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Benchmarking binding energy calculations for organic structure-directing agents in pure-silica zeolites

revised on 21.01.2021, 02:28 and posted on 22.01.2021, 06:42 by Daniel Schwalbe-Koda, Rafael Gomez-Bombarelli
Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, there is no consensus on the best calculation strategy for high-throughput virtual screening undertakings. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. Enabled by automation software, we show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and provide robust and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.


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