Marinova, V;
Dodd, L;
Lee, S-J;
Wood, G;
Marziano, I;
Salvalaglio, M;
(2021)
Identifying conformational isomers of organic molecules in solution via unsupervised clustering.
Journal of Chemical Information and Modeling
, 61
(5)
pp. 2263-2273.
10.1021/acs.jcim.0c01387.
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Abstract
We present a systematic approach for the identification of statistically relevant conformational macrostates of organic molecules from molecular dynamics trajectories. The approach applies to molecules characterized by an arbitrary number of torsional degrees of freedom and enables the transferability of the macrostates definition across different environments. We formulate a dissimilarity measure between molecular configurations that incorporates information on the characteristic energetic cost associated with transitions along all relevant torsional degrees of freedom. Such metric is employed to perform unsupervised clustering of molecular configurations based on the Fast Search and Find of Density Peaks algorithm. We apply this method to investigate the equilibrium conformational ensemble of Sildenafil, a conformationally complex pharmaceutical compound, in different environments including the crystal bulk, the gas phase, and three different solvents (acetonitrile, 1-butanol, and toluene). We demonstrate that while Sildenafil can adopt more than 100 metastable conformational configurations, only 12 are significantly populated across all of the environments investigated. Despite the complexity of the conformational space, we find that the most abundant conformers in solution are the closest to the conformers found in the most common Sildenafil crystal phase.
| Type: | Article |
|---|---|
| Title: | Identifying conformational isomers of organic molecules in solution via unsupervised clustering |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1021/acs.jcim.0c01387 |
| Publisher version: | https://doi.org/10.1021/acs.jcim.0c01387 |
| Language: | English |
| Additional information: | © 2021 The Authors. Published by American Chemical Society. This work is licensed under a CC BY 4.0 License. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Chemical Engineering |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10125890 |
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