Hydrophobic Collapse of Alkanes in Water

The hydrophobic effect is the thermodynamics of interactions between oil and water. Oil-water mixing has been found to have an unusual dependence on temperature, where at a given temperature, a coil-to-globule transition can be entropically or enthapically driven. As the hydrophobic effect has a key role in the biological and chemical processes, such as in the formation of membranes and protein folding, understanding how the temperature and solvent type affect the conformation of large alkanes can have major implications for chemistry and biology. Thus, numerous studies have concentrated on understanding the collapse of long alkane chains and the associated dynamics of these chains in water. We investigate the temperature-induced hydrophobic collapse of tetracontane and icosane in silico with water/ethanol mixtures using replica-exchange molecular dynamics. We use radius of gyration and developed our own method of counting continuous contacts to distinguish collapsed and extended conformation populations in two-dimensional probability density plots. We also found the relative free energy associated with each conformation, the trend in which the relative conformation populations change with temperature and identified the entropy of the system as a thermodynamic property influencing the prevalence of collapsed conformations. We are currently developing diffusion maps to find the dynamical pathways alkane chains take to collapse from a coil to globule conformation.