Understanding partial charges has implications for molecular modeling, especially computational exploration of drug-protein binding. Charge density refinement refers to the refinement of a diffuse electron density model to fit X-ray diffraction (XRD) data. Unlike standard whole-atom-model refinement, which uses spherical neutral atoms, in more realistic models the distribution of charge across the molecule varies. A common problem when modeling atomic partial charges using computation is that the computed charges vary depending on the method used. We are developing a simplified approach to partial charge determination by partial-occupancy refinement of a spherical atom model of X-ray crystal structure. XRD data for 1-butyl-2,3-bis(dicyclohexylamino)cyclopropenimine has been collected and its structure has been elucidated. Partial charge determination will be performed using our novel variable occupancy refinement technique developed in our lab. 1-butyl-2,3-bis(dicyclohexylamino)cyclopropenimine has a disordered alkyl chain, which will be used to probe how molecular disorder affects the determination of partial atomic charge. Also presented will be partial charge analysis on novel transition metal complexes synthesized in our lab.

Partial-occupancy analysis of unknown organic crystal structures

ACS Spring 2022

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