Numerical calculation of molecular orientation considering Au-S dipole in self-assembled monolayer of helical peptides on gold

We numerically investigate molecular arrangement and orientation in the self-assembled monolayer (SAM) of helical peptide adsorbed on gold, considering dipoles of each amide group in peptides and a dipole due to the Au-S bond at the chemisorption site. We calculate the energy of the SAM in crystals, and in random molecular arrangements by using the Metropolis Monte Carlo method. Comparing these results, we find the most stable arrangement is a crystal. However, the most stable molecular orientation depends on the composition of SAM: A normally standing orientation is most stable when it is a SAM of equimolar mixture of two peptides whose dipole moments are in opposite sense to each other; a tilting orientation is most stable when it is a SAM of one peptide.