Kinetic redox reactions

[NKampman]

Hi - I had a general question about the form of the reaction formulas defined in KINETICS, for RATES involving redox reactions. I am modeling bacterial sulfate reduction in the presence of a dissolved fatty acid and subsequent H2S generation.

As an example I include extracts of the RATES and KINETICS blocks I am using, below (similar to example 15 in the PHREEQC documentation)

My question was - what valence state does phreeqc take for elements used in the KINETICS block '-formula'? Does phreeqc automatically use a valence that means the total change in 'elements' in '-formula' is charged balanced? For example, in the case I am looking at, metabolism of acetate releases carbon to solution - only the total change in 'C' is defined in '-formula' e.g. 'C  -0.66' . How does phreeqc decide whether to use C(-4) rather than C(4) when adding this new carbon to solution? Am I correct in thinking that following the KINETICS step PHREEQC recalculates the species equilibria to distribute the change in redox that occurs as a result of this reaction amongst all the redox sensitive species?

Any insight would be much appreciated!

Thanks



RATES
Acetate-
-start
10 Kc = 0.01
20 Ks = 0.01
30 qm = 1.69444E-05 # maximum specific growth rate (h-1)
40 f1 = MOL("Acetate-")/(Kc+MOL("Acetate-"))
50 f2 = MOL("SO4-2")/(Ks + MOL("SO4-2"))
60 rate = -qm*MOL("Biomass")*f1*f2
70 moles = rate * TIME
80 REM Do not consume more than what is available
90 IF (moles > M) THEN moles = M
100 PUT(rate, 1)   # save the rate for use in Biomass rate calculation
200 SAVE moles
-end
#
BiomassRate
        -start
10 Y = 33.77   # microbial yield coefficient (g cells/mol acetate)
20 D = 0.035/3600 # bacterial decay rate  (hr-1) 
30 rate = GET(1)  # uses rate calculated in acetate rate calculation
40 rate = -Y*rate-D*MOL("Biomass")
50 moles = -rate * TIME
60 if (MOL("Biomass") + moles) < 0 then moles = -MOL("Biomass")
200 SAVE moles
        -end

KINETICS
Acetate-
    -formula  Acetate-  1 N 0.25 C  -0.66 H  -1.25 O -1.5
    -m        0
    -m0       0
    -tol      1e-08
BiomassRate
    -formula  Biomass  1
    -m        0
    -m0       0
    -tol      1e-08

[dlparkhurst]

You should not try to choose the electron acceptor for a redox reaction. The kinetic reaction should only specify the change in moles of elements in solution. For your acetate reaction, Acetate should decrease in the system with a consequent increase in C, H, and O. The amount of N in the system probably does not change.

So you probably want the formula

-formula Acetate -1 CH3COO +1

or,equivalently, because the net reaction is the same,

-formula AcetateH -1 CH3COOH +1

The formula does not consider charge on the reactants. The CH3COO will be added to the solution, and redox equilibria will determine the electron acceptor. This will work out as expected, where O2, NO3, SO4 will be used in sequence.