BeginPackage["BiochemThermo`BasicBiochemData3`"];

BasicBiochemData3.nb

Robert A. Alberty
Department of Chemistry 6-215
Massachusetts Institute of Technology
Cambridge, MA 02139
alberty@mit.edu

Abstract:  The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties.  Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties.  These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values.  The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species).  It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives.  The species database in this package contains data matrices for 199 reactants.  For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength.  For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants.  For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated.  The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants.  It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94 reactants.  Thus loading this package makes available 774 mathematical functions for these properties.  These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

1  Introduction

Chemical reaction systems are discussed in terms of species, and many chemical thermodynamic properties can be calculated from the species properties given in the next section, for example pKs.  However, in making calculations on enzyme-catalyzed reactions it is useful to take the pH as an independent variable.  When this is done the principal thermodynamic properties of a reactant are the standard transformed Gibbs energy of formation (Subscript[Δ, f])G ' °, the standard transformed enthalpy of formation (Subscript[Δ, f])H' °, the standard transformed entropy of formation  (Subscript[Δ, f])S ' °, and the average number of hydrogen atoms in the reactant (Subscript[\(N\&_\), H]).  These properties are related by the following equations:

(Subscript[Δ, f])(Subscript[H, i])'° = -(T^2)((∂((Subscript[Δ, f])(Subscript[G, i])'°/T))/(∂T))										(1)

(Subscript[Δ, f])(Subscript[S, i])'° = - ((∂(Subscript[Δ, f])(Subscript[G, i])'°)/(∂T))												(2)

(Subscript[\(N\&_\), H])(i) = (1/(RTln(10)))((∂(Subscript[Δ, f])(Subscript[G, i])'°)/(∂pH))											(3)

These equations emphasize the importance of being able to express (Subscript[Δ, f])G ' ° as a function of temperature, pH, and ionic strength because the other three properties can be calculated by taking partial derivatives.  
	The calculation of (Subscript[Δ, f])G° and (Subscript[Δ, f])H° of species from experimental data on apparent equilibrium constants and transformed enthalpies of reaction is described in R. A. Alberty, Thermodynamics of Biochemical Reactions, Wiley, Hoboken, NJ (2003) and a number of places in the literature.  That is not discussed here because this package is oriented toward the derivation of mathematical functions to calculate thermodynamic properties at specified T, pH, and ionic strength.  There are two types of biochemical reactants in the database: 
(1) reactants for which (Subscript[Δ, f])((G )^o) values are known for all species that are significant in the range pH 5 - 9
(2) reactants for which (Subscript[Δ, f])((G )^o) and (Subscript[Δ, f])(H^o) are known for all species that are significant in the range pH 5 - 9
There are 199 reactants of the first type and 94 reactants of the second type. For the first type of reactant, it is possible to calculate (Subscript[Δ, f])G ' ° and (Subscript[\(N\&_\), H]) as functions of pH and ionic strength at 298.15 K.  For the second type of reactant, it is possible to calculate (Subscript[Δ, f])G ' °,  (Subscript[Δ, f])H ' °, (Subscript[Δ, f])S ' °, and (Subscript[\(N\&_\), H]) as functions of temperature, pH , and ionic strength.  The equations for calculating these transformed properties from species properties are quite complicated, and so it is fortunate that they can be derived by using Mathematica's symbolic capabilities.  The program calcdGmat is used with the first type of reactants to derive the functions of pH and ionic strength at 298.15 K.  The program derivetrGT is used with the second type of reactants to derive the functions of temperature, pH, and ionic strength.  
	The transformed thermodynamic properties of biochemical reactions (K ', (Subscript[Δ, r]) ((G '  )^o), (Subscript[Δ, r]) ((H '  )^o), \(TraditionalForm\`\(Δ\_r\) \(\(S'\)\(\ \)\)\^\(\(\ \)\(o\)\)\), and (Subscript[Δ, r])(Subscript[N, H])) are related to properties of reactants by the following equations:

(Subscript[Δ, r])\(G'\^\(\(\ \)\(o\)\)\)= ∑ (Subscript[ν, i])'(Subscript[Δ, f])\(G\_i'\^\(\(\ \)\(o\)\)\)= - RT ln K '									(4)

(Subscript[Δ, r])((H' )^o)= ∑ (Subscript[ν, i])'(Subscript[Δ, f])(((Subscript[H, i])' )^o)												(5)

(Subscript[Δ, r])((S' )^o)= ∑ (Subscript[ν, i])'(Subscript[Δ, f])(((Subscript[S, i])' )^o)												(6)

(Subscript[Δ, r])(Subscript[N, H])= ∑ (Subscript[ν, i])'(Subscript[\(N\&_\), H])													(7)

The (Subscript[ν, i])' are the stoichiometric numbers of reactants in the biochemical equation (positive for reactants on the right side of the equation and negative for reactants on the left side).  The prime is needed on the stoichiometric numbers to distinguish them from the stoichiomeric numbers in the underlying chemical reactions.  
	This package provides mathematical functions for the following properties of reactants:

(1) Functions of pH and ionic strength at 298.15 K for (Subscript[Δ, f])(((Subscript[G, i])' )^( o)) for 199 reactants, for example, atp.
(2) Functions of pH and ionic strength at 298.15 K for (Subscript[\(N\&_\), H]) for 199 reactants, for example, atpNH.
(3) Functions of temperature, pH and ionic strength for (Subscript[Δ, f])(((Subscript[G, i])'  )^o) for 94 reactants, for example, atpGT.
(4) Functions of temperature, pH and ionic strength for (Subscript[Δ, f])(((Subscript[H, i])' )^( o)) for 94 reactants, for example, atpHT
(5) Functions of temperature, pH and ionic strength for (Subscript[Δ, f])(((Subscript[S, i])'  )^o) for 94 reactants, for example, atpST
(6) Functions of temperature, pH and ionic strength for (Subscript[\(N\&_\), H]) for 94 reactants, for example, atpNHT

These functions can be evaluated at desired temperatures, pHs, and ionic strengths by use of the operation ReplaceAll: for example, atpGT/.t->313.15/.pH->7/.is->0.25.  They can also be used to make tables and plots.
	The functions for biochemical reactants can be added and subtracted to obtain standard transformed thermodynamic properties for enzyme-catalyzed reactions and their apparent equilibrium constants.  The standard transformed Gibbs energy of reaction for atp + h2o = adp + pi is given as a function of temperature, pH, and ionic strength by adpGT+h2oGT-(atpGT+h2oGT).  The other properties can also be calculated by changing the suffixes.  These functions can also be used to produce plots and tables.

Instructions for the use of the package BasicBiochemData3.m

When the notebook BasicBiochemData3.nb was made, a package version BasicBiochemData3.m was made automatically.  The package consists of the Mathematica input without the text.  When the 199 small matrices of species data or the 774 functions are needed, the command     <<BiochemThermo`BasicBiochemData3`
is used to make this information available.  It is necessary for the user of this book to put BasicBiochemData3.m in their computer so that  
<<BiochemThermo`BasicBiochemData3` 
will work.  To load this package properly, it is first necessary to create a folder named BiochemThermo and put BasicBiochemData3.m into this folder.  Then it is necessary to find out where to put this folder as follows:  Open a Mathematica session and evaluate $UserBaseDirectory.  On my Mac computer, this yields /Users/robertalberty/Library/Mathematica.  In this Mathematica file, you will find Applications.  Put the folder BiochemThermo (with BasicBiochemData3.m in it) into this Applications directory.  Now this package becomes available whenever you load it using
<<BiochemThermo`BasicBiochemData3`  
Each chapter should be opened in a fresh workspace.  When this package is loaded, all the species data on 199 reactants and the 774 functions under this package will be available for calculations.  The properties for adenosine triphosphate are named atpsp, atp, atpNH, atpGT, atpHT, atpST, and atpNHT.  These functions are all protected; that is, none of them can be changed without unprotecting them.

Off[General::spell1];
Off[General::spell];

Usage statements for the programs used to derive functions of temperature, pH, and ionic strength for reactants:

calcdGmat::usage="calcdGmat[species_] 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 mol^-1.";

calcNHmat::usage="calcNHmat[speciesmat_]  
produces the function of pH and ionic strength (is) that gives the average 
number of hydrogen atoms in 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.";

derivetrGibbsT::usage="derivetrGibbsT[speciesmat_] derives the function of T 
(in Kelvin), pH, and ionic strength (is) that gives 
the standard transformed Gibbs energy of 
formation of a reactant (sum of species).  The input speciesmat is a matrix 
that gives the standard Gibbs energy of formation in kJ mol^-1 at 298.15 K and 
zero ionic strength, the standard enthalpy of formation in kJ mol^-1 at 298.15 K 
and zero ionic strength, 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 standard transformed Gibbs energies 
of the species. The corresponding functions for other transformed properties 
can be obtained by taking partial derivatives.  The standard transformed Gibbs 
energy of formation of a reactant in kJ mol^-1 can be calculated at any temperature 
in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, and any ionic 
strength in the range 0 to 0.35 M by use of ReplaceAll (/.).";

derivetrHT::usage="derivetrHT[speciesmat_] derives the function of T (in Kelvin), 
pH, and ionic strength (is) that gives the standard transformed enthalpy of 
formation of a reactant (sum of species).  The input speciesmat is a matrix 
that gives the standard Gibbs energy of formation in kJ mol^-1 at 298.15 K and 
zero ionic strength, the standard enthalpy of formation in kJ mol^-1 at 298.15 K 
and zero ionic strength, 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 standard transformed Gibbs energies 
of the species.  This program applies the Gibbs-Helmholtz equation to the 
function for the standard transformed Gibbs energy of formation of a reactant.  The 
standard transformed enthalpy of formation of a reactant in kJ mol^-1 can be 
calculated at any temperature in the range 273.15 K to 313.15 K, any pH in the 
range 5 to 9, and any ionic strength in the range 0 to 0.35 M by use of ReplaceAll (/.).";

derivetrST::usage="derivetrST[speciesmat_] derives the function of T 
 (in Kelvin), pH, and ionic strength (is) that gives the stndard transformed 
 entropy of formation of a reactant (sum of species).  The input speciesmat 
 is a matrix that gives the standard Gibbs energy of formation in kJ mol^-1 
 at 298.15 K and zero ionic strength, the standard enthalpy of formation in 
 kJ mol^-1 at 298.15 K and zero ionic strength, 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 
 standard transformed Gibbs energies of the species.  This program applies 
 the equation for the entropy to the function for the standard transformed 
 Gibbs energy of formation of a reactant.  The standard transformed entropy 
 of formation of a reactant in kJ K^-1 mol^-1 can be calculated at any 
 temperature in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, 
 and any ionic strength in the range 0 to 0.35 M by use of ReplaceAll (/.).";
 
 deriveNHT::usage="deriveNHT[speciesmat_] derives the function of T (in Kelvin), pH, 
and ionic strength (is) that gives the average number of hydrogen atoms in a 
reactant (sum of species).  The input speciesmat is a matrix that gives the 
standard Gibbs energy of formation in kJ mol^-1 at 298.15 K and zero ionic 
strength, the standard enthalpy of formation in kJ mol^-1 at 298.15 K and 
zero ionic strength, 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 standard transformed 
Gibbs energies of the species. The average number can be calculated at any 
temperature in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, 
and any ionic strength in the range 0 to 0.35 M by use of ReplaceAll (/.).";

Remove all the names to be used.

Remove [acetaldehydesp,acetatesp,acetoacetatesp,acetoacetylcoAsp,acetonesp,
acetylcoAsp,acetylphossp,aconitatecissp,adeninesp,adenosinesp,
adenosinephosphosulfatesp,adpsp,alaninesp,ammoniasp,ampsp,arabinosesp,
arabinose5phossp,asparagineLsp,aspartatesp,atpsp,bpgsp,butanalsp,butanolnsp,
butyratesp,cellobiosesp,citratesp,citrateisosp,co2gsp,co2totsp,coAsp,
coAglutathionesp,coaqsp,cogsp,creatinesp,creatininesp,cyclicampsp,cysteineLsp,
cystineLsp,cytochromecoxsp,cytochromecredsp,deoxyadenosinesp,deoxyadpsp,
deoxyampsp,deoxyatpsp,deoxyribosesp,deoxyribose1phossp,deoxyribose5phossp,
dihydroxyacetonesp,dihydroxyacetonephossp,ethaneaqsp,ethanolsp,
ethylacetatesp,fadenzoxsp,fadenzredsp,fadoxsp,fadredsp,ferredoxinoxsp,
ferredoxinredsp,ferricsp,ferroussp,fmnoxsp,fmnredsp,formatesp,fructosesp,
fructose16phossp,fructose6phossp,fumaratesp,galactono14lactonesp,
galactosesp,galactose1phossp,galactose6phossp,gluconolactonesp,
gluconolactone6phossp,glucosesp,glucose1phossp,glucose6phossp,glutamatesp,
glutaminesp,glutathioneoxsp,glutathioneredsp,glyceraldehydesp,
glyceraldehydephossp,glyceratesp,glycerolsp,glycerol3phossp,glycinesp,
glycolatesp,glycylglycinesp,glyoxylatesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,
h2saqsp,hydroxy2oxoglutaratesp,hydroxyglutaratesp,hydroxypropionatebsp,
hydroxypyruvatesp,hypoxanthinesp,i2crsp,iditolsp,idpsp,impsp,indolesp,
inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaramatesp,ketoglutaratesp,
lactatesp,lactosesp,lactulosesp,leucineisoLsp,leucineLsp,lyxosesp,malatesp,
maleatesp,maltosesp,malylcoAsp,mannitol1phossp,mannitolDsp,mannosesp,
mannose1phossp,mannose6phossp,methaneaqsp,methanegsp,methanolsp,methionineLsp,
methyl2oxopentanoatesp,methylmalatesp,methylmaleatesp,methylmalonylcoAsp,
n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,nadpredsp,nadredsp,
nicotinamideribonucleotidesp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,
oxalatesp,oxaloacetatesp,oxalosuccinatesp,oxalylcoAsp,oxoprolinesp,
palmitatesp,pepsp,phenylalanineLsp,phosphoglycerate2sp,phosphoglycerate3sp,
phosphohydroxypyruvatesp,phosphoserinesp,pisp,ppisp,propanol2sp,propanolnsp,
propanoylcoAsp,prppsp,pyruvatesp,retinalsp,retinolsp,ribitolsp,ribosesp,
ribose1phossp,ribose5phossp,ribulosesp,ribulose5phossp,serineLsp,sorbitolsp,
sorbitol6phossp,sorbosesp,succinatesp,succinylcoAsp,sucrosesp,sulfatesp,
sulfitesp,sulfurcrsp,thioredoxinoxsp,thioredoxinredsp,threoninesp,
transcinnamatesp,trehalosesp,tryptophanLsp,tyrosineLsp,ubiquinoneoxsp,
ubiquinoneredsp,uratesp,ureasp,uricacidsp,valineLsp,xylitolsp,xylosesp,
xylulosesp]

