Groupcontribution

assignThermoToModel(model, Alberty2006, Legendre, LegendreCHI, useKeqData, printToFile, GCpriorityMetList, metGroupCont, metSpeciespKa)[source]

Assigns thermodynamic data to model at given temperature, pH, ionic strength and electrical potential.

Physicochemically, this is the most important function for setting up a thermodynamic model. It takes the standard Gibbs energies of the metabolite species and uses this data to create a standard transformed Gibbs energy for each reactant. It uses the metabolite species standard Gibbs energies of formation backcalculated from equilibrium constants, in preference to the group contribution estimates.

USAGE

[model,computedSpeciesData] = assignThermoToModel (model, Alberty2006, Legendre, LegendreCHI, useKeqData, printToFile, GCpriorityMetList, metGroupCont, metSpeciespKa)

INPUTS

  • model – structure with fields:

    • model.T - temperature 298.15 K to 313.15 K

    • model.ph(p) - real pH in compartment defined by letter p

    • model.is(p) - ionic strength (0 - 0.35M) in compartment defined by letter p

    • model.chi(p) - electrical potential (mV) in compartment defined by letter p

    • model.cellCompartments(p) - 1 x # cell array of distinct compartment letters

    • model.NaNdfG0GCMetBool(m) - m x 1 boolean vector with 1 when no group contribution data is available for a metabolite

  • Alberty2006 – Alberty’s data

OPTIONAL INPUTS

  • Legendre – {(1), 0} Legendre Transformation for specifc real pH?

  • LegendreCHI – {(1), 0} Legendre Transformation for specifc electrical potential?

  • useKeqData – {(1), 0} Use dGf0 back calculated from Keq?

  • printToFile – {(0), 1} 1 = print out repetitive material to log file

  • metGroupCont – Structure containing output from Jankowski et al.’s 2008 implementation of the group contribution method (GCM). Contains the following fields for each metabolite:

    • .abbreviation: Metabolite ID

    • .formulaMarvin: Metabolite formula output by GCM

    • .delta_G_formation: Estimated standard Gibbs energy of formation

    • .delta_G_formation_uncertainty: Uncertainty in estimated delta_G_formation

    • .chargeMarvin: Metabolite charge output by GCM

  • metSpeciespKa – Structure containing pKa for acid-base equilibria between metabolite species. pKa are estimated with ChemAxon’s pKa calculator plugin (see function assignpKasToSpecies).

OUTPUTS

model – structure with fields:

  • model.dfG0(m) - standard Gibbs energy of formation

  • model.dfG(m) - Gibbs energy of formation

  • model.dfGt0(m) - standard transformed Gibbs energy of formation

  • model.dHzerot(m) - standard transformed enthalpy of formation

  • model.dfGt0Source(m) - origin of data, Keq or groupContFileName.txt

  • model.dfGt0Keq(m)

  • model.dfGt0GroupCont(m)

  • model.dfHt0Keq(m)

  • model.mf(m) - mole fraction of each species within a pseudoisomer group

  • model.aveZi(m) - average charge

  • model.chi - electrical potential

  • model.aveHbound(m) - average number of protons bound to a reactant

  • modelT.gasConstant - Gas Constant (deprecated)

  • model.faradayConstant - Faraday Constant

  • modelT.temp - Temperature (deprecated)

  • model.ph(p) - real pH in compartment defined by letter p

  • model.is(p) - ionic strength (0 - 0.35M) in compartment defined by letter p

  • model.chi(p) - electrical potential (mV) in compartment defined by letter p

createComputedSpeciesData(metSpeciespKa, metGroupCont)[source]

Use group contribution estimated standard Gibbs energies of formation for predominant metabolite species at pH 7, and ChemAxon estimated pKa for species equilibria, to calculate standard Gibbs energies of formation for nonpredominant metabolite species.

USAGE

computedSpeciesData = createComputedSpeciesData (metSpeciespKa, metGroupCont)

INPUTS

  • metSpeciespKa – Structure containing pKa for acid-base equilibria between metabolite species. pKa are estimated with ChemAxon’s pKa calculator plugin (see function “assignpKasToSpecies”)

  • metGroupCont – Structure array with group contribution method output mapped to BiGG metabolites.

OUTPUT

computedSpeciesData – Structure with thermodynamic data for metabolite species. Contains two fields for each metabolite:

  • .abbreviation: Metabolite abbreviation

  • .basicData: Cell array with 4 columns; 1. dGf0 (kJ/mol), 2. dHf0, 3. charge, 4. #Hydrogens