scholarly journals Molecular Dynamics Studies on the Effects of Water Speciation on Interfacial Structure and Dynamics in Silica-Filled PDMS Composites

2001 ◽  
Vol 710 ◽  
Author(s):  
Richard H. Gee ◽  
Robert S. Maxwell ◽  
Long N. Dinh ◽  
Bryan Balazs
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Local Density ◽  
Experimental Studies ◽  
Structural Features ◽  
Distribution Functions ◽  
Interfacial Structure ◽  
Structure And Dynamics ◽  
Contact Distance ◽  
Physisorbed Water

ABSTRACTSignificant changes in materials properties of siloxane based polymers can be obtained by the addition of inorganic fillers. In silica-filled polydimethylsiloxane (PDMS) based composites the mechanism of this reinforcing behavior is presumably hydrogen bonding between surface hydroxyls and backbone siloxane species. We have chosen to investigate in detail the effect of chemisorbed (hydroxyls) and physisorbed water on the interfacial structure and dynamics in silica-filled PDMS based composites. Toward this end, we have combined molecular dynamics simulations and experimental studies employing DMA and NMR analysis. Our results suggest that the polymer-silica contact distance and the mobility of interfacial polymer chains significantly decreased as the hydration (hydroxyl and/or physisorbed water) level at the interface was reduced. The reduced mobility of the PDMS chains in the interfacial domain reduced the overall motional properties of the polymer, thus causing an effective "stiffening" of the polymer matrix. The role of the long-ranged Coulombic interactions on the structural features and chain dynamics of the polymer were also examined. Both are found to be strongly influenced by the electrostatic interactions as identified by the bond orientation time correlation function and local density distribution functions. These results have important implications for the design of nanocomposite silica-siloxane materials.

scholarly journals Insight into the Structure and Dynamics of Polymers by Neutron Scattering Combined with Atomistic Molecular Dynamics Simulations

Polymers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3067
Author(s):  
Arantxa Arbe ◽  
Fernando Alvarez ◽  
Juan Colmenero
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Structural Features ◽  
Length Scales ◽  
Polymeric Systems ◽  
Structure And Dynamics ◽  
Dynamical Features ◽  
Dynamics Simulations ◽  
Insight Into

Combining neutron scattering and fully atomistic molecular dynamics simulations allows unraveling structural and dynamical features of polymer melts at different length scales, mainly in the intermolecular and monomeric range. Here we present the methodology developed by us and the results of its application during the last years in a variety of polymers. This methodology is based on two pillars: (i) both techniques cover approximately the same length and time scales and (ii) the classical van Hove formalism allows easily calculating the magnitudes measured by neutron scattering from the simulated atomic trajectories. By direct comparison with experimental results, the simulated cell is validated. Thereafter, the information of the simulations can be exploited, calculating magnitudes that are experimentally inaccessible or extending the parameters range beyond the experimental capabilities. We show how detailed microscopic insight on structural features and dynamical processes of various kinds has been gained in polymeric systems with different degrees of complexity, and how intriguing questions as the collective behavior at intermediate length scales have been faced.

scholarly journals Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
P. M. Pieczywek ◽  
W. Płaziński ◽  
A. Zdunek
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Large Scale ◽  
Dissipative Particle Dynamics ◽  
Three Dimensional ◽  
Structural Features ◽  
Particle Dynamics ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Dynamics Model

Abstract In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.

Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides

2016 ◽  
Vol 138 (20) ◽  
pp. 6532-6540 ◽  
Author(s):  
Stacy L. Chin ◽  
Qing Lu ◽  
Eric L. Dane ◽  
Laura Dominguez ◽  
Christopher J. McKnight ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Structure And Dynamics ◽  
Dynamics Simulations

Structure and Dynamics of NaCl in Methanol. A Molecular Dynamics Study

1991 ◽  
Vol 46 (10) ◽  
pp. 887-897 ◽  
Author(s):  
D. Marx ◽  
K. Heinzinger ◽  
G. Pálinkás ◽  
I. Bakó
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Nacl Solution ◽  
Geometrical Arrangement ◽  
Self Diffusion ◽  
Site Model ◽  
Structure And Dynamics ◽  
Dynamical Properties

AbstractA recently developed flexible three-site model for methanol was employed to perform a Molecular Dynamics simulation of a 0.6 molal NaCl solution. The ion-methanol and ion-ion potential functions were derived from ab initio calculations. The structural properties of the solution are discussed on the basis of radial and angular distribution functions, the orientation of the methanol molecules, and their geometrical arrangement in the solvation shells of the ions. The dynamical properties of the solution - like self-diffusion coefficients, hindered translations, librations, and internal vibrations of the methanol molecules - are calculated from various autocorrelation functions.

