CHNOSZ (version 1.1.0)

nonideal: Activity coefficients of aqueous species

Description

Calculate activity coefficients and non-ideal contributions to apparent standard molal properties of aqueous species.

Usage

nonideal(species, proptable, IS, T)

Arguments

species

names or indices of species for which to calculate nonideal properties

proptable

list of dataframes of species properties

IS

numeric, ionic strength(s) used in nonideal calculations, mol kg\(^{-1}\)

T

numeric, temperature (K) (lines.water, nonideal)

Warning

The logarithms of activity coefficients (loggam) returned by nonideal use the natural logarithm (cf. Alberty, 2003 Eq. 3.6-1). To maintain consistency with the conventions used elsewhere in the package (i.e. for logarithms of equilibrium constants and of chemical activities), the values of loggam returned by subcrt are expressed using the common (base 10) logarithm. Note that the first example below uses loggam returned by subcrt, therefore requiring a base of 10 for calculating gamma.

Details

nonideal takes a list of dataframes (in proptable) containing the standard molal properties of the identified species. The function bypasses (leaves unchanged) properties of all species whose charge (determined by the number of Z in their makeup) is equal to zero. The proton (H+) and electron (e-) are also bypassed by default; to apply the calculations to H+ and/or e-, change thermo$opt$ideal.H or ideal.e to FALSE. The values of IS are combined with Alberty's (2003) equation 3.6-1 (extended Debye-H<U+00FC>ckel equation) and its derivatives, to calculate apparent molal properties at the specified ionic strength(s) and temperature(s). The lengths of IS and T supplied in the arguments should be equal to the number of rows of each dataframe in proptable, or one to use single values throughout. The apparent molal properties that can be calculated include G, H, S and Cp; any columns in the dataframes of proptable with other names are left untouched. A column named loggam (logarithm of gamma, the activity coefficient) is appended to the output dataframe of species properties.

References

Alberty, R. A. (2003) Thermodynamics of Biochemical Reactions, John Wiley & Sons, Hoboken, New Jersey, 397 p. http://www.worldcat.org/oclc/51242181

Examples

# NOT RUN {
### Examples following Alberty, 2003 

## p. 273-276: activity coefficient (gamma)
## as a function of ionic strength and temperature
T <- c(0, 25, 40)
col <- c("blue", "black", "red")
IS <- seq(0, 0.25, 0.0025)
thermo.plot.new(xlim=range(IS), ylim=c(0, 1), xlab=axis.label("IS"), ylab="gamma")
for(j in 1:3) {
  s <- subcrt(c("H2PO4-", "HADP-2", "HATP-3", "ATP-4"), IS=IS, grid="IS", T=T[j])
  for(i in 1:4) lines(IS, 10^s$out[[i]]$loggam, col=col[j])
}
text(0.125, 0.8, "Z = -1")
text(0.1, 0.42, "Z = -2")
text(0.075, 0.18, "Z = -3")
text(0.05, 0.08, "Z = -4")
title(main=paste("activity coefficient (gamma) of -1,-2,-3,-4",
  "charged species at 0, 25, 40 deg C, after Alberty, 2003",
  sep="\n"), cex.main=0.95)
legend("topright", lty=c(NA, 1, 1, 1), col=c(NA, "blue", "black", "red"),
  legend=c(as.expression(axis.label("T")), 0, 25, 40))

## p. 16 Table 1.3: apparent pKa of acetic acid with
## changing ionic strength
# we set this option to FALSE so that nonideal() will calculate activity
# coefficients for the proton (makes for better replication of the values
# in Alberty's book)
thermo$opt$ideal.H <<- FALSE
subcrt(c("acetic acid", "acetate", "H+"), c(-1, 1, 1),
  IS=c(0, 0.1, 0.25), T=25, property="logK")
# note that *apparent* values equal *standard* values at IS=0
# reset option to default
thermo$opt$ideal.H <<- TRUE

## p. 95: basis and elemental stoichiometries of species 
# (this example doesn't use activity coefficients)
basis(c("ATP-4", "H+", "H2O", "HPO4-2", "O2", "NH3"))
# cf Eq. 5.1-33: basis composition
species(c("ATP-4", "H+", "H2O", "HPO4-2", "ADP-3", "HATP-3", "HADP-2",
  "H2PO4-"))

### A different example

# speciation of phosphate as a function of ionic strength
opar <- par(mfrow=c(2, 1))
basis("CHNOPS+")
Ts <- c(25, 100)
species(c("PO4-3", "HPO4-2", "H2PO4-"))
for(T in Ts) {
  a <- affinity(IS=c(0, 0.14), T=T)
  e <- equilibrate(a)
  if(T==25) diagram(e, ylim=c(-3.0, -2.6), legend.x=NULL)
  else d <- diagram(e, ylim=c(-3.0, -2.6), add=TRUE, col="red")
}
title(main="Non-ideality model for phosphate species")
dp <- describe.property(c("pH", "T", "T"), c(7, Ts))
legend("topright", lty=c(NA, 1, 1), col=c(NA, "black", "red"), legend=dp)
text(0.07, -2.76, expr.species("HPO4-2"))
text(0.07, -2.90, expr.species("H2PO4-"))
#
# phosphate predominance f(IS,pH)
a <- affinity(IS=c(0, 0.14), pH=c(6, 13), T=Ts[1])
d <- diagram(a, fill=NULL)
a <- affinity(IS=c(0, 0.14), pH=c(6, 13), T=Ts[2])
d <- diagram(a, add=TRUE, names=NULL, col="red")
par(opar)
# }