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Kinetics- writing a custom reaction in the line editor


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[admin notice: the below is from the former GWB users group email distribution list. This message was originally posted 12/17/2005]

 

Posted by: Nikolay Sidenko

 

I try to model simple reductive dissolution of

Fe(OH)3(ppd). I use acetic acid as an electron donor

as surrogate for DOC. As well I have to use Fe (OH)3aq

instead of Fe(OH)3(ppd) (as React does not let me to

input solid phases for enzymatic redox reaction).

Monod kinetics is assumed with respect to Fe(OH)3.

When I try to run I get message "Primary product H2O

is not loaded in the current system". Water is in,

because it is solvent! Could you help me with this

problem, please? React script in the attachment.

 

Thank you in advance,

 

Nikolay

 

 

Posted by: Craig Bethke

 

Hi Nikolay,

 

Reverse the positions of H2O and Fe++ on the right side of your kinetic reaction and I think you'll be OK.

 

What's going on? The (dual) Michaelis-Menton equation is derived for a transformation reaction

A + E <=> A:E <=> P + E

where A is the reactant, P the product, and E the enzyme. The activities/concentrations of A, P, and E figure in the rate law.

 

In real life, some kinetic reactions are transformation reactions, but many involve hydrolysis, (de)protonation, electron transfer, and so on. As such, they involve species besides A, P, and E. We generally know A and P from context. In your case, they are Fe(OH)3 and Fe++.

 

But the program isn't so smart, so it takes the first species on the left of the reaction to be the reactant A, and the first on the right to be the product P. For more info, see pages 37-38 of the Reaction Modeling Guide.

 

BTW, you might consider using the custom rate law feature of the program, which lets you prepare a Basic script or C++ function defining your rate law. It sounds a little intimidating, but it's not too difficult and it will let you set a rate law any way you wish.

 

Hope this helps,

 

Craig

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