scholarly journals Aggregation of cyclic polypeptoids bearing zwitterionic end-groups with attractive dipole–dipole and solvophobic interactions: a study by small-angle neutron scattering and molecular dynamics simulation

2017 ◽  
Vol 19 (22) ◽  
pp. 14388-14400 ◽  
Author(s):  
Pu Du ◽  
Ang Li ◽  
Xin Li ◽  
Yueheng Zhang ◽  
Changwoo Do ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Aggregation Behavior ◽  
Dynamics Simulation ◽  
End Groups ◽  
Solvophobic Interactions

The aggregation behavior of cyclic polypeptoids has been studied using experiments and simulations.

Effect of the solute–solvent interface on small-angle neutron scattering from organic solutions of short alkyl chain molecules as revealed by molecular dynamics simulation

2013 ◽  
Vol 46 (2) ◽  
pp. 372-378 ◽  
Author(s):  
Roman A. Eremin ◽  
Kholmirzo Kholmurodov ◽  
Viktor I. Petrenko ◽  
László Rosta ◽  
Mikhail V. Avdeev
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Scattering Length ◽  
Solvent Molecule ◽  
Dynamics Simulation ◽  
Time Averaging ◽  
Acid Molecule

The problem of describing the experimental small-angle neutron scattering (SANS) from diluted solutions of saturated monocarboxylic acids with short chain lengths (myristic and stearic acids) in deuterated decalin is considered. The method of classical molecular dynamics simulation (MDS) is used to obtain the atomic number density distributions, and, as a consequence, the scattering length density (SLD) distribution in the solute–solvent interface area (about 1 nm around the acid molecules), assuming the acid molecules to be rigid and non-associated in the solutions. MDS is performed for solutions in a parallelepiped cell of 5.5 × 5.3 × 5.3 nm (one acid molecule per cell) under normal conditions. The time averaging of the obtained distributions is done over 2 ns (after the system thermalization). It is shown that a specific short-range ordering organization of the solvent molecules in the vicinity of the acid molecules has a significant effect on the scattering, which is mainly determined by a relatively large ratio between the effective size of the solvent molecule and the cross-section diameter of the acid molecule. Various approximations to the simulated SLD distributions, based on the cylinder-type symmetry of the acid molecules, are probed to achieve the best consistency with the experimental SANS curves by varying the residual incoherent background.

Quantification of the Surface Morphology of Lubricant Films With Polar End Groups Using Molecular Dynamics Simulation: Periodic Changes in Morphology Depending on Film Thickness

2008 ◽  
Vol 130 (2) ◽  
Author(s):  
Susumu Ogata ◽  
Hedong Zhang ◽  
Kenji Fukuzawa ◽  
Yasunaga Mitsuya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Surface Morphology ◽  
Film Thickness ◽  
Film Surface ◽  
Dynamics Simulation ◽  
Molecular Probe ◽  
Coarse Grained ◽  
End Groups ◽  
Lubricant Films

Using a coarse-grained molecular dynamics simulation based on the bead-spring polymer model, we reproduced the film distribution of molecularly thin lubricant films with polar end groups coated on the disk surface and quantified the film-surface morphology using a molecular-probe scanning method. We found that the film-surface morphology changed periodically with increasing film thickness. The monolayer of a polar lubricant that entirely covers the solid surface provides a flat lubricant surface by exposing its nonpolar backbone outside of the monolayer. By increasing film thickness, the end beads aggregate to make clusters, and bulges form on the lubricant surface, accompanying an increase in surface roughness. The bulges continue to grow even though the averaged film thickness reaches or exceeds the bilayer thickness. With further increases in film thickness, the clusters start to be uniformly distributed in the lateral direction to clearly form a third layer. As for the formation of fourth and fifth layers, the process is basically the same as that for the second and third layers. Through our calculations of the intermolecular potential field and the intermolecular force field, these values are found to change periodically and are synchronized with the formation of molecule aggregations, which explains the mechanism of forming the layered structure that is inherent to a polar lubricant.

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