Brute force denitrifying?

[peterwadeuk]

Greetings good persons.

I am working with a conceptual model of a system in which nitrogen added to soil pore water as an agricultural fertiliser is transformed to nitrate, which is transported away from the soil through groundwater percolation and into streams, wetlands and maybe even marine reducing conditions.

I am a novice in the nitrogen cycling modelling arena.

I am wanting to simulate generation of nitrate under some conditions, with subsequent denitrification and replacement of the nitrate anion by bicarbonate anion.

The overall denitrifying reaction is as follows (in wateq4f.dat): 2 NO3- + 12 H+ + 10 e- = N2 + 6 H2O

If I try to model this reaction as a kinetic expression, or via REACTION as follows:

TITLE DENITRIFICATION
SOLUTION 1
    temp      25
    pH        8.24
    pe        12.471
    redox     pe
    units     mg/l
    density   1
    Al        0.065
    Ba        0.737
    C(4)      1 CO2(g)     -3.39
    Ca        32.4
    Cl        6.774
    F         1.029
    Fe        0.335
    K         1.349
    Li        0.003
    Mg        1.52
    Mn        0.003
    N(3)      0.824
    N(5)      29.286 charge
    Na        4.235
    S(6)      6.249
    Si        3.337
    Sr        0.085
    Ti        0.007
    Zn        0.165
   -water    1 # kg
EQUILIBRIUM_PHASES 1
#    O2(g)      -0.678 10
    CO2(g)    -3.39 10
REACTION 1
    H+1        -12
    H2O        6
    N2         1
    NO3-1      -2
    e-1        -10
    2.0362E-04 moles in 1 steps


 then PHREEQC simply does as it should and balances all the species, yielding:

Reaction 1.   

     2.036e-04 moles of the following reaction have been added:

                    Relative
   Reactant            moles

   H+1                -12.00000
   H2O                  6.00000
   N2                   1.00000
   NO3-1               -2.00000
   e-1                -10.00000

                    Relative
   Element             moles
   H                    0.00000
   N                    0.00000
   O                    0.00000
   e                  -10.00000

The increased amount of electrons is insufficient to change the redox status of the nitrate.

If I include more of a realistic scenario of actual CH2O reacting, with the Amm.dat database and the input file:

TITLE DENITRIFICATION
SOLUTION 1
    temp      25
    pH        8.24
    pe        12.471
    redox     pe
    units     mg/l
    density   1
    Al        0.065
    Ba        0.737
    C(4)      1 CO2(g)     -3.39
    Ca        32.4
    Cl        6.774
    F         1.029
    Fe        0.335
    K         1.349
    Li        0.003
    Mg        1.52
    Mn        0.003
    N(3)      0.824
    N(5)      29.286 charge
    Na        4.235
    S(6)      6.249
    Si        3.337
    Sr        0.085
    Ti        0.007
    Zn        0.165
    -water    1 # kg
EQUILIBRIUM_PHASES 1
#    O2(g)      -0.678 10
    CO2(g)    -3.39 10
REACTION 1
CH2O           1.0
3.75 mmol
END

I get the satisfying result that all nitrate has been transformed into dissolved nitrogen.

But I have added carbon and complicated my model with respect to carbon.

I could go this route and get my head around balancing the system for carbon and then present how much carbonate was generated in the system by denitrification.

But I would appreciate a simpler model. Such as the following, which gives me conceptual problems:

TITLE DENITRIFICATION
SOLUTION 1
    temp      25
    pH        8.24
    pe        12.471
    redox     pe
    units     mg/l
    density   1
    Al        0.065
    Ba        0.737
    C(4)      1 CO2(g)     -3.39
    Ca        32.4
    Cl        6.774
    F         1.029
    Fe        0.335
    K         1.349
    Li        0.003
    Mg        1.52
    Mn        0.003
    N(3)      0.824
    N(5)      29.286 charge
    Na        4.235
    S(6)      6.249
    Si        3.337
    Sr        0.085
    Ti        0.007
    Zn        0.165
    -water    1 # kg
EQUILIBRIUM_PHASES 1
#    O2(g)      -0.678 10
    CO2(g)    -3.39 10
REACTION 1
    H+1        -1
    NO3-1      -1
    4.072E-04 moles in 1 steps
END

At first glance I get similar pH levels between the simulation involving addition of organic matter as CH2O and subtraction of nitric acid from the system. There are differences between carbonate concentrations.

Before I go into detail on comparing the systems, I ask:

Is the method of "subtracting" nitric acid too brutal for a simulation of denitrification?
Should I stick with the addition of organic material as a reducing agent?

All the best,
Peter

Without detailed and careful accounting to check if the

[dlparkhurst]

I would use the following approach, which adds CH2O to reduce nitrate.

Code: [Select]

SOLUTION 1
pH 7
Na 1
N(5) 1
END
USE solution 1
REACTION
CH2O 1
0.001 moles
END

The Amm.dat database keeps Amm as a separate element and has removed N(-3) and NH3 species. Using it, nitrification would be done by REACTION or KINETICS. If O2(aq) is present, you can simply use the following:

REACTION
Amm -1
NH3   +1
0.0001 moles
END

Alternatively, if N(-3) is present and O2(aq) is absent, you can use phreeqc.dat to oxidize ammonium. You need to redefine the N2(aq) species with a log K many orders of magnitude smaller. Thus when you add O2 by REACTION, EQUILIBRIUM_PHASES, or KINETICS, N(-3) will oxidize to N(5) and skip N(0).  Denitirification would have to be done by REACTION or KINETICS including N, Ntg, and C.