Search results for "molecular dynamics"
showing 10 items of 1075 documents
Atomistic Simulations of Functional Au_{144}(SR)_{60} Gold Nanoparticles in Aqueous Environment
2012
Charged monolayer-protected gold nanoparticles (AuNPs) have been studied in aqueous solution by performing atomistic molecular dynamics simulations at physiological temperature (310 K). Particular attention has been paid to electrostatic properties that modulate the formation of a complex comprised of the nanoparticle together with surrounding ions and water. We focus on Au-144 nanoparticles that comprise a nearly spherical Au core (diameter similar to 2 nm), a passivating Au-S interface, and functionalized alkanethiol chains. Cationic and anionic AuNPs have been modeled with amine and carboxyl terminal groups and Cl-/Na+ counterions, respectively. The radial distribution functions show tha…
Increased Acid Dissociation at the Quartz/Water Interface.
2018
As shown by a quite significant amount of literature, acids at the water surface tend to be “less” acid, meaning that their associated form is favored over the conjugated base. What happens at the solid/liquid interface? In the case of the silica/water interface, we show how the acidity of adsorbed molecules can instead increase. Using a free energy perturbation approach in combination with electronic structure-based molecular dynamics simulations, we show how the acidity of pyruvic acid at the quartz/water interface is increased by almost two units. Such increased acidity is the result of the specific microsolvation at the interface and, in particular, of the stabilization of the deprotona…
Molecular dynamics of supercooled polymer films
2000
We present results of molecular dynamics simulations for a supercooled polymer melt confined between two smooth and purely repulsive walls. The thickness D of the film is about 7 times the bulk radius of gyration. For all temperatures studied, a significant increase of the monomer and chain mobilities with respect to the bulk is observed. Preliminary results suggest that structural relaxation times exhibit a power-law behavior in the vicinity of a critical temperature T c (D) 0.39 (in Lennard-Jones units). This estimate of T c (D) is about 14% smaller than the corresponding bulk value. Despite this significant decrease the time dependence of various mean-square displacements seems to be una…
Understanding Noncovalent Interactions of Small Molecules with Carbon Nanotubes
2017
We combine experimental methods, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations in the quantitative analysis of noncovalent interactions between (6,5)-enriched single-walled carbon nanotubes (SWNTs), as hosts, and a set of pyrene derivatives with different electronic properties and surface areas, as guests. The experiments and calculations were carried out in two solvents with markedly different polarities, namely 1,1',2,2'-tetrachloroethane (TCE) and N,N-dimethylformamide (DMF). Our results show that dispersion forces govern the supramolecular association of small molecules with (6,5)-SWNTs, with negligible contributions from ground-state charge-trans…
Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalyzed by HG3.17
2015
A recently designed enzyme, HG3.17, obtained by directed evolution, has shown a catalytic activity close to natural enzymes. Hybrid QM/MM molecular dynamics simulations for the Kemp elimination in this new enzyme have provided a deep insight into the origin of its catalytic efficiency. In this case, we have first demonstrated the presence of different conformations with significantly different reactivity. The larger reactivity is related with a better electrostatic preorganization of the environment that creates a more favorable electrostatic potential for the reaction to proceed. In HG3.17, efforts to improve the catalytic properties must be focused in possible mutations increasing the pre…
Flexible Chirality in Self-Assembled N-Annulated Perylenedicarboxamides.
2017
N-annulated perylenedicarboxamides 1-3 form supramolecular polymers with a strong tendency to aggregate. The bundles of fibers formed generate a spontaneous anisotropy that conditions the chiroptical features of the described molecules in solution; a strong linear dichroism effect accompanies the circular dichroism (CD) outcome. There is no influence of the point chirality existing at the side chains of 1 and 2, and these molecules present the same chiroptical features as achiral 3. Mechanical rotary stirring increases the CD response and the sign of the dichroic signal changes with the stirring direction. Theoretical calculations indicate that the self-assembly of 1-3 in helical columnar s…
A slow process in confined polymer melts: layer exchange dynamics at a polymer solid interface
2010
Employing Molecular Dynamics simulations of a chemically realistic model of 1,4-polybutadiene between graphite walls we show that the mass exchange between layers close to the walls is a slow process already in the melt state. For the glass transition of confined polymers this process competes with the slowing down due to packing effects and intramolecular rotation barriers.
Glassy dynamics in thin polymer films: recent MD results
2002
The influence of a film geometry on the glass transition is investigated via molecular dynamics (MD) simulations of a (non-entangled) polymer melt. The confinement is realized by two identical potential barriers of the form U wall = z -9 , where z denotes the distance of a particle from the wall. Despite the geometric confinement, basic qualitative features of the system dynamics can be well described in the framework of the mode-coupling theory (MCT). Examples are the two-step relaxation of the incoherent intermediate scattering function, the time-temperature superposition property of the late time α-process and the space-time factorization of the scattering function on the intermediate ti…
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…