File(s) under permanent embargo
Benchmarking of computational methods for creation of retention models in quantitative structure-retention relationships studies
journal contribution
posted on 2023-05-19, 14:56 authored by Amos, RIJ, Tyteca, E, Mohammad TalebiMohammad Talebi, Paul HaddadPaul Haddad, Szucs, R, Dolan, JW, Pohl, CAQuantitative structure-retention relationship (QSRR) models are powerful techniques for the prediction of retention times of analytes, where chromatographic retention parameters are correlated with molecular descriptors encoding chemical structures of analytes. Many QSRR models contain geometrical descriptors derived from the three-dimensional (3D) spatial coordinates of computationally predicted structures for the analytes. Therefore, it is sensible to calculate these structures correctly, as any error is likely to carry over to the resulting QSRR models. This study compares molecular modeling, semiempirical, and density functional methods (both B3LYP and M06) for structure optimization. Each of the calculations was performed in a vacuum, then repeated with solvent corrections for both acetonitrile and water. We also compared Natural Bond Orbital analysis with the Mulliken charge calculation method. The comparison of the examined computational methods for structure calculation shows that, possibly due to the error inherent in descriptor creation methods, a quick and inexpensive molecular modeling method of structure determination gives similar results to experiments where structures are optimized using an expensive and time-consuming level of computational theory. Also, for structures with low flexibility, vacuum or gas phase calculations are found to be as effective as those calculations with solvent corrections added.
Funding
Australian Research Council
Pfizer
Thermo Fisher Scientific Australia
History
Publication title
Journal of Chemical Information and ModelingVolume
57Issue
11Pagination
2754-2762ISSN
1549-9596Department/School
School of Natural SciencesPublisher
American Chemical SocietyPlace of publication
United StatesRights statement
Copyright 2017 American Chemical SocietyRepository Status
- Restricted