Charge of hydrogen atoms

A user have asked the following question:








I use cxcalc to calculate the atomic propeties.





In some mol file, Hydrogen was not included. But I also need the properties of Hydrongen.





Is it possible to add hydrogen by using the command - cxcalc?





Ethylene was used as an example,





The command line is : cxcalc -S ethylene.mol charge


The output is :








Marvin 09120618282D





2 1 0 0 0 0 999 V2000


-3.7813 0.7188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-3.0668 1.1313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1 2 2 0 0 0 0


M END


> <CHARGE>


-0.11;-0.11





$$$$


I also want to get the charge of hydrogen.

There are two different solutions for the problem:





1. cxcalc option for the sum of charge on H atoms:





You can use the "cxcalc <calculation> --help" command to get plugin-specific


help, for example:

Code:

cxcalc charge --help

The help states that you can use the following option for cxcalc:

Code:

-i, --implh [true|false] implicit H charge sum shown in brackets (for sigma and total charge only) (default: false)

Example for your structure:

Code:

$ cxcalc -S input.mol charge --implh true Marvin 09110616192D 2 1 0 0 0 0 999 V2000 -2.4687 -0.0937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6437 -0.0937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M END > > <CHARGE> -0.07 (0.07);-0.07 (0.07) $$$$

2. Add explicit hydrogen atoms for the structure before performing


the calculation:





Add explicit hydrogens with standardizer:

Code:

$ standardize input.mol -c "addExplicitH" -f mol -o out.mol

Charges are calculated for all atoms (including hydrogens):

Code:

$ cxcalc -S out.mol charge Marvin 09110616232D 8 7 0 0 0 0 999 V2000 -2.4687 -0.0937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6437 -0.0937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4687 -0.9187 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4687 0.7313 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2937 -0.0937 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6437 0.7313 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6437 -0.9187 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8187 -0.0937 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 1 4 1 0 0 0 0 1 5 1 0 0 0 0 2 6 1 0 0 0 0 2 7 1 0 0 0 0 2 8 1 0 0 0 0 M END > > <CHARGE> -0.07;-0.07;0.02;0.02;0.02;0.02;0.02;0.02 $$$$

Best regards,


Zsolt