Page 219 - Thermodynamics of Biochemical Reactions
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BasicBiochemData2 219
These tables have been given to 0.01 kJ mol-' . In general this overemphasizes the accuracy with which these
formation properties are known. However for some reactants for which species are in classical tables, this accuracy is
warranted. An error of 0.01 kJ mol-' in the standard transformed Gibbs energy of a reaction at 298 K corresponds with an
error of about 18 in the value of the apparent equilibrium constant. It is important to understand that the large number of
digits in these tables is required because the thermodynamic information is in differences between entries.
These tables can be used to calculate changes in standard transformed Gibbs energies of reaction and standard
transformed enthalpies of reaction for any biochemical reaction for which all the reactants are in the tables. Standard trans-
fomed entropies of formation and of reaction can also be calculated. The advantage of having this notebook is that these
propertiec can be calculated at any desired'pH in the range 5 to 9 and any ionic strength in the range 0 to 0.35 M.
I 9.0 Examples of calculations using the database on species
w 9.1 Calculation of pKs of weak acids
When weak acids have pKs in the range between 4 to 10, the standard Gibbs energies of formation at 298.15 K and zero ionic
strength of the various species are given in the database on species. In using the program calcpK, it is necessary to give the
number associated with the pK. pKs are numbered 1, 2, 3, ... from the highest to the lowest in the pH range approximately 4
to 10.
calcpK[ speciesmat-, no-, is-] : =
Module[(lnkzero, sigmanuzsq, lnK),(*Calculates ~Ks for a weak acid at 298.15 K at
specified ionic strengths (is) when the number no of the pK is specified. ~Ks are
numbered 1.2, 3,... from the highest pK to the lowest pK, but the highest pK for a
weak acid may be omitted if it is outside of the range 5 tO 9. For h3P04,
pK1=CalC[piSp,l,{0)] = 7.22.*)
lnkzero = (speciesrnat[[no + 1,111 - speciesmat~[no,lll)/
(8.31451*0.29815); sigmanuzsq = speciesrnat[[no,311*2 -
speciesmat[[no + 1,311*2 + 1;
1nK = lnkzero + (1.17582*isA0.5*sigmanuzsg)/
(1 + 1.6*isA0.5); N[-(lnK/Log[lOl )I1
6.46502
calcpK[atpsp,2,.251
3.82652
9.2 Calculation of changes in thermodynamic properties of reactions
calctrGerx[ac, pHlist-, islist-] :I
Module[{energy}, (*Calculates the standard transformed
Gibbs energy of reaction in kJ mol*-l at specified pHs and ionic
strengths for a biochemical reaction typed in the form atp+h2o+de:=
adp+pi. The names of reactants call the appropriate functions of
pH and ionic strength. pHlist and is list can be lists.*)
energy = Solve [eq, de] ; energyul, 1, 21 /. pH -i pHlist /. is + islist]