Adding Organic Acid Species to Thermo Database

[Jamison Ward]

Hello,

I'm attempting to use GWB to model a solution of lead(II) citrate exposed to atmospheric conditions. I see that citrate is not contained within the thermo.com.V8.R6+ database, so I've attempted to add all 4 species of this triprotic organic acid (citric acid, citric acid monobasic, citric acid dibasic, and citrate) to the database; however, I can't get my species to appear when I try to run a simulation in React. I've added citric acid as a redox species by the reaction: Citric_acid(aq) + 2 H2O + 4.5 O2(aq) = 6 H+ + 6 HCO3-, but I do not know the reaction's logK. Additionally, I've added each of the 3 deprotonated forms of the acid as aqueous species defined by the appropriate deprotonation reactions whose logK values are known.

This seems to be the same approach that was used to add other organic acids to this thermo database such as acetic acid. I'm not sure why I can't swap in my Citric_acid(aq) reagent for HCO3- in React as I can for other organic acids such as acetic acid. I've attached the version of the thermo.com.V8.R6+ database file I've modified with my citric acid additions.

Thank you for any assistance you can provide.

Best,

Jamison

thermo.com.V8.R6+.tdat

[Jia Wang]

Hello Jamison,

Thank you for posting your dataset. I see that you have added a log K of 200 at 25C for your citric_acid reaction. Is this correct? Or did you mean to attach another dataset? As for the ability to swap, I was able to swap in citric acid once I added the HCO3- component to the basis of a system. Did you look under "aqueous species" when performing the swap on HCO3-?

Adding a reaction as a redox species allows users the flexibility to disable redox equilibrium in various calculations. By default, all redox couples are enabled, meaning that a bulk concentration prescribed for that element is distributed between all oxidation states. In thermo.V8.R6+, many of the organic species are written as redox reactions of HCO3-. In this case, you can specify the bulk carbon concentration by adding in the HCO3- component and the program will automatically calculate species concentration assuming all redox states are in equilibrium. You can disable any of the equilibrium reactions at run time and that will allow you to add in the bulk concentration for each oxidation state separately into the basis. For example, if you disable the HCO3-/Acetic_acid, you can now add in both HCO3- and Acetic_acid to your basis in React. For more information, please see section 2.4 Redox couples and 7.4 Redox disequilibrium in the GWB Essentials Guide. 

If you want the program to calculate mass distribution to various oxidation state of carbon, you will need to find and add the appropriate Log K for the HCO3-/Citric acid reaction.

If you do not need the capability to calculate mass distribution between citric acid and other carbon oxidation states, there are a couple of options. You can add citric acid as a basis species, which permanently decouples citric acid from other species. In this case, you also don't need a log K for the reaction between HCO3- and Citric acid. You can use the "break couple' feature to move a redox species into the basis species section in the dataset attached. Please see section 9.2.9 Adjusting redox coupling in the GWB Essentials guide for more information. Alternatively, keep your dataset as is and add an appropriate log K for the HCO3-/Citric acid reaction. You can disable the redox couple at runtime in React under "Config" -> "Redox couples...".

Note that there are a lot of other organic species in this thermo dataset. If some are forming and you are not expecting, you can use the suppress feature ("Config" -> "Suppress...") to exclude them from React's calculation. The program considers all possible reactions unless otherwise specified by the user.

Hope this helps,
Jia Wang
Aqueous Solutions LLC

[Jamison Ward]

Hi Jia,

Thanks for your detailed reply. The log K of 200 at 25C is just a placeholder until I can get my citric acid reagent to appear in the React Basis. I tried restarting my computer, but I am still unable to swap my citric acid reagent in for HCO3- in the React Basis; even when clicking on the "Aqueous..." option, it does not appear in the list of species. Do I need to add the citric acid as an aqueous species in the thermo database I am editing? I tried this earlier, but I received a "circular reaction" warning since I already had the 3 deprotonated species entered as aqueous species. I also do not see an option to decouple my citric acid reagent from HCO3- in the "Config" -> "Redox couples..." window.

Sincerely,

Jamison

[Jia Wang]

Hi Jamison,

This is very strange. You do not need to add citric acid to both sections. I downloaded the dataset you attached and loaded it into a React run and I was able to find Citric_acid just fine (in both the swap options for HCO3- and the Redox Couples dialog). Could you double-check that the dataset you have loaded in your current run is correct? To open the current dataset loaded for your run in React, go to "File" -> "View" -> select the thermo dataset that ends with the extension .tdat. Check that the dataset includes everything you have added.

I encourage that you also change the name of the thermo file so that it is different from what is installed with the software. In general, it is good practice to create a copy and save with a unique name when you customize a dataset.

Best,
Jia

[Jamison Ward]

Hi Jia,

Thank you very much again for your assistance. I was able to add my citric acid species to the basis in React! As you pointed out, the problem was that I needed to make a copy of the original thermo.com.V8.R6+ dataset and then add my citric acid species. For some reason, the program was not recognizing my custom species when I simply added them to the original dataset.

Best,

Jamison