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,pH=NULL,pKa_Donor=NA,pKa_Accept=NA)

Arguments

chem.name

Either the chemical name or the CAS number must be specified.

chem.cas

Either the chemical name or the CAS number must be specified.

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.

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

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: $z w i t t e r / n e t u r a l = 1$ $f o r (i i n 1 : p k a b o v e) n e g a t i v e = n e g a t i v e + 10^{(} i * p H - p K a 1 - . . . - p K a i)$ $f o r (i i n 1 : p k b e l o w) p o s i t i v e = p o s i t i v e + 10^{(} p K a 1 + . . . + p K a i - i * p H)$ 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.

Examples

Run this code

# NOT RUN {
calc_ionization(chem.name='bisphenola',pH=7.4)
calc_ionization(pKa_Donor=8,pKa_Accept=c(1,4),pH=9)
# }