httk: calc_ionization – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

calc_ionization

Calculate the ionization.

Description

This function calculates the ionization of a compound at a given pH. The pKa's are either entered as parameters or taken from a specific compound in the package.

Usage

calc_ionization(
  chem.cas = NULL,
  chem.name = NULL,
  dtxsid = NULL,
  parameters = NULL,
  pH = NULL,
  pKa_Donor = NA,
  pKa_Accept = NA
)

Arguments

`chem.cas`	Either the chemical name or the CAS number must be specified.
`chem.name`	Either the chemical name or the CAS number must be specified.
`dtxsid`	EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard) the chemical must be identified by either CAS, name, or DTXSIDs
`parameters`	Chemical parameters from a parameterize_MODEL function, overrides chem.name and chem.cas.
`pH`	pH where ionization is evaluated.
`pKa_Donor`	Compound H dissociation equilibirum constant(s). Overwrites chem.name and chem.cas.
`pKa_Accept`	Compound H association equilibirum constant(s). Overwrites chem.name and chem.cas.

Details

The fractions are calculated by determining the coefficients for each species and dividing the particular species by the sum of all three. The positive, negative and zwitterionic/neutral coefficients are given by:

zwitter/netural = 1

for(i in 1:pkabove) negative = negative + 10^(i * pH - pKa1 - ... - pKai)

for(i in 1:pkbelow) positive = positive + 10^(pKa1 + ... + pKai - i * pH)

where i begins at 1 and ends at the number of points above(for negative) or below(for positive) the neutral/zwitterionic range. The neutral/zwitterionic range is either the pH range between 2 pKa's where the number of acceptors above is equal to the number of donors below, everything above the pKa acceptors if there are no donors, or everything below the pKa donors if there are no acceptors. Each of the terms in the sums represent a different ionization.

Value

`fraction_neutral`	fraction of compound neutral
`fraction_charged`	fraction of compound charged
`fraction_negative`	fraction of compound negative
`fraction_positive`	fraction of compound positive
`fraction_zwitter`	fraction of compound zwitterionic

Author(s)

Robert Pearce and John Wambaugh

References

Pearce, Robert G., et al. "Evaluation and calibration of high-throughput predictions of chemical distribution to tissues." Journal of pharmacokinetics and pharmacodynamics 44.6 (2017): 549-565.

Examples

calc_ionization(chem.name='bisphenola',pH=7.4)
calc_ionization(pKa_Donor=8,pKa_Accept=c(1,4),pH=9)

httk

High-Throughput Toxicokinetics

v2.0.4

GPL-3

Authors

John Wambaugh [aut, cre] (<https://orcid.org/0000-0002-4024-534X>), Robert Pearce [aut] (<https://orcid.org/0000-0003-3168-4049>), Caroline Ring [aut] (<https://orcid.org/0000-0002-0463-1251>), Greg Honda [aut] (<https://orcid.org/0000-0001-7713-9850>), Mark Sfeir [aut], Matt Linakis [aut] (<https://orcid.org/0000-0003-0526-2395>), Sarah Davidson [aut] (<https://orcid.org/0000-0002-2891-9380>), Miyuki Breen [ctb] (<https://orcid.org/0000-0001-8511-4653>), Shannon Bell [ctb], Xiaoqing Chang [ctb] (<https://orcid.org/0000-0003-0752-1848>), Jimena Davis [ctb], James Sluka [ctb] (<https://orcid.org/0000-0002-5901-1404>), Nisha Sipes [ctb] (<https://orcid.org/0000-0003-4203-6426>), Barbara Wetmore [ctb] (<https://orcid.org/0000-0002-6878-5348>), Woodrow Setzer [ctb] (<https://orcid.org/0000-0002-6709-9186>)

Initial release

2021-05-07