reactantContribution

acidDissociationConstant(metAbbr, Alberty2006, metAbbrAlbertyAbbr, temp, is, chi)

Acid dissociation constant for the different metabolite species that make up a reactant

Usage

[Ka, pKa] = acidDissociationConstant(metAbbr, Alberty2006, metAbbrAlbertyAbbr, temp, is, chi)

Inputs

• metAbbr – reconstruction reactant abbreviation
• Alberty2006 – Basic data on the metabolite species that make up a reactant, compiled by Robert A. Alberty, Massachusetts Institute of Technology. In Print: Robert A. Alberty, Biochemical Thermodynamics: Applications of Mathematica. John Wiley & Sons, 2006. p391-395 Online: BasicBioChemData3.nb http://library.wolfram.com/infocenter/MathSource/5704/
• metAbbrAlbertyAbbr – mapping from model metabolite primary key to primary key of reactants in Alberty2006

Optional inputs

• temp – temperature (default 298.15 K)
• is – ionic strength (default 0 M)
• chi – electrical potential (default 0)

Outputs

• Ka – apparent equilibrium constants
• pKa – \(-log_{10}(Ka)\)

calcdGHT(dGzero, dHzero, zi, nH, pHr, is, temp, chi, Legendre, LegendreCHI, printLevel)

Calculates the standard transformed Gibbs energy of a reactant

Reproduces the function of T (in Kelvin), pHa (electrode pH), and ionic strength (is) that gives the standard transformed Gibbs energy of formation of a reactant (sum of species) and the standard transformed enthalpy of a reactant.

Assuming p pseudoisomer species corresponding to one reactant

Optional output dependent on multiple precision toolbox

Usage

[dGf0, dHf0, mf, aveHbound, aveZi, lambda, gpfnsp] = calcdGHT(dGzero, dHzero, zi, nH, pHr, is, temp, chi, Legendre, LegendreCHI, printLevel)

Inputs

• dGzero – p x 1 standard Gibbs energy of formation at 298.15 K
• zi – p x 1 electric charge
• nH – p x 1 number of hydrogen atoms in each species
• pHr – real pH of 5 to 9 (see realpH.m)
• is – ionic strength 0 to 0.35 M
• temp – temperature 273.15 K to 313.15 K

Optional inputs

• dHzero – p x 1 standard enthalpy of formation at 298.15 K
• chi – electrical potential
• Legendre – {(1), 0} Legendre Transformation for specifc pHr?
• LegendreCHI – {(1), 0} Legendre Transformation for specifc electrical potential?

Outputs

• dGf0 – reactant standard transformed Gibbs energy of formation
• dHf0 – reactant standard transformed enthalpy of formation
• mf – mole fraction of each species within a pseudoisomer group
• aveHbound – average number of protons bound to a reactant
• aveZi – average charge of a reactant
• lambda – activity coefficient for each metabolite species
• gpfnsp – metabolite species standard transformed Gibbs energy of formation

Optional output

• dHf0 – standard transformed enthalpy of formation

The values of the standard transformed Gibbs energy of formation and the standard transformed enthalpy of formation can be calculated temperature in the range 273.15 K to 313.15 K, using the van’t Hoff equation. pHr in the range 5 to 9 (these correspond to the pH range of the species in Alberty’s tables) ionic strength in the range 0 to 0.35 M. See Mathematica program calcdGHT p289 Alberty 2003

The changes in the values of standard transformed Gibbs energy of formation and the standard transformed enthalpy of formation might be improved if knowlegde of standard molar heat capacity was available for each species See p41 Alberty 2003

Multiple Precision Toolbox for MATLAB by Ben Barrowes (mptoolbox_1.1) http://www.mathworks.com/matlabcentral/fileexchange/6446

setCommonZeroStandardGibbsEnergyOfFormation(model, adjustedMetList)

Sets all Alberty’s cofactor metabolites to have a common thermodynamic baseline.

Sets all the exceptional metabolites to have a common baseline. i.e. Standard transformed Gibbs energies of reactants with the baseline adjusted for certain paired cofactors e.g. fad & fadh2, such that the difference between the two is the same as in Albertys data but the absolute values are consistent with the group contribution data

Usage

model = setCommonZeroStandardGibbsEnergyOfFormation(model, adjustedMetList)

Input

• model – Thermodynamic model:
  • .met(m).dGft0 - standard transformed Gibbs energy of formation(kJ/mol)
  • .met(m).dGft0Keq - standard transformed Gibbs energy of formation(kJ/mol)
  • .met(m).dGft0Source - origin of data, Keq or groupContFileName.txt
  • .met(m).dGft0GroupCont - group. cont. estimate of standard transformed Gibbs energy of formation(kJ/mol)

Optional input

• adjustedMetList

Output

• model – structure with field:
  • .met(m).dGft0 - Standard transformed Gibbs energies of reactants with the baseline adjusted for certain paired cofactors e.g. fad & fadh2, such that the difference between the two is the same as in Albertys data but the absolute values are consistent with the group contribution data

singleMetaboliteSpeciesReaction(model)

Identifies reactions involving reactants with only one metabolite species.

Identifies the reactions involving one substrate metabolite species reactant, one product metabolite species reactant and where each reactant is composed of only one metabolite species.

Usage

[rxnBool, nSpecies] = singleMetaboliteSpeciesReaction(model)

Input

• model – structure with fields:
  • .S
  • .met(m).mf - mole fraction of each species

thermodynamicAdjustmentToStoichiometry(model)

Thermodynamic adjustments to the stoichiometric matrix for ‘co2’, ‘h2o’, and bound cofactors.

In aqueous phase, carbon dioxide is distributed between ‘CO2(aq)’, ‘H2CO3’, ‘HCO3^-‘, ‘CO3^2-‘. For each ‘CO2(tot)’ in a reaction add an ‘H2O’ to the other side of reaction, and change the formula for carbon dioxide to ‘CO2.H20’ = ‘H2CO3’ see p150 Alberty 2003.

Also adjust stoichiometric matrix to account for the fact that the cofactors of succinate dehydrogenase, FAD/FADH, are bound.

Usage

model = thermodynamicAdjustmentToStoichiometry(model)

Input

• model – structure with fields:
  • .S
  • .mets
  • .rxns

Output

• model – structure with fields:
  • .S - thermodynamically adjusted stoichiometric matrix
  • .mets
  • .rxns
  • .Sold