Graph theory approach to determine configurations of multidentate and high coverage adsorbates for heterogeneous catalysis
Abstract Heterogeneous catalysts constitute a crucial component of many industrial processes, and to gain an understanding of the atomic-scale features of such catalysts, ab initio density functional theory is widely employed. Recently, growing computational power has permitted the extension of such studies to complex reaction networks involving either high adsorbate coverages or multidentate adsorbates, which bind to the surface through multiple atoms. Describing all possible adsorbate configurations for such systems, however, is often not possible based on chemical intuition alone. To systematically treat such complexities, we present a generalized Python-based graph theory approach to convert atomic scale models into undirected graph representations. These representations, when combined with workflows such as evolutionary algorithms, can systematically generate high coverage adsorbate models and classify unique minimum energy multidentate adsorbate configurations for surfaces of low symmetry, including multi-elemental alloy surfaces, steps, and kinks. Two case studies are presented which demonstrate these capabilities; first, an analysis of a coverage-dependent phase diagram of absorbate NO on the Pt 3 Sn(111) terrace surface, and second, an investigation of adsorption energies, together with identifying unique minimum energy configurations, for the reaction intermediate propyne (CHCCH 3 *) adsorbed on a PdIn(021) step surface. The evolutionary algorithm approach reproduces high coverage configurations of NO on Pt 3 Sn(111) using only 15% of the number of simulations required for a brute force approach. Furthermore, the screening of potentially hundreds of multidentate adsorbates is shown to be possible without human intervention. The strategy presented is quite general and can be applied to a spectrum of complex atomic systems.