User e4efcc5789

21-03-2011 22:30:25

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?

ChemAxon fa971619eb

22-03-2011 16:54:19

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

User e4efcc5789

22-03-2011 17:43:51

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!

User e05b1833aa

21-02-2012 14:22:59

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

ChemAxon fa971619eb

22-02-2012 11:49:55

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

User e05b1833aa

24-02-2012 14:45:53

Thanks Tim,

This is exactly what I wanted.

Cheers,

Evert