Remove[acetaldehyde,acetate,acetoacetate,acetoacetylcoA,acetone,acetylcoA,
acetylphos,aconitatecis,adenine,adenosine,adenosinephosphosulfate,adp,
alanine,ammonia,amp,arabinose,arabinose5phos,asparagineL,aspartate,atp,bpg,
butanal,butanoln,butyrate,cellobiose,citrate,citrateiso,co2g,co2tot,coA,
coAglutathione,coaq,cog,creatine,creatinine,cyclicamp,cysteineL,cystineL,
cytochromecox,cytochromecred,deoxyadenosine,deoxyadp,deoxyamp,deoxyatp,
deoxyribose,deoxyribose1phos,deoxyribose5phos,dihydroxyacetone,
dihydroxyacetonephos,ethaneaq,ethanol,ethylacetate,fadenzox,fadenzred,fadox,
fadred,ferredoxinox,ferredoxinred,ferric,ferrous,fmnox,fmnred,formate,
fructose,fructose16phos,fructose6phos,fumarate,galactono14lactone,galactose,
galactose1phos,galactose6phos,gluconolactone,gluconolactone6phos,glucose,
glucose1phos,glucose6phos,glutamate,glutamine,glutathioneox,glutathionered,
glyceraldehyde,glyceraldehydephos,glycerate,glycerol,glycerol3phos,glycine,
glycolate,glycylglycine,glyoxylate,h2aq,h2g,h2o,h2o2aq,h2saq,hydroxy2oxoglutarate,
hydroxyglutarate,hydroxypropionateb,hydroxypyruvate,hypoxanthine,i2cr,iditol,
idp,imp,indole,inosine,iodideion,isomaltose,itp,ketoglutaramate,ketoglutarate,
lactate,lactose,lactulose,leucineisoL,leucineL,lyxose,malate,maleate,maltose,
malylcoA,mannitol1phos,mannitolD,mannose,mannose1phos,mannose6phos,methaneaq,
methaneg,methanol,methionineL,methyl2oxopentanoate,methylmalate,methylmaleate,
methylmalonylcoA,n2aq,n2g,n2oaq,nadox,nadpox,nadpred,nadred,
nicotinamideribonucleotide,nitrate,nitrite,noaq,o2aq,o2g,oxalate,oxaloacetate,
oxalosuccinate,oxalylcoA,oxoproline,palmitate,pep,phenylalanineL,
phosphoglycerate2,phosphoglycerate3,phosphohydroxypyruvate,phosphoserine,pi,
ppi,propanol2,propanoln,propanoylcoA,prpp,pyruvate,retinal,retinol,ribitol,
ribose,ribose1phos,ribose5phos,ribulose,ribulose5phos,serineL,sorbitol,
sorbitol6phos,sorbose,succinate,succinylcoA,sucrose,sulfate,sulfite,sulfurcr,
thioredoxinox,thioredoxinred,threonine,transcinnamate,trehalose,tryptophanL,
tyrosineL,ubiquinoneox,ubiquinonered,urate,urea,uricacid,valineL,xylitol,
xylose,xylulose]

Remove[acetaldehydeNH,acetateNH,acetoacetateNH,acetoacetylcoANH,acetoneNH,
acetylcoANH,acetylphosNH,aconitatecisNH,adenineNH,adenosineNH,
adenosinephosphosulfateNH,adpNH,alanineNH,ammoniaNH,ampNH,arabinoseNH,
arabinose5phosNH,asparagineLNH,aspartateNH,atpNH,bpgNH,butanalNH,butanolnNH,
butyrateNH,cellobioseNH,citrateNH,citrateisoNH,co2gNH,co2totNH,coANH,
coAglutathioneNH,coaqNH,cogNH,creatineNH,creatinineNH,cyclicampNH,cysteineLNH,
cystineLNH,cytochromecoxNH,cytochromecredNH,deoxyadenosineNH,deoxyadpNH,
deoxyampNH,deoxyatpNH,deoxyriboseNH,deoxyribose1phosNH,deoxyribose5phosNH,
dihydroxyacetoneNH,dihydroxyacetonephosNH,ethaneaqNH,ethanolNH,
ethylacetateNH,fadenzoxNH,fadenzredNH,fadoxNH,fadredNH,ferredoxinoxNH,
ferredoxinredNH,ferricNH,ferrousNH,fmnoxNH,fmnredNH,formateNH,fructoseNH,
fructose16phosNH,fructose6phosNH,fumarateNH,galactono14lactoneNH,
galactoseNH,galactose1phosNH,galactose6phosNH,gluconolactoneNH,
gluconolactone6phosNH,glucoseNH,glucose1phosNH,glucose6phosNH,glutamateNH,
glutamineNH,glutathioneoxNH,glutathioneredNH,glyceraldehydeNH,
glyceraldehydephosNH,glycerateNH,glycerolNH,glycerol3phosNH,glycineNH,
glycolateNH,glycylglycineNH,glyoxylateNH,h2aqNH,h2gNH,h2oNH,h2o2aqNH,
h2saqNH,hydroxy2oxoglutarateNH,hydroxyglutarateNH,hydroxypropionatebNH,
hydroxypyruvateNH,hypoxanthineNH,i2crNH,iditolNH,idpNH,impNH,indoleNH,
inosineNH,iodideionNH,isomaltoseNH,itpNH,ketoglutaramateNH,
ketoglutarateNH,lactateNH,lactoseNH,lactuloseNH,leucineisoLNH,leucineLNH,
lyxoseNH,malateNH,maleateNH,maltoseNH,malylcoANH,mannitol1phosNH,mannitolDNH,
mannoseNH,mannose1phosNH,mannose6phosNH,methaneaqNH,methanegNH,methanolNH,
methionineLNH,methyl2oxopentanoateNH,methylmalateNH,methylmaleateNH,
methylmalonylcoANH,n2aqNH,n2gNH,n2oaqNH,nadoxNH,nadpoxNH,nadpredNH,nadredNH,
nicotinamideribonucleotideNH,nitrateNH,nitriteNH,noaqNH,o2aqNH,o2gNH,
oxalateNH,oxaloacetateNH,oxalosuccinateNH,oxalylcoANH,oxoprolineNH,
palmitateNH,pepNH,phenylalanineLNH,phosphoglycerate2NH,phosphoglycerate3NH,
phosphohydroxypyruvateNH,phosphoserineNH,piNH,ppiNH,propanol2NH,propanolnNH,
propanoylcoANH,prppNH,pyruvateNH,retinalNH,retinolNH,ribitolNH,riboseNH,
ribose1phosNH,ribose5phosNH,ribuloseNH,ribulose5phosNH,serineLNH,sorbitolNH,
sorbitol6phosNH,sorboseNH,succinateNH,succinylcoANH,sucroseNH,sulfateNH,
sulfiteNH,sulfurcrNH,thioredoxinoxNH,thioredoxinredNH,threonineNH,
transcinnamateNH,trehaloseNH,tryptophanLNH,tyrosineLNH,ubiquinoneoxNH,
ubiquinoneredNH,urateNH,ureaNH,uricacidNH,valineLNH,xylitolNH,xyloseNH,
xyluloseNH]

Remove[acetaldehydeGT,acetateGT,acetoneGT,adenineGT,adenosineGT,adpGT,
alanineGT,ammoniaGT,ampGT,arabinoseGT,asparagineLGT,aspartateGT,atpGT,
citrateGT,co2gGT,co2totGT,coaqGT,cogGT,ethaneaqGT,ethanolGT,ethylacetateGT,
ferricGT,ferrousGT,formateGT,fructoseGT,fructose16phosGT,fructose6phosGT,
fumarateGT,galactoseGT,glucoseGT,glucose6phosGT,glutamateGT,glutamineGT,
glycerolGT,glycerol3phosGT,glycineGT,glycylglycineGT,h2aqGT,h2gGT,h2oGT,
h2o2aqGT,h2saqGT,i2crGT,idpGT,impGT,indoleGT,inosineGT,iodideionGT,
isomaltoseGT,itpGT,ketoglutarateGT,lactateGT,lactoseGT,leucineLGT,malateGT,
maltoseGT,mannoseGT,mannose6phosGT,methaneaqGT,methanegGT,methanolGT,n2aqGT,
n2gGT,n2oaqGT,nadoxGT,nadpoxGT,nadpredGT,nadredGT,nitrateGT,nitriteGT,
noaqGT,o2aqGT,o2gGT,oxaloacetateGT,pepGT,piGT,ppiGT,propanol2GT,pyruvateGT,
riboseGT,ribose1phosGT,ribose5phosGT,ribuloseGT,sorboseGT,succinateGT,
sucroseGT,sulfateGT,sulfiteGT,sulfurcrGT,tryptophanLGT,ureaGT,valineLGT,
xyloseGT,xyluloseGT]

Remove[acetaldehydeHT,acetateHT,acetoneHT,adenineHT,adenosineHT,adpHT,alanineHT,
ammoniaHT,ampHT,arabinoseHT,asparagineLHT,aspartateHT,atpHT,citrateHT,co2gHT,
co2totHT,coaqHT,cogHT,ethaneaqHT,ethanolHT,ethylacetateHT,ferricHT,ferrousHT,
formateHT,fructoseHT,fructose16phosHT,fructose6phosHT,fumarateHT,galactoseHT,
glucoseHT,glucose6phosHT,glutamateHT,glutamineHT,glycerolHT,glycerol3phosHT,
glycineHT,glycylglycineHT,h2aqHT,h2gHT,h2oHT,h2o2aqHT,h2saqHT,i2crHT,idpHT,
impHT,indoleHT,inosineHT,iodideionHT,isomaltoseHT,itpHT,ketoglutarateHT,
lactateHT,lactoseHT,leucineLHT,malateHT,maltoseHT,mannoseHT,mannose6phosHT,
methaneaqHT,methanegHT,methanolHT,n2aqHT,n2gHT,n2oaqHT,nadoxHT,nadpoxHT,
nadpredHT,nadredHT,nitrateHT,nitriteHT,noaqHT,o2aqHT,o2gHT,oxaloacetateHT,
pepHT,piHT,ppiHT,propanol2HT,pyruvateHT,riboseHT,ribose1phosHT,ribose5phosHT,
ribuloseHT,sorboseHT,succinateHT,sucroseHT,sulfateHT,sulfiteHT,sulfurcrHT,
tryptophanLHT,ureaHT,valineLHT,xyloseHT,xyluloseHT]

Remove[acetaldehydeST,acetateST,acetoneST,adenineST,adenosineST,adpST,alanineST,
ammoniaST,ampST,arabinoseST,asparagineLST,aspartateST,atpST,citrateST,co2gST,
co2totST,coaqST,cogST,ethaneaqST,ethanolST,ethylacetateST,ferricST,ferrousST,
formateST,fructoseST,fructose16phosST,fructose6phosST,fumarateST,galactoseST,
glucoseST,glucose6phosST,glutamateST,glutamineST,glycerolST,glycerol3phosST,
glycineST,glycylglycineST,h2aqST,h2gST,h2oST,h2o2aqST,h2saqST,i2crST,idpST,
impST,indoleST,inosineST,iodideionST,isomaltoseST,itpST,ketoglutarateST,
lactateST,lactoseST,leucineLST,malateST,maltoseST,mannoseST,mannose6phosST,
methaneaqST,methanegST,methanolST,n2aqST,n2gST,n2oaqST,nadoxST,nadpoxST,
nadpredST,nadredST,nitrateST,nitriteST,noaqST,o2aqST,o2gST,oxaloacetateST,
pepST,piST,ppiST,propanol2ST,pyruvateST,riboseST,ribose1phosST,ribose5phosST,
ribuloseST,sorboseST,succinateST,sucroseST,sulfateST,sulfiteST,sulfurcrST,
tryptophanLST,ureaST,valineLST,xyloseST,xyluloseST]

Remove[acetaldehydeNHT,acetateNHT,acetoneNHT,adenineNHT,adenosineNHT,adpNHT,
alanineNHT,ammoniaNHT,ampNHT,arabinoseNHT,asparagineLNHT,aspartateNHT,atpNHT,
citrateNHT,co2gNHT,co2totNHT,coaqNHT,cogNHT,ethaneaqNHT,ethanolNHT,
ethylacetateNHT,ferricNHT,ferrousNHT,formateNHT,fructoseNHT,fructose16phosNHT,
fructose6phosNHT,fumarateNHT,galactoseNHT,glucoseNHT,glucose6phosNHT,
glutamateNHT,glutamineNHT,glycerolNHT,glycerol3phosNHT,glycineNHT,
glycylglycineNHT,h2aqNHT,h2gNHT,h2oNHT,h2o2aqNHT,h2saqNHT,i2crNHT,idpNHT,
impNHT,indoleNHT,inosineNHT,iodideionNHT,isomaltoseNHT,itpNHT,
ketoglutarateNHT,lactateNHT,lactoseNHT,leucineLNHT,malateNHT,maltoseNHT,
mannoseNHT,mannose6phosNHT,methaneaqNHT,methanegNHT,methanolNHT,n2aqNHT,
n2gNHT,n2oaqNHT,nadoxNHT,nadpoxNHT,nadpredNHT,nadredNHT,nitrateNHT,nitriteNHT,
noaqNHT,o2aqNHT,o2gNHT,oxaloacetateNHT,pepNHT,piNHT,ppiNHT,propanol2NHT,
pyruvateNHT,riboseNHT,ribose1phosNHT,ribose5phosNHT,ribuloseNHT,sorboseNHT,
succinateNHT,sucroseNHT,sulfateNHT,sulfiteNHT,sulfurcrNHT,tryptophanLNHT,
ureaNHT,valineLNHT,xyloseNHT,xyluloseNHT]

Unprotect all the names to be used.

Unprotect [t,pH, is, 
acetaldehydesp,acetatesp,acetoacetatesp,acetoacetylcoAsp,acetonesp,
acetylcoAsp,acetylphossp,aconitatecissp,adeninesp,adenosinesp,
adenosinephosphosulfatesp,adpsp,alaninesp,ammoniasp,ampsp,arabinosesp,
arabinose5phossp,asparagineLsp,aspartatesp,atpsp,bpgsp,butanalsp,butanolnsp,
butyratesp,cellobiosesp,citratesp,citrateisosp,co2gsp,co2totsp,coAsp,
coAglutathionesp,coaqsp,cogsp,creatinesp,creatininesp,cyclicampsp,cysteineLsp,
cystineLsp,cytochromecoxsp,cytochromecredsp,deoxyadenosinesp,deoxyadpsp,
deoxyampsp,deoxyatpsp,deoxyribosesp,deoxyribose1phossp,deoxyribose5phossp,
dihydroxyacetonesp,dihydroxyacetonephossp,ethaneaqsp,ethanolsp,
ethylacetatesp,fadenzoxsp,fadenzredsp,fadoxsp,fadredsp,ferredoxinoxsp,
ferredoxinredsp,ferricsp,ferroussp,fmnoxsp,fmnredsp,formatesp,fructosesp,
fructose16phossp,fructose6phossp,fumaratesp,galactono14lactonesp,
galactosesp,galactose1phossp,galactose6phossp,gluconolactonesp,
gluconolactone6phossp,glucosesp,glucose1phossp,glucose6phossp,glutamatesp,
glutaminesp,glutathioneoxsp,glutathioneredsp,glyceraldehydesp,
glyceraldehydephossp,glyceratesp,glycerolsp,glycerol3phossp,glycinesp,
glycolatesp,glycylglycinesp,glyoxylatesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,
h2saqsp,hydroxy2oxoglutaratesp,hydroxyglutaratesp,hydroxypropionatebsp,
hydroxypyruvatesp,hypoxanthinesp,i2crsp,iditolsp,idpsp,impsp,indolesp,
inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaramatesp,
ketoglutaratesp,lactatesp,lactosesp,lactulosesp,leucineisoLsp,leucineLsp,
lyxosesp,malatesp,maleatesp,maltosesp,malylcoAsp,mannitol1phossp,mannitolDsp,
mannosesp,mannose1phossp,mannose6phossp,methaneaqsp,methanegsp,methanolsp,
methionineLsp,methyl2oxopentanoatesp,methylmalatesp,methylmaleatesp,
methylmalonylcoAsp,n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,nadpredsp,nadredsp,
nicotinamideribonucleotidesp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,
oxalatesp,oxaloacetatesp,oxalosuccinatesp,oxalylcoAsp,oxoprolinesp,
palmitatesp,pepsp,phenylalanineLsp,phosphoglycerate2sp,phosphoglycerate3sp,
phosphohydroxypyruvatesp,phosphoserinesp,pisp,ppisp,propanol2sp,propanolnsp,
propanoylcoAsp,prppsp,pyruvatesp,retinalsp,retinolsp,ribitolsp,ribosesp,
ribose1phossp,ribose5phossp,ribulosesp,ribulose5phossp,serineLsp,sorbitolsp,
sorbitol6phossp,sorbosesp,succinatesp,succinylcoAsp,sucrosesp,sulfatesp,
sulfitesp,sulfurcrsp,thioredoxinoxsp,thioredoxinredsp,threoninesp,
transcinnamatesp,trehalosesp,tryptophanLsp,tyrosineLsp,ubiquinoneoxsp,
ubiquinoneredsp,uratesp,ureasp,uricacidsp,valineLsp,xylitolsp,xylosesp,
xylulosesp];

