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Ekaterina Marchenko

Publications and source records attributed to Ekaterina Marchenko.

2 recordsLinked to original sources

Artificial bees collect diverse conformers of small organic molecules

The conformational mobility of organic molecules defined as a variability of practically accessible conformers plays a critical role in determining electronic, chemical, and physical properties within computational methods. At the same time, there is a challenge of identifying compact set of global and local conformers for the comprehensive description of potential energy surface. Here we apply nature-inspired algorithms to resolve this issue. Among all the considered algorithms, the artificial bee colony optimizer exhibits the highest performance in discovering conformers detected both in gas and condensed phases. We hope that our approach enables researchers to make a next step in organic crystal packing studies.

physics.chem-ph

Transferable and extensible machine learning derived atomic charges for modeling hybrid nanoporous materials

Nanoporous materials have attracted significant interest as an emerging platform for adsorption-related applications. The high-throughput computational screening became a standard technique to access the performance of thousands of candidates, but its accuracy is highly dependent on a partial charge assignment method. In this study, we propose a machine learning model that can reconcile the benefits of two main approaches-the high accuracy of density-derived electrostatic and chemical charge (DDEC) method and the scalability of charge equilibration (Qeq) method. The mean absolute deviation of predicted partial charges from the original DDEC counterparts archive an excellent level of 0.01e. The model, initially designed for metal-organic frameworks, is also capable of assigning charges to another class of nanoporous materials, covalent organic frameworks, with acceptable accuracy. Adsorption properties of carbon dioxide, calculated by means of machine learning derived charges, are consistent with the reference data obtained with DDEC charges.

physics.comp-ph