Search patterns used for SIMPOL.1 functional groups

This dataframe documents how functional groups for the SIMPOL.1 and Meredith et al. method are defined using SMARTS strings or ChemmineR functions.

Usage

smarts_simpol1

Format

method

Either "simpol1" for functional groups only used with the SIMPOL.1 method, or "meredith" for additional groups used in the Meredith et al. method.

functional_groups

These correspond to matching column names in the results of get_fx_groups().

description

Functional group description from Table 5 of Pankow & Asher (2008)

smarts

SMARTS strings used to capture groups, when applicable

fun

The function used to capture the functional group. When smarts is not NA, this is always "ChemmineR::smartsSearchOB". Other groups are captured with other ChemmineR functions or as calculations using other functional groups.

notes

Notes including how any functional group counts are corrected when there is overlap. E.g. when one SMARTS pattern is a subset of another pattern, but the two groups are counted separately without overlap in the SIMPOL.1 method.

References

Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D, Tfaily M, Krechmer J. 2023. Automating methods for estimating metabolite volatility. Frontiers in Microbiology. doi:10.3389/fmicb.2023.1267234

Pankow, J.F., Asher, W.E. 2008. SIMPOL.1: a simple group contribution method for predicting vapor pressures and enthalpies of vaporization of multifunctional organic compounds. Atmos. Chem. Phys. doi:10.5194/acp-8-2773-2008