Way to define dissolved oxygen.

[Sol-Chan Han]

Hello, Phreeqc users.

I am confusing about defining dissolved oxygen in the solution.
The below data shows the chemical properties of the solution.
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pH 4.0 / Temp(oC) 30 / Eh(mV) 380.7 (pe:6.33) / DO(mg/L) 5.2 / SO4-2(mg/L) 7.5 / Ca(mg/L) 0.8 / SiO2(mg/L) 0.5 / Na(mg/L) 0.8 / K(mg/L) 0.4 / Mg(mg/L) 0.2 / Al(mg/L) 0.0395 / Cl-(mg/L) 1.6 / NO3-2(mg/L) 0.4
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The Phreeqc manual instructed that DO can be defined by O(0).
Therefore, the dissolved oxygen in my solution can be defined as O(0) 5.2 when the default TDB is used.
However, in the database which I used, the gfw_formula for O(0) (solution master species) is defined as O2.
In this case, I guess that DO should be defined as O(0) 5.2×2. Am I correct?

I defined the solution as belows.
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SOLUTION 1
pH   4.0
pe   6.33
-temp   30
-unit mg/l
O(0)   10.4
S(6)   7.5   as   SO4
Ca   0.8
Si   0.5
Na   0.8
K   0.4
Mg   0.2
Al   0.0395   gfw   26.981541
Cl(-1)   1.6
N(5)   0.4   as   NO3
END
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In addition, the simulation results showed that the N(5) is present predominantly as not NO3-2 but as NH3.
The chemical analysis data, that I have, indicates the concentration of NO3-2 is 0.4 mg/l.
I am confusing about the difference between the actual concentration of NO3-2 and the calculated result.

Can anyone give me any comments?
Thank you in advance for your help.

p.s. I attached the TDB that I used.

[dlparkhurst]

It's a little confusing, but PHREEQC needs to know the number of moles of O in the O(0) valence state, not the number of moles of O2(aq). Dissolved oxygen is normally reported as mg/L of O2, which is also the total mg/L of O(0). In a nutshell, the easiest way to do this is to take the total number of milligrams of O(0), which is 5.2 in your case, and divide by the gram formula weight of an atom of O, which is 16 g/mol. So, you can do one of the following:

Change your database to use the values in phreeqc.dat.

Code: [Select]

SOLUTION_MASTER_SPECIES
O H2O 0 O 16.0
O(0) O2 0 O

2. Define the dissolved oxygen as follows:

Code: [Select]

O(0) 5.2 gfw 16

3. Define the dissolved oxygen as follows:

Code: [Select]

O(0) 5.2 as O

The number of moles of O in the O(0) redox state for your solution is 5.6/16 = 0.325 mmol/L, and the concentration of O2(aq) is 0.325/2 = 0.1625 mmol/L. In the distribution of species you find the following concentrations in mol/kgw:

Code: [Select]

O(0)          3.250e-04
   O2              1.625e-04   1.625e-04    -3.789    -3.789     0.000     (0)

For comparison, equilibrium with the atmosphere at 30 C gives 0.47 mmol/kgw O(0) and 0.23 mmol/kgw O2(aq), or ~7.36 mg/L O2, as calculated with phreeqc.dat. Note, I think there must be a mistake in your database for the definition of O2(g), because it gives a log partial pressure of -40 for O2(g) for your solution; phreeqc.dat gives -0.86, which is similar to that expected from atmospheric equilibrium (-0.7).

[Sol-Chan Han]

Thank you for your help David L. Parkhurst.

Modifying the TDB is a little bit sensitive issue in my work, the method #2 and #3 you suggested as follows would be proper to me.

Code: [Select]

O(0)5.2 gfw 16

Code: [Select]

O(0)O(0) 5.2 as O
After your comment, I recalculated the simulation and I also found that SI reported for O2(g) is nearly -40. However, I do not have a clear answer to this at the moment.

In the previous post, I asked for some help also with N(5). When I calculated with phreeqc.dat, most of N(5) was present as NO3- but NH3 was predominant when my database was used. Could you give me some clue about this one?

[dlparkhurst]

PHREEQC is a bit picky about how valence states are defined in SOLUTION_SPECIES. The rule is that the reaction for only one species of a valence state should be defined with e- or O2(aq) in the reaction. This species is called the "secondary master species". All other species of the the valence state should be defined using the secondary master species. Failure to follow this rule can result in PHREEQC getting the valence states confused, in this case, NH3 incorrectly falls into the N(5) set of species.

