Calculated field: Arrhenius equation

I'd like to set up a calculated field to display rate constants (k) calculated from the Arrhenius equation:

k=A*e^(-Ea/RT)

A and Ea are variables, R and T are constants.

I haven't been able to make this work (validate). Is it possible to do this calculation in Instant JChem 5.4.1? 

Could you clarify how you are trying to do this.

Do you have fields that contain the the values of A and Ea, and want to calculate the result according to that formula?

If so then I think this might be what you need:

A * Math.exp(-Ea / (8.3144 * 237))

A and Ea are the field values that you pass in, 8.3144 and 237 are the values for R and T (which of course you could combine into a single constant for better efficiency) .

Please check the results to ensure this is correct!

Tim

Yes, I have fields that contain the values for A and Ea. I tried the formula you suggested and it worked! I was missing the "Math." before "exp". Thanks!

sounds good to me

will come back and leave further comments

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Hi Tim,

I've meant to ask something similar for  while and would like to take the opportunity. Ligand Efficiency LE is defined as

LE = deltaG/Heavy Atom Count

with deltaG = -RTln(Kd), or -0.59ln(Kd)

with Kd being the dissociation constant in molar

What would be the correct syntax, assuming that values for Kd and Heavy Atom Count (= matchCount("[!H]") would be available?

Thanks,

Evert

Hi Evert,

FIrstly I wouldn't use the matchCount() chemcial terms expression as this requires running of a substructure search. The heavy atom count can be better determined with this chemical terms expression:

atomCount - atomCount('1')

Then to calculate the ligand efficiency I think you need something like this as your calculated field expression:

-0.59 * Math.log(kd) / heavyAtoms

assuming you have defined appropriate fields caleld kd and heavyAtoms.

Tim

 

 

Thanks Tim,

This is exactly what I wanted.

Cheers,

Evert