Force Field Parameter Development for the Thiolate/Defective Au(111) Interface

Abstract

A molecular-level understanding of the interplay between self-assembled monolayers (SAMs) of thiolates and gold surface is of great importance to a wide range of applications in surface science and nanotechnology. Despite theoretical research progress of the past decade, an atomistic model, capable of describing key features of SAMs at reconstructed gold surfaces, is still missing. In this work, periodic ab initio density functional theory (DFT) calculations were utilized to develop a new atomistic force field model for alkanethiolate (AT) SAMs on a reconstructed Au(111) surface. The new force field parameters were carefully trained to reproduce the key features, including vibrational spectra and torsion energy profiles of ethylthiolate (C 2 S) in the bridge or staple motif model on the Au(111) surface, wherein, the force constants of the bond and angle terms were trained by matching the vibrational spectra, while the torsion parameters of the dihedral angles were trained via fitting the torsion energy profiles from DFT calculations. To validate the developed force field parameters, we performed classical molecular dynamics (MD) simulations for both pristine and reconstructed Au−S interface models with a (2√3 × 3) unit cell, which includes four dodecanethiolate (C 10 S) molecules on the Au(111) surface. The simulation results showed that the geometrical features of the investigated Au−S interface models and structural properties of the C 10 S SAMs are in good agreement with the ab initio MD studies. The newly developed atomistic force field model provides new fundamental insights into AT SAMs on the reconstructed Au(111) surface and adds advancement to the existing interface research knowledge.

Highly Sensitive Electrochemical Sensor for an miR-200c Assay Based on Ligation-Assisted DNA Strand Displacements

“…Next, the sum of probe C strands from the two subsequent SDA reactions can be consumed in the third SDA at the electrode surface. Hairpin-structured probe D is modified on the surface of the electrode via Au–S interaction . Probe C is able to open the hairpin structure, and the released single-stranded 3′ end captures methylene blue (MB)-labeled probe E by hybridization.…”

“…Hairpin-structured probe D is modified on the surface of the electrode via Au−S interaction. 21 Probe C is able to open the hairpin structure, and the released single-stranded 3′ end captures methylene blue (MB)-labeled probe E by hybridization. In this place, probe E is used as the primer of the third SDA.…”