total charge

Hi,





I would like to calculate the total charge of a set of molecules at pH=7.4.


I've used Instant JChem and the chemical term: sum (charge("7.4")) but the result is always a low negative value. Apparently, the hydrogen charges are not being summed.





Any suggestion to solve this problem?





Thanks

macneves wrote:

Hi, I would like to calculate the total charge of a set of molecules at pH=7.4. I've used Instant JChem and the chemical term: sum (charge("7.4")) but the result is always a low negative value. Apparently, the hydrogen charges are not being summed. Any suggestion to solve this problem? Thanks

Hi,





You are right, the hydrogen charges are not being summed. Chemical Terms expression to calculate the charges with hydrogens:

Code:

sum(charge("7.4")) + sum(charge("implh", "7.4"))

Unfortunately, the

Code:

sum(charge("implh", "7.4"))

part of the expression does not return the result (it is a bug!), so the whole expression will not return the correct result.





We will fix this bug in the next version.





Best regards,


Zsolt

I suppose, that the current solution is a bit confusing, so we will change this function to include the charges of all atoms (either implicit or explicit). Thanks for drawing our attention to this problem!

In the next JChem version (JChem 3.2.6) a new function will be available for calculating the total charge of a molecule:

Code:

totalCharge()

To get the total charge of major microspecies at pH 7.4 this expression can be used (from JChem version 3.2.6):

Code:

totalCharge(majorms("7.4"))

The

Code:

sum(charge("7.4")) + sum(charge("implh", "7.4"))

will also work (we have fixed the bug), but we recommend to use the totalCharge() function (it is faster).





Best regards,


Zsolt