Theoretical identification of alignments for polypeptides adsorbed onto periodic interfaces, and, Molecular dynamics simulation of alcohol monolayers: A study of structure and thermodynamics

The controlled formation of inorganic minerals and inhibition of ice nucleation by polypeptides are of great importance in crystal engineering and material science. However, identifying the minimum energy alignments for polypeptides adsorbed onto specific interfaces is a challenging problem. We have developed a program referred as POINTER (POlypeptide INTerface E&barbelow;nergy Landscape MappeR&barbelow;) to identify the global minimum energy orientations for polypeptides on specific minerals and ice interfaces. By using a simple force field and Cα, Cβ virtual bond representation, POINTER can identify the chain alignments for our nine benchmark systems.; We also studied the alcohol C31 and C30 monolayers using molecular dynamics simulation with RESPA algorithm in the canonical ensemble. It is well known that alcohol monolayers can induce ice nucleation. But experimental data can not explain why the ice nucleation temperature for super-cooled water under alcohol C31 monolayer is 5.5 degree higher than that for water under alcohol C30 monolayer, even though they both have the similar crystalline structure to serve as the templates for ice nucleation. From our simulation, we have found that the head groups of alcohol C31 monolayer were distributed in a surface with roughness of 0.11 angstrom while the head groups of alcohol C30 monolayer were distributed in a surface with roughness of 0.43 angstrom. The average number of the hydrogen bond between individual alcohol C31 and water molecules is (2.71) greater than the hydrogen bonding number (1.66) of alcohol C30. We conclude that the difference in surface characteristics between alcohol C31 and C30 monolayers leads to a difference in ice nucleation temperature.