Unprotect[acetaldehyde,acetate,acetoacetate,acetoacetylcoA,acetone,acetylcoA,
acetylphos,aconitatecis,adenine,adenosine,adenosinephosphosulfate,adp,alanine,
ammonia,amp,arabinose,arabinose5phos,asparagineL,aspartate,atp,bpg,butanal,
butanoln,butyrate,cellobiose,citrate,citrateiso,co2g,co2tot,coA,
coAglutathione,coaq,cog,creatine,creatinine,cyclicamp,cysteineL,cystineL,
cytochromecox,cytochromecred,deoxyadenosine,deoxyadp,deoxyamp,deoxyatp,
deoxyribose,deoxyribose1phos,deoxyribose5phos,dihydroxyacetone,
dihydroxyacetonephos,ethaneaq,ethanol,ethylacetate,fadenzox,fadenzred,fadox,
fadred,ferredoxinox,ferredoxinred,ferric,ferrous,fmnox,fmnred,formate,
fructose,fructose16phos,fructose6phos,fumarate,galactono14lactone,galactose,
galactose1phos,galactose6phos,gluconolactone,gluconolactone6phos,glucose,
glucose1phos,glucose6phos,glutamate,glutamine,glutathioneox,glutathionered,
glyceraldehyde,glyceraldehydephos,glycerate,glycerol,glycerol3phos,glycine,
glycolate,glycylglycine,glyoxylate,h2aq,h2g,h2o,h2o2aq,h2saq,
hydroxy2oxoglutarate,hydroxyglutarate,hydroxypropionateb,hydroxypyruvate,
hypoxanthine,i2cr,iditol,idp,imp,indole,inosine,iodideion,isomaltose,itp,
ketoglutaramate,ketoglutarate,lactate,lactose,lactulose,leucineisoL,
leucineL,lyxose,malate,maleate,maltose,malylcoA,mannitol1phos,mannitolD,
mannose,mannose1phos,mannose6phos,methaneaq,methaneg,methanol,methionineL,
methyl2oxopentanoate,methylmalate,methylmaleate,methylmalonylcoA,n2aq,n2g,
n2oaq,nadox,nadpox,nadpred,nadred,nicotinamideribonucleotide,nitrate,
nitrite,noaq,o2aq,o2g,oxalate,oxaloacetate,oxalosuccinate,oxalylcoA,
oxoproline,palmitate,pep,phenylalanineL,phosphoglycerate2,phosphoglycerate3,
phosphohydroxypyruvate,phosphoserine,pi,ppi,propanol2,propanoln,
propanoylcoA,prpp,pyruvate,retinal,retinol,ribitol,ribose,ribose1phos,
ribose5phos,ribulose,ribulose5phos,serineL,sorbitol,sorbitol6phos,sorbose,
succinate,succinylcoA,sucrose,sulfate,sulfite,sulfurcr,thioredoxinox,
thioredoxinred,threonine,transcinnamate,trehalose,tryptophanL,tyrosineL,
ubiquinoneox,ubiquinonered,urate,urea,uricacid,valineL,xylitol,xylose,
xylulose];

Unprotect[acetaldehydeNH,acetateNH,acetoacetateNH,acetoacetylcoANH,acetoneNH,
acetylcoANH,acetylphosNH,aconitatecisNH,adenineNH,adenosineNH,
adenosinephosphosulfateNH,adpNH,alanineNH,ammoniaNH,ampNH,arabinoseNH,
arabinose5phosNH,asparagineLNH,aspartateNH,atpNH,bpgNH,butanalNH,butanolnNH,
butyrateNH,cellobioseNH,citrateNH,citrateisoNH,co2gNH,co2totNH,coANH,
coAglutathioneNH,coaqNH,cogNH,creatineNH,creatinineNH,cyclicampNH,cysteineLNH,
cystineLNH,cytochromecoxNH,cytochromecredNH,deoxyadenosineNH,deoxyadpNH,
deoxyampNH,deoxyatpNH,deoxyriboseNH,deoxyribose1phosNH,deoxyribose5phosNH,
dihydroxyacetoneNH,dihydroxyacetonephosNH,ethaneaqNH,ethanolNH,
ethylacetateNH,fadenzoxNH,fadenzredNH,fadoxNH,fadredNH,ferredoxinoxNH,
ferredoxinredNH,ferricNH,ferrousNH,fmnoxNH,fmnredNH,formateNH,fructoseNH,
fructose16phosNH,fructose6phosNH,fumarateNH,galactono14lactoneNH,
galactoseNH,galactose1phosNH,galactose6phosNH,gluconolactoneNH,
gluconolactone6phosNH,glucoseNH,glucose1phosNH,glucose6phosNH,glutamateNH,
glutamineNH,glutathioneoxNH,glutathioneredNH,glyceraldehydeNH,
glyceraldehydephosNH,glycerateNH,glycerolNH,glycerol3phosNH,glycineNH,
glycolateNH,glycylglycineNH,glyoxylateNH,h2aqNH,h2gNH,h2oNH,h2o2aqNH,
h2saqNH,hydroxy2oxoglutarateNH,hydroxyglutarateNH,hydroxypropionatebNH,
hydroxypyruvateNH,hypoxanthineNH,i2crNH,iditolNH,idpNH,impNH,indoleNH,
inosineNH,iodideionNH,isomaltoseNH,itpNH,ketoglutaramateNH,
ketoglutarateNH,lactateNH,lactoseNH,lactuloseNH,leucineisoLNH,leucineLNH,
lyxoseNH,malateNH,maleateNH,maltoseNH,malylcoANH,mannitol1phosNH,mannitolDNH,
mannoseNH,mannose1phosNH,mannose6phosNH,methaneaqNH,methanegNH,methanolNH,
methionineLNH,methyl2oxopentanoateNH,methylmalateNH,methylmaleateNH,
methylmalonylcoANH,n2aqNH,n2gNH,n2oaqNH,nadoxNH,nadpoxNH,nadpredNH,nadredNH,
nicotinamideribonucleotideNH,nitrateNH,nitriteNH,noaqNH,o2aqNH,o2gNH,
oxalateNH,oxaloacetateNH,oxalosuccinateNH,oxalylcoANH,oxoprolineNH,
palmitateNH,pepNH,phenylalanineLNH,phosphoglycerate2NH,phosphoglycerate3NH,
phosphohydroxypyruvateNH,phosphoserineNH,piNH,ppiNH,propanol2NH,propanolnNH,
propanoylcoANH,prppNH,pyruvateNH,retinalNH,retinolNH,ribitolNH,riboseNH,
ribose1phosNH,ribose5phosNH,ribuloseNH,ribulose5phosNH,serineLNH,sorbitolNH,
sorbitol6phosNH,sorboseNH,succinateNH,succinylcoANH,sucroseNH,sulfateNH,
sulfiteNH,sulfurcrNH,thioredoxinoxNH,thioredoxinredNH,threonineNH,
transcinnamateNH,trehaloseNH,tryptophanLNH,tyrosineLNH,ubiquinoneoxNH,
ubiquinoneredNH,urateNH,ureaNH,uricacidNH,valineLNH,xylitolNH,xyloseNH,
xyluloseNH];

Unprotect[acetaldehydeGT,acetateGT,acetoneGT,adenineGT,adenosineGT,adpGT,
alanineGT,ammoniaGT,ampGT,arabinoseGT,asparagineLGT,aspartateGT,atpGT,
citrateGT,co2gGT,co2totGT,coaqGT,cogGT,ethaneaqGT,ethanolGT,ethylacetateGT,
ferricGT,ferrousGT,formateGT,fructoseGT,fructose16phosGT,fructose6phosGT,
fumarateGT,galactoseGT,glucoseGT,glucose6phosGT,glutamateGT,glutamineGT,
glycerolGT,glycerol3phosGT,glycineGT,glycylglycineGT,h2aqGT,h2gGT,h2oGT,
h2o2aqGT,h2saqGT,i2crGT,idpGT,impGT,indoleGT,inosineGT,iodideionGT,
isomaltoseGT,itpGT,ketoglutarateGT,lactateGT,lactoseGT,leucineLGT,malateGT,
maltoseGT,mannoseGT,mannose6phosGT,methaneaqGT,methanegGT,methanolGT,n2aqGT,
n2gGT,n2oaqGT,nadoxGT,nadpoxGT,nadpredGT,nadredGT,nitrateGT,nitriteGT,
noaqGT,o2aqGT,o2gGT,oxaloacetateGT,pepGT,piGT,ppiGT,propanol2GT,pyruvateGT,
riboseGT,ribose1phosGT,ribose5phosGT,ribuloseGT,sorboseGT,succinateGT,
sucroseGT,sulfateGT,sulfiteGT,sulfurcrGT,tryptophanLGT,ureaGT,valineLGT,
xyloseGT,xyluloseGT];

Unprotect[acetaldehydeHT,acetateHT,acetoneHT,adenineHT,adenosineHT,adpHT,alanineHT,
ammoniaHT,ampHT,arabinoseHT,asparagineLHT,aspartateHT,atpHT,citrateHT,co2gHT,
co2totHT,coaqHT,cogHT,ethaneaqHT,ethanolHT,ethylacetateHT,ferricHT,ferrousHT,
formateHT,fructoseHT,fructose16phosHT,fructose6phosHT,fumarateHT,galactoseHT,
glucoseHT,glucose6phosHT,glutamateHT,glutamineHT,glycerolHT,glycerol3phosHT,
glycineHT,glycylglycineHT,h2aqHT,h2gHT,h2oHT,h2o2aqHT,h2saqHT,i2crHT,idpHT,
impHT,indoleHT,inosineHT,iodideionHT,isomaltoseHT,itpHT,ketoglutarateHT,
lactateHT,lactoseHT,leucineLHT,malateHT,maltoseHT,mannoseHT,mannose6phosHT,
methaneaqHT,methanegHT,methanolHT,n2aqHT,n2gHT,n2oaqHT,nadoxHT,nadpoxHT,
nadpredHT,nadredHT,nitrateHT,nitriteHT,noaqHT,o2aqHT,o2gHT,oxaloacetateHT,
pepHT,piHT,ppiHT,propanol2HT,pyruvateHT,riboseHT,ribose1phosHT,ribose5phosHT,
ribuloseHT,sorboseHT,succinateHT,sucroseHT,sulfateHT,sulfiteHT,sulfurcrHT,
tryptophanLHT,ureaHT,valineLHT,xyloseHT,xyluloseHT];

Unprotect[acetaldehydeST,acetateST,acetoneST,adenineST,adenosineST,adpST,alanineST,
ammoniaST,ampST,arabinoseST,asparagineLST,aspartateST,atpST,citrateST,co2gST,
co2totST,coaqST,cogST,ethaneaqST,ethanolST,ethylacetateST,ferricST,ferrousST,
formateST,fructoseST,fructose16phosST,fructose6phosST,fumarateST,galactoseST,
glucoseST,glucose6phosST,glutamateST,glutamineST,glycerolST,glycerol3phosST,
glycineST,glycylglycineST,h2aqST,h2gST,h2oST,h2o2aqST,h2saqST,i2crST,idpST,
impST,indoleST,inosineST,iodideionST,isomaltoseST,itpST,ketoglutarateST,
lactateST,lactoseST,leucineLST,malateST,maltoseST,mannoseST,mannose6phosST,
methaneaqST,methanegST,methanolST,n2aqST,n2gST,n2oaqST,nadoxST,nadpoxST,
nadpredST,nadredST,nitrateST,nitriteST,noaqST,o2aqST,o2gST,oxaloacetateST,
pepST,piST,ppiST,propanol2ST,pyruvateST,riboseST,ribose1phosST,ribose5phosST,
ribuloseST,sorboseST,succinateST,sucroseST,sulfateST,sulfiteST,sulfurcrST,
tryptophanLST,ureaST,valineLST,xyloseST,xyluloseST];

Unprotect[acetaldehydeNHT,acetateNHT,acetoneNHT,adenineNHT,adenosineNHT,adpNHT,
alanineNHT,ammoniaNHT,ampNHT,arabinoseNHT,asparagineLNHT,aspartateNHT,atpNHT,
citrateNHT,co2gNHT,co2totNHT,coaqNHT,cogNHT,ethaneaqNHT,ethanolNHT,
ethylacetateNHT,ferricNHT,ferrousNHT,formateNHT,fructoseNHT,fructose16phosNHT,
fructose6phosNHT,fumarateNHT,galactoseNHT,glucoseNHT,glucose6phosNHT,
glutamateNHT,glutamineNHT,glycerolNHT,glycerol3phosNHT,glycineNHT,
glycylglycineNHT,h2aqNHT,h2gNHT,h2oNHT,h2o2aqNHT,h2saqNHT,i2crNHT,idpNHT,
impNHT,indoleNHT,inosineNHT,iodideionNHT,isomaltoseNHT,itpNHT,
ketoglutarateNHT,lactateNHT,lactoseNHT,leucineLNHT,malateNHT,maltoseNHT,
mannoseNHT,mannose6phosNHT,methaneaqNHT,methanegNHT,methanolNHT,n2aqNHT,
n2gNHT,n2oaqNHT,nadoxNHT,nadpoxNHT,nadpredNHT,nadredNHT,nitrateNHT,nitriteNHT,
noaqNHT,o2aqNHT,o2gNHT,oxaloacetateNHT,pepNHT,piNHT,ppiNHT,propanol2NHT,
pyruvateNHT,riboseNHT,ribose1phosNHT,ribose5phosNHT,ribuloseNHT,sorboseNHT,
succinateNHT,sucroseNHT,sulfateNHT,sulfiteNHT,sulfurcrNHT,tryptophanLNHT,
ureaNHT,valineLNHT,xyloseNHT,xyluloseNHT];

2 Basic data on the species that make up a reactant

The rows in the data matrices are of the form {(Subscript[Δ, f])G° , (Subscript[Δ, f])H° , z, (Subscript[N, H])}, where the energies are in kJ (mol^(-1)) at 298.15 K and zero ionic strength, z is the charge number, and (Subscript[N, H]) is the number of hydrogen atoms in the species.

