Molecular Dynamics Study of Naturally Occurring Defects in Self-Assembled Monolayer Formation

Abstract

One of the major challenges for nanofabrication, in particular microcontact printing (mu-CP), is the control of molecular diffusion, or "ink spreading", for the creation of nanopatterns with minimized "smudging" at pattern boundaries. In this study, fully atomistic computer simulations were used to measure the impact of naturally occurring domain boundaries on the diffusion of excess alkanethiol ink molecules on printed alkanethiol self-assembled monolayers (SAM). A periodic unit cell containing approximately one million atoms and with a surface area of 56 nm x 55 nm was used to model a hexadecanethiol SAM on Au(111), featuring SAM domain boundaries and a range of concentrations of excess hexadecanethiol ink molecules diffusing on top. This model was simulated for a total of approximately 80 ns of molecular dynamics. The simulations reveal that domain boundaries impede the diffusion of excess ink molecules and can, in some cases, permanently trap excess inks. There is competition between ink spreading and ink trapping, with the ink/SAM interaction strongly dependent on both the ink concentration and the SAM orientation at domain boundaries. SAM defects thus provide potential diffusion barriers for the control of excess ink spreading, and simulations also illustrate atom-scale mechanisms for the repair of damaged areas of the SAM via self-healing. The ability of domain boundaries to trap excess ink molecules is accounted for using an accessible volume argument, and trapping is discussed in relation to experimental efforts to reduce molecular spreading on SAMs for the creation of ultrahigh resolution nanopatterns.

Probing How Defects in Self-assembled Monolayers Affect Peptide Adsorption with Molecular Simulation

“…The easy preparation of SAMs with different terminal chemical functionalities has made them convenient for far-reaching and numerous applications, including bio-related technologies such as biosensors and medical implants, nano-and microfabrication, nanodevices, and corrosion protection. Experimental microscopy studies have long shown that SAMs have high concentrations of defects [1][2][3]; in some cases, as with the nanofabrication method of microcontact printing, naturally occurring imperfections in the SAMs were shown to play a beneficial role in the process [4]. In most cases, however, defects in the monolayers can have unexpected and perhaps undesirable consequences.…”

“…Though molecular simulation can offer unique insights into the consequences of SAM structural imperfections, it has only rarely been done [5][6][7][8][9]; limitations of small simulation cell sizes and/or insufficient sampling times have prevented the explicit exploration of defects in typical SAM modeling studies [4]. We have employed the enhanced sampling method parallel tempering metadynamics using the well-tempered ensemble (PTMetaD-WTE), which we have used successfully in several prior studies to study peptide/protein adsorption at interfaces [10][11][12].…”

First-principle-based MD description of azobenzene molecular rods

“…Molecular modeling at the classical atomistic level has already proved to be useful in the interpretation of the behavior of a SAM [9,10]; in particular, it has been successfully applied to the study of elastic properties of azobenzene SAMs at the nanoscale [11].…”

Barrier height distribution and dipolar relaxation in metal-insulator-semiconductor junctions with molecular insulator: Ageing effects

“…11,12 Strong covalent grafting produces robust assemblies, however irreversible binding to the semiconductor substrate may lead to substantial fluctuations in molecular packing density and formation of domains with variable average orientation. 1,13,14 In spite of the intrinsic topological disorder of organic monolayers (OML) covalently bound to semiconductor (SC) surfaces, electrical transport properties of such M-OML-SC devices have been widely studied due to their relatively low density of electrically active defects at the OML-Si interface, at least in their as-grown state. 28,32,34,[38][39][40][41][42] Linear saturated (n-alkyl) chains play the role of a nanometer-thick tunnel barrier (TB); however steric molecular constraints do not allow a full passivation of Si(111) surface sites, which remain subject to post-grafting oxidation at the ambient.…”