Two-dimensional molecular recognition studies of the six polyaromatic hydro-carbons that can be formed from the combination of four benzene rings: tetracene, pyrene, 1,2-benzanthracene, 3,4-benzphenanthrene, triphenylene, and chrysene were explored for each of these six molecules interacting with six different graphene layer site-specific nanopores. Computational studies were done for the gas phase adsorption on single layer graphene, bilayer graphene, and six molecule-specific graphene bilayer nanopores. Molecular mechanics MM2 parameters have been shown previously to provide good comparisons to experimental adsorption energies for aromatic hydrocarbons adsorption on graphitic surfaces. These binding energies are dominated by van der Waals forces. Just as a jigsaw puzzle hole can accommodate only a specific piece, two-dimensional shape specific sites were created in the top layer of a graphene bilayer to match each one of the six adsorbate molecules. The purpose of this study was to examine the molecular recognition possibilities of site specific adsorption in these simple two-dimensional nanopores based on dispersion forces and molecular shape. For example, triphenylene has a calculated surface binding energy of 24.5 kcal/mol on the graphene bilayer and 30.2 kcal/mol in its own site specific pore. The interaction energy of this molecule in the other five sites ranged from 17.6 to 23.8 kcal/mol. All the molecules tetracene, pyrene, 1,2-benzanthracene, triphenylene and chrysene had higher binding energies in their matched molecule bilayer sites than on either single or double layer graphene. In addition, each one of these five molecules had a stronger binding in their own shape specific (puzzle-ene) site than any of the other molecular sites. The results suggest that two-dimensional molecular recognition based on shape specific pores may allow selectivity useful for applications such as sensors, separations, nanofabrication, or information storage.
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