The CEMDATA18.1-16-01-2019-phaseVol - copy Ca.dat database has both NH4+ and NH3 defined with e- in the reactions. Because NH4+ is defined to be the secondary master species in SOLUTION_MASTER_SPECIES, the reaction for NH4+ is okay. However, NH3 should be defined by a reaction of NH4+. It is necessary to rewrite the NH3 reaction by subtracting the first commented reaction from the second commented reaction in the block below. I have simply subtracted the log_Ks; you need to subtract the terms of the analytical expression as well.

Code: [Select]

SOLUTION_SPECIES
#NO3- + 8e- + 10H+ = NH4+ + 3H2O
# -analytical_expression -103.801782 0 44761.476983 29.424107 0 0 0
# -gamma 2.5 0.064
# -log_K 119.136999

#NO3- + 8e- + 9H+ = NH3 + 3H2O
# -analytical_expression -107.400094 0 42212.00396 30.601079 0 0 0
# -gamma 0.0 0
# -log_K 109.900031

NH4+ = NH3 + H+
-gamma 0.0 0
       log_k -9.236968


You can include this SOLUTION_SPECIES data block in your input file, if you do not want to change the database. You don't need to include the comments, but you should calculate the new analytical expression.

As for O2(g) log partial pressure, the calculation is being made with the specified pe (6.33), pH (4.0), and the equation O2(g) + 4e- + 4H+ = 2H2O. It would be better to use the equation O2(g) = O2(aq) because then the log partial pressure would depend on the dissolved oxygen concentration, rather than estimates of pe and pH. In reaction calculations, there would not be a difference between using either equation because redox equilibrium applies, but in initial solution pH, pe, and O(0) can be defined independently and equilibrium between O2, and pe and pH likely does not obtain.

You can add the following definition, which is derived by adding the two commented equations taken from the CEMDATA database. Again, I have not added the terms of the analytical expression. The new definition will give a more reasonable estimate of log P[O2(g)] when O(0) is defined in initial solution (SOLUTION) calculations.

Code: [Select]

#2H2O = O2(aq) + 4e- + 4H+
# -analytical_expression -37.318475 0 -27028.699677 16.968388 0 0 0
# -gamma 0.0 0
# -log_K -85.986052
#O2(g)
# O2(g) + 4e- + 4H+ = 2H2O
# -Vm 24789.71191
# -analytical_expression -39.356141 0 30857.471179 7.664541 0 0 0
# -log_K 83.104854
PHASES
O2(g)
O2 = O2
-log_k   -2.881198
END


[Sol-Chan Han]

Hello, David L. Parkhurst.
Thank you for your kind reply and comments.
If you allowed, I want to check that I understand correctly.

The half-reaction as follows is right because both NO3- and NH4+ are defined as "secondary master species" for N(5) and N(-3), respectively.

Code: [Select]

SOLUTION_SPECIES
#NO3- + 8e- + 10H+ = NH4+ + 3H2O
# -analytical_expression -103.801782 0 44761.476983 29.424107 0 0 0
# -gamma 2.5 0.064
# -log_K 119.136999

However, another half-reaction is wrong because NH3 was not defined as "secondary master species". In addition, the valence state of N in NH3 is -3, therefore, it should be defined by using N(-3) "secondary master species", i.e. NH4+. In my database, NH3 was defined by using NO3-, therefore, Phreeqc gives me a result that NH3 has a valence state of +5 in spite of the actual valence state is -3.

Code: [Select]

#NO3- + 8e- + 9H+ = NH3 + 3H2O
# -analytical_expression -107.400094 0 42212.00396 30.601079 0 0 0
# -gamma 0.0 0
# -log_K 109.900031

Did I understand correctly?

Thank you again.

[dlparkhurst]

Yes.

The rules are that there must be one and only one secondary master species for a valence state (SOLUTION_MASTER_SPECIES), and all species (SOLUTION_SPECIES) of a valence state, excluding the secondary master species, must be written in terms of species of the valence state. The second rule allows you to have a chain of reactions like the following with CO3-2 as the secondary master species for C(4), where the second reaction is not explicitly written in terms of the secondary master species.

CO3-2 + H+ = HCO3-
HCO3- + H+ = H2CO3

[Sol-Chan Han]

Hello, David L. Parkhurst.
Thank you again for your kind reply and comments.

Could you allow me to share this one with the developer of my database?

[dlparkhurst]

Please share. This forum is public, and PHREEQC is in the public domain.

[Sol-Chan Han]

I appreciate your generous help.