scholarly journals Ab initio Molecular Dynamics of CdSe Quantum Dots Doped Glasses

2019 ◽  
Author(s):  
Wenke Li ◽  
Xiujian Zhao ◽  
Chao Liu ◽  
François-Xavier Coudert
Keyword(s):  
Molecular Dynamics ◽  
Quantum Dots ◽  
Ab Initio ◽  
Glass Matrix ◽  
Distribution Functions ◽  
Interfacial Structure ◽  
Ab Initio Molecular Dynamics ◽  
Cdse Quantum Dots ◽  
Cdse Qds ◽  
Doped Glasses

<div> <div> <div> <p>We have probed the local atomic structure of the interfacial structure between the CdSe quantum dots (QDs) and sodium silicate glass matrix. Using ab initio molecular dynamics simulations, we determined the structural properties and bond length, in excellent agreement with previous experimental observations. Based on analysis of radial distribution functions, coordination environment and ring structures, we demonstrate that huge structure reconstruction occurs at the interface between the CdSe QDs and the glass matrix. The incorporation of the CdSe QDs disrupts the Na-O bonds, while stronger SiO4 tetrahedra are reformed. The existence of the glass matrix breaks the stable 4-member (4MR) and 6-member (6MR) of Cd-Se rings, and we observe a disassociated Cd atom dissolved in the glass matrix. Besides, the formation of Se-Na and Cd-O linkages is observed at the CdSe QDs/glass interface. These results significantly extend our understanding of the interfacial structure of the CdSe QDs doped glasses, and provide physical and chemical insight into the possible defect structure origin of CdSe QDs, of interest to the fabrication of the highly luminescent CdSe QDs doped glasses. </p> </div> </div> </div>

scholarly journals Ab initio Molecular Dynamics of CdSe Quantum Dots Doped Glasses

2019 ◽  
Author(s):  
Wenke Li ◽  
Xiujian Zhao ◽  
Chao Liu ◽  
François-Xavier Coudert
Keyword(s):  
Molecular Dynamics ◽  
Quantum Dots ◽  
Ab Initio ◽  
Glass Matrix ◽  
Distribution Functions ◽  
Interfacial Structure ◽  
Ab Initio Molecular Dynamics ◽  
Cdse Quantum Dots ◽  
Cdse Qds ◽  
Doped Glasses

<div> <div> <div> <p>We have probed the local atomic structure of the interfacial structure between the CdSe quantum dots (QDs) and sodium silicate glass matrix. Using ab initio molecular dynamics simulations, we determined the structural properties and bond length, in excellent agreement with previous experimental observations. Based on analysis of radial distribution functions, coordination environment and ring structures, we demonstrate that huge structure reconstruction occurs at the interface between the CdSe QDs and the glass matrix. The incorporation of the CdSe QDs disrupts the Na-O bonds, while stronger SiO4 tetrahedra are reformed. The existence of the glass matrix breaks the stable 4-member (4MR) and 6-member (6MR) of Cd-Se rings, and we observe a disassociated Cd atom dissolved in the glass matrix. Besides, the formation of Se-Na and Cd-O linkages is observed at the CdSe QDs/glass interface. These results significantly extend our understanding of the interfacial structure of the CdSe QDs doped glasses, and provide physical and chemical insight into the possible defect structure origin of CdSe QDs, of interest to the fabrication of the highly luminescent CdSe QDs doped glasses. </p> </div> </div> </div>

scholarly journals Adsorption of metallic ions from aqueous solution on surfactant aggregates: a molecular dynamics study

2021 ◽  
Vol 24 (2) ◽  
pp. 23601
Author(s):  
E. H. Chavez-Martinez ◽  
E. Cedillo-Cruz ◽  
H. Dominguez
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Sodium Dodecyl ◽  
Lead Sulfate ◽  
Distribution Functions ◽  
Metallic Ions ◽  
Positive Ions ◽  
Surfactant Aggregates ◽  
Aluminum Ions ◽  
Dynamics Simulations

Metallic ion adsorption on surfactant aggregates were studied with Molecular dynamics simulations. Using ionic salts, such as lead sulfate (PbSO4) and aluminum sulfate [Al2(SO4)3], adsorption of lead and aluminum were investigated at different salt concentrations and different surfactant aggregates (micelles) sizes. The micelles were constructed with spherical shapes composed of sodium dodecyl sulfate (SDS) anionic surfactants. The electrostatic interactions between the positive ions and the negative SDS headgroups promote capture of the metal particles on the aggregate surface. Metal adsorption was analyzed in terms of radial density profiles, partial pair distribution functions and adsorption isotherms. It is showed that SDS micelles adsorb better lead than aluminum ions regardless of the size of the aggregates and salt concentrations.

