Interaction of the (2 root 3 x 3)rect. Adsorption-Site Basis and Alkyl- Chain Close Packing in Alkanethiol Self-Assembled Monolayers on Au(111): A Molecular Dynamics Study of Alkyl-Chain Conformation

S Bhattacharya and MP Yothers and LL Huang and LA Bumm, ACS OMEGA, 5, 13802-13812 (2020).

DOI: 10.1021/acsomega.0c01111

We show that the adsorption site basis of the (2 root 3 x 3)rect. phase of n-alkanethiol self-assembled monolayers plays a key role in determining the molecular conformation of the close-packed alkyl chains. Ten proposed reconstructed Au-S interfaces are used to explore the minimized energy alkyl-chain packing of n-decanethiol molecules using molecular dynamics with the all-atom description. In this comparative study, all models have the same alkyl-chain surface density of four molecules per unit cell; thus, Alkyl Chain Conformation differences are due to the headgroup spacing within the 4-molecule basis as opposed to the average surface density. We demonstrate for the first time the 4 -molecule-basis twist structure driven by the packing of alkanethiol molecules in a large simulation box (100 molecules, 25 unit cells) using molecular dynamics. Our results validate the prediction put forward by Mar and Klein that to achieve the 4-molecule-basis twist symmetry observed by the experiment, the headgroups must deviate from the high- symmetry (root 3 x root 3)R30 degrees sites. The key structural parameters: tilt, twist, and end-group height, as well as their spatial order, are compared with experimental results, which we show is a highly sensitive approach that can be used to vet proposed Au-S interfacial models.

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