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 hydrogensare 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 eachindividual 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 thetotal charge of the structure is zero, and the structure containsindividual 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 manipulationand 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.