scholarly journals Potential Mean Force for Chitosan and Glyphosate

2020 ◽  
Author(s):  
Roberto Ribeiro Faria ◽  
Lourival Rodrigues de Sousa Neto ◽  
Victor de Sousa Batista ◽  
Keli Cristina Barbosa dos Reis ◽  
Odonírio Abrahão Junior
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Experimental Studies ◽  
High Capacity ◽  
Umbrella Sampling ◽  
Carcinogenic Activity ◽  
Different Temperatures ◽  
Amine Groups ◽  
Jarzynski’S Equality ◽  
Herbicide Glyphosate

Glyphosate is the most widely consumed herbicide in the world and has threatening and harmful properties to living beings due to its chronic toxicity and carcinogenic activity. That is why the proposal to remove glyphosate through chitosan in an aqueous medium arose, due to the high capacity of the biopolymer to chelate contaminants. This can be achieved computationally, simulating models representing real systems, such as the Molecular Dynamics (MD) methodology, mainly in models of atomistic force fields such as OPLS-AA (Optimized Potentials for Atomistic Liquid Simulations) used here, through the computational software GROMACS 4.6 (Groningen Machine for Chemical Simulations). However, this work aims to calculate the Potential Mean Force (PMF) of chitosan and glyphosate binding through 594 simulations by Steered Molecular Dynamics (SMD) using umbrella sampling method, performing the gradual removal of the herbicide in 3 different Cartesian axes ( + x; + y; + z) and in 3 different temperatures (288 K, 298 K, and 308 K) adding 9 systems with 66 simulations for each axis and 198 simulations for each temperature. The glyphosate adsorption process occurs mainly by formation of electrostatic interactions caused by its high polarity groups, such as phosphonate, carboxylate, and amine with the chitosan's groups such as non-acetylated amine groups, primary and secondary hydroxyls. The energy barriers showed very close values in all systems, indicating enough disturbance samples to satisfy Jarzynski's equality. This fact suggested the lack of specificity regarding the axis of untying of the herbicide in relation to chitosan since the great proximity between all the PMF calculations performed was evident. Therefore, the promising potential of chitosan as a glyphosate adsorbent was theoretically confirmed, it agrees with experimental studies of the attempt to remove the herbicide glyphosate in chitosan in desorption processes.

scholarly journals Exploring electrostatic patterns of human, murine, equine and canine TLR4/MD-2 receptors

2019 ◽  
Vol 26 (5) ◽  
pp. 364-380
Author(s):  
Jorge Lozano-Aponte ◽  
Thomas Scior ◽  
Francisco Noé Mendoza Ambrosio ◽  
Minerva González-Melchor ◽  
Christian Alexander
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Protein Complexes ◽  
Structural Features ◽  
Variable Degree ◽  
Phosphate Binding ◽  
Toll Like Receptor 4 ◽  
Sequence Composition ◽  
Myeloid Differentiation Factor ◽  
Phosphate Groups

Electrostatic interactions between phosphate anions and Toll-like receptor 4 / Myeloid differentiation factor-2 (TLR4/MD-2) protein complexes of human, murine, equine and canine species were computed. Such knowledge can provide mechanistic information about recognising LPS-like ligands, since anionic phosphate groups belong to the structural features of LPS with their diphosphorylated diglucosamine backbone. Sequence composition analyses, electrostatic interaction potentials and docked energies as well as molecular dynamics studies evaluated the phosphate interactions within the triangular LPS binding site (wedge). According to electrostatic analyses, human, horse and dog wedges possess phosphate-binding sites with indistinct positive and negative charge distributions, but the murine wedge shows a unique strong negative net charge at the site where antagonists bind in other species (Pan). Docking of a phosphate mono-anion (probe) confirmed its repulsion at this Pan site, but the Pag site of the murine wedge attracted the probe. It is occupied by phosphate groups of agonists in other species (Pag). Molecular dynamics trajectories show a variable degree of random walk across the wedges, that is, not following electrostatic preferences (neither Pag nor Pan). In summary, two opposing electrostatic patterns exist –murine versus human, equine and canine species – all of which reflect the potential dual activity mode of under-acylated ligands such as lipid IVA.

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