title: Large-scale molecular dynamics simulations of alkanethiol self-assembled monolayers.
abstract: Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing, and molecular chain length. Our simulations show that the alkanethiol chains of 13-carbons tilt from the surface normal by a collective angle of 25 degrees along next-nearest-neighbor direction at 300 K. The tilt structure of 13-carbon alkanethiol system is found to depend strongly on temperature and exhibits hysteresis. At 350 K the 13-carbon alkanethiol system transforms to a disordered phase characterized by small collective tilt angle, flexible tilt direction, and random distribution of backbone planes. The tilt structure also depends on lattice spacing: With increasing lattice spacing a the tilt angle increases rapidly from a nearly zero value at a=4.7 A to as high as 34 degrees at a=5.3 A at 300 K for 13-carbon alkanethiol system. Finally, the effects of the molecular chain length on the tilt structure are significant at high temperatures.
authors.affiliation: Biological Computation and Visualization Center, Department of Physics & Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
authors.forename: Satyavani
authors.initials: S
authors.lastname: Vemparala
authors.forename: Bijaya B
authors.initials: BB
authors.lastname: Karki
authors.forename: Rajiv K
authors.initials: RK
authors.lastname: Kalia
authors.forename: Aiichiro
authors.initials: A
authors.lastname: Nakano
authors.forename: Priya
authors.initials: P
authors.lastname: Vashishta
mesh_terms: D000473:Alkanes / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D044367:Phase Transition; D013438:Sulfhydryl Compounds / Q000737:chemistry*; D013696:Temperature
chemical_list: D000473:Alkanes; D013438:Sulfhydryl Compounds