acetaldehydesp={{-139.,-212.23,0,4}};
acetatesp={{-369.31,-486.01,-1,3},{-396.45,-485.76,0,4}};
acetoacetatesp={{-482.49,_,0,5}};
acetoacetylcoAsp={{-285.32,_,0,5}};
acetonesp={{-159.7,-221.71,0,6}};
acetylcoAsp={{-180.36,_,0,3}};
acetylphossp={{-1219.49,_,-2,3},{-1269.08,_,-1,4},{-1298.26,_,0,5}};
aconitatecissp={{-917.13,_,-3,3}};
adeninesp={{313.40,129.5,0,5},{289.43,109.4,1,6}};
adenosinesp={{-194.5,-621.3,0,13},{-214.28,-637.7,1,14}};
adenosinephosphosulfatesp={{-1541.98,_,-1,12}};
adpsp={{-1906.13,-2626.54,-3,12},{-1947.1,-2620.94,-2,
        13},{-1971.98,-2638.54,-1,14}};
alaninesp={{-371.,-554.8,0,7}};
ammoniasp={{-26.5,-80.29,0,3},{-79.31,-132.51,1,4}};
ampsp={{-1040.45,-1635.37,-2,12},{-1078.86,-1629.97,-1,
        13},{-1101.63,-1648.07,0,14}};
arabinosesp={{-742.23,-1043.79,0,10}};
arabinose5phossp={{-1598.34,_,-2,9},{-1636.53,_,-1,10}};
asparagineLsp={{-525.93,-766.09,0,8}};
aspartatesp={{-695.88,-943.41,-1,6}};
atpsp={{-2768.1,-3619.21,-4,12},{-2811.48,-3612.91,-3,
        13},{-2838.18,-3627.91,-2,14}};
bpgsp={{-2356.14,_,-4,4},{-2401.58,_,-3,5}};
butanalsp={{-129.87,_,0,8}};
butanolnsp={{-171.84,_,0,10}};
butyratesp={{-352.63,_,-1,7}};
cellobiosesp={{-1585.94,_,0,22}};
citratesp={{-1162.69,-1515.11,-3,5},{-1199.18,-1518.46,-2,
        6},{-1226.33,-1520.88,-1,7}};
citrateisosp={{-1156.04,_,-3,5},{-1192.57,_,-2,6},{-1219.47,_,-1,7}};
co2gsp={{-394.36,-393.5,0,0}};
co2totsp={{-527.81,-677.14,-2,0},{-586.77,-691.99,-1,1},{-623.11,-699.63,0,
        2}};
coAsp={{0,_,-1,0},{-47.83,_,0,1}};
coAglutathionesp={{-35.85,_,-1,15}};
coaqsp={{-119.9,-120.96,0,0}};
cogsp={{-137.17,-110.53,0,0}};
creatinesp={{-259.2,_,0,9}};
creatininesp={{-23.14,_,0,7}};
cyclicampsp={{-629.68,_,-1,7}};
cysteineLsp={{-291.,_,-1,6},{-338.82,_,0,7}};
cystineLsp={{-666.51,_,0,12}};
cytochromecoxsp={{0,_,3,0}};
cytochromecredsp={{-24.51,_,2,0}};
deoxyadenosinesp={{-46.64,_,0,13},{-66.42,_,1,14}};
deoxyadpsp={{-1758.27,_,-3,12},{-1799.24,_,-2,13},{-1824.12,_,-1,14}};
deoxyampsp={{-892.59,_,-2,12},{-931.0,_,-1,13},{-953.77,_,0,14}};
deoxyatpsp={{-2620.24,_,-4,12},{-2663.62,_,-3,13},{-2690.32,_,-2,14}};
deoxyribosesp={{-604.14,_,0,10}};
deoxyribose1phossp={{-1439.84,_,-2,9},{-1478.02,_,-1,10}};
deoxyribose5phossp={{-1447.92,_,-2,9},{-1486.11,_,-1,10}};
dihydroxyacetonesp={{-451.0,_,0,6}};
dihydroxyacetonephossp={{-1296.26,_,-2,5},{-1328.8,_,-1,6}};
ethaneaqsp={{-17.01,-102.09,0,6}};
ethanolsp={{-181.64,-288.3,0,6}};
ethylacetatesp={{-337.65,-482.,0,8}};
fadenzoxsp={{0,_,-2,31}};
fadenzredsp={{-88.6,_,-2,33}};
fadoxsp={{0,_,-2,31}};
fadredsp={{-38.88,_,-2,33}};
ferredoxinoxsp={{0,_,1,0}};
ferredoxinredsp={{38.07,_,0,0}};
ferricsp={{-4.70,-48.5,3,0}};
ferroussp={{-78.90,-89.10,2,0}};
fmnoxsp={{0,_,-2,19}};
fmnredsp={{-38.88,_,-2,21}};
formatesp={{-351.,-425.55,-1,1}};
fructosesp={{-915.51,-1259.38,0,12}};
fructose16phossp={{-2601.4,-3343.25,-4,10},{-2639.36,-3341.45,-3,11},{-2673.\
\
89,-3339.65,-2,12}};
fructose6phossp={{-1760.8,-2265.17,-2,11},{-1796.6,-2263.37,-1,12}};
fumaratesp={{-601.87,-777.39,-2,2},{-628.14,-774.46,-1,3},{-645.8,-774.88,0,
        4}};
galactono14lactonesp={{-905.34,_,0,10}};
galactosesp={{-908.93,-1255.2,0,12}};
galactose1phossp={{-1756.69,_,-2,11},{-1791.77,_,-1,12}};
galactose6phossp={{-1756.81,_,-2,11},{-1793.57,_,-1,12}};
gluconolactonesp={{-903.50,_,0,10}};
gluconolactone6phossp={{-1746.08,_,-2,9},{-1782.73,_,-1,10}};
glucosesp={{-915.9,-1262.19,0,12}};
glucose1phossp={{-1756.87,_,-2,11},{-1793.98,_,-1,12}};
glucose6phossp={{-1763.94,-2276.44,-2,11},{-1800.59,-2274.64,-1,12}};
glutamatesp={{-697.47,-979.89,-1,8}};
glutaminesp={{-528.02,-805.,0,10}};
glutathioneoxsp={{0,_,-2,30}};
glutathioneredsp={{34.17,_,-2,15},{-13.44,_,-1,16}};
glyceraldehydesp={{-440.02,_,0,6}};
glyceraldehydephossp={{-1288.6,_,-2,5},{-1321.14,_,-1,6}};
glyceratesp={{-661.01,_,-1,5}};
glycerolsp={{-497.48,-676.55,0,8}};
glycerol3phossp={{-1358.96,-1724.59,-2,7},{-1397.04,-1722.79,-1,8}};
glycinesp={{-379.91,-523.,0,5}};
glycolatesp={{-530.95,_,-1,3}};
glycylglycinesp={{-520.2,-734.25,0,8}};
glyoxylatesp={{-468.6,_,-1,1}};
h2aqsp={{17.6,-4.2,0,2}};
h2gsp={{0,0,0,2}};
h2osp={{-237.19,-285.83,0,2}};
h2o2aqsp={{-134.03,-191.17,0,2}};
h2saqsp={{85.8,33.1,-2,0},{12.08,-17.6,-1,1},{-27.83,-39.7,0,2}};
hydroxy2oxoglutaratesp={{-951.78,_,-2,4}};
hydroxyglutaratesp={{-840.18,_,-2,6}};
hydroxypropionatebsp={{-518.4,_,-1,5}};
hydroxypyruvatesp={{-608.55,_,-1,3}};
hypoxanthinesp={{89.5,_,0,4}};
i2crsp={{0,0,0,0}};
iditolsp={{-944.73,_,0,14}};
idpsp={{-2066.44,-2797.18,-4,10},{-2121.01,-2825.88,-3,
        11},{-2161.99,-2820.28,-2,12}};
impsp={{-1200.43,-1799.61,-3,10},{-1255.42,-1834.71,-2,
        11},{-1293.84,-1829.31,-1,12}};
indolesp={{223.8,97.5,0,7}};
inosinesp={{-358.02,-792.74,-1,11},{-409.15,-819.84,0,12}};
iodideionsp={{-51.57,-55.19,-1,0}};
isomaltosesp={{-1587.71,-2244.48,0,22}};
itpsp={{-2925.31,-3794.65,-5,10},{-2982.90,-3818.60,-4,
        11},{-3026.28,-3812.25,-3,12}};
ketoglutaramatesp={{-595.88,_,-1,5}};
ketoglutaratesp={{-793.41,-1044.06,-2,4}};
lactatesp={{-516.72,-686.64,-1,5}};
lactosesp={{-1567.33,-2233.08,0,22}};
lactulosesp={{-1575.22,_,0,22}};
leucineisoLsp={{-343.9,_,0,13}};
leucineLsp={{-352.25,-643.37,0,13}};
lyxosesp={{-749.14,_,0,10}};
malatesp={{-842.66,-1079.79,-2,4},{-872.68,-1079.95,-1,5}};
maleatesp={{-592.09,_,-2,2}};
maltosesp={{-1574.69,-2238.06,0,22}};
malylcoAsp={{-663.44,_,-1,4},{-687.47,_,0,5}};
mannitol1phossp={{-1793.58,_,-2,13},{-1830.68,_,-1,14}};
mannitolDsp={{-942.61,_,0,14}};
mannosesp={{-910.,-1258.66,0,12}};
mannose1phossp={{-1754.56,_,-2,11},{-1791.32,_,-1,12}};
mannose6phossp={{-1759.87,-2273.71,-2,11},{-1796.63,-2271.90,-1,12}};
methaneaqsp={{-34.33,-89.04,0,4}};
methanegsp={{-50.72,-74.81,0,4}};
methanolsp={{-175.31,-245.93,0,4}};
methionineLsp={{-502.92,_,0,11}};
methyl2oxopentanoatesp={{-445.14,_,-1,9}};
methylmalatesp={{-843.90,_,-2,6}};
methylmaleatesp={{-600.7,_,-2,4},{-636.49,_,-1,5}};
methylmalonylcoAsp={{-502.48,_,-1,4},{-526.51,_,0,5}};
n2aqsp={{18.7,-10.54,0,0}};
n2gsp={{0,0,0,0}};
n2oaqsp={{104.2,82.05,0,0}};
nadoxsp={{0,0,-1,26}};
nadpoxsp={{-835.18,-1007.48,-3,25}};
nadpredsp={{-809.71,-1036.66,-4,26}};
nadredsp={{22.65,-31.94,-2,27}};
nicotinamideribonucleotidesp={{840.08,_,-2,14},{803.32,_,-1,15}};
nitratesp={{-108.74,-205.0,-1,0},{-111.25,-207.36,0,1}};
nitritesp={{-32.2,-104.6,-1,0},{-50.6,-119.2,0,1}};
noaqsp={{86.55,90.25,0,0}};
o2aqsp={{16.4,-11.7,0,0}};
o2gsp={{0,0,0,0}};
oxalatesp={{-673.9,825.1,-2,0},{-698.33,_,-1,1}};
oxaloacetatesp={{-793.29,-959.90,-2,2}};
oxalosuccinatesp={{-1138.88,_,-2,4}};
oxalylcoAsp={{-509.96,_,-1,0}};
oxoprolinesp={{-469.15,_,-1,6}};
palmitatesp={{-259.4,_,-1,31}};
pepsp={{-1263.65,-1621.38,-3,2},{-1303.61,-1619.58,-2,3}};
phenylalanineLsp={{-207.1,_,0,11}};
phosphoglycerate2sp={{-1496.38,_,-3,4},{-1539.99,_,-2,5}};
phosphoglycerate3sp={{-1502.54,_,-3,4},{-1545.52,_,-2,5}};
phosphohydroxypyruvatesp={{-1448.67,_,-3,2}};
phosphoserinesp={{-1360.75,_,-2,6},{-1397.51,_,-1,7}};
pisp={{-1096.1,-1299.,-2,1},{-1137.3,-1302.6,-1,2}};
ppisp={{-1919.86,-2293.47,-4,0},{-1973.86,-2294.87,-3,
        1},{-2012.21,-2295.37,-2,2},{-2025.11,-2290.37,-1,
        3},{-2029.85,-2281.17,0,4}};
propanol2sp={{-185.23,-330.83,0,8}};
propanolnsp={{-175.81,_,0,8}};
propanoylcoAsp={{-179.14,_,0,5}};
prppsp={{-3284.25,_,-5,8},{-3325.23,_,-4,9},{-3363.42,_,-3,10}};
pyruvatesp={{-472.27,-596.22,-1,3}};
retinalsp={{0,_,0,28}};
retinolsp={{-27.91,_,0,30}};
ribitolsp={{-774.8,_,0,12}};
ribosesp={{-752.00,-1034.00,0,10}};
ribose1phossp={{-1587.70,-2041.48,-2,9},{-1625.88,-2030.18,-1,10}};
ribose5phossp={{-1595.78,-2041.48,-2,9},{-1633.96,-2030.18,-1,10}};
ribulosesp={{-735.94,-1023.02,0,10}};
ribulose5phossp={{-1595.32,_,-2,9},{-1633.50,_,-1,10}};
serineLsp={{-510.87,_,0,7}};
sorbitolsp={{-946.36,_,0,14}};
sorbitol6phossp={{-1793.10,_,-2,13},{-1829.75,_,-1,14}};
sorbosesp={{-911.95,-1263.3,0,12}};
succinatesp={{-690.44,-908.68,-2,4},{-722.62,-908.84,-1,5},{-746.64,-912.2,0,
        6}};
succinylcoAsp={{-509.72, _, -1, 4}, {-533.76, _, 0, 
  5}};
sucrosesp={{-1564.7,-2199.87,0,22}};
sulfatesp={{-744.53,-909.27,-2,0},{-755.91,-887.34,-1,1}};
sulfitesp={{-486.5,-635.5,-2,0},{-527.78,-626.22,-1,1}};
sulfurcrsp={{0,0,0,0}};
thioredoxinoxsp={{0,_,0,0}};
thioredoxinredsp={{69.88,_,-2,0},{20.56,_,-1,1},{-25.37,_,0,2}};
threoninesp={{-528.89,_,0,9}};
transcinnamatesp={{-128.75,_,-1,7}};
trehalosesp={{-1582.76,_,0,22}};
tryptophanLsp={{-114.7,-405.2,0,12}};
tyrosineLsp={{-370.7,_,0,11}};
ubiquinoneoxsp={{0,_,0,90}};
ubiquinoneredsp={{-89.92,_,0,92}};
uratesp={{-325.9,_,-1,3}};
ureasp={{-202.8,-317.65,0,4}};
uricacidsp={{-356.9,_,0,4}};
valineLsp={{-358.65,-611.99,0,11}};
xylitolsp={{-784.09,_,0,12}};
xylosesp={{-750.49,-1045.94,0,10}};
xylulosesp={{-746.15,-1029.65,0,10}};

Begin["Private`"];

3 Programs that are used

calcdGmat[speciesmat_] := 
  Module[{dGzero, dHzero, 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 mol^-1.*) 
    {dGzero, dHzero, zi, nH} = 
     Transpose[speciesmat]; 
     pHterm = nH*8.31451*0.29815*Log[10^(-pH)]; 
    isterm = 2.91482*(zi^2 - nH)*(is^0.5/(1 + 1.6*is^0.5)); 
    gpfnsp = dGzero - pHterm - isterm; 
    -8.31451*0.29815*Log[Plus @@ 
       Exp[-(gpfnsp/(8.31451*0.29815))]]]
       
calcNHmat[speciesmat_] := 
Module[{dGzero, dHzero,zi, nH, pHterm, isterm,gpfnsp,trgef},(*This program 
produces the function of pH and ionic strength (is) that gives the average 
number of hydrogen atoms in 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.*)
{dGzero,dHzero,zi,nH}=Transpose[speciesmat];
pHterm = nH*8.31451*.29815*Log[10^-pH];
isterm = 2.91482*((zi^2) - nH)*(is^.5)/(1 + 1.6*is^.5);
gpfnsp=dGzero - pHterm - isterm;
trgef=-8.31451*.29815*Log[Apply[Plus,Exp[-1*gpfnsp/(8.31451*.29815)]]];
D[trgef,pH]/(8.31451*.29815*Log[10])]
       
derivetrGibbsT[speciesmat_]:=Module[{dGzero,dGzeroT,dHzero,zi,nH,gibbscoeff
,pHterm, isterm,gpfnsp},(*This program derives the function of T (in Kelvin), 
pH, and ionic strength (is) that gives the standard transformed Gibbs energy 
of formation of a reactant (sum of species).  The input speciesmat is a matrix 
that gives the standard Gibbs energy of formation in kJ mol^-1 at 298.15 K and 
zero ionic strength, the standard enthalpy of formation in kJ mol^-1 at 298.15 K 
and zero ionic strength, 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 standard transformed Gibbs energies 
of the species. The corresponding functions for other transformed properties 
can be obtained by taking partial derivatives.  The standard transformed Gibbs 
energy of formation of a reactant in kJ mol^-1 can be calculated at any temperature 
in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, and any ionic 
strength in the range 0 to 0.35 M by use of ReplaceAll (/.).*) 
{dGzero,dHzero,zi,nH}=Transpose[speciesmat]; 
gibbscoeff=(9.20483*t)/10^3-(1.284668*t^2)/10^5+(4.95199*t^3)/10^8; 
dGzeroT=(dGzero*t)/298.15+dHzero*(1-t/298.15); 
pHterm=(nH*8.31451*t*Log[10^(-pH)])/1000; 
istermG=(gibbscoeff*(zi^2-nH)*is^0.5)/(1+1.6*is^0.5); 
gpfnsp=dGzeroT-pHterm-istermG; 
-((8.31451*t*Log[Plus@@(E^(-(gpfnsp/((8.31451*t)/1000))))])/1000)]

