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]
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