Neutralize

The action neutralizes charged molecules. Neutralization logic is described below through examples.

Example :

Action

Input

Output

Comment

Neutralize
(neutralize)

images/download/attachments/1803701/neutralize1_in.png

images/download/attachments/1803701/neutralize1_out.png

Charges of non-metal atoms are set to zero and implicit hydrogens

are added/removed to neutralize the molecule.

images/download/attachments/1803701/sodium_ion.png

images/download/attachments/1803701/sodium_ion.png

Metal ions are not neutralized.

images/download/attachments/1803701/neutralize3_in.png

images/download/attachments/1803701/neutralize3_out.png

Charged structures with counterions are neutralized if each

individual entity can be neutralized separately.

images/download/attachments/1803701/neutralize2_inout.png

images/download/attachments/1803701/neutralize2_inout.png

Charged structures with counterions are not neutralized if the

total charge of the structure is zero, and the structure contains

individual entities which cannot be neutralized separately.

images/download/attachments/1803701/neutralize4_inout.png

images/download/attachments/1803701/neutralize4_inout.png

If the molecule cannot be neutralized by charge manipulation

and hydrogen addition/removal without violating valence rules,

it remains unchanged.

images/download/attachments/1803701/neutralize5_inout.png

images/download/attachments/1803701/neutralize5_inout.png

Mesomer structures with adjacent opposite charges remain intact.

Note :

The action only operates through hydrogen manipulation, i.e. adds or removes hydrogens to create a neutral compound.