Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Host–guest inclusion complexes between peracetylated β-cyclodextrin and diphenyl(4-phenylphenyl)phosphine : computational studies
2006
PM3 and molecular dynamic calculations were performed upon the inclusion complexation of peracetylated β-cyclodextrin (Per-Ac-β-CD) with diphenyl(4-phenylphenyl)phosphine (DBP). Results show that the 4-phenylphenyl part of the DBP phosphine fits tightly in the cavity of the Per-Ac-β-CD, leading to the formation of stable inclusion complexes. Complexation energies indicate that the complex formed via the primary side of the Per-Ac-β-CD is more stable than that formed via the secondary side. Electrostatic potential mapping and frontier orbital analysis suggest that van der Waals interaction constitute a major driving force in the complexation of the DBP and Per-Ac-β-CD.
Interactions between proteins and poly(ethylene-glycol) investigated using molecular dynamics simulations
2017
Poly(ethylene-glycol) (PEG) is a polymer used to coat therapeutic preparations, like drugs or drug nanocarriers, and improve their efficacy. This effect is probably due to a reduction of the interactions of the coated species with the host organism. Nevertheless, experiments show that PEGylated materials do interact with the surrounding biological milieu, and in particular with blood proteins. Here, we use atomistic molecular dynamics simulations to characterize the interactions between the polymer and several blood proteins. In these simulations, the proteins are immersed in a mixture of PEG and water molecules. We observe how PEG distributes around the protein surface and measure PEG-prot…
Interactions Between Blood Proteins and Nanoparticles Investigated Using Molecular Dynamics Simulations
2019
In the development of new therapeutic agents based on nanoparticles it is of fundamental importance understanding how these substances interact with the underlying biological milieu. Our research is focussed on simulating in silico these interactions using accurate atomistic models, and gather from these information general pictures and simplified models of the underlying phenomena. Here we report results about the interactions of blood proteins with promising hydrophilic polymers used for the coating of therapeutic nanoparticles, about the salt dependent behavior of one of these polymers (poly-(ethylene glycol)) and about the interactions of blood proteins with silica, one of the most used…
Stability of negatively charged platelets in calcium-rich anionic copolymer solutions.
2014
Controlling the stability of anisotropic particles is key to the development of advanced materials. Here, we report an investigation, by means of mesoscale molecular dynamics simulations, of the stability and structural change of calcium-rich dispersions containing negatively charged nanoplatelets, neutralized by calcium counterions, in the presence of either comb copolymers composed of anionic backbones with attached neutral side chains or anionic-neutral linear block copolymers. In agreement with experimental observations, small stacks of platelets (tactoids) are formed, which are greatly stabilized in the presence of copolymers. In the absence of polymers, tactoids will grow and aggregat…
Thermodynamics and Kinetics of the Interactions Between Proteins and Hydrophilic Polymers
2021
Hydrophilic polymers are being investigated as possible coating agents for therapeutic nanoparticles because of their capacity to reduce immune response and increase circulation life time. The mechanism of action of these coatings is not well understood although it is clear that they unspecifically reduce the amount of proteins adsorbing on the nanoparticle surface coming in contact with biological fluids. Here we have investigated, using state-of-the-art atomistic molecular dynamics simulations, the equilibrium and kinetic properties of the interactions forming between human serum albumin, the most abundant protein in the blood stream, and two different and promising polymers poly(ethylene…
Phase Separation and Nematic Order in Lyotropic Solutions: Two Types of Polymers with Different Stiffnesses in a Common Solvent
2021
The interplay of the isotropic-nematic transition and phase separation in lyotropic solutions of two types of semiflexible macromolecules with pronounced difference in chain stiffness is studied by Density Functional Theory and Molecular Dynamics simulations. While the width of the isotropic-nematic two-phase coexistence region is narrow for solutions with a single type of semiflexible chain, the two-phase coexistence region widens for solutions containing two types of chains with rather disparate stiffness. In the nematic phase, both types of chains contribute to the nematic order, with intermediate values of the order parameter compared to the corresponding single component solutions. As …
Compression-induced anti-nematic order in glassy and semicrystalline polymers
2020
We provide new insights into the molecular origin of the asymmetry between uniaxial tensile and compressive deformation of glassy and semicrystalline polymers using molecular dynamics simulations. The difference between the two responses strongly depends on the chain length and is the largest at intermediate chain lengths. Irrespective of chain length, the intra- and interchain organization of polymers under extension and compression are remarkably distinct. The chains align along the tensile axis leading to a global nematic order of the bonds and end-to-end vectors, whereas compression reorganizes polymers to lie in planes perpendicular to the compressive axis resulting in the emergence of…
Structure and dynamics of dibutylphosphate/n-propylamine ionic liquid: A multi-scale theoretical study
2021
Abstract Owing to the amphiphilic nature of their constituent molecules, binary mixtures of pure liquid surfactants are usually characterized by enhanced nano-segregation and thus can exhibit interesting transport properties and complex macroscopic behavior. In this ambit it was recently shown by Turco Liveri et al. (2018) that mixtures of short aliphatic chains compounds at room temperature, such as dibutyl phosphate (DBP) and n-propylamine (PA) liquids, display ionic liquid–like behavior ascribed to phosphate-to-amine proton transfer. To gain a detailed molecular picture of the system structure and dynamics and to understand the molecular mechanisms at the basis of the observed behavior, …
GLASS TRANSITION IN THIN POLYMER FILMS: A MOLECULAR DYNAMICS STUDY
2002
A melt of nonentangled polymer chains confined between two smooth and purely repulsive walls is studied for various film thicknesses D and temperatures. The dynamics of the supercooled films is qualitatively identical to that of the bulk, but the walls lead to faster relaxation. To quantify this observation we analyze the data by the mode-coupling theory (MCT) of the glass transition. We find that the critical temperature of MCT, Tc(D), decreases with D and that T - Tc(D) is a relevant temperature scale. The static structure factor and dynamic correlation functions at intermediate times coincide with bulk behavior when compared to the same T - Tc(D).
Dynamics of weak interactions in the ligand layer of meta-mercaptobenzoic acid protected gold nanoclusters Au68(m-MBA)32 and Au144(m-MBA)40
2020
Atomically precise metal nanoclusters, stabilized and functionalized by organic ligands, are emerging nanomaterials with potential applications in plasmonics, nano-electronics, bio-imaging, nanocatalysis, and as therapeutic agents or drug carriers in nanomedicine. The ligand layer has an important role in modifying the physico-chemical properties of the clusters and in defining the interactions between the clusters and the environment. While this role is well recognized from a great deal of experimental studies, there is very little theoretical information on dynamical processes within the layer itself. Here, we have performed extensive molecular dynamics simulations, with forces calculated…