Single molecular insight into steric effect on C-terminal amino acids with various hydrogen bonding sites

Abstract

Amino acids are basic units to construct a protein with the assistance of various interactions. During this building process, steric hindrance derived from amino acid side groups or side chains is a factor that could not be ignored. In this contribution, adsorption behaviors of C-terminal amino acid derivatives with amino acid residues fused in 3,4,9,10-perylenetetracarboxylic dianhydride were investigated by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations at various liquid/solid interfaces. STM results at 1-phenyloctane/HOPG interface show that N,N'-3,4,9,10-perylenedicarboximide (GP) and N,N'-methyl-3,4,9,10-perylenedicarboximide (AP) formed linear and herringbone structures, respectively. The driving force could be attributed to different H-bonding sites induced by steric hindrance at side groups. N,N'-Benzyl-3,4,9,10-perylenedicarboximide (PP) generates both linear and herringbone structures because steric hindrance changes the H-bonding sites between PP molecules, whereas N,N'-isopropyl-3,4,9,10-perylenedicarboximide (LP) failed to be imaged because of strong steric hindrance coming from larger side group. To further investigate the impact of steric hindrance, we utilized octanoic acid (OA) as solvent to capture the adsorption details of LP and PP. We found that OA molecules drag PP and LP molecules in a different direction to generate linear structure, impeding the molecular rotation. The structure–solvent relationship shows that the steric hindrance is brought by the large side group, which makes it easier to recognize OA molecules at the interface. These results demonstrate that steric effect plays a significant role in altering interaction sites of the compounds during the adsorption process at the liquid/solid interface.