But percolation probabilities and mean cluster sizes near the threshold were different between both cases. Those results implied that the threshold density was consistent with the conventional theory, but the forming of water clusters near the threshold was influenced by the hydrophilicity on the ice nucleation protein.

scholarly journals Nanoscale friction and wear of a polymer coated with graphene

2022 ◽  
Vol 13 ◽  
pp. 63-73
Author(s):  
Robin Vacher ◽  
Astrid S de Wijn
Keyword(s):  
Molecular Dynamics ◽  
Polyvinyl Alcohol ◽  
Viscoelastic Properties ◽  
Friction And Wear ◽  
Indentation Depth ◽  
Polymer Chains ◽  
Graphene Sheets ◽  
Challenging Problem ◽  
Flat Sheet ◽  
Dynamics Simulations

Friction and wear of polymers at the nanoscale is a challenging problem due to the complex viscoelastic properties and structure. Using molecular dynamics simulations, we investigate how a graphene sheet on top of the semicrystalline polymer polyvinyl alcohol affects the friction and wear. Our setup is meant to resemble an AFM experiment with a silicon tip. We have used two different graphene sheets, namely an unstrained, flat sheet, and one that has been crumpled before being deposited on the polymer. The graphene protects the top layer of the polymer from wear and reduces the friction. The unstrained flat graphene is stiffer, and we find that it constrains the polymer chains and reduces the indentation depth.

scholarly journals Molecular Dynamics on Wood-Derived Lignans Analyzed by Intermolecular Network Theory

Molecules ◽  
2018 ◽  
Vol 23 (8) ◽  
pp. 1990 ◽  
Author(s):  
Thomas Sandberg ◽  
Christian Weinberger ◽  
Jan-Henrik Smått
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Conformation ◽  
Molecular Structures ◽  
New Approach ◽  
Chemical Systems ◽  
Key Factor ◽  
Solvent Molecules ◽  
Dynamics Simulations

The dynamics of interactions to a solvent is a key factor in the proper characterization of new molecular structures. In molecular dynamics simulations, the solvent molecules are explicitly present, thereby defining a more accurate description on how the solvent molecules affect the molecular conformation. Intermolecular interactions in chemical systems, e.g., hydrogen bonds, can be considered as networks or graphs. Graph theoretical analyses can be an outstanding tool in analyzing the changes in interactions between solvent and solute. In this study, the software ChemNetworks is applied to interaction studies between TIP4P solvent molecules and organic solutes, i.e., wood-derived lignan-based ligands called LIGNOLs, thereby supporting the research of interaction networks between organic molecules and solvents. This new approach is established by careful comparisons to studies using previously available tools. In the hydration studies, tetramethyl 1,4-diol is found to be the LIGNOL which was most likely to form hydrogen bonds to the TIP4P solvent.

scholarly journals Tunable transition from hydration to monomer-supported lubrication in zwitterionic monolayers revealed by molecular dynamics simulation

Soft Matter ◽  
2015 ◽  
Vol 11 (17) ◽  
pp. 3340-3346 ◽  
Author(s):  
Christoph Klein ◽  
Christopher R. Iacovella ◽  
Clare McCabe ◽  
Peter T. Cummings
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Separation Distance ◽  
Dynamics Simulation ◽  
Lubrication Regime ◽  
Dynamics Simulations

Molecular dynamics simulations of zwitterionic monolayers reveal a transition from a hydration lubrication dominated shearing regime to a monomer-supported lubrication regime as the separation distance between surfaces decreases.

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