Evaluation of packing single and multiple atoms and molecules in the porous organic cage CC3-R

The absorption of multiple atoms and molecules, including Kr, Xe, CH₄, CO₂, C₂H₂, H₂O, and SF₆, within CC3-R, a Porous Organic Cage (POC), was calculated and analyzed. The CC3-R molecule has one central cavity and four window sites. Most adsorbents were modeled with either one unit in the central cavity, four units in the window sites, or with five units in both sites. For Xe, the most favorable site was the central one. The CO₂ molecule binds about 3 kcal mol^-1 in free energy more strongly than CH₄ in the central cavity of CC3-R at 300 K which may be enough to allow useful discrimination. Four C₂H₂ units and four CO₂ units are calculated to bind similarly inside CC3-R (ΔH(298 K) = -8.6 and -7.7 kcal mol^-1 per unit, respectively). Since H₂O is smaller, more waters can easily fit inside. For twelve water molecules, the binding enthalpy per water is ΔH(298 K) = -16.4 kcal mol^-1. For comparison, the binding enthalpy of (H₂O)₁₂ at the same level of theory (B3LYP/6-31G(d,p)-D3BJ//M06-2X/6-31G(d)) is predicted to be -12.3 kcal mol^-1 per water. Finally, the dimerization of CC3-R and the association of CC3-R with CC3-S was studied as well as 3 to 9 iodine atoms enclosed in CC3-R.