User 75309100fd
19-07-2012 12:41:27
Hi! I am new here using marvin plugins. I use the command line input as below:
cxcalc charge -p 2 -H 7 "[NH3]"
and it generates results: Total charge -0.02
However as we all know that Amonia in pH7 condition should carry +1 charge. Where is the problem?
thx a lot!
ChemAxon afdac7b783
20-07-2012 06:47:57
Hi,
Charge plugin calculates partial charges: sigma, pi, or total partial charge of an atom. Read more about charge caluclation here.
If you want to calculate the total charge of the molecule, you should use the "formalcharge" calculation of cxcalc:
$ cxcalc formalcharge -H 7 "[NH3]"
id Formal charge
1 1
$ cxcalc formalcharge -H 9 "[NH3]"
id Formal charge
1 0
Hope these help.
Best Regards,
Viktoria
User 75309100fd
20-07-2012 11:04:56
vpalfi wrote: |
Hi,
Charge plugin calculates partial charges: sigma, pi, or total partial charge of an atom. Read more about charge caluclation here.
If you want to calculate the total charge of the molecule, you should use the "formalcharge" calculation of cxcalc:
$ cxcalc formalcharge -H 7 "[NH3]" id Formal charge 1 1
$ cxcalc formalcharge -H 9 "[NH3]" id Formal charge 1 0
Hope these help.
Best Regards,
Viktoria
|
Yeah, this surely helps! I really appreciated it.
However using this method sometimes returns nothing as result.
eg. cxcalc formalcharge "O=[O-1]"
id Formal charge
1
How does this happen? Forgive me for my igorant. :( Thanks for your help.
ChemAxon afdac7b783
20-07-2012 11:29:10
In case of your example, the molecular structure contains valence error, i.e., cxcalc cannot return the result.
You can see the error message "formalcharge: Inconsistent molecular structure" above the returned result:
$ cxcalc formalcharge "O=[O-1]"
O=[O-] 1 "formalcharge: Inconsistent molecular structure."
id Formal charge
1
The following examples do not contain errors, and results are retuned:
$ cxcalc formalcharge "O[O-]"
id Formal charge
1 -1
$ cxcalc formalcharge "[O+][O-]"
id Formal charge
1 0
BR,
Viktoria
User 75309100fd
20-07-2012 15:29:48
you guys are great! thanks!!