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.
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
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_neutralfraction of compound neutral
fraction_chargedfraction of compound charged
fraction_negativefraction of compound negative
fraction_positivefraction of compound positive
fraction_zwitterfraction 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:
$$zwitter/netural = 1$$
$$for(i in 1:pkabove) negative = negative + 10^(i * pH - pKa1 - ... - pKai)$$
$$for(i in 1:pkbelow) positive = positive + 10^(pKa1 + ... + pKai - i * pH)$$
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.