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Adding oxalate to thermodynamic databases


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I have seen publications using oxalate to model speciation (e.g. file:///C:/Users/Cansu%20Floyd/Downloads/Biotransformation_of_lanthanum_by_Aspergillus_nige.pdf) using Act2 module. I want oxalic acid, oxalate, Li-oxalate, Mg-oxalate, and Li-carbonate in my models.  I could not see any of them in the dropdown species list in the default thermodynamic database. Could you walk me through how to find or add them to databases?

Thanks in advance!

Cansu Floyd

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Hello Cansu,

I think a good place to start is to look at some of the databases that are installed with the GWB software (located in the Gtdata folder). thermo_minteq.tdat is a database released with Visual Minteq 2.40 and contains many of the species you are looking for. thermo.com.V8.R6+.tdat is an expanded dataset published by Lawrence Livermore National Laboratory that contains some oxalate species.

You can add reactions to create a customized database if the necessary reactions are available for your work. For the new reactions to be considered in a simulation, you must at least designate one log K value when adding it into your database. You can find more information regarding TEdit, in section 9 of the GWB Essentials Guide. For dataset formats, please see the Thermo datasets chapter in the GWB Reference Manual.

If you are adding or editing one of the installed databases for your work, I recommend saving the edited version with a new name so you will always have the original dataset to refer to. If you do overwrite them, you can always download the files again from our Thermo webpage.

Hope this helps,
Jia Wang
Aqueous Solutions LLC

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Just an additional note about the "add" dropdown menu. The list will only display basis species from the thermo dataset loaded. If you wish to add a redox species, you would need to first decouple it in the "Redox Couples..." dialog (found under the Config menu) . For example, oxalic_acid(aq) is a redox reaction in thermo.com.V8.R6+.tdat and would appear on the "add" list if you decouple it from HCO3-. Decoupling a redox reaction allows the user to constrain each oxidation state of the element separately. For more information, refer to sections 2.4 Redox Couples and 7.3 Redox Disequilibrium in the GWB Essentials User's Guide.

Best regards,
Jia

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