Calculation of average charge of molecule at a given pH

Hi,


I'm trying to compute the average charge of a molecule at a given pH, that is, the weighted sum of charges of all the microspecies of that molecule at the given pH (the weight for each microspecies would be the fraction of the molecule at the ionization state of the corresponding microspecies).


I've seen that you have that information in the curve data that you get when you compute the isoelectric point in MarvinView. Unfortunately I want this calculation for a sdf file with lots of molecules, so I can't afford manually copying and pasting all those data from MarvinView.


I tried cxcalc isoelectricpoint, but in that case I only get the isoelectric point, not the desired average charge at a given pH.


Any idea on how to compute this? I guess it's probably trivial, but I'm new to ChemAxon software.


Thanks in advance,


Gonzalo

Hi,





Find my answer here: http://www.chemaxon.com/forum/viewpost18850.html#18850.





Zsolt

Could it be possible to get this by a chemical terms expression in Instan JChem? Sorry I'm not familiar with c.t.e's.

Thanks,

Gonzalo

From Marvin 5.2 this calculation is available in cxcalc, but there is no Chemical Terms function for this yet.

Help: chargedistribution calculation in cxcalc

Usage example (cxcalc):

$ cxcalc chargedistribution "C[C@H](N)C(O)=O"
id Charge
1 0.00 1.00
  1.00 0.97
  2.00 0.75
  3.00 0.23
  4.00 0.03
  5.00 0.00
  6.00 -0.00
  7.00 -0.00
  8.00 -0.03
  9.00 -0.25
 10.00 -0.77
 11.00 -0.97
 12.00 -1.00
 13.00 -1.00
 14.00 -1.00

$ cxcalc chargedistribution -H 9 "C[C@H](N)C(O)=O"
id Charge
1 9.00 -0.25

$ cxcalc chargedistribution -l 4 -u 8 -s 2 "C[C@H](N)C(O)=O"
id Charge
1 4.00 0.03
  6.00 -0.00
  8.00 -0.03

We will add a Chemical Terms function for this calculation soon. The name of the calculation may change.

Zsolt