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Tom Meuzelaar

Database format and redox couple

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[admin note: this post represents recovered forum content after a critical hard drive failure - it is not in it's original form]

>>>>>>>>>>

Jul 19 2007, 11:43 PM

Hi,

We're buffering pH of your experiments using the acetic acid/acetate buffer. That involves decoupling the acitic_acid_aq/acetate redox couple. No problem with GWB's <thermo.com.V8.R6+.dat>, but with our modified database we some redox couples (e.g. Malonate) remain in the calculations (and end up buffering the Eh, which we do not want). The way around it is to suppress these species, but I'm wondering what I need to do to change the database.

Our version is based on

* THERMODYNAMIC DATABASE: thermo.com.R7beta

* generated by GEMBOCHS.V2-Jewel.src.R9 19-nov-1999 10:03:44

whereas GWB's is

* THERMODYNAMIC DATABASE: thermo.com.V8.R6.full

* generated by GEMBOCHS.V2-Jewel.src.R6 03-dec-1996 16:55:04

The difference seems to be that H-Malonate is defined relative to Malonic acid in the original database, and acedic acid in our personal database. Am I wrong to think that GWB should see through this and have the correct behaviour even with our private database?

Thanks!

Joel

=======================

in GWB the Malonate are defined:

=======================

(redox couple)

Malonic_acid(aq)

* formula= C3H4O4

charge= 0.0 ion size= 3.0 A mole wt.= 104.0624 g

4 species in reaction

-1.0000 H2O -2.0000 O2(aq) 3.0000 H+

3.0000 HCO3-

158.2234 144.1431 127.5278 111.9097

96.0054 82.9156 71.7342 61.6814

* gflag = 1 [reported delG0f used]

* extrapolation algorithm: supcrt92 [92joh/oel]

* reference-state data source = 95sho

* delG0f = -175.420 kcal/mol

* delH0f = -207.870 kcal/mol

* S0PrTr = 55.700 cal/(mol*K)

(aqueous species)

H-Malonate

* formula= C3H3O4-

charge= -1.0 ion size= 4.0 A mole wt.= 103.0544 g

2 species in reaction

1.000 Malonic_acid(aq) -1.000 H+

2.8919 2.8513 2.9059 3.0681

3.3691 3.7531 4.2224 4.8286

* gflag = 1 [reported delG0f used]

* extrapolation algorithm: supcrt92 [92joh/oel]

* reference-state data source = 95sho

* delG0f = -171.530 kcal/mol

* delH0f = -207.850 kcal/mol

* S0PrTr = 42.700 cal/(mol*K)

And in OUR database:

(redox couple)

Malonic_acid(aq)

* formula= C3H4O4

charge= 0.0 ion size= 3.0 A mole wt.= 104.0624 g

4 species in reaction

-1.0000 H2O -2.0000 O2(aq) 3.0000 H+

3.0000 HCO3-

158.2234 144.1431 127.5278 111.9097

96.0054 82.9156 71.7342 61.6814

* gflag = 1 [reported delG0f used]

* P-T extrapolation algorithm: Cp(T),V(P) integration

* P-T extrapolation alg. ref.: 88tan/hel, 92joh/oel

* reference-state data source: 95sho

* delG0f = -175.420 kcal/mol

* delH0f = -207.870 kcal/mol

* S0PrTr = 55.700 cal/(mol*K)

(aqueous species)

H-Malonate

* formula= C3H3O4-

charge= -1.0 ion size= 4.0 A mole wt.= 103.0544 g

4 species in reaction

-1.0000 H+ -1.0000 H2O 1.0000 O2(aq)

1.5000 Acetic_acid(aq)

-72.5490 -65.9939 -58.2272 -50.8835

-43.3587 -37.1373 -31.8219 -27.0816

* gflag = 1 [reported delG0f used]

* P-T extrapolation algorithm: Cp(T),V(P) integration

* P-T extrapolation alg. ref.: 88tan/hel, 92joh/oel

* reference-state data source: 95sho

* delG0f = -171.530 kcal/mol

* delH0f = -207.850 kcal/mol

* S0PrTr = 42.700 cal/(mol*K)

>>>>>>>>>>

Jul 26 2007, 02:53 PM

Hi Joel:

Since I don't have access to your modified database or scripts, I can't respond with certainty, but it sounds like you're looking in the right place. In your database, you should be able to decouple Malonic_acid from HCO3-, meaning that it will need to be independently constrained in order to appear in your results. H-Malonate, on the other hand, is defined as an aqueous species whose reaction is written in terms of acetic_acid, so it will be in the pool of possible species unless suppressed.

In thermo.com.V8.R6+.dat, since H-Malonate is defined in terms of Malonic_acid, decoupling the latter from HCO3- removes both from consideration (unless either is independently constrained in your basis setup).

Regards,

Tom

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