Polycyclic Aromatic Hydrocarbon Molecule-Surface Binding Energies in Site Specific Graphene Bilayer Nanopores: A Puzzle-ene Force Field Calculation

Abstract

Two-dimensional molecular recognition studies of the six polyaromatic hydrocarbons 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.

Modeling Enhanced Adsorption of Explosive Molecules on a Hydroxylated Graphene Pore

“…In addition, by considering molecule-molecule nearest neighbor interactions, calculated monolayer coverage binding energies also compared well to thermal program desorption (TPD) experiments. For example, TPD experiments and MM2 calculations for monolayer desorption gave 0.50 and 0.52, 0.72 and 0.71, and 1.41 and 1.47 eV for benzene, o-dichlorobenzene, and coronene, respectively [28]. When calculating the theoretical moles of a low concentration adsorbate adhering to a surface or surface site, the viral coefficient of physical adsorption may be considered [30].…”

“…Again, most of the interaction was from van der Waal's forces, and the newly designed pore successfully attracted the TNT molecule down into the bilayer's pore. In a prior study, the adsorption was enhanced for different shaped polycyclic aromatic hydrocarbons (PAH) by pores with matching shaped flat graphene bilayer pores[28].…”

Clar Covers of Overlapping Benzenoids: Case of Two Identically-Oriented Parallelograms

“…Benzenoid hydrocarbons are an intensively studied class of aromatic molecules attracting attention of scientists specializing in various fields of chemistry including organic synthesis [1,2] and characterization [3][4][5], combustion chemistry [6,7], nanoscience [8,9], atmospheric chemistry [10,11], astrochemistry [12,13], computational chemistry [14,15], and chemical graph theory [16,17]. Enumeration and construction of Clar covers for benzenoid hydrocarbons constitutes one of the important branches of chemical graph theory.…”

“…These two interfaces-intersected by the blue elementary cuts I 8 and I 9 (a) and I 7 and I 14 (b) in Figure 5-can be characterized as the interfaces containing, respectively, the leftmost and rightmost interface bonds of the intersection region M(µ, ν). Let us denote by o µ ≡ ord(i n 2 +m 2 −µ ) and o ν ≡ ord(i n 2 +m 2 −ν ) the interface orders of these two interfaces as determined from Equation (8). For the two structures MvM shown in Figure 5…”