Molecular dynamics simulations have been used to study the formation of nanoscale islands of self-assembled monolayers (SAMs) starting from alkanethiol molecules initially lying down in a disordered physisorbed layer on gold. These islands form when tens of alkane thiols stand up together within tens of ns after chemisorption begins. The alkane chains in these islands are found to be tilted, and the tilt direction precesses around the center of the island. This precession, together with the packing of the sulfur atoms, signals the formation of a SAM island, occurring prior to the tilting and orientation ordering of the chains.

A subnanometer gap-separated linear chain gold nanoparticle (AuNP) silica nanotube peapod (SNTP) was fabricated by self-assembly. The geometrical configurations of the AuNPs inside the SNTPs were managed in order to pose either a single-line or a double-line nanostructure by controlling the diameters of the AuNPs and the orifice in the silica nanotubes (SNTs). The AuNPs were internalized and self-assembled linearly inside the SNTs by capillary force using a repeated wet-dry process on a rocking plate. Transmission electron microscopy (TEM) images clearly indicated that numerous nanogap junctions with sub-1-nm distances were formed among AuNPs inside SNTs. Finite-dimension time domain (FDTD) calculations were performed to estimate the electric field enhancements. Polarization-dependent surface-enhanced Raman scattering (SERS) spectra of bifunctional aromatic linker p-mercaptobenzoic acid (p-MBA)-coated AuNP-embedded SNTs supported the linearly aligned nanogaps. We could demonstrate a silica wall-protected nanopeapod sensor with single nanotube sensitivity. SNTPs have potential application to intracellular pH sensors after endocytosis in mammalian cells for practical purposes. The TEM images indicated that the nanogaps were preserved inside the cellular constituents. SNTPs exhibited superior quality SERS spectra in vivo due to well-sustained nanogap junctions inside the SNTs, when compared to simply using AuNPs without any silica encapsulation. By using these SNTPs, a robust intracellular optical pH sensor could be developed with the advantage of the sustained nanogaps, due to silica wall-protection.

In this study, the cost of working electrode was reduced greatly by replacing glassy carbon electrode (GCE) with 2B pencil. The pencil lead was modified with carbon nanotubes (CNTs) for simultaneous and quantitative detection of hydroquinone (HQ) and catechol (CT). The surface morphology of CNT-modified pencil electrode (PE-CNT) was studied by scanning electron microscopy (SEM) whereas electron transfer properties were evaluated through electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). This electrode evinced an enhanced redox reversibility and superior electrocatalytic performance concerning HQ and CT. Consecutive concentration variation studies exhibited linearity in oxidation peak responses up to 300 μM for each of the analytes with a detection limit (S/N = 3) as low as 1.5 and 0.7 μM for HQ and CT, respectively. We proposed a possible mechanism for their sensitive detection. The developed sensor was successfully examined for real sample analysis with tap water and it exhibited a stable and reliable recovery data with high reproducibility. The cost of the 2B pencil is 1000 times lower than that of GCE. Thus, the 2B pencil can be a good alternative to GCE in electrochemical sensor fabrication due to its economic advantage.

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.

Using molecular dynamics simulations, we show that the minimum diameter of ordered self-assembled monolayer (SAM) structures of alkanethiols on Au(111) is 1.9 nm at room temperature. This presumably sets the ultimate resolution of the SAM patterns created by nanolithography. For SAMs larger than 1.9 nm, the tilt direction of the alkyl chain precesses around the center of the SAM. This precession changes direction on a time scale that increases from picoseconds to nanoseconds as the SAM size varies from 2 to 3 nm.