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Supramolecular Recognition in Crystalline Nanocavities Through Monte Carlo and Voronoi Network Algorithms

submitted on 09.11.2020, 23:15 and posted on 10.11.2020, 12:15 by Daniel Schwalbe-Koda, Rafael Gomez-Bombarelli
Computational screening of templating molecules enables the discovery of new synthesis routes for zeolites. Despite decades of work in molecular modeling of organic structure-directing agents (OSDAs), the development and benchmarking of algorithms for docking molecules in nanoporous materials has received scarce attention. Here, we introduce Voronoi Organic-Inorganic Docker (VOID) a method based on Voronoi diagrams to dock molecules in crystalline materials, and release it as a Python package. Benchmarks of the implementation show it generates docked poses up to 95 times faster than the traditional Monte Carlo docking scheme. We then evaluate the algorithm by obtaining binding energies for about 120 zeolite-OSDA pairs of industrial relevance. The computed host-guest interactions explain experimental outcomes for traditional synthesis routes from the literature. The results further suggest new OSDAs to synthesize known zeolites. Finally, we exemplify the generality of VOID by docking molecules inside a metal-organic framework and on a metal surface. The proposed method and software provide a low-cost computational approach for generating molecule-material interfaces.


MIT Energy Initiative Seed Fund

MIT Energy Fellowship

MIT International Science and Technology Initiatives Seed Fund


Email Address of Submitting Author


Massachusetts Institute of Technology


United States of America

ORCID For Submitting Author


Declaration of Conflict of Interest

No conflict of interest

Version Notes

initial submission