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Thermodynamic and methanogenesis. validation of calculation

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Hello everyone,

I know perhaps this in not the right forum to ask this question but all the users are using GWB software and would be well versed with thermodynamics. So though this queries are nor related to GWB software, i would appreciate a help.


I am Mustafa Vohra, working on a project involving CO2 sequestration and methane production from coal. My works includes understanding microbial syntrophy in my consortia and production of methane from coal. I am microbiologist by nature and have some calculations on calculation of free energy for my reactions. After going through literature, I have finally calculated the free energy for my reactions but I need to validate it. So I am requesting you to go through my calculations and check for its correctness. Please don’t mind for some naïve questions since I am not an expert in it. Any help, suggestion, reference, guidance appreciated.


1) Calculation of partial pressure and mmoles of gases.

I do analysis of gas (CH4, H2 and CO2) with the help of GC. From the area, I calculate % of gas.


• After 30 days of analysis, CH4 = 2.042% = % 0.02042


• The gauge pressure measured from needle manometer, after 30 days in bottle = 0.5 psi

Now 1 atm pressure =101.3 KPa =760mm Hg = 14.7 psi

Therefore, 0.5 psi = 0.5 x 101.3 = 3.44 KPa



• Absolute total pressure (PT) = Gauge pressure, KPa + Atmospheric pressure, KPa

= 3.44 KPa + 101.3 KPa

= 104.74 KPa

• CH4 gas partial pressure (PCH4)

PCH4 = % CH4 x PT

= 0.02042 x 104.74

= 2.138 KPa



My question is, whether in the calculations of partial pressure, should I include total pressure or guage pressure?


Thermodynamic calculations


Consider the following reaction

CH3COO- + H+ + 4H2O = 2HCO3+ + 2H+ + 4H2O


Calculation of ΔG

ΔG = ΔGo + RT ln{ [HCO3+]2 [H+]2 [pH2]4

/[CH3COO-] [H+] }


Query 1: Should I use ΔGo or ΔGoI :

ΔGo is free energy under standard conditions of temp= 25oC, pressure =1 atm, conc= 1 M and pH=0. While ΔGoI is free energy under physiological condition of pH=7.

Now, the pH of my medium for this reaction is suppose 5.9 and I want to take this in to consideration, than I think I should use ΔGo and take account of the concentration of H+ ions [H+].

I think [H+] can be calculated by [H+] = - log pH

If not, is it necessary to consider pH of reaction i.e should I use ΔGoI for my equation. If yes than should I consider H+ in my equation?


Query 2: Temperature effect:

ΔGo or ΔGoI are calculated at 25oC but my reaction goes at 60oC. Below is the calculation done to correct my ΔGo for 60oC

ΔGoT = ΔHo – RBT

Where, ΔGoT = ΔGo at corrected temperature

ΔHo = change in enthalpy, R= ideal gas constant,

B = integration constant

Also RB = S (entropy)

 The integration constant B can be calculated from above equation using ΔGo value at 25oC and T= 298oK

 ΔHo is not dependent of temp up to 0 to 100oC and so value of Hf at 25oC can be used.

I calculated, ΔHo by taking Hf value of all the component involved in my reaction. Then I calculated B. From these values, I calculated ΔGoT

Is this the correct way?


Query 3: [pCO2] or [HCO3+]

In most of the references, I have seen people use [HCO3+] for free energy calculations but in some papers I have seen people using [pCO2]. Which one should I use?

If I have to use [HCO3+] than I dint measure it and had to calculate it from pCO2 value.

Now [H+] X [HCO3+] = [H2CO3] = [CO2] X [H2O]

Taken from aquatic chemistry by stuns

[H2CO3] = KH pCO2

Where KH = henry coefficient

Putting value & Calculating further we get, log [H2CO3] = -1.5 + log PCO2

Further deriving I get final equation,

Log [HCO3+] = - 6.4 + pH + log [H2CO3] 1


In some reference from net, I got another equation

pH = 6.4 + log {[HCO3+]

/0.03 pCO2 } 2

Here I think they consider [H+] X [HCO3+] = [CO2] X [H2O] without taking [H2CO3] in to consideration. So according to me eq 1 should be used for this conversion. What do you think?


Query 4: Calculate ΔGoT or critical pH2


I want to understand syntrophy between my acetogen and methanogens. To prove syntrophy, I will need to do thermodynamics calculation. There are two ways it is done

1) Calculate ΔGoT from above equation and tell whether reaction is exergonic or endergonic. Or

2) Calculate critical pH2 by taking ΔGoT = 0. Usually syntrophy depends on interspecies H2 or formate transfer and most of the people have used critical pH2 value for their discussion.

What do think I sould calculate? Any reason?


Query 5: Software?

I have lots of such free any calculations to do. Is there any software I can use? Can GWB software be used? I have heard and downloaded SUPCRAT92 and PHREEQC. Are they useful for my work? How should I use them?

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Hello Mustafa,


I'll try to focus on how The Geochemist’s Workbench can make solving this problem easier for you. Perhaps someone else can check your hand calculations.


A very brief background: GWB uses thermodynamic datasets in its calculations. Each dataset contains a list of Basis species (H2O, O2(aq) for O, H+ for H, HCO3- for C, Ca++ for Ca, etc.). These Basis species are the building blocks for constructing all secondary species (H2CO3 or CO2(aq), CO3--, etc.), redox species (Basis species in alternate redox states, like CH4(aq), CH3COO-, H2(aq), etc.), minerals, or gases (CH4(g), H2(g)) that you want to consider in your system. The thermo dataset is a compilation of reactions for these various secondary species, redox species, minerals, or gases, written in terms of the Basis species. Each reaction has an associated equilibrium constant at several discrete temperatures (generally ranging from 0 to 300 C).


I recommend looking for the Geochemical and Biogeochemical Reaction Modeling textbook by Craig Bethke. Chapter 7, Redox disequilibrium, contains an example for the program SpecE8 which describes what you’re looking to do.


Basically, you’ll want to take your water analysis and use it to add species to your Basis, then constrain your entries by setting pH, concentration, fugacity, etc.. You should decouple the redox pairs between species in different oxidation states (HCO3- and CH4, for example), then constrain the concentration of each independently. Since you have a partial pressure for CH4(g), you would replace CH4(aq) in your Basis with CH4(g) by performing a “Basis swap.” Then you would specify the fugacity of CH4, which is like the partial pressure in atm (be sure to use the total, not guage pressure, to calculate the partial pressure of CH4). You can do the same thing for CO2(g) by swapping it in for HCO3-.


You can set the temperature of your system directly. The program will use the grid of equilibrium constants at different temperatures to solve for the equilibrium state at your conditions of interest. That way, you won’t have to mess around with calculating integration constants or using the Van ‘t Hoff equation.


When you run your model, the program will perform a speciation analysis, listing the actual concentrations (and thermodynamic activity) of all the species in your system. It will also calculate the redox potential (Eh) for each electron donating and accepting half-cell reaction. By combining different donating and accepting reactions, you can calculate the free energy available from various redox reactions. Since you can easily modify your input (pH, fugacity, concentration, T) you can quickly run a number of analyses without being slowed down by the repetitive hand calculations.


I'll contact you about a trial license of the software. Please let me know if you have any questions.




Brian Farrell

Aqueous Solutions LLC

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