# Charge of hydrogen atoms

ChemAxon 9c0afc9aaf

11-09-2006 13:53:01

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.

ChemAxon e08c317633

11-09-2006 15:12:27

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)

 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 > > -0.07 (0.07);-0.07 (0.07) \$\$\$\$

2. Add explicit hydrogen atoms for the structure before performing

the calculation:

 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 > > -0.07;-0.07;0.02;0.02;0.02;0.02;0.02;0.02 \$\$\$\$

Best regards,

Zsolt