derivetrHT[speciesmat_]:=Module[{dGzero,dGzeroT,dHzero,zi,nH,gibbscoeff,
pHterm,isterm,gpfnsp,gibbsereactant},(*This program derives the function of T (in 
Kelvin), pH, and ionic strength (is) that gives the stndard transformed enthalpy of 
formation of a reactant (sum of species).  The input speciesmat is a matrix 
that gives the standard Gibbs energy of formation in kJ mol^-1 at 298.15 K and 
zero ionic strength, the standard enthalpy of formation in kJ mol^-1 at 298.15 K 
and zero ionic strength, 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 standard transformed Gibbs energies 
of the species.  This program applies the Gibbs-Helmholtz equation to the function 
for the standard transformed Gibbs energy of formation of a reactant.  The 
standard transformed enthalpy of formation of a reactant in kJ mol^-1 can be 
calculated at any temperature in the range 273.15 K to 313.15 K, any pH in the 
range 5 to 9, and any ionic strength in the range 0 to 0.35 M by use of ReplaceAll (/.).*) 
{dGzero,dHzero,zi,nH}=Transpose[speciesmat]; 
gibbscoeff=(9.20483*t)/10^3-(1.284668*t^2)/10^5+(4.95199*t^3)/10^8; 
dGzeroT=(dGzero*t)/298.15+dHzero*(1-t/298.15); 
pHterm=(nH*8.31451*t*Log[10^(-pH)])/1000; 
istermG=(gibbscoeff*(zi^2-nH)*is^0.5)/(1+1.6*is^0.5); 
gpfnsp=dGzeroT-pHterm-istermG; 
gibbsereactant=-((8.31451*t*Log[Plus@@(E^(-(gpfnsp/((8.31451*t)/1000))))])/1000);
-t^2*D[gibbsereactant/t,t]]

derivetrST[speciesmat_]:=Module[{dGzero,dGzeroT,dHzero,zi,nH,gibbscoeff,pHterm,
 isterm,gpfnsp,gibbsereactant},(*This program derives the function of T 
 (in Kelvin), pH, and ionic strength (is) that gives the stndard transformed 
 entropy of formation of a reactant (sum of species).  The input speciesmat 
 is a matrix that gives the standard Gibbs energy of formation in kJ mol^-1 
 at 298.15 K and zero ionic strength, the standard enthalpy of formation in 
 kJ mol^-1 at 298.15 K and zero ionic strength, 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 
 standard transformed Gibbs energies of the species.  This program applies 
 the equation for the entropy to the function for the standard transformed 
 Gibbs energy of formation of a reactant.  The standard transformed entropy 
 of formation of a reactant in kJ K^-1 mol^-1 can be calculated at any 
 temperature in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, 
 and any ionic strength in the range 0 to 0.35 M by use of ReplaceAll (/.).*) 
{dGzero,dHzero,zi,nH}=Transpose[speciesmat]; 
gibbscoeff=(9.20483*t)/10^3-(1.284668*t^2)/10^5+(4.95199*t^3)/10^8; 
dGzeroT=(dGzero*t)/298.15+dHzero*(1-t/298.15); 
pHterm=(nH*8.31451*t*Log[10^(-pH)])/1000; 
istermG=(gibbscoeff*(zi^2-nH)*is^0.5)/(1+1.6*is^0.5); 
gpfnsp=dGzeroT-pHterm-istermG; 
gibbsereactant=-((8.31451*t*Log[Plus@@(E^(-(gpfnsp/((8.31451*t)/1000))))])/1000);
-D[gibbsereactant,t]]

deriveNHT[speciesmat_]:=Module[{dGzero,dGzeroT,dHzero,zi,nH,gibbscoeff,pHterm, 
isterm,gpfnsp,trgefT},(*This program derives the function of T (in Kelvin), pH, 
and ionic strength (is) that gives the average number of hydrogen atoms in a 
reactant (sum of species).  The input speciesmat is a matrix that gives the 
standard Gibbs energy of formation in kJ mol^-1 at 298.15 K and zero ionic 
strength, the standard enthalpy of formation in kJ mol^-1 at 298.15 K and 
zero ionic strength, 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 standard transformed 
Gibbs energies of the species. The average number can be calculated at any 
temperature in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, 
and any ionic strength in the range 0 to 0.35 M by use of ReplaceAll (/.).*) 
{dGzero,dHzero,zi,nH}=Transpose[speciesmat]; 
gibbscoeff=(9.20483*t)/10^3-(1.284668*t^2)/10^5+(4.95199*t^3)/10^8; 
dGzeroT=(dGzero*t)/298.15+dHzero*(1-t/298.15); 
pHterm=(nH*8.31451*t*Log[10^(-pH)])/1000; 
istermG=(gibbscoeff*(zi^2-nH)*is^0.5)/(1+1.6*is^0.5); 
gpfnsp=dGzeroT-pHterm-istermG; 
trgefT=-((8.31451*t*Log[Plus@@(E^(-(gpfnsp/((8.31451*t)/1000))))]));
D[trgefT,pH]/(8.31451*t*Log[10])]

4 Calculation of the functions of pH and ionic strength for the standard transformed Gibbs energies of formation of reactants at 298.15 K and desired pHs and ionic strengths

These functions are given the following Mathematica names of reactants, which have to be cleared first.

Clear[acetaldehyde,acetate,acetoacetate,acetoacetylcoA,acetone,acetylcoA,
acetylphos,aconitatecis,adenine,adenosine,adenosinephosphosulfate,adp,alanine,
ammonia,amp,arabinose,arabinose5phos,asparagineL,aspartate,atp,bpg,butanal,
butanoln,butyrate,cellobiose,citrate,citrateiso,co2g,co2tot,coA,
coAglutathione,coaq,cog,creatine,creatinine,cyclicamp,cysteineL,cystineL,
cytochromecox,cytochromecred,deoxyadenosine,deoxyadp,deoxyamp,deoxyatp,
deoxyribose,deoxyribose1phos,deoxyribose5phos,dihydroxyacetone,
dihydroxyacetonephos,ethaneaq,ethanol,ethylacetate,fadenzox,fadenzred,fadox,
fadred,ferredoxinox,ferredoxinred,ferric,ferrous,fmnox,fmnred,formate,
fructose,fructose16phos,fructose6phos,fumarate,galactono14lactone,galactose,
galactose1phos,galactose6phos,gluconolactone,gluconolactone6phos,glucose,
glucose1phos,glucose6phos,glutamate,glutamine,glutathioneox,glutathionered,
glyceraldehyde,glyceraldehydephos,glycerate,glycerol,glycerol3phos,glycine,
glycolate,glycylglycine,glyoxylate,h2aq,h2g,h2o,h2o2aq,h2saq,
hydroxy2oxoglutarate,hydroxyglutarate,hydroxypropionateb,hydroxypyruvate,
hypoxanthine,i2cr,iditol,idp,imp,indole,inosine,iodideion,isomaltose,itp,
ketoglutaramate,ketoglutarate,lactate,lactose,lactulose,leucineisoL,
leucineL,lyxose,malate,maleate,maltose,malylcoA,mannitol1phos,mannitolD,
mannose,mannose1phos,mannose6phos,methaneaq,methaneg,methanol,methionineL,
methyl2oxopentanoate,methylmalate,methylmaleate,methylmalonylcoA,n2aq,n2g,
n2oaq,nadox,nadpox,nadpred,nadred,nicotinamideribonucleotide,nitrate,
nitrite,noaq,o2aq,o2g,oxalate,oxaloacetate,oxalosuccinate,oxalylcoA,
oxoproline,palmitate,pep,phenylalanineL,phosphoglycerate2,phosphoglycerate3,
phosphohydroxypyruvate,phosphoserine,pi,ppi,propanol2,propanoln,
propanoylcoA,prpp,pyruvate,retinal,retinol,ribitol,ribose,ribose1phos,
ribose5phos,ribulose,ribulose5phos,serineL,sorbitol,sorbitol6phos,sorbose,
succinate,succinylcoA,sucrose,sulfate,sulfite,sulfurcr,thioredoxinox,
thioredoxinred,threonine,transcinnamate,trehalose,tryptophanL,tyrosineL,
ubiquinoneox,ubiquinonered,urate,urea,uricacid,valineL,xylitol,xylose,
xylulose]

The program calcdGmat is applied in a single step by use of Map.

Evaluate[{acetaldehyde,acetate,acetoacetate,acetoacetylcoA,acetone,acetylcoA,
acetylphos,aconitatecis,adenine,adenosine,adenosinephosphosulfate,adp,alanine,
ammonia,amp,arabinose,arabinose5phos,asparagineL,aspartate,atp,bpg,butanal,
butanoln,butyrate,cellobiose,citrate,citrateiso,co2g,co2tot,coA,
coAglutathione,coaq,cog,creatine,creatinine,cyclicamp,cysteineL,cystineL,
cytochromecox,cytochromecred,deoxyadenosine,deoxyadp,deoxyamp,deoxyatp,
deoxyribose,deoxyribose1phos,deoxyribose5phos,dihydroxyacetone,
dihydroxyacetonephos,ethaneaq,ethanol,ethylacetate,fadenzox,fadenzred,fadox,
fadred,ferredoxinox,ferredoxinred,ferric,ferrous,fmnox,fmnred,formate,
fructose,fructose16phos,fructose6phos,fumarate,galactono14lactone,galactose,
galactose1phos,galactose6phos,gluconolactone,gluconolactone6phos,glucose,
glucose1phos,glucose6phos,glutamate,glutamine,glutathioneox,glutathionered,
glyceraldehyde,glyceraldehydephos,glycerate,glycerol,glycerol3phos,glycine,
glycolate,glycylglycine,glyoxylate,h2aq,h2g,h2o,h2o2aq,h2saq,
hydroxy2oxoglutarate,hydroxyglutarate,hydroxypropionateb,hydroxypyruvate,
hypoxanthine,i2cr,iditol,idp,imp,indole,inosine,iodideion,isomaltose,itp,
ketoglutaramate,ketoglutarate,lactate,lactose,lactulose,leucineisoL,
leucineL,lyxose,malate,maleate,maltose,malylcoA,mannitol1phos,mannitolD,
mannose,mannose1phos,mannose6phos,methaneaq,methaneg,methanol,methionineL,
methyl2oxopentanoate,methylmalate,methylmaleate,methylmalonylcoA,n2aq,n2g,
n2oaq,nadox,nadpox,nadpred,nadred,nicotinamideribonucleotide,nitrate,
nitrite,noaq,o2aq,o2g,oxalate,oxaloacetate,oxalosuccinate,oxalylcoA,
oxoproline,palmitate,pep,phenylalanineL,phosphoglycerate2,phosphoglycerate3,
phosphohydroxypyruvate,phosphoserine,pi,ppi,propanol2,propanoln,
propanoylcoA,prpp,pyruvate,retinal,retinol,ribitol,ribose,ribose1phos,
ribose5phos,ribulose,ribulose5phos,serineL,sorbitol,sorbitol6phos,sorbose,
succinate,succinylcoA,sucrose,sulfate,sulfite,sulfurcr,thioredoxinox,
thioredoxinred,threonine,transcinnamate,trehalose,tryptophanL,tyrosineL,
ubiquinoneox,ubiquinonered,urate,urea,uricacid,valineL,xylitol,xylose,
xylulose}]=Map[\
calcdGmat,{acetaldehydesp,acetatesp,acetoacetatesp,acetoacetylcoAsp,acetonesp,
acetylcoAsp,acetylphossp,aconitatecissp,adeninesp,adenosinesp,
adenosinephosphosulfatesp,adpsp,alaninesp,ammoniasp,ampsp,arabinosesp,
arabinose5phossp,asparagineLsp,aspartatesp,atpsp,bpgsp,butanalsp,butanolnsp,
butyratesp,cellobiosesp,citratesp,citrateisosp,co2gsp,co2totsp,coAsp,
coAglutathionesp,coaqsp,cogsp,creatinesp,creatininesp,cyclicampsp,cysteineLsp,
cystineLsp,cytochromecoxsp,cytochromecredsp,deoxyadenosinesp,deoxyadpsp,
deoxyampsp,deoxyatpsp,deoxyribosesp,deoxyribose1phossp,deoxyribose5phossp,
dihydroxyacetonesp,dihydroxyacetonephossp,ethaneaqsp,ethanolsp,
ethylacetatesp,fadenzoxsp,fadenzredsp,fadoxsp,fadredsp,ferredoxinoxsp,
ferredoxinredsp,ferricsp,ferroussp,fmnoxsp,fmnredsp,formatesp,fructosesp,
fructose16phossp,fructose6phossp,fumaratesp,galactono14lactonesp,
galactosesp,galactose1phossp,galactose6phossp,gluconolactonesp,
gluconolactone6phossp,glucosesp,glucose1phossp,glucose6phossp,glutamatesp,
glutaminesp,glutathioneoxsp,glutathioneredsp,glyceraldehydesp,
glyceraldehydephossp,glyceratesp,glycerolsp,glycerol3phossp,glycinesp,
glycolatesp,glycylglycinesp,glyoxylatesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,
h2saqsp,hydroxy2oxoglutaratesp,hydroxyglutaratesp,hydroxypropionatebsp,
hydroxypyruvatesp,hypoxanthinesp,i2crsp,iditolsp,idpsp,impsp,indolesp,
inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaramatesp,
ketoglutaratesp,lactatesp,lactosesp,lactulosesp,leucineisoLsp,leucineLsp,
lyxosesp,malatesp,maleatesp,maltosesp,malylcoAsp,mannitol1phossp,mannitolDsp,
mannosesp,mannose1phossp,mannose6phossp,methaneaqsp,methanegsp,methanolsp,
methionineLsp,methyl2oxopentanoatesp,methylmalatesp,methylmaleatesp,
methylmalonylcoAsp,n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,nadpredsp,nadredsp,
nicotinamideribonucleotidesp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,
oxalatesp,oxaloacetatesp,oxalosuccinatesp,oxalylcoAsp,oxoprolinesp,
palmitatesp,pepsp,phenylalanineLsp,phosphoglycerate2sp,phosphoglycerate3sp,
phosphohydroxypyruvatesp,phosphoserinesp,pisp,ppisp,propanol2sp,propanolnsp,
propanoylcoAsp,prppsp,pyruvatesp,retinalsp,retinolsp,ribitolsp,ribosesp,
ribose1phossp,ribose5phossp,ribulosesp,ribulose5phossp,serineLsp,sorbitolsp,
sorbitol6phossp,sorbosesp,succinatesp,succinylcoAsp,sucrosesp,sulfatesp,
sulfitesp,sulfurcrsp,thioredoxinoxsp,thioredoxinredsp,threoninesp,
transcinnamatesp,trehalosesp,tryptophanLsp,tyrosineLsp,ubiquinoneoxsp,
ubiquinoneredsp,uratesp,ureasp,uricacidsp,valineLsp,xylitolsp,xylosesp,
xylulosesp}];

5  Calculation of the functions of pH and ionic strength for the average number of hydrogen atoms in the reactants at 298.15 K and desired pHs and ionic strengths

The function of pH and ionic stength that gives the average number of hydrogen atoms (Subscript[\(N\&_\), H]) in a reactant can be derived by differentiating the function for the standard transformed Gibbs energy of formation. The names to be assigned to these functions are given by the following list:

