Thermodynamics of Malonamide Aggregation Deduced from Molecular Dynamics Simulations

Abstract

The aggregation of malonamide extractants diluted in an aliphatic solvent phase has been studied in the presence of water by molecular dynamics simulation. Using association criteria based on distances between molecules and graphs theory, the aggregate distribution has been computed and the corresponding Gibbs energy of aggregates and mass action law constants have been determined. Finally, a model allowing us to the compute critical micelle concentration and osmotic data for a variable concentration of extractants, with or without a correction of the organic phase activity, was developed. It appears however that the accurate depiction of the aggregation allows modeling the thermodynamics of the solution even without an explicit calculation of the activity: both models give results in good agreement with the experiments.

Long-Range Organization Study of Piperidinium-Based Ionic Liquids by Polarizable Molecular Dynamics Simulations

“…In order to probe the size of polar and apolar microdomains in [EBPip + ]­[NTf 2 – ] and [EOPip + ]­[NTf 2 – ] and compare them to those obtained in imidazolium-based ILs, we used the statistical tool introduced in the study of Shimizu et al which gives the average domain size by where P ( N a ) is the probability of finding an atom in a domain of size N a , SN a is the domain number of size N a , n F is the total frame number used in the computation, and n tot is the total atom number. The aggregates’ distribution as a function of their size S N a was obtained from the graph theory as the one developed in the study of Vatin et al For the polar domain, the C ring and A mid CoMs were chosen to define the aggregation with a minimum distance of 8.8 Å, that is, the minimum of the g ( r ) first peak (Figure S5). As in the study of Shimizu et al, we demonstrated that the polar network is continuous regardless of the size of the cation carbon tail.…”

Mesostructuring in Liquid–Liquid Extraction Organic Phases Originating from Critical Points

“…At high concentration, polar regions of DMDBPMA head groups and nonpolar regions of aliphatic tails and solvent are interspersed in a bicontinuous-like fashion. Malonamide self-association is quantified by cluster analysis, an intuitive description of amphiphile aggregation that is accessible from simulation trajectories, ,− as described in the Supporting Information. Cluster size distributions are plotted in Figure .…”

“…A connection between the Ornstein–Zernike correlation length and simulation clustering is desirable: it would link the former, an experimentally observable feature of interest, to the latter, a physically intuitive description of solution structure that is commonly applied to quantify extractant aggregation. ,, To that end, we compute a cluster correlation length, ξ cluster , from the malonamide clusters to qualitatively compare with ξ O‑Z . Here, ξ cluster is defined for N total molecules by where r ij is the distance between molecules i and j with δ ij being unity if the molecules are on the same cluster and zero otherwise .…”

Improved delivery and competitive adsorption of paclitaxel and mitomycin C anticancer drugs on boron nitride nanoparticles: a molecular dynamics insight

“…In order to simulate biological phenomena, molecular dynamics simulation methods provided more reliable results. 67–69 Here, all simulations were done using the NAMD-2.12 package 70 with the force field of CHARMM-36. 71 The VMD 72 program was also used for visualization and graphical analyses.…”