Page 203 - Thermodynamics of Biochemical Reactions

BasicBiochemData2 203

sorbosesp=({-911.95,-1263.3,0,12}};
succinatesg=i{-690.44,-908.68,-2,4},{-722.62,-908.84,-1,5},~-746.64,-912.2,0,
611;
succinylcoAsp={{-509.72, -, -1, 41, {-533.76, -, 0,
511;
sucrosesp={{-l564.7,-2199.87,0,22}};
thioredoxinoxsp=ii0,_,010));
thioredoxinredsp={(69.88,-,-2,0~,~20.56,-,-1,1~,~-25.37,-,0,2});
trygtophaneLsp={(-114.7,-405.2,0,12}};
tyrosineLsp=({-370.7,_,O,ll));
ubiguinoneoxsp={{O,-,O,90}};
ubiguinoneredsp=({-89.92,_,0,92));
uratesp={{-325.9,_,-1,3)};
ureasp={(-202.8,-317.65,0,41};
uricacidsp={{-356.9,-,0,4}};
valineLsp={{-358.65,-611.99,0,11}};
~~1~~~~~~{{-750.49,-1045.94,0,10}};
XylUlOSeS~=~{-746.15.-1029.65,~,~~}};

These thermodynamic values are based on the usual conventions of chemical thermodynamic tables that Af Go = At H" = 0
for elements in defined reference states and for H+(a=l). Additional conventions are that AfCo = AfH" = 0 for
coA- , FAD,, 2-, FADenz2-, cytochr~mec~', ferred~xin,,-~, FMN2-,
glutathiomeox2-, NAD,, -' , NADP,, 3-, retinal', thioredoxin,, O, and ubiquinoneOx 0 .

I 3.0 Calculation of the functions of pH and ionic strength for the standard

transformed Gibbs energy of formation of reactants.

calcdQnat [speciesmat-1 : =
Module[(dGzero, zi, nH, pHterm, isterm,gpfnsp),(*This program produces the function of
pH and ionic strength (is) that gives the standard transformed Gibbs energy of
formation of a reactant (sum of species) at 298.15 K. The input speciesmat 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 each species.
There is a row in the matrix for each species of the reactant. gpfnsp is a list of the
functions for the species. Energies are expressed in kJ rnol"-l.*)
dGzero = speciesmat[[Al1,111;
zi = speciesmat 1 [All, 31 1 ;
nH = speciesmat~[A11,411;
pHterm = nH*8.31451*.29815*Log[1OA-pHI;
isterm = 2.91482*((ziA2) - nH)*(isA.5)/(1 + 1.6*isA.5);
gpfnsp=dGzero - pHterm - isterm;
-8.31451*.298l5*Log[ApplyIPlus,Exg[-l*g~fnsp/(8.31451*.29815)11II

The following is a list of names of the reactants. After the calculation using calcdGmat, typing one of these names yields the
function of pH and ionic strength that gives the standard transformed Gibbs energy of formation of the reactant at 298.15 K
in dilute aqueous solution.