Page 213 - Thermodynamics of Biochemical Reactions

BasicBiochemData2 213

6.0 Calculation of the functions of pH and ionic strength for the standard
transformed enthalpies of formation of reactants

calcdmat [speciesmat-] : =
Module[(dHzero, zi, nH, dhfnsp, dGzero, pHterm, isenth, dgfnsp, doreactant, ri),
(*This program produces the function of ionic strength (is) that gives the standard
transformed enthalpy of formation of a reactant (sum of species) at 298.15
K. The input is a matrix that gives the standard Gibbs energy of formation,
the standard enthalpy of formation, the electric charge,
and the number of hydrogen atoms in the species in the reactant. There is
a row in the matrix for each species of the reactant. dhfnsp is a list
of the functions for the species. Energies are expressed in kJ mol"-l.*)
dHzero = speciesmat [ [All, 21 ] ;
zi = speciesmat [ [All, 31 ] ;
nH= speciesmat[[All, 411;
isenth=1.4775* ((zi"2) -nH) * (isA.5) / (1+1.6*isA.5);
dhfnsp = dlizero+isenth;
(*Now calculate the functions for
the standard Gibbs energies of formation of the species.*)
dGzero = speciesmat [ [All, 11 ] ;
pHterm = nH * 8.31451 * .29815 * Log [ 10 A - pH] ;
gpfnsp = dGzero - pHterm - isenth * 2.91482 / 1.44775;
(*Now calculate the standard
transformed Gibbs energy of formation for the reactant.*)
dGreactant = -8.31451* .29815*Log[Apply[Plus, Exp[-l*gpfnsp/ (8.31451* .29815)]]];
(*Now calculate the equilibrium mole fractions of the species
in the reactant and the mole fraction-weighted average of the
functions for the standard transformed enthalpies of the species.*)
ri = Exp[ (dGreactant - gpfnsp) / (8.31451 * .29815) 1;
ri.dhfnsp]
The following is a list of functions for the reactants with which the standard transformed enthalpies of formation can be
calculated. It is shorter than the list of reactants for the transformed Gibbs energies because these is less information about
standard enthalpies of formation of species.

listreactantsh={"acetaldehyde", "acetate", "adenosine", lladpml, "alanine", rgammonia
'I, IIamp", l*arabinose", "asparagineL", llaspartatell, lvatpil, "citrate", "c02g1', "c02tot", IIcoaq", "C
ogl', "ethanol11, "ethylacetate", "formateml, "fructose", rlf~rate", "galactose", "glucose", "glu
cose6phos", "glutamatell, "glutaminemt, lrglycerollr, l'glycinell, Eiglycylglycineii, Irh2aq", "h2g", "h
20", 'th202aq1t, "indole", "lactate", lvlactosela, "leucineL", "maltose", 19nannose", "methaneg", "me
thaneaq" , "methanol", ilmethylamineionrl, iin2aql*, **n2gra, tlnadox*l, "nadpox" , "nadpred" , %adred", ''
02aq", 1102g~~, "pi", "ppi", 11propano12", iipyruvatei', "ribose", "ribose5phos", "ribulose", "sorbos
;
ell, "succinate", "sucroset1, "tryptophaneL1'. "urea", lsvalineL'l, "xylose", "xylulosetm)