Search results for "molecular dynamics"

Selective recognition of aromatic hydrocarbons by endo-functionalized molecular tubes via C/N-H⋅⋅⋅π interactions

2018

Abstract Molecular recognition of aromatic hydrocarbons by four endo -functionalized molecular tubes has been studied by 1 H NMR spectroscopy, computational methods, and single crystal X-ray crystallography. The binding selectivity is rationalized by invoking shape complementarity and dipole alignment. The non-covalent interactions are proved to predominantly be C/N-H⋅⋅⋅ π interactions.

Computer Simulations of Undercooled Fluids and Glasses

2007

An introduction to the Molecular Dynamics (MD) simulation of chemically realistic models for undercooled fluids and glasses is given, emphasizing silicatic materials such as molten silicon dioxide and its mixtures with sodium oxide and aluminium oxide, and comparing the simulation results to experimental data whenever possible.

Energetic analysis of succinic acid in water droplets: insight into the size-dependent solubility of atmospheric nanoparticles

2021

<p>Size-dependent solubility is prevalent in atmospheric nanoparticles, but a molecular level understanding is still insufficient, especially for organic compounds. Here, we performed molecular dynamics simulations to investigate the size dependence of succinic acid solvation on the scale of ~1-4 nm with the potential of mean forces method. Our analyses reveal that the surface preference of succinic acid is stronger for a droplet than the slab of the same size, and the surface propensity is enhanced due to the curvature effect as the droplet becomes smaller. Energetic analyses show that such surface preference is primarily an enthalpic effect in both systems, while the entropi…

Density functional/molecular dynamics simulations of phase-change materials

2013

Computational methods and theory for ion channel research

2022

Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.

Liquid structure of a choline chloride-water natural deep eutectic solvent: A molecular dynamics characterization

2021

The liquid structure of a representative of the first water-in-salt (WiS) Natural Deep Eutectic Solvents (NADES), hereinafter indicated as aquoline, a mixture of choline chloride (ChCl) and water with molar ratio 1:3.33, is ex- plored at ambient conditions. Using Molecular Dynamics (MD) simulation tools, we extract structural informa- tion at atomistic level on the nature of inter-correlations between the different moieties. Despite being a very fluid liquid, with much lower viscosity than other common ChCl-based DES, aquoline turns out to be very struc- tured. Computed X-ray and neutron weighted scattering patterns (the latter also on selectively deuterated mix- tures) highlight the existe…

Structural Features of β-Cyclodextrin Solvation in the Deep Eutectic Solvent, Reline

2020

The inherently amphiphilic nature of native cyclodextrins (CDs) determines their peculiar molecular encapsulation features, enabling applications such as targeted drug nanodelivery, aroma protection, etc. On the contrary, it may also lead to poor solubility in water and other organic solvents and to potentially detrimental flocking in these media, thus posing limitations to more extensive usage. Here we use small angle X-ray scattering to show that deep eutectic solvent reline (1:2 choline chloride:urea) succeeds in dissolving large amounts of beta-CD (at least 800 mg/mL, compared with the solubility in water of 18 mg/mL), without aggregation phenomena occurring. At the microscopic level, m…

What Contributes to the Measured Chiral Optical Response of the Glutathione-Protected Au25 Nanocluster?

2023

The water-soluble glutathione-protected [Au25(GSH)18]−1 nanocluster was investigated by integrating several methodologies such as molecular dynamics simulations, essential dynamics analysis, and state-of-the-art time-dependent density functional theory calculations. Fundamental aspects such as conformational, weak interactions and solvent effects, especially hydrogen-bonds, were included and found to play a fundamental role in assessing the optical response of this system. Our analysis demonstrated not only that the electronic circular dichroism is extremely sensitive to the solvent presence but also that the solvent itself plays an active role in the optical activity of such system, formin…

Dynamics and toxicity of proteins with a high homology of sequences: approach by molecular dynamics and ab-initio calculations

2008

The elucidation of the structure and the biological function of proteins is a major stake for its implications in the biomedical research as well as in biotechnologies. In addition, there is a glass or dynamical transition for the proteins which occurs at around 200K: it has been observed by Neutron Scattering, X-ray diffraction and Mossbauer spectroscopy for different proteins. Above the transition temperature, the biological function is activated as the protein may diffuse between conformational sub-states. The microscopic origin of this transition is still debated in spite of significant advances in recent years showing the significant role of hydration. By using all-atoms classical mole…

Structural behaviour differences in low methoxy pectin solutions in the presence of divalent cations (Ca 2+ and Zn 2+ ): a process driven by the bind…

2014

International audience; In this paper, we compare the interactions between low methoxy pectin (LMP) and either Ca2+ or Zn2+ in semi-dilute solutions. Intrinsic viscosity and turbidity measurements reveal that pectin-calcium solutions are more viscous, but yet less turbid, than pectin-zinc ones. To get a molecular understanding on the origin of this rather unexpected behavior, we further performed isothermal titration calorimetry, small angle neutron scattering experiments, as well as molecular dynamics simulations. Our results suggest that calcium cations induce the formation of a more homogeneous network of pectin than zinc cations do. The molecular dynamics simulations indicate that this …