Accurate Estimates of Infinite-Dilution Chemical Potentials of Small Hydrocarbons in Water via Molecular Dynamics Simulation

Methanol as a hydrate inhibitor and hydrate activator

During their transport to processing plants, produced hydrocarbon streams are always accompanied by water appearing as a separate phase in contact with the hydrocarbons. Dramatic temperature and pressure changes during processing can lead to condensation of water and possibly hazardous formation of ice and hydrates. Historically, methanol has been the dominating chemical agent added to prevent the formation of solid water phases. In this work, the technique of molecular dynamics simulation has been utilized to investigate and illustrate the impact of methanol as a surfactant in a water-methane system. We have found that adding 5% of methanol boosted the diffusion of methane through the interface by more than 40% compared to the reference system. The amount of methane accumulated in the aqueous phase was also significantly higher. This effect will likely also result in a significant increase in homogeneous and heterogeneous hydrate formation in these regions in the case of the methanol-stimulated system, and thus necessitate the application of classical nucleation theory. In particular, our analysis emphasised the fact that several different hydrates may form in this scenario. In case of the homogeneous hydrate formation, there will theoretically exist an infinite number of hydrate phases corresponding to concentrations spanning the range between methane's solubility and its hydrate stability limit.

Density functional theory for protein transfer free energy

We cast the problem of protein transfer free energy within the formalism of density functional theory (DFT), treating the protein as a source of external potential that acts upon the solvent. Solvent excluded volume, solvent-accessible surface area, and temperature dependence of the transfer free energy all emerge naturally within this formalism, and may be compared with simplified "back of the envelope" models, which are also developed here. Depletion contributions to osmolyte induced stability range from 5 to 10 kBT for typical protein lengths. The general DFT transfer theory developed here may be simplified to reproduce a Langmuir isotherm condensation mechanism on the protein surface in the limits of short-ranged interactions, and dilute solute. Extending the equation of state to higher solute densities results in non-monotonic behavior of the free energy driving protein or polymer collapse. Effective interaction potentials between protein backbone or side chains and TMAO are obtained, assuming a simple backbone/side chain two-bead model for the protein with an effective 6-12 potential with the osmolyte. The transfer free energy δg shows significant entropy: d(δg)/dT ≈ 20 kB for a 100-residue protein. The application of DFT to effective solvent forces for use in implicit-solvent molecular dynamics is also developed. The simplest DFT expressions for implicit-solvent forces contain both depletion interactions and an "impeded-solvation" repulsive force at larger distances.

Hybrid integral equation/simulation model for enhancing free energy computations

Integral equation theory is used for extrapolating free energy data from molecular simulations of a reference state with respect to a modification of the interaction potential. The methodology is applied to the correction of artefacts arising from potential shifting and truncation. Corrective contributions for the hydration free energy with respect to the full potential are analysed for the case that both the solute-solvent as well as the solvent-solvent potentials are truncated and modified by a shifted-force term, reaching beyond the range of the dielectric continuum approximation and simple long-range correction expressions. The model systems argon in water and pure water are used as examples for apolar and polar solutes, revealing significant correction contributions even for the short-ranged dispersive interactions and the magnitude of solute-solvent and solvent-solvent components. In comparison with simulation-based extrapolation techniques the integral equation method is shown to be capable of quantitatively predicting truncation artefacts at negligible computational overhead.

On the use of the quasi-Gaussian entropy theory in the study of simulated dilute solutions

In a recent paper [M. D'Alessandro, M. D'Abramo, G. Brancato, A. Di Nola, and A. Amadei, J. Phys. Chem. B 106, 11843 (2002)] we showed how to combine molecular dynamics simulations with the quasi-Gaussian entropy theory, in order to model the statistical mechanics and thermodynamics of ionic (water) solutions. In this paper we extend the method to treat nonspherical solutes, describe more thoroughly its theoretical basis and apply it to a set of more complex solute molecules in water (i.e., water, methane, ethane, methanol, and ethanol). Results show that this approach can really provide an excellent theoretical description of solute-solvent systems over a wide range of temperatures.

Molecular theory of hydrophobic effects: "She is too mean to have her name repeated."

This paper reviews the molecular theory of hydrophobic effects relevant to biomolecular structure and assembly in aqueous solution. Recent progress has resulted in simple, validated molecular statistical thermodynamic theories and clarification of confusing theories of decades ago. Current work is resolving effects of wider variations of thermodynamic state, e.g., pressure denaturation of soluble proteins, and more exotic questions such as effects of surface chemistry in treating stability of macromolecular structures in aqueous solution.