search

ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
Creative Commons Attribution 4.0 International
46 stars 10 forks source link

neutral/ionic form #408

Open muthuvenkat opened 19 years ago

muthuvenkat commented 19 years ago

Question:

I don't understand why you distinguish neutral/ionic form of a chemical compound? In solution, both species coexist, isn't it?

Reported by: pauladematos

muthuvenkat commented 19 years ago

Logged In: YES user_id=802919

We do distinguish between different molecular entities because they have different properties. The very same argument (how many species coexist in solution) can be applied to any chemical reaction, however nobody argues that reactant and product are the different entities. Fundamentally, (Bronsted) acid/base reactions are no different from any other chemical reaction where a bond is formed/broken:

AH --> A- + H+

There is a long-going discussion about so-called 'biochemical equations' (as opposed to 'chemical equations'; see http://www.chem.qmul.ac.uk/iubmb/newsletter/1996/news7.html ) In short, Alberty argued that charges have to be omitted from 'biochemical equations'.

However, when 'biochemical' representation of NAD(P)/NADH(2) [as opposed to NAD(P)+/NAD(P)H + H+] were introduced into EC niomenclature, lot of people complained (see http://www.chem.qmul.ac.uk/iubmb/newsletter/2004/item4.html\#NAD ) so now it has reverted back to charged forms.

Biochemists often refer to "glutamate" meaning mixture of glutamic acid (neutral), hydrogen glutamate (1-) and glutamate (2-). So far, we do not have mixtures in ChEBI although we may need to introduce them in the future.

Original comment by: kiri11