Molecular Dynamics Simulations of a Characteristic DPC Micelle in Water

We present the first comparative molecular dynamics investigation for a dodecylphosphocholine (DPC) micelle performed in condensed phase using the CHARMM36, GROMOS53A6, GROMOS54A7, and GROMOS53A6/Berger force fields and a set of parameters developed anew. Our potential consists of newly derived RESP atomic charges, which are associated with the Amber99SB force field developed for proteins. This new potential is expressly designed for simulations of peptides and transmembrane proteins in a micellar environment. To validate this new ensemble, molecular dynamics simulations of a DPC micelle composed of 54 monomers were carried out in explicit water using a “self-assembling” approach. Characteristic micellar properties such as aggregation kinetic, volume, size, shape, surface area, internal structure, surfactant conformation, and hydration were thoroughly examined and compared with experiments. Derived RESP charge values combined with parameters taken from Amber99SB reproduce reasonably well important structural properties and experimental data compared to the other tested force fields. However, the headgroup and alkyl chain conformations or the micelle hydration simulated with the Amber99SB force field display some differences. In particular, we show that Amber99SB slightly overestimates the trans population of the alkyl Csp³–Csp³–Csp³–Csp³ dihedral angle (i.e., CCCC) and reduces the flexibility of the DPC alkyl chain. In agreement with experiments and previously published studies, the DPC micelle shows a slightly ellipsoidal shape with a radius of gyration of ∼17 Å for the different potentials evaluated. The surface of contact between the DPC headgroup and water molecules represents between 70% and 80% of the total micelle surface independently of the force field considered. Finally, molecular dynamics simulations show that water molecules form various hydrogen-bond patterns with the surfactant headgroup, as noted previously for phospholipids with a phosphatidylcholine headgroup

Atomistic Simulations of the Surface Coverage of Large Gold Nanocrystals

Here, the adsorption of alkanethiols (from ethane to dodecanethiol) on icosahedral gold nanocrystals with diameters up to 10 nm is studied by molecular dynamics simulations in a vacuum. The surface coverage of the nanocrystals obtained in the simulations is in good agreement with experimental data. We show that the average surface per adsorbed thiol does not markedly depend on the nanocrystal size and ligand and is only about 10% lower than the value observed on a flat Au(111) surface. We observe two different molecular organizations of the thiolates on the edges and in the centers of the nanocrystal facets. The incompatibility between both organizations explains the fact that the formation of self-assembled monolayers usually observed on flat Au(111) surfaces is hindered for nanocrystals smaller than 6 nm. We also show that the organization of thiolates on the edges is at the origin of the lower average surface per adsorbed thiol found for the nanocrystal