Clear[acetaldehydeNH,acetateNH,acetoacetateNH,acetoacetylcoANH,acetoneNH,
acetylcoANH,acetylphosNH,aconitatecisNH,adenineNH,adenosineNH,
adenosinephosphosulfateNH,adpNH,alanineNH,ammoniaNH,ampNH,arabinoseNH,
arabinose5phosNH,asparagineLNH,aspartateNH,atpNH,bpgNH,butanalNH,butanolnNH,
butyrateNH,cellobioseNH,citrateNH,citrateisoNH,co2gNH,co2totNH,coANH,
coAglutathioneNH,coaqNH,cogNH,creatineNH,creatinineNH,cyclicampNH,cysteineLNH,
cystineLNH,cytochromecoxNH,cytochromecredNH,deoxyadenosineNH,deoxyadpNH,
deoxyampNH,deoxyatpNH,deoxyriboseNH,deoxyribose1phosNH,deoxyribose5phosNH,
dihydroxyacetoneNH,dihydroxyacetonephosNH,ethaneaqNH,ethanolNH,
ethylacetateNH,fadenzoxNH,fadenzredNH,fadoxNH,fadredNH,ferredoxinoxNH,
ferredoxinredNH,ferricNH,ferrousNH,fmnoxNH,fmnredNH,formateNH,fructoseNH,
fructose16phosNH,fructose6phosNH,fumarateNH,galactono14lactoneNH,
galactoseNH,galactose1phosNH,galactose6phosNH,gluconolactoneNH,
gluconolactone6phosNH,glucoseNH,glucose1phosNH,glucose6phosNH,glutamateNH,
glutamineNH,glutathioneoxNH,glutathioneredNH,glyceraldehydeNH,
glyceraldehydephosNH,glycerateNH,glycerolNH,glycerol3phosNH,glycineNH,
glycolateNH,glycylglycineNH,glyoxylateNH,h2aqNH,h2gNH,h2oNH,h2o2aqNH,
h2saqNH,hydroxy2oxoglutarateNH,hydroxyglutarateNH,hydroxypropionatebNH,
hydroxypyruvateNH,hypoxanthineNH,i2crNH,iditolNH,idpNH,impNH,indoleNH,
inosineNH,iodideionNH,isomaltoseNH,itpNH,ketoglutaramateNH,
ketoglutarateNH,lactateNH,lactoseNH,lactuloseNH,leucineisoLNH,leucineLNH,
lyxoseNH,malateNH,maleateNH,maltoseNH,malylcoANH,mannitol1phosNH,mannitolDNH,
mannoseNH,mannose1phosNH,mannose6phosNH,methaneaqNH,methanegNH,methanolNH,
methionineLNH,methyl2oxopentanoateNH,methylmalateNH,methylmaleateNH,
methylmalonylcoANH,n2aqNH,n2gNH,n2oaqNH,nadoxNH,nadpoxNH,nadpredNH,nadredNH,
nicotinamideribonucleotideNH,nitrateNH,nitriteNH,noaqNH,o2aqNH,o2gNH,
oxalateNH,oxaloacetateNH,oxalosuccinateNH,oxalylcoANH,oxoprolineNH,
palmitateNH,pepNH,phenylalanineLNH,phosphoglycerate2NH,phosphoglycerate3NH,
phosphohydroxypyruvateNH,phosphoserineNH,piNH,ppiNH,propanol2NH,propanolnNH,
propanoylcoANH,prppNH,pyruvateNH,retinalNH,retinolNH,ribitolNH,riboseNH,
ribose1phosNH,ribose5phosNH,ribuloseNH,ribulose5phosNH,serineLNH,sorbitolNH,
sorbitol6phosNH,sorboseNH,succinateNH,succinylcoANH,sucroseNH,sulfateNH,
sulfiteNH,sulfurcrNH,thioredoxinoxNH,thioredoxinredNH,threonineNH,
transcinnamateNH,trehaloseNH,tryptophanLNH,tyrosineLNH,ubiquinoneoxNH,
ubiquinoneredNH,urateNH,ureaNH,uricacidNH,valineLNH,xylitolNH,xyloseNH,
xyluloseNH]

The program calcNHmat is applied in a single step by use of Map.

Evaluate[{acetaldehydeNH,acetateNH,acetoacetateNH,acetoacetylcoANH,acetoneNH,
acetylcoANH,acetylphosNH,aconitatecisNH,adenineNH,adenosineNH,
adenosinephosphosulfateNH,adpNH,alanineNH,ammoniaNH,ampNH,arabinoseNH,
arabinose5phosNH,asparagineLNH,aspartateNH,atpNH,bpgNH,butanalNH,butanolnNH,
butyrateNH,cellobioseNH,citrateNH,citrateisoNH,co2gNH,co2totNH,coANH,
coAglutathioneNH,coaqNH,cogNH,creatineNH,creatinineNH,cyclicampNH,cysteineLNH,
cystineLNH,cytochromecoxNH,cytochromecredNH,deoxyadenosineNH,deoxyadpNH,
deoxyampNH,deoxyatpNH,deoxyriboseNH,deoxyribose1phosNH,deoxyribose5phosNH,
dihydroxyacetoneNH,dihydroxyacetonephosNH,ethaneaqNH,ethanolNH,
ethylacetateNH,fadenzoxNH,fadenzredNH,fadoxNH,fadredNH,ferredoxinoxNH,
ferredoxinredNH,ferricNH,ferrousNH,fmnoxNH,fmnredNH,formateNH,fructoseNH,
fructose16phosNH,fructose6phosNH,fumarateNH,galactono14lactoneNH,
galactoseNH,galactose1phosNH,galactose6phosNH,gluconolactoneNH,
gluconolactone6phosNH,glucoseNH,glucose1phosNH,glucose6phosNH,glutamateNH,
glutamineNH,glutathioneoxNH,glutathioneredNH,glyceraldehydeNH,
glyceraldehydephosNH,glycerateNH,glycerolNH,glycerol3phosNH,glycineNH,
glycolateNH,glycylglycineNH,glyoxylateNH,h2aqNH,h2gNH,h2oNH,h2o2aqNH,
h2saqNH,hydroxy2oxoglutarateNH,hydroxyglutarateNH,hydroxypropionatebNH,
hydroxypyruvateNH,hypoxanthineNH,i2crNH,iditolNH,idpNH,impNH,indoleNH,
inosineNH,iodideionNH,isomaltoseNH,itpNH,ketoglutaramateNH,
ketoglutarateNH,lactateNH,lactoseNH,lactuloseNH,leucineisoLNH,leucineLNH,
lyxoseNH,malateNH,maleateNH,maltoseNH,malylcoANH,mannitol1phosNH,mannitolDNH,
mannoseNH,mannose1phosNH,mannose6phosNH,methaneaqNH,methanegNH,methanolNH,
methionineLNH,methyl2oxopentanoateNH,methylmalateNH,methylmaleateNH,
methylmalonylcoANH,n2aqNH,n2gNH,n2oaqNH,nadoxNH,nadpoxNH,nadpredNH,nadredNH,
nicotinamideribonucleotideNH,nitrateNH,nitriteNH,noaqNH,o2aqNH,o2gNH,
oxalateNH,oxaloacetateNH,oxalosuccinateNH,oxalylcoANH,oxoprolineNH,
palmitateNH,pepNH,phenylalanineLNH,phosphoglycerate2NH,phosphoglycerate3NH,
phosphohydroxypyruvateNH,phosphoserineNH,piNH,ppiNH,propanol2NH,propanolnNH,
propanoylcoANH,prppNH,pyruvateNH,retinalNH,retinolNH,ribitolNH,riboseNH,
ribose1phosNH,ribose5phosNH,ribuloseNH,ribulose5phosNH,serineLNH,sorbitolNH,
sorbitol6phosNH,sorboseNH,succinateNH,succinylcoANH,sucroseNH,sulfateNH,
sulfiteNH,sulfurcrNH,thioredoxinoxNH,thioredoxinredNH,threonineNH,
transcinnamateNH,trehaloseNH,tryptophanLNH,tyrosineLNH,ubiquinoneoxNH,
ubiquinoneredNH,urateNH,ureaNH,uricacidNH,valineLNH,xylitolNH,xyloseNH,
xyluloseNH}]=Map[calcNHmat,{acetaldehydesp,acetatesp,acetoacetatesp,
acetoacetylcoAsp,acetonesp,
acetylcoAsp,acetylphossp,aconitatecissp,adeninesp,adenosinesp,
adenosinephosphosulfatesp,adpsp,alaninesp,ammoniasp,ampsp,arabinosesp,
arabinose5phossp,asparagineLsp,aspartatesp,atpsp,bpgsp,butanalsp,butanolnsp,
butyratesp,cellobiosesp,citratesp,citrateisosp,co2gsp,co2totsp,coAsp,
coAglutathionesp,coaqsp,cogsp,creatinesp,creatininesp,cyclicampsp,cysteineLsp,
cystineLsp,cytochromecoxsp,cytochromecredsp,deoxyadenosinesp,deoxyadpsp,
deoxyampsp,deoxyatpsp,deoxyribosesp,deoxyribose1phossp,deoxyribose5phossp,
dihydroxyacetonesp,dihydroxyacetonephossp,ethaneaqsp,ethanolsp,
ethylacetatesp,fadenzoxsp,fadenzredsp,fadoxsp,fadredsp,ferredoxinoxsp,
ferredoxinredsp,ferricsp,ferroussp,fmnoxsp,fmnredsp,formatesp,fructosesp,
fructose16phossp,fructose6phossp,fumaratesp,galactono14lactonesp,
galactosesp,galactose1phossp,galactose6phossp,gluconolactonesp,
gluconolactone6phossp,glucosesp,glucose1phossp,glucose6phossp,glutamatesp,
glutaminesp,glutathioneoxsp,glutathioneredsp,glyceraldehydesp,
glyceraldehydephossp,glyceratesp,glycerolsp,glycerol3phossp,glycinesp,
glycolatesp,glycylglycinesp,glyoxylatesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,
h2saqsp,hydroxy2oxoglutaratesp,hydroxyglutaratesp,hydroxypropionatebsp,
hydroxypyruvatesp,hypoxanthinesp,i2crsp,iditolsp,idpsp,impsp,indolesp,
inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaramatesp,
ketoglutaratesp,lactatesp,lactosesp,lactulosesp,leucineisoLsp,leucineLsp,
lyxosesp,malatesp,maleatesp,maltosesp,malylcoAsp,mannitol1phossp,mannitolDsp,
mannosesp,mannose1phossp,mannose6phossp,methaneaqsp,methanegsp,methanolsp,
methionineLsp,methyl2oxopentanoatesp,methylmalatesp,methylmaleatesp,
methylmalonylcoAsp,n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,nadpredsp,nadredsp,
nicotinamideribonucleotidesp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,
oxalatesp,oxaloacetatesp,oxalosuccinatesp,oxalylcoAsp,oxoprolinesp,
palmitatesp,pepsp,phenylalanineLsp,phosphoglycerate2sp,phosphoglycerate3sp,
phosphohydroxypyruvatesp,phosphoserinesp,pisp,ppisp,propanol2sp,propanolnsp,
propanoylcoAsp,prppsp,pyruvatesp,retinalsp,retinolsp,ribitolsp,ribosesp,
ribose1phossp,ribose5phossp,ribulosesp,ribulose5phossp,serineLsp,sorbitolsp,
sorbitol6phossp,sorbosesp,succinatesp,succinylcoAsp,sucrosesp,sulfatesp,
sulfitesp,sulfurcrsp,thioredoxinoxsp,thioredoxinredsp,threoninesp,
transcinnamatesp,trehalosesp,tryptophanLsp,tyrosineLsp,ubiquinoneoxsp,
ubiquinoneredsp,uratesp,ureasp,uricacidsp,valineLsp,xylitolsp,xylosesp,
xylulosesp}];

6  Calculation of the functions of temperature, pH and ionic strength for the standard transformed Gibbs energies of formation for reactants for which standard enthalpies of formation of the species are known

When (Subscript[Δ, f])H° are known for all species of a reactant, (Subscript[Δ, f])G' ° , (Subscript[\(N\&_\), H]), (Subscript[Δ, f])H' °, and (Subscript[Δ, f])S' ° can be calculated at temperatures in the range 273.15 - 313.15 K, pHs in the range 5 - 9, and ionic strengths in the range zero to 0.35 M.  The names of the 94 reactants for which all (Subscript[Δ, f])H° are known are given by

Clear[acetaldehydeGT,acetateGT,acetoneGT,adenineGT,adenosineGT,adpGT,
alanineGT,ammoniaGT,ampGT,arabinoseGT,asparagineLGT,aspartateGT,atpGT,
citrateGT,co2gGT,co2totGT,coaqGT,cogGT,ethaneaqGT,ethanolGT,ethylacetateGT,
ferricGT,ferrousGT,formateGT,fructoseGT,fructose16phosGT,fructose6phosGT,
fumarateGT,galactoseGT,glucoseGT,glucose6phosGT,glutamateGT,glutamineGT,
glycerolGT,glycerol3phosGT,glycineGT,glycylglycineGT,h2aqGT,h2gGT,h2oGT,
h2o2aqGT,h2saqGT,i2crGT,idpGT,impGT,indoleGT,inosineGT,iodideionGT,
isomaltoseGT,itpGT,ketoglutarateGT,lactateGT,lactoseGT,leucineLGT,malateGT,
maltoseGT,mannoseGT,mannose6phosGT,methaneaqGT,methanegGT,methanolGT,n2aqGT,
n2gGT,n2oaqGT,nadoxGT,nadpoxGT,nadpredGT,nadredGT,nitrateGT,nitriteGT,
noaqGT,o2aqGT,o2gGT,oxaloacetateGT,pepGT,piGT,ppiGT,propanol2GT,pyruvateGT,
riboseGT,ribose1phosGT,ribose5phosGT,ribuloseGT,sorboseGT,succinateGT,
sucroseGT,sulfateGT,sulfiteGT,sulfurcrGT,tryptophanLGT,ureaGT,valineLGT,
xyloseGT,xyluloseGT]

Evaluate[{acetaldehydeGT,acetateGT,acetoneGT,adenineGT,adenosineGT,adpGT,
alanineGT,ammoniaGT,ampGT,arabinoseGT,asparagineLGT,aspartateGT,atpGT,
citrateGT,co2gGT,co2totGT,coaqGT,cogGT,ethaneaqGT,ethanolGT,ethylacetateGT,
ferricGT,ferrousGT,formateGT,fructoseGT,fructose16phosGT,fructose6phosGT,
fumarateGT,galactoseGT,glucoseGT,glucose6phosGT,glutamateGT,glutamineGT,
glycerolGT,glycerol3phosGT,glycineGT,glycylglycineGT,h2aqGT,h2gGT,h2oGT,
h2o2aqGT,h2saqGT,i2crGT,idpGT,impGT,indoleGT,inosineGT,iodideionGT,
isomaltoseGT,itpGT,ketoglutarateGT,lactateGT,lactoseGT,leucineLGT,malateGT,
maltoseGT,mannoseGT,mannose6phosGT,methaneaqGT,methanegGT,methanolGT,n2aqGT,
n2gGT,n2oaqGT,nadoxGT,nadpoxGT,nadpredGT,nadredGT,nitrateGT,nitriteGT,
noaqGT,o2aqGT,o2gGT,oxaloacetateGT,pepGT,piGT,ppiGT,propanol2GT,pyruvateGT,
riboseGT,ribose1phosGT,ribose5phosGT,ribuloseGT,sorboseGT,succinateGT,
sucroseGT,sulfateGT,sulfiteGT,sulfurcrGT,tryptophanLGT,ureaGT,valineLGT,
xyloseGT,xyluloseGT}]=Map[derivetrGibbsT,{acetaldehydesp,acetatesp,acetonesp,
adeninesp,adenosinesp,adpsp,alaninesp,ammoniasp,ampsp,arabinosesp,
asparagineLsp,aspartatesp,atpsp,citratesp,co2gsp,co2totsp,coaqsp,cogsp,
ethaneaqsp,ethanolsp,ethylacetatesp,ferricsp,ferroussp,formatesp,fructosesp,
fructose16phossp,fructose6phossp,fumaratesp,galactosesp,glucosesp,
glucose6phossp,glutamatesp,glutaminesp,glycerolsp,glycerol3phossp,glycinesp,
glycylglycinesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,h2saqsp,i2crsp,idpsp,impsp,
indolesp,inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaratesp,lactatesp,
lactosesp,leucineLsp,malatesp,maltosesp,mannosesp,mannose6phossp,
methaneaqsp,methanegsp,methanolsp,n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,
nadpredsp,nadredsp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,oxaloacetatesp,
pepsp,pisp,ppisp,propanol2sp,pyruvatesp,ribosesp,ribose1phossp,ribose5phossp,
ribulosesp,sorbosesp,succinatesp,sucrosesp,sulfatesp,sulfitesp,sulfurcrsp,
tryptophanLsp,ureasp,valineLsp,xylosesp,xylulosesp}];

7  Calculation of the functions of temperature, pH and ionic strength for the standard transformed enthalpies of formation of reactants for which standard enthalpies of formation of the species are known

The function of T, pH, and ionic strength that gives the standard transformed enthalpy of formation (Subscript[Δ, f])H' ° for a reactant can be derived by differentiating the function for the standard transformed Gibbs energy of formation.  This is done by the program derivetrHT.

