new terms: ketones

[muthuvenkat]

Hello,

Can the following be added to ChEBI:

name: oxyketones def: Compounds with the general formula R2C=O (R≠H) where one or more of the R groups contains an oxy (-O-) group. is_a: ChEBI:17087 ! ketones

name: α-oxyketones def: Compounds with the general formula R2C(=O) (R≠H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are bonded to adjacent carbon atoms. is_a: ChEBI:new? ! oxyketones

name: β-oxyketones def: Compounds with the general formula R2C(=O) (R≠H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are separated by a carbon atom. is_a: ChEBI:new? ! oxyketones

name: aryloxyketones def: Compounds with the general formula R2C=O (R≠H) where one or more of the R groups contains an oxy (-O-) group bonded to an aryl group. is_a: ChEBI:new? ! oxyketones

name: 2-aryloxyketones def: Compounds with the general formula R2C=O (R≠H) containing an oxyaryl (-OAr) group bonded to the carbon adjacent to the ketone carbonyl group. synonym: α-aryloxyketones is_a: ChEBI:new? ! aryloxyketones

Can quinone be added to ChEBI?

name: quinone InChI=1/C6H4O2/c7-5-1-2-6(8)4-3-5/h1-4H/i1-12,2-12,3-12,4-12,5-12,6-12,7-16,8-16 is_a: ChEBI:36141 ! quinones

name: quinone methanes def: Quinones in which one or more of the quinonoid oxygens have been replaced by methylene groups. synonyms: quinomethanes is_a: ChEBI:36141 ! quinones

name: quinone dimethanes def: Quinones in which both quinonoid oxygens have been replaced by methylene groups. synonyms: quinodimethanes, xylylenes is_a: CHEBI:new? ! quinone methanes

Thanks Hilary Burch

Reported by: burchh

[muthuvenkat]

and also the following xylylenes:

name: azaxylylenes def: Quinone dimethanes in which one or more of the methylene groups have been replaced by =NH or =NR. is_a: CHEBI:new? ! quinone dimethanes

name: o-azaxylylenes def: Quinone dimethanes in which one or more of the methylene groups, which are situated ortho to each other, have been replaced by =NH or =NR. synonyms: ortho-azaxylylenes is_a: CHEBI:new? ! azaxylylenes

name: p-azaxylylenes def: Quinone dimethanes in which one or more of the methylene groups, which are situated para to each other, have been replaced by =NH or =NR. synonyms: para-azaxylylenes is_a: CHEBI:new? ! azaxylylenes

Original comment by: burchh

[muthuvenkat]

Hello,

The InChI for quinone here was generated by a dodgy version of ChemDraw. It should read:

InChI=1/C6H4O2/c7-5-1-2-6(8)4-3-5/h1-4H

Many thanks, Colin.

Original comment by: batchelorc

[muthuvenkat]

Hi Hilary

1. Can you please supply examples (preferably ones already in ChEBI or, if not, as much detail as possible) of α-oxyketones, β-oxyketones, 2-aryloxyketones, quinone methanes, quinone dimethanes, o-azaxylylenes and p-azaxylylenes?

2. The InChI which Colin has supplied for 'quinone' corresponds with that for 1,4-benzoquinone which is already in ChEBI as CHEBI:16509. Is this what you mean?

Thanks

Marcus

Original comment by: mennis

[muthuvenkat]

Hi Marcus,

1. See examples below

α-oxyketones 1-hydroxylimonen-2-one (CHEBI:50246)

β-oxyketones pyrethrolone (CHEBI:39107)

2-aryloxyketones 2-methoxy-1-phenylethanone (synonym: 2-methoxyacetophenone) InChI=1/C9H10O2/c1-11-7-9(10)8-5-3-2-4-6-8/h2-6H,7H2,1H3

(see Enthaler.pdf)

quinone methanes 4-methylenecyclohexa-2,5-dienone (synonym: p-quinomethane) InChI=1/C7H6O/c1-6-2-4-7(8)5-3-6/h2-5H,1H2

quinone dimethanes 3,6-dimethylenecyclohexa-1,4-diene (synonym: p-quinodimethane) InChI=1/C8H8/c1-7-3-5-8(2)6-4-7/h3-6H,1-2H2

(see IUPAC Gold Book Q05012 for both)

azaxylylenes All of the azaxylylenes are either o- or p- (m- doesn't seem to exist) so I haven't got an example for this.

o-azaxylylenes (can we also have aza-o-xylylenes and aza-ortho-xylylenes as synonyms for this class) 6-methylenecyclohexa-2,4-dienimine InChI=1/C7H7N/c1-6-4-2-3-5-7(6)8/h2-5,8H,1H2 (can we also have aza-o-xylylenes and aza-ortho-xylylenes as synonyms for this class)

p-azaxylylenes 4-methylenecyclohexa-2,5-dienimine InChI=1/C7H7N/c1-6-2-4-7(8)5-3-6/h2-5,8H,1H2 (can we also have aza-p-xylylenes and aza-para-xylylenes as synonyms for this class)

(see Fishwick.pdf)

We may as well have diazaxylylenes for completeness.

name: diazaxylylenes def: Quinone dimethanes in which both of the methylene groups have been replaced by =NH or =NR. is_a: CHEBI:new? ! azaxylylenes

example: cyclohexa-3,5-diene-1,2-diimine InChI=1/C6H6N2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H

(there doesn't seem to be any o- or p-diazaxylylenes in the literature)

2. Yes, please can 'quinone' be a synonym for CHEBI:16509.

I've e-mailed the PDFs to you as this tracker won't let me upload anything over 256 kB.

Thanks,

Hilary

Original comment by: burchh

[muthuvenkat]

Hi Hilary

All completed now. I've had to make a number of changes to the definitions and ontology parentage. For example, I have defined a quinomethane (aka quinone methane) not as a quinone which has been modified, but as cyclic ketone which is formed by formal replacement of one or more of the quinonoid oxygens. The class of quinomethanes cannot be linked to quinones by an is_a relationship, as although formally derived from quinones, the quinomethanes are not themselves quinones and such a relationship would therefore be invalid within the ontology branch.

By a similar argument azaxylylenes should not have quinone dimethanes as is_a parents, owing to the presence of the imine group. I have therefore reclassified these as imines.

One particular difficulty was with the dual meaning which quinomethane (or quinone methane) has. Thus it can mean both the singly substituted cyclic ketone and (according to the Gold Book) the parent of both singly and doubly substituted quinones. I have therefore had to resort to use of the plural form to indicate the common parent and the singular to denote the singly substituted compound. I think that this works OK, although a further problem with this approach was that I needed a common parent for both the quinomonomethanes and quinodimethanes. In the end I had to settle for is_a carbocylic compound.

Note that we are trying to move away from use of plurals to indicate classes and I am slowly changing these to singular whenever I have other occasion to access the entries for classes. In some cases though (like above) the plural forms need to be retained. We know that this is a problem to the ontologists and are working on ways to get around this.

All the new entries will go live on May 27. Let me know if you need the ChEBI IDs for all or any of the terms.

Cheers

Marcus

Original comment by: mennis