Help Validating free energy calculation for my methanogeneis reaction

[jakkaas]

Hello everyone,

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 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.

Thermodynamic calculations

Consider the following reaction

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

Calculation of ΔG

ΔG = ΔG^o + RT ln {[HCO₃⁺]² [H⁺]² [pH₂]⁴ / [CH₃COO^-] [H⁺] }

Query 1: Should I use ΔG^oor ΔG^oI:

ΔG^o is free energy under standard conditions of temp= 25^oC, pressure =1 atm, conc= 1 M and pH=0. While ΔG^oI 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 ΔG^o 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 ΔG^oI for my equation.
If yes than should I consider H⁺ in my equation?

Query 2: Temperature effect:

ΔG^o or ΔG^oI are calculated
at 25^oC but my reaction goes at 60^oC. Below is the
calculation done to correct my ΔG^o for 60^oC

ΔG^o_T = ΔH^o – RBT

Where, ΔG^o_T
= ΔG^o at corrected temperature

ΔH^o = 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 ΔG^o value at 25^oC and T= 298^oK

• 
  ΔH^o is not dependent of temp up to 0 to 100^oC and so value of H_f at 25^oC can be used.

I calculated, ΔH^o by taking H_f value of all the component involved in my reaction. Then I calculated B. From these values, I calculated ΔG^o_T

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] = K_H pCO₂

Where K_H = 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 ΔG^o_T 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 ΔG^o_T
   from above equation and tell whether reaction is exergonic or endergonic. Or

1. 
   Calculate critical pH₂ by taking ΔG^o_T = 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?

[Brett Nortje]

 

 

Hello everyone,

 

 

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 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.

 

 

Thermodynamic calculations

Consider the following reaction

 

 

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

 

 

Calculation of ΔG

 

ΔG = ΔG^o + RT ln {[HCO₃⁺]² [H⁺]² [pH₂]⁴ / [CH₃COO^-] [H⁺] }

Query 1: Should I use ΔG^oor ΔG^oI:

 

ΔG^o is free energy under standard conditions of temp= 25^oC, pressure =1 atm, conc= 1 M and pH=0. While ΔG^oI 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 ΔG^o 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 ΔG^oI for my equation.

If yes than should I consider H⁺ in my equation?

 

If the pH is supposed to be 5.9, but it is 7, then something is wrong immediately. It is 7, and you want it to be 5.9? how do you change that?

 

Well, if you were to add hydrogen atoms to it, it would be better? If you were to compress it further, yes, but how do you know where to stop?

 

I suggest you try to 'fill it right up', then you take 420 of them, and lower them to the minimum concentration, and add all that together, you will have your ratio or whatever of 5.9? How does that sound? [H] is pH without the p, so, take that into consideration.

 

 

 

Query 2: Temperature effect:

 

ΔG^o or ΔG^oI are calculated

at 25^oC but my reaction goes at 60^oC. Below is the

calculation done to correct my ΔG^o for 60^oC

 

ΔG^o_T = ΔH^o – RBT

 

Where, ΔG^o_T

= ΔG^o at corrected temperature

 

ΔH^o = 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 ΔG^o value at 25^oC and T= 298^oK

 

• ΔH^o is not dependent of temp up to 0 to 100^oC and so value of H_f at 25^oC can be used.

 

I calculated, ΔH^o by taking H_f value of all the component involved in my reaction. Then I calculated B. From these values, I calculated ΔG^o_T

 

Is this the correct way?

 

Okay, so it looks to me like you take your entrophy state, and minus that from the H thing. then you work out the power of the o on top of the equations, and then you got your answer. well, very basically.

 

 

 

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] = K_H pCO₂

 

Where K_H = 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?

 

Well, if you consider [pCO₂] or [HCO₃⁺] you just need to consider which is more important to the 'thing,' being either p in the former equation, or H in the latter equation?

 

 

 

 

 

Query 4: Calculate ΔG^o_T 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 ΔG^o_T

   from above equation and tell whether reaction is exergonic or endergonic. Or

 

1. Calculate critical pH₂ by taking ΔG^o_T = 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?

 

Exergonic is the one you are looking for, as it is associated with free energy, I read on google.

 

 

 

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?

 

 

 

Why don't you go to freenode? this chat server is full of programmers who can help you.

[hypervalent_iodine]

!

Moderator Note

Brett, I mean no offense here, but it might be better if you refrain from answering questions about content you are unsure of. If you have your own questions, please feel free to start your own thread.

[jakkaas]

Thank you Brett for you precious time but this was not i was asking for

[EdEarl]

Thank you Brett for you precious time but this was not i was asking for

I am confused by your post. Thermodynamics tells us there is no "Free Energy". What do you mean by free energy? Moreover, exothermic reactions using of coal or methane made from coal increase CO2 in the atmosphere and increase global warming. Why would you want to do that?

 

I am not a chemist and cannot help you. I am merely curious and like to learn.