Clear[acetaldehydeHT,acetateHT,acetoneHT,adenineHT,adenosineHT,adpHT,alanineHT,
ammoniaHT,ampHT,arabinoseHT,asparagineLHT,aspartateHT,atpHT,citrateHT,co2gHT,
co2totHT,coaqHT,cogHT,ethaneaqHT,ethanolHT,ethylacetateHT,ferricHT,ferrousHT,
formateHT,fructoseHT,fructose16phosHT,fructose6phosHT,fumarateHT,galactoseHT,
glucoseHT,glucose6phosHT,glutamateHT,glutamineHT,glycerolHT,glycerol3phosHT,
glycineHT,glycylglycineHT,h2aqHT,h2gHT,h2oHT,h2o2aqHT,h2saqHT,i2crHT,idpHT,
impHT,indoleHT,inosineHT,iodideionHT,isomaltoseHT,itpHT,ketoglutarateHT,
lactateHT,lactoseHT,leucineLHT,malateHT,maltoseHT,mannoseHT,mannose6phosHT,
methaneaqHT,methanegHT,methanolHT,n2aqHT,n2gHT,n2oaqHT,nadoxHT,nadpoxHT,
nadpredHT,nadredHT,nitrateHT,nitriteHT,noaqHT,o2aqHT,o2gHT,oxaloacetateHT,
pepHT,piHT,ppiHT,propanol2HT,pyruvateHT,riboseHT,ribose1phosHT,ribose5phosHT,
ribuloseHT,sorboseHT,succinateHT,sucroseHT,sulfateHT,sulfiteHT,sulfurcrHT,
tryptophanLHT,ureaHT,valineLHT,xyloseHT,xyluloseHT]

Evaluate[{acetaldehydeHT,acetateHT,acetoneHT,adenineHT,adenosineHT,adpHT,alanineHT,
ammoniaHT,ampHT,arabinoseHT,asparagineLHT,aspartateHT,atpHT,citrateHT,co2gHT,
co2totHT,coaqHT,cogHT,ethaneaqHT,ethanolHT,ethylacetateHT,ferricHT,ferrousHT,
formateHT,fructoseHT,fructose16phosHT,fructose6phosHT,fumarateHT,galactoseHT,
glucoseHT,glucose6phosHT,glutamateHT,glutamineHT,glycerolHT,glycerol3phosHT,
glycineHT,glycylglycineHT,h2aqHT,h2gHT,h2oHT,h2o2aqHT,h2saqHT,i2crHT,idpHT,
impHT,indoleHT,inosineHT,iodideionHT,isomaltoseHT,itpHT,ketoglutarateHT,
lactateHT,lactoseHT,leucineLHT,malateHT,maltoseHT,mannoseHT,mannose6phosHT,
methaneaqHT,methanegHT,methanolHT,n2aqHT,n2gHT,n2oaqHT,nadoxHT,nadpoxHT,
nadpredHT,nadredHT,nitrateHT,nitriteHT,noaqHT,o2aqHT,o2gHT,oxaloacetateHT,
pepHT,piHT,ppiHT,propanol2HT,pyruvateHT,riboseHT,ribose1phosHT,ribose5phosHT,
ribuloseHT,sorboseHT,succinateHT,sucroseHT,sulfateHT,sulfiteHT,sulfurcrHT,
tryptophanLHT,ureaHT,valineLHT,xyloseHT,xyluloseHT}]=Map[derivetrHT,{acetaldehydesp,
acetatesp,acetonesp,adeninesp,adenosinesp,adpsp,alaninesp,
ammoniasp,ampsp,arabinosesp,asparagineLsp,aspartatesp,atpsp,citratesp,co2gsp,
co2totsp,coaqsp,cogsp,ethaneaqsp,ethanolsp,ethylacetatesp,ferricsp,ferroussp,
formatesp,fructosesp,fructose16phossp,fructose6phossp,fumaratesp,galactosesp,
glucosesp,glucose6phossp,glutamatesp,glutaminesp,glycerolsp,glycerol3phossp,
glycinesp,glycylglycinesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,h2saqsp,i2crsp,idpsp,
impsp,indolesp,inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaratesp,
lactatesp,lactosesp,leucineLsp,malatesp,maltosesp,mannosesp,mannose6phossp,
methaneaqsp,methanegsp,methanolsp,n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,
nadpredsp,nadredsp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,oxaloacetatesp,
pepsp,pisp,ppisp,propanol2sp,pyruvatesp,ribosesp,ribose1phossp,ribose5phossp,
ribulosesp,sorbosesp,succinatesp,sucrosesp,sulfatesp,sulfitesp,sulfurcrsp,
tryptophanLsp,ureasp,valineLsp,xylosesp,xylulosesp}];

8  Calculation of the functions of temperature, pH and ionic strength for the standard transformed entropies of formation of reactants for which standard enthalpies of formation of the species are known

The function of T, pH, and ionic strength that gives the standard transformed entropy of formation (Subscript[Δ, f])S' ° for a reactant can be derived by differentiating the function for the standard transformed Gibbs energy of formation.  This is done by the program derivetrST.

Clear[acetaldehydeST,acetateST,acetoneST,adenineST,adenosineST,adpST,alanineST,
ammoniaST,ampST,arabinoseST,asparagineLST,aspartateST,atpST,citrateST,co2gST,
co2totST,coaqST,cogST,ethaneaqST,ethanolST,ethylacetateST,ferricST,ferrousST,
formateST,fructoseST,fructose16phosST,fructose6phosST,fumarateST,galactoseST,
glucoseST,glucose6phosST,glutamateST,glutamineST,glycerolST,glycerol3phosST,
glycineST,glycylglycineST,h2aqST,h2gST,h2oST,h2o2aqST,h2saqST,i2crST,idpST,
impST,indoleST,inosineST,iodideionST,isomaltoseST,itpST,ketoglutarateST,
lactateST,lactoseST,leucineLST,malateST,maltoseST,mannoseST,mannose6phosST,
methaneaqST,methanegST,methanolST,n2aqST,n2gST,n2oaqST,nadoxST,nadpoxST,
nadpredST,nadredST,nitrateST,nitriteST,noaqST,o2aqST,o2gST,oxaloacetateST,
pepST,piST,ppiST,propanol2ST,pyruvateST,riboseST,ribose1phosST,ribose5phosST,
ribuloseST,sorboseST,succinateST,sucroseST,sulfateST,sulfiteST,sulfurcrST,
tryptophanLST,ureaST,valineLST,xyloseST,xyluloseST]

Evaluate[{acetaldehydeST,acetateST,acetoneST,adenineST,adenosineST,adpST,alanineST,
ammoniaST,ampST,arabinoseST,asparagineLST,aspartateST,atpST,citrateST,co2gST,
co2totST,coaqST,cogST,ethaneaqST,ethanolST,ethylacetateST,ferricST,ferrousST,
formateST,fructoseST,fructose16phosST,fructose6phosST,fumarateST,galactoseST,
glucoseST,glucose6phosST,glutamateST,glutamineST,glycerolST,glycerol3phosST,
glycineST,glycylglycineST,h2aqST,h2gST,h2oST,h2o2aqST,h2saqST,i2crST,idpST,
impST,indoleST,inosineST,iodideionST,isomaltoseST,itpST,ketoglutarateST,
lactateST,lactoseST,leucineLST,malateST,maltoseST,mannoseST,mannose6phosST,
methaneaqST,methanegST,methanolST,n2aqST,n2gST,n2oaqST,nadoxST,nadpoxST,
nadpredST,nadredST,nitrateST,nitriteST,noaqST,o2aqST,o2gST,oxaloacetateST,
pepST,piST,ppiST,propanol2ST,pyruvateST,riboseST,ribose1phosST,ribose5phosST,
ribuloseST,sorboseST,succinateST,sucroseST,sulfateST,sulfiteST,sulfurcrST,
tryptophanLST,ureaST,valineLST,xyloseST,xyluloseST}]=Map[derivetrST,{acetaldehydesp,
acetatesp,acetonesp,adeninesp,adenosinesp,adpsp,alaninesp,
ammoniasp,ampsp,arabinosesp,asparagineLsp,aspartatesp,atpsp,citratesp,co2gsp,
co2totsp,coaqsp,cogsp,ethaneaqsp,ethanolsp,ethylacetatesp,ferricsp,ferroussp,
formatesp,fructosesp,fructose16phossp,fructose6phossp,fumaratesp,galactosesp,
glucosesp,glucose6phossp,glutamatesp,glutaminesp,glycerolsp,glycerol3phossp,
glycinesp,glycylglycinesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,h2saqsp,i2crsp,idpsp,
impsp,indolesp,inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaratesp,
lactatesp,lactosesp,leucineLsp,malatesp,maltosesp,mannosesp,mannose6phossp,
methaneaqsp,methanegsp,methanolsp,n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,
nadpredsp,nadredsp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,oxaloacetatesp,
pepsp,pisp,ppisp,propanol2sp,pyruvatesp,ribosesp,ribose1phossp,ribose5phossp,
ribulosesp,sorbosesp,succinatesp,sucrosesp,sulfatesp,sulfitesp,sulfurcrsp,
tryptophanLsp,ureasp,valineLsp,xylosesp,xylulosesp}];

9  Calculation of the functions of temperature, pH and ionic strength for the average numbers of hydrogen atoms in reactants for which standard enthalpies of formation of the species are known

The function of temperature, pH. and ionic stength that gives the average number of hydrogen atoms (Subscript[\(N\&_\), H]) in a reactant can be derived by differentiating the function for the standard transformed Gibbs energy of formation.  This is done by the program deriveNHT.

Clear[acetaldehydeNHT,acetateNHT,acetoneNHT,adenineNHT,adenosineNHT,adpNHT,
alanineNHT,ammoniaNHT,ampNHT,arabinoseNHT,asparagineLNHT,aspartateNHT,atpNHT,
citrateNHT,co2gNHT,co2totNHT,coaqNHT,cogNHT,ethaneaqNHT,ethanolNHT,
ethylacetateNHT,ferricNHT,ferrousNHT,formateNHT,fructoseNHT,fructose16phosNHT,
fructose6phosNHT,fumarateNHT,galactoseNHT,glucoseNHT,glucose6phosNHT,
glutamateNHT,glutamineNHT,glycerolNHT,glycerol3phosNHT,glycineNHT,
glycylglycineNHT,h2aqNHT,h2gNHT,h2oNHT,h2o2aqNHT,h2saqNHT,i2crNHT,idpNHT,
impNHT,indoleNHT,inosineNHT,iodideionNHT,isomaltoseNHT,itpNHT,
ketoglutarateNHT,lactateNHT,lactoseNHT,leucineLNHT,malateNHT,maltoseNHT,
mannoseNHT,mannose6phosNHT,methaneaqNHT,methanegNHT,methanolNHT,n2aqNHT,
n2gNHT,n2oaqNHT,nadoxNHT,nadpoxNHT,nadpredNHT,nadredNHT,nitrateNHT,nitriteNHT,
noaqNHT,o2aqNHT,o2gNHT,oxaloacetateNHT,pepNHT,piNHT,ppiNHT,propanol2NHT,
pyruvateNHT,riboseNHT,ribose1phosNHT,ribose5phosNHT,ribuloseNHT,sorboseNHT,
succinateNHT,sucroseNHT,sulfateNHT,sulfiteNHT,sulfurcrNHT,tryptophanLNHT,
ureaNHT,valineLNHT,xyloseNHT,xyluloseNHT]

Evaluate[{acetaldehydeNHT,acetateNHT,acetoneNHT,adenineNHT,adenosineNHT,adpNHT,
alanineNHT,ammoniaNHT,ampNHT,arabinoseNHT,asparagineLNHT,aspartateNHT,atpNHT,
citrateNHT,co2gNHT,co2totNHT,coaqNHT,cogNHT,ethaneaqNHT,ethanolNHT,
ethylacetateNHT,ferricNHT,ferrousNHT,formateNHT,fructoseNHT,fructose16phosNHT,
fructose6phosNHT,fumarateNHT,galactoseNHT,glucoseNHT,glucose6phosNHT,
glutamateNHT,glutamineNHT,glycerolNHT,glycerol3phosNHT,glycineNHT,
glycylglycineNHT,h2aqNHT,h2gNHT,h2oNHT,h2o2aqNHT,h2saqNHT,i2crNHT,idpNHT,
impNHT,indoleNHT,inosineNHT,iodideionNHT,isomaltoseNHT,itpNHT,
ketoglutarateNHT,lactateNHT,lactoseNHT,leucineLNHT,malateNHT,maltoseNHT,
mannoseNHT,mannose6phosNHT,methaneaqNHT,methanegNHT,methanolNHT,n2aqNHT,
n2gNHT,n2oaqNHT,nadoxNHT,nadpoxNHT,nadpredNHT,nadredNHT,nitrateNHT,nitriteNHT,
noaqNHT,o2aqNHT,o2gNHT,oxaloacetateNHT,pepNHT,piNHT,ppiNHT,propanol2NHT,
pyruvateNHT,riboseNHT,ribose1phosNHT,ribose5phosNHT,ribuloseNHT,sorboseNHT,
succinateNHT,sucroseNHT,sulfateNHT,sulfiteNHT,sulfurcrNHT,tryptophanLNHT,
ureaNHT,valineLNHT,xyloseNHT,xyluloseNHT}]=Map[deriveNHT,{acetaldehydesp,
acetatesp,acetonesp,adeninesp,adenosinesp,adpsp,alaninesp,
ammoniasp,ampsp,arabinosesp,asparagineLsp,aspartatesp,atpsp,citratesp,co2gsp,
co2totsp,coaqsp,cogsp,ethaneaqsp,ethanolsp,ethylacetatesp,ferricsp,ferroussp,
formatesp,fructosesp,fructose16phossp,fructose6phossp,fumaratesp,galactosesp,
glucosesp,glucose6phossp,glutamatesp,glutaminesp,glycerolsp,glycerol3phossp,
glycinesp,glycylglycinesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,h2saqsp,i2crsp,idpsp,
impsp,indolesp,inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaratesp,
lactatesp,lactosesp,leucineLsp,malatesp,maltosesp,mannosesp,mannose6phossp,
methaneaqsp,methanegsp,methanolsp,n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,
nadpredsp,nadredsp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,oxaloacetatesp,
pepsp,pisp,ppisp,propanol2sp,pyruvatesp,ribosesp,ribose1phossp,ribose5phossp,
ribulosesp,sorbosesp,succinatesp,sucrosesp,sulfatesp,sulfitesp,sulfurcrsp,
tryptophanLsp,ureasp,valineLsp,xylosesp,xylulosesp}];

End[]

Now we protect all the names that have been assigned so that they cannot be changed.

