Reactantcontribution

acidDissociationConstant(metAbbr, Alberty2006, metAbbrAlbertyAbbr, temp, is, chi)[source]

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 INPUT

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)[source]

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 INPUT:

  • 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?

  • printLevel – verbosity control; if > 0, prints diagnostic output. Default is 0.

OUTPUT:

  • 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)[source]

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:

  • .S - m x n stoichiometric matrix

  • .mets - m x 1 cell array of metabolite identifiers

  • .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 – cell array of metabolite abbreviations to place on a common thermodynamic baseline. Defaults to a built-in list of Alberty cofactors.

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)[source]

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 - m x n stoichiometric matrix

  • .SExRxnInd - indices of external (exchange/demand/sink) reactions

  • .rxns - n x 1 cell array of reaction identifiers

  • .met(m).mf - mole fraction of each species of metabolite m

OUTPUTS:

  • rxnBool – n x 1 logical, true for reactions where each reactant is a single metabolite species

  • nSpecies – m x 1 vector with the number of species of each metabolite

thermodynamicAdjustmentToStoichiometry(model)[source]

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 - m x n stoichiometric matrix

  • .mets - m x 1 cell array of metabolite identifiers

  • .rxns - n x 1 cell array of reaction identifiers

  • .metFormulas - m x 1 cell array of metabolite formulas

  • .metNames - m x 1 cell array of metabolite names

  • .rxnNames - n x 1 cell array of reaction names

  • .subSystems - n x 1 cell array of reaction subsystem annotations

  • .SIntRxnBool - n x 1 logical, true for internal (mass-balanced) reactions

OUTPUT:

model – structure with fields:

  • .S - thermodynamically adjusted stoichiometric matrix

  • .oldS - copy of the original (pre-adjustment) stoichiometric matrix

  • .mets - m x 1 cell array of metabolite identifiers

  • .rxns - n x 1 cell array of reaction identifiers

  • .metFormulas - metabolite formulas, adjusted for co2/h2o

  • .metNames - metabolite names, with bound cofactors appended

  • .rxnNames - reaction names, with bound cofactors annotated

  • .subSystems - subsystem annotations

  • .SIntRxnBool - n x 1 logical, true for internal reactions

  • .SExRxnBool - n x 1 logical, true for external reactions

waterGibbsEnergyOfFormation(T)[source]

Standard Gibbs energy of formation of liquid water at temperature T

Uses the NIST Shomate equation (heat capacity, enthalpy and entropy integrals) to compute the standard Gibbs energy of formation of liquid water as a function of temperature.

USAGE:

dGf0 = waterGibbsEnergyOfFormation (T)

INPUT:

T – temperature in Kelvin

OUTPUT:

dGf0 – standard Gibbs energy of formation of liquid water (kJ/mol)

Note

Shomate coefficients from NIST: http://webbook.nist.gov/cgi/cbook.cgi?ID=C7732185&Units=SI&Mask=2#ref-2