Molecular modeling of Tol inside the Pd6L412+ cage to estimate distances between substrate methyl C─H bonds and cage Pd2+ centers
This protocol is extracted from research article:
Ultrafast photoactivation of C─H bonds inside water-soluble nanocages
Sci Adv, Feb 22, 2019; DOI: 10.1126/sciadv.aav4806

The initial coordinates of the Pd6L412+ (Pd, ethylenediamine-palladium) cationic cage were obtained from the Cambridge Crystallographic Data Centre (CCDC number 277006) and optimized using density functional theory (DFT) at a B3LYP/Lanl2dz/6-31G* level of theory. Then, a single Tol molecule was placed close to one of the four triazine moieties of the optimized cationic cage using the distance constraints (see table S1) obtained from 2D ROESY NMR experiments (Fig. 5A). The Tol-cage complex was then minimized in water with the polarizable continuum model (PCM) (67), keeping the cage structure fixed and using the same level of theory mentioned above. For the resultant optimized Tol-cage complex, average distances between all hydrogen atom pairs of Tol and cage and between Tol H and Pd atoms were calculated and compared with NMR ROESY experimental data (see section S1.3).

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