Graph theory-based exploration of structure and dynamics of surface organometallic catalysis

• MD-graph theory integration explores catalyst configurational space intuitively. • Graph theory distinguishes meaningful isomers from conformers in MD trajectories. • Local amorphous support strain significantly influences active site diversity. Capturing the dynamic behavior of active sites on complex, amorphous supports is a significant challenge in modeling single-site catalysts, particularly in surface organometallic catalysts. These systems are characterized by a well-defined chemical bonding pattern that coexists with the fluxionality of ancillary ligands and the inherent complexity of the support. Here, we present a conceptual workflow that integrates reactive molecular dynamics with advanced graph theory-based analysis to systematically explore the configurational space of supported catalysts. First, we used enhanced molecular dynamics to overcome local energy barriers and generate a diverse ensemble of structures. Then, we applied graph-based algorithms to distinguish truly distinct isomers from mere conformers and rotamers. Applying this approach to the model system of 1,1′-bis(n-butyl-cyclopentadienyl) zirconium dihydride on a dehydrated amorphous silica model, our method reveals the significant role of local silica strain in shaping the ensemble of active site configurations: catalysts grafted on silanol groups with strained confinement exhibit a diverse array of reaction pathways and significant energy stabilization, whereas less-strained environments yield a more restricted set of accessible configurations. This work demonstrates that combining molecular dynamics with graph theory provides an intuitive framework for unraveling the complex, fluxional behavior of supported catalysts.