Molecular dynamics and free energy calculations in unconventional surfactants and proteins

Abstract

Protein solvation is a fundamental process in biology and a detailed understanding of its basic principle is of paramount importance in current research. The study of the solvation properties of proteins in solvents different from water could lead to a better understanding of protein folding and the effects of non-bonded interactions in biological systems. Building upon past experimental and computational studies, the solvation free energies of the side chain analogues of 18 of the natural occurring amino acids are calculated using molecular dynamics simulations in cyclohexane and ethanol. Moreover the entropy-enthalpy balance is carefully assessed by singling out the energetic terms. In parallel, the aggregation properties of unconventional surfactants, synthesized here at the department of molecular science and nano-systems, are also studied. These molecules were experimentally shown to aggregate in an apolar medium without the presence of water. We implement molecular dynamics simulations also for this case both in water and in cyclohexane, and compute the critical micelle concentration (CMC) to guide new experimental studies in this framework.