title: Ab initio modeling of amide-stabilized, oligo(ethylene glycol)-terminated self-assemblies: in-SAM molecular geometry, orientation, and hydrogen bonding.
abstract: Under the constraint that sulfur atoms form a hexagonal (square root 3 x square root 3)R30 degrees overlayer on the (111) gold surface, the optimized geometry of periodic arrays of HS(CH2)3CONH-(CH2CH2O)3H molecules has been found ab initio, by exploiting the BP86 exchange-correlation functional with 6-31G and "general" basis sets. The obtained data suggests that several prominent features of in-SAM molecular geometry and orientation stand out from conclusions based on single-molecule modeling. In particular, changing of amide-related dihedrals is shown to dominate in adjustment of molecular constituents to the assembly environment and to result in a substantial shortening of the hydrogen bond distance between nearest-neighbor amides. First demonstrated here, the full account to the intermolecular interaction within periodic arrays of amide-bridged, oligo(ethylene glycol)-terminated alkanethiolates forms a new platform for arguable modeling of SAM apparent properties.
authors.forename: Lyuba
authors.initials: L
authors.lastname: Malysheva
authors.forename: Alexander
authors.initials: A
authors.lastname: Onipko
authors.forename: Bo
authors.initials: B
authors.lastname: Liedberg
mesh_terms: D000577:Amides / Q000737:chemistry*; D002627:Chemistry, Physical / Q000379:methods; D019855:Ethylene Glycol / Q000737:chemistry; D006046:Gold / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D013055:Spectrophotometry, Infrared / Q000379:methods; D013499:Surface Properties
chemical_list: D000577:Amides; D006046:Gold; D019855:Ethylene Glycol