Jump to content
Geochemist's Workbench Support Forum

Input organics

Recommended Posts


Sure, there are many calculations you can do involving dissolved organics:

You can set the total concentration of a dissolved organic and determine its speciation in solution. For example, you can look at a ligand like EDTA or acetate to see how much is present in free form, in various protonated or deprotonated forms, and complexed with various metals, and see how the distribution of mass changes as a function of pH, temperature, concentration, etc..

You can create Eh-pH or Pourbaix diagrams to see under what conditions a dissolved organic is stable and when it would tend to mineralize to inorganic carbon, or form various other organic compounds. 

You can also set up disequilibrium simulations in which a dissolved organic is oxidized or reduced with time, at a rate determined by a kinetic rate law you specify. You can account for abiotic reactions in solution, catalysis on mineral surfaces, biodegradation (a simple model of enzymatic catalysis), or microbial catabolism coupled to growth and decay.

The program does not currently consider non-aqueous phase organics, however. You can’t find the solubility of an organic in water the same way you would a mineral, unless you create a fictive “organic mineral” with a log K to control the solubility.

To set up a simulations involving organics, you’ll first need to load a thermodynamic dataset that contains your organics of interest. The GWB’s default dataset, thermo.tdat, does not have any data for hexane. However, the thermo.com.V8.R6+.tdat dataset, a later release from Lawrence Livermore National Lab, does contain data for one hexane isomer, n-Hexane(aq), along with many other organic species. Many organic species are found in the redox coupling reactions section of the dataset, in a reaction with inorganic carbon. Please note that there is only one reaction for n-hexane, though. I’m not familiar with the chemistry of hexane, but if you expect it to form complexes, you might need to modify one of the existing thermo dataset. You can do so in a text editor like Notepad, or in the GWB’s graphical thermo data editor, the TEdit app.

Next, you’ll have to decide in the GWB app (e.g. React) what redox reactions should be in equilibrium. To look at speciation of acetate as a function of oxidation state and pH, for example, assuming equilibrium with inorganic carbon, you’d load thermo.com.V8.R6+.tdat into React, add basis entries HCO3-, O2(aq), H+, and constrain those values. In a redox equilibrium model, the HCO3- component includes inorganic carbon species as well as various organics. The oxidation state you specify determines how much is present at equilibrium as inorganic carbon, how much as acetate, methane, ethanol, benzene, and so on (all reactions are considered by default). You can disable one or more redox coupling reactions if you’d like. If you disable all coupling reactions involving carbon except for the one involving acetate, you can look at the distribution of mass between inorganic carbon and acetate. And you decouple all coupling reactions. In that case, you can add acetate directly, without needing to specify the oxidation state or amount of inorganic carbon. Then, you can look at speciation as a function of T, pH, concentration, etc., as mentioned above. 

For more information, please see sections 2.1 Configuring a calculation, 2.4 Redox couples, 7.2 Equilibrium models, and 7.3 Redox disequilibrium in the GWB Essentials Guide. Please see as well section 4.6 Kinetics of redox reactions in the GWB Reaction Modeling Guide, and the Thermo datasets chapter in the GWB Reference Manual.

Hope this helps,

Brian Farrell
Aqueous Solutions

Share this post

Link to post
Share on other sites

Join the conversation

You can post now and register later. If you have an account, sign in now to post with your account.

Reply to this topic...

×   Pasted as rich text.   Paste as plain text instead

  Only 75 emoji are allowed.

×   Your link has been automatically embedded.   Display as a link instead

×   Your previous content has been restored.   Clear editor

×   You cannot paste images directly. Upload or insert images from URL.


  • Create New...