Molecular Dynamics Study on the Self-Assembled Monolayer Grown from a Droplet of Alkanethiol

Abstract

Direct-write lithography, where a nanoscale tip or a stamp serves as a molecular source, is used widely to fabricate self-assembled monolayers (SAMs), nanometers in size. The spatially narrow deposition of molecules creates a droplet, which then spreads to form an ordered SAM. Currently, the dynamics and mechanism for this spreading are largely unknown. Herein, the evolution of a droplet of 1-octadecanethiol into a circular island of SAM, where the sulfur atoms and alkyl chains are densely and orderly packed, was examined by using molecular dynamics simulations. The packing of sulfur atoms preceded the alignment and packing of alkyl chains. The SAM islands resembled the bulk SAM, but it contained defects where the molecules were standing upside down on the surface. We found two mechanisms pertaining to the growth of a SAM island in the direct-write lithography. In the first mechanism, the molecules penetrated into the SAM islands by pushing away the molecules below. In the other mechanism, the molecules diffused, reached the periphery of the SAM islands, and slid down to the surface. The chemisorption of sulfur atoms made the present droplet spread more slowly than a droplet interacting nonspecifically with a surface. A droplet laterally moving across the surface was also simulated to gain insight into the growth of a SAM line. The alkyl chains of the SAM line were directed preferentially toward the line direction.

Structural Characterization of Alkylsilane and Fluoroalkylsilane Self-Assembled Monolayers on SiO2 by Molecular Dynamics Simulations

“…25 To account for thermal and structural disorder from a computational point of view, in particular for quantitatively predicting the change in surface potential induced by the SAM, it is necessary to resort to classical models that allow simulating sufficiently large structures 3 (composed at the very minimum by hundreds of molecules). 26,27 By employing the atomistic molecular dynamics technique, we investigate and compare the microscopic structure of two popular SAMs with different polarity, formed by either n-octadecyltrichlorosilane (OTS) or perfluorodecyltrichlorosilane (FDTS) (Figure 1). The recent simulation literature on octadecyl SAMs on metal surfaces is quite abundant, in particular with many studies by Saha and coworkers describing the SAM stability and its dynamics at different partial coverages on gold substrates.…”

“…The recent simulation literature on octadecyl SAMs on metal surfaces is quite abundant, in particular with many studies by Saha and coworkers describing the SAM stability and its dynamics at different partial coverages on gold substrates. [27][28][29][30][31] Turning to SiO 2 surfaces, alkoxysilane-coated SiO 2 nanoparticles have been simulated both in vacuum 32 and in alkane solvents; 26 Ewers and Batteas also studied functionalized silica interfaces, focusing on the modification of friction and attractive forces introduced by OTS coatings. 33 and forming, to mimic the SAM formation process, 36 but obtaining tilt angles quite far from experimental estimates.…”

Thermal Effect on Positive Patterned Self‐Assembled Monolayer Grown from a Droplet of Alkanethiol

“…Another distinct mechanism, namely hopping down, was accounted by Saha et al for the adsorption of ODT molecules on the bare surface. In the hopping‐down process, the molecules diffuse on top of the SAM island reach to the edge of the SAMs island and slid down to the surface . But, at room temperature, we did not observe such mechanism due to the presence of bulk DDT SAM matrix which restricted this adsorption pathway by causing unavailable space and hindrance.…”

“…In serial pushing mechanism (Fig. ), the numbered molecules sitting on top of the ODT SAM island push the molecules below away, perforate down, and eventually adsorb to the surface . Another distinct mechanism, namely hopping down, was accounted by Saha et al for the adsorption of ODT molecules on the bare surface.…”

“…Theoretical study of orientation, conformation, and the phase separation reproduced the experimental observation for a mixed SAM composed of short‐ and long‐chain alkanethiols, whereas the latter ones form a denser crystalline‐like assembly on spherical gold nanoparticles . Saha et al revealed that the SAM island grown from a droplet of 1‐octadecanethiol (ODT) resembled the bulk SAM in terms of stability and order, but it incorporates defects where the molecules were in an overturned position on the surface . The subjects regarding the range of formation of these structures, the thermal stability, nature of the defects, etc., are still unsettled.…”