Protect [t,pH, is, 
acetaldehydesp,acetatesp,acetoacetatesp,acetoacetylcoAsp,acetonesp,
acetylcoAsp,acetylphossp,aconitatecissp,adeninesp,adenosinesp,
adenosinephosphosulfatesp,adpsp,alaninesp,ammoniasp,ampsp,arabinosesp,
arabinose5phossp,asparagineLsp,aspartatesp,atpsp,bpgsp,butanalsp,butanolnsp,
butyratesp,cellobiosesp,citratesp,citrateisosp,co2gsp,co2totsp,coAsp,
coAglutathionesp,coaqsp,cogsp,creatinesp,creatininesp,cyclicampsp,cysteineLsp,
cystineLsp,cytochromecoxsp,cytochromecredsp,deoxyadenosinesp,deoxyadpsp,
deoxyampsp,deoxyatpsp,deoxyribosesp,deoxyribose1phossp,deoxyribose5phossp,
dihydroxyacetonesp,dihydroxyacetonephossp,ethaneaqsp,ethanolsp,
ethylacetatesp,fadenzoxsp,fadenzredsp,fadoxsp,fadredsp,ferredoxinoxsp,
ferredoxinredsp,ferricsp,ferroussp,fmnoxsp,fmnredsp,formatesp,fructosesp,
fructose16phossp,fructose6phossp,fumaratesp,galactono14lactonesp,
galactosesp,galactose1phossp,galactose6phossp,gluconolactonesp,
gluconolactone6phossp,glucosesp,glucose1phossp,glucose6phossp,glutamatesp,
glutaminesp,glutathioneoxsp,glutathioneredsp,glyceraldehydesp,
glyceraldehydephossp,glyceratesp,glycerolsp,glycerol3phossp,glycinesp,
glycolatesp,glycylglycinesp,glyoxylatesp,h2aqsp,h2gsp,h2osp,h2o2aqsp,
h2saqsp,hydroxy2oxoglutaratesp,hydroxyglutaratesp,hydroxypropionatebsp,
hydroxypyruvatesp,hypoxanthinesp,i2crsp,iditolsp,idpsp,impsp,indolesp,
inosinesp,iodideionsp,isomaltosesp,itpsp,ketoglutaramatesp,
ketoglutaratesp,lactatesp,lactosesp,lactulosesp,leucineisoLsp,leucineLsp,
lyxosesp,malatesp,maleatesp,maltosesp,malylcoAsp,mannitol1phossp,mannitolDsp,
mannosesp,mannose1phossp,mannose6phossp,methaneaqsp,methanegsp,methanolsp,
methionineLsp,methyl2oxopentanoatesp,methylmalatesp,methylmaleatesp,
methylmalonylcoAsp,n2aqsp,n2gsp,n2oaqsp,nadoxsp,nadpoxsp,nadpredsp,nadredsp,
nicotinamideribonucleotidesp,nitratesp,nitritesp,noaqsp,o2aqsp,o2gsp,
oxalatesp,oxaloacetatesp,oxalosuccinatesp,oxalylcoAsp,oxoprolinesp,
palmitatesp,pepsp,phenylalanineLsp,phosphoglycerate2sp,phosphoglycerate3sp,
phosphohydroxypyruvatesp,phosphoserinesp,pisp,ppisp,propanol2sp,propanolnsp,
propanoylcoAsp,prppsp,pyruvatesp,retinalsp,retinolsp,ribitolsp,ribosesp,
ribose1phossp,ribose5phossp,ribulosesp,ribulose5phossp,serineLsp,sorbitolsp,
sorbitol6phossp,sorbosesp,succinatesp,succinylcoAsp,sucrosesp,sulfatesp,
sulfitesp,sulfurcrsp,thioredoxinoxsp,thioredoxinredsp,threoninesp,
transcinnamatesp,trehalosesp,tryptophanLsp,tyrosineLsp,ubiquinoneoxsp,
ubiquinoneredsp,uratesp,ureasp,uricacidsp,valineLsp,xylitolsp,xylosesp,
xylulosesp];

Protect[acetaldehyde,acetate,acetoacetate,acetoacetylcoA,acetone,acetylcoA,
acetylphos,aconitatecis,adenine,adenosine,adenosinephosphosulfate,adp,alanine,
ammonia,amp,arabinose,arabinose5phos,asparagineL,aspartate,atp,bpg,butanal,
butanoln,butyrate,cellobiose,citrate,citrateiso,co2g,co2tot,coA,
coAglutathione,coaq,cog,creatine,creatinine,cyclicamp,cysteineL,cystineL,
cytochromecox,cytochromecred,deoxyadenosine,deoxyadp,deoxyamp,deoxyatp,
deoxyribose,deoxyribose1phos,deoxyribose5phos,dihydroxyacetone,
dihydroxyacetonephos,ethaneaq,ethanol,ethylacetate,fadenzox,fadenzred,fadox,
fadred,ferredoxinox,ferredoxinred,ferric,ferrous,fmnox,fmnred,formate,
fructose,fructose16phos,fructose6phos,fumarate,galactono14lactone,galactose,
galactose1phos,galactose6phos,gluconolactone,gluconolactone6phos,glucose,
glucose1phos,glucose6phos,glutamate,glutamine,glutathioneox,glutathionered,
glyceraldehyde,glyceraldehydephos,glycerate,glycerol,glycerol3phos,glycine,
glycolate,glycylglycine,glyoxylate,h2aq,h2g,h2o,h2o2aq,h2saq,
hydroxy2oxoglutarate,hydroxyglutarate,hydroxypropionateb,hydroxypyruvate,
hypoxanthine,i2cr,iditol,idp,imp,indole,inosine,iodideion,isomaltose,itp,
ketoglutaramate,ketoglutarate,lactate,lactose,lactulose,leucineisoL,
leucineL,lyxose,malate,maleate,maltose,malylcoA,mannitol1phos,mannitolD,
mannose,mannose1phos,mannose6phos,methaneaq,methaneg,methanol,methionineL,
methyl2oxopentanoate,methylmalate,methylmaleate,methylmalonylcoA,n2aq,n2g,
n2oaq,nadox,nadpox,nadpred,nadred,nicotinamideribonucleotide,nitrate,
nitrite,noaq,o2aq,o2g,oxalate,oxaloacetate,oxalosuccinate,oxalylcoA,
oxoproline,palmitate,pep,phenylalanineL,phosphoglycerate2,phosphoglycerate3,
phosphohydroxypyruvate,phosphoserine,pi,ppi,propanol2,propanoln,
propanoylcoA,prpp,pyruvate,retinal,retinol,ribitol,ribose,ribose1phos,
ribose5phos,ribulose,ribulose5phos,serineL,sorbitol,sorbitol6phos,sorbose,
succinate,succinylcoA,sucrose,sulfate,sulfite,sulfurcr,thioredoxinox,
thioredoxinred,threonine,transcinnamate,trehalose,tryptophanL,tyrosineL,
ubiquinoneox,ubiquinonered,urate,urea,uricacid,valineL,xylitol,xylose,
xylulose];

Protect[acetaldehydeNH,acetateNH,acetoacetateNH,acetoacetylcoANH,acetoneNH,
acetylcoANH,acetylphosNH,aconitatecisNH,adenineNH,adenosineNH,
adenosinephosphosulfateNH,adpNH,alanineNH,ammoniaNH,ampNH,arabinoseNH,
arabinose5phosNH,asparagineLNH,aspartateNH,atpNH,bpgNH,butanalNH,butanolnNH,
butyrateNH,cellobioseNH,citrateNH,citrateisoNH,co2gNH,co2totNH,coANH,
coAglutathioneNH,coaqNH,cogNH,creatineNH,creatinineNH,cyclicampNH,cysteineLNH,
cystineLNH,cytochromecoxNH,cytochromecredNH,deoxyadenosineNH,deoxyadpNH,
deoxyampNH,deoxyatpNH,deoxyriboseNH,deoxyribose1phosNH,deoxyribose5phosNH,
dihydroxyacetoneNH,dihydroxyacetonephosNH,ethaneaqNH,ethanolNH,
ethylacetateNH,fadenzoxNH,fadenzredNH,fadoxNH,fadredNH,ferredoxinoxNH,
ferredoxinredNH,ferricNH,ferrousNH,fmnoxNH,fmnredNH,formateNH,fructoseNH,
fructose16phosNH,fructose6phosNH,fumarateNH,galactono14lactoneNH,
galactoseNH,galactose1phosNH,galactose6phosNH,gluconolactoneNH,
gluconolactone6phosNH,glucoseNH,glucose1phosNH,glucose6phosNH,glutamateNH,
glutamineNH,glutathioneoxNH,glutathioneredNH,glyceraldehydeNH,
glyceraldehydephosNH,glycerateNH,glycerolNH,glycerol3phosNH,glycineNH,
glycolateNH,glycylglycineNH,glyoxylateNH,h2aqNH,h2gNH,h2oNH,h2o2aqNH,
h2saqNH,hydroxy2oxoglutarateNH,hydroxyglutarateNH,hydroxypropionatebNH,
hydroxypyruvateNH,hypoxanthineNH,i2crNH,iditolNH,idpNH,impNH,indoleNH,
inosineNH,iodideionNH,isomaltoseNH,itpNH,ketoglutaramateNH,
ketoglutarateNH,lactateNH,lactoseNH,lactuloseNH,leucineisoLNH,leucineLNH,
lyxoseNH,malateNH,maleateNH,maltoseNH,malylcoANH,mannitol1phosNH,mannitolDNH,
mannoseNH,mannose1phosNH,mannose6phosNH,methaneaqNH,methanegNH,methanolNH,
methionineLNH,methyl2oxopentanoateNH,methylmalateNH,methylmaleateNH,
methylmalonylcoANH,n2aqNH,n2gNH,n2oaqNH,nadoxNH,nadpoxNH,nadpredNH,nadredNH,
nicotinamideribonucleotideNH,nitrateNH,nitriteNH,noaqNH,o2aqNH,o2gNH,
oxalateNH,oxaloacetateNH,oxalosuccinateNH,oxalylcoANH,oxoprolineNH,
palmitateNH,pepNH,phenylalanineLNH,phosphoglycerate2NH,phosphoglycerate3NH,
phosphohydroxypyruvateNH,phosphoserineNH,piNH,ppiNH,propanol2NH,propanolnNH,
propanoylcoANH,prppNH,pyruvateNH,retinalNH,retinolNH,ribitolNH,riboseNH,
ribose1phosNH,ribose5phosNH,ribuloseNH,ribulose5phosNH,serineLNH,sorbitolNH,
sorbitol6phosNH,sorboseNH,succinateNH,succinylcoANH,sucroseNH,sulfateNH,
sulfiteNH,sulfurcrNH,thioredoxinoxNH,thioredoxinredNH,threonineNH,
transcinnamateNH,trehaloseNH,tryptophanLNH,tyrosineLNH,ubiquinoneoxNH,
ubiquinoneredNH,urateNH,ureaNH,uricacidNH,valineLNH,xylitolNH,xyloseNH,
xyluloseNH];

Protect[acetaldehydeGT,acetateGT,acetoneGT,adenineGT,adenosineGT,adpGT,
alanineGT,ammoniaGT,ampGT,arabinoseGT,asparagineLGT,aspartateGT,atpGT,
citrateGT,co2gGT,co2totGT,coaqGT,cogGT,ethaneaqGT,ethanolGT,ethylacetateGT,
ferricGT,ferrousGT,formateGT,fructoseGT,fructose16phosGT,fructose6phosGT,
fumarateGT,galactoseGT,glucoseGT,glucose6phosGT,glutamateGT,glutamineGT,
glycerolGT,glycerol3phosGT,glycineGT,glycylglycineGT,h2aqGT,h2gGT,h2oGT,
h2o2aqGT,h2saqGT,i2crGT,idpGT,impGT,indoleGT,inosineGT,iodideionGT,
isomaltoseGT,itpGT,ketoglutarateGT,lactateGT,lactoseGT,leucineLGT,malateGT,
maltoseGT,mannoseGT,mannose6phosGT,methaneaqGT,methanegGT,methanolGT,n2aqGT,
n2gGT,n2oaqGT,nadoxGT,nadpoxGT,nadpredGT,nadredGT,nitrateGT,nitriteGT,
noaqGT,o2aqGT,o2gGT,oxaloacetateGT,pepGT,piGT,ppiGT,propanol2GT,pyruvateGT,
riboseGT,ribose1phosGT,ribose5phosGT,ribuloseGT,sorboseGT,succinateGT,
sucroseGT,sulfateGT,sulfiteGT,sulfurcrGT,tryptophanLGT,ureaGT,valineLGT,
xyloseGT,xyluloseGT];

Protect[
acetaldehydeHT,acetateHT,acetoneHT,adenineHT,adenosineHT,adpHT,alanineHT,
ammoniaHT,ampHT,arabinoseHT,asparagineLHT,aspartateHT,atpHT,citrateHT,co2gHT,
co2totHT,coaqHT,cogHT,ethaneaqHT,ethanolHT,ethylacetateHT,ferricHT,ferrousHT,
formateHT,fructoseHT,fructose16phosHT,fructose6phosHT,fumarateHT,galactoseHT,
glucoseHT,glucose6phosHT,glutamateHT,glutamineHT,glycerolHT,glycerol3phosHT,
glycineHT,glycylglycineHT,h2aqHT,h2gHT,h2oHT,h2o2aqHT,h2saqHT,i2crHT,idpHT,
impHT,indoleHT,inosineHT,iodideionHT,isomaltoseHT,itpHT,ketoglutarateHT,
lactateHT,lactoseHT,leucineLHT,malateHT,maltoseHT,mannoseHT,mannose6phosHT,
methaneaqHT,methanegHT,methanolHT,n2aqHT,n2gHT,n2oaqHT,nadoxHT,nadpoxHT,
nadpredHT,nadredHT,nitrateHT,nitriteHT,noaqHT,o2aqHT,o2gHT,oxaloacetateHT,
pepHT,piHT,ppiHT,propanol2HT,pyruvateHT,riboseHT,ribose1phosHT,ribose5phosHT,
ribuloseHT,sorboseHT,succinateHT,sucroseHT,sulfateHT,sulfiteHT,sulfurcrHT,
tryptophanLHT,ureaHT,valineLHT,xyloseHT,xyluloseHT];

Protect[acetaldehydeST,acetateST,acetoneST,adenineST,adenosineST,adpST,alanineST,
ammoniaST,ampST,arabinoseST,asparagineLST,aspartateST,atpST,citrateST,co2gST,
co2totST,coaqST,cogST,ethaneaqST,ethanolST,ethylacetateST,ferricST,ferrousST,
formateST,fructoseST,fructose16phosST,fructose6phosST,fumarateST,galactoseST,
glucoseST,glucose6phosST,glutamateST,glutamineST,glycerolST,glycerol3phosST,
glycineST,glycylglycineST,h2aqST,h2gST,h2oST,h2o2aqST,h2saqST,i2crST,idpST,
impST,indoleST,inosineST,iodideionST,isomaltoseST,itpST,ketoglutarateST,
lactateST,lactoseST,leucineLST,malateST,maltoseST,mannoseST,mannose6phosST,
methaneaqST,methanegST,methanolST,n2aqST,n2gST,n2oaqST,nadoxST,nadpoxST,
nadpredST,nadredST,nitrateST,nitriteST,noaqST,o2aqST,o2gST,oxaloacetateST,
pepST,piST,ppiST,propanol2ST,pyruvateST,riboseST,ribose1phosST,ribose5phosST,
ribuloseST,sorboseST,succinateST,sucroseST,sulfateST,sulfiteST,sulfurcrST,
tryptophanLST,ureaST,valineLST,xyloseST,xyluloseST];

Protect[acetaldehydeNHT,acetateNHT,acetoneNHT,adenineNHT,adenosineNHT,adpNHT,
alanineNHT,ammoniaNHT,ampNHT,arabinoseNHT,asparagineLNHT,aspartateNHT,atpNHT,
citrateNHT,co2gNHT,co2totNHT,coaqNHT,cogNHT,ethaneaqNHT,ethanolNHT,
ethylacetateNHT,ferricNHT,ferrousNHT,formateNHT,fructoseNHT,fructose16phosNHT,
fructose6phosNHT,fumarateNHT,galactoseNHT,glucoseNHT,glucose6phosNHT,
glutamateNHT,glutamineNHT,glycerolNHT,glycerol3phosNHT,glycineNHT,
glycylglycineNHT,h2aqNHT,h2gNHT,h2oNHT,h2o2aqNHT,h2saqNHT,i2crNHT,idpNHT,
impNHT,indoleNHT,inosineNHT,iodideionNHT,isomaltoseNHT,itpNHT,
ketoglutarateNHT,lactateNHT,lactoseNHT,leucineLNHT,malateNHT,maltoseNHT,
mannoseNHT,mannose6phosNHT,methaneaqNHT,methanegNHT,methanolNHT,n2aqNHT,
n2gNHT,n2oaqNHT,nadoxNHT,nadpoxNHT,nadpredNHT,nadredNHT,nitrateNHT,nitriteNHT,
noaqNHT,o2aqNHT,o2gNHT,oxaloacetateNHT,pepNHT,piNHT,ppiNHT,propanol2NHT,
pyruvateNHT,riboseNHT,ribose1phosNHT,ribose5phosNHT,ribuloseNHT,sorboseNHT,
succinateNHT,sucroseNHT,sulfateNHT,sulfiteNHT,sulfurcrNHT,tryptophanLNHT,
ureaNHT,valineLNHT,xyloseNHT,xyluloseNHT];

EndPackage[]