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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, CA
Quantitative 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 Modeling

Volume

57

Issue

11

Pagination

2754-2762

ISSN

1549-9596

Department/School

School of Natural Sciences

Publisher

American Chemical Society

Place of publication

United States

Rights statement

Copyright 2017 American Chemical Society

Repository Status

  • Restricted

Socio-economic Objectives

Expanding knowledge in the chemical sciences

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