#19 fused vs bridged

[Kirill Degtyarenko]

We have

%CHEBI:33635 polycyclic compounds
%CHEBI:35293 fused compounds
%CHEBI:33640 cage compounds
%CHEBI:33599 spiro compounds
%CHEBI:35990 bridged compounds

I canot find a good definition of "bridged compounds".

Currently it is:

"Polycyclic compounds in which two rings have two or more atoms in common."
(don't remember where I got it from, but since the definition of bridge is
"A valence bond or an atom or an unbranched chain of atoms connecting two different parts of a molecule", and if the bridge=bond, then only two atomas are in common)

in this case, CHEBI:35293 fused compounds should be
is_a CHEBI:35990 bridged compounds

but appears to be wrong even though I am not be sure why.

E.g. the Blue Book draft says

"P-25.4.1.1 Bridged fused ring system. A ring system in which some of the rings constitute a fused ring system (see P-25.0 - P-25.3) and the remaining rings are created by one or more bridges."

(i.e. there need to be clear distinction between fused ring systems and bridged ring systems; bridged fused ring system will be is_a child of both)

P-25.4.1.2 Bridge. An atom or group of atoms is named as a bridge by means of a prefix if it fulfills one or more of the following:
(a) if it connects two or more non-adjacent positions of the same ring in a fused ring system;
(b) if it connects two or more positions of different rings of a fused ring system and does not thereby form a new ortho- and peri-fused ring;
(c) if it connects positions of a ring of a fused ring system to a previously described bridge but cannot be included as part of that bridge;
(d) if it connects the atoms at the end of a bond common to two rings of a fused ring system;
(e) if it is used to describe a system with only ortho- or ortho- and peri-fusions that cannot be named entirely by fusion principles."

The criterion (e) is interesting: it says that the purely fused systems can be *named* using the bridge. But are they really bridged?

example:
is bicyclo[4.2.0]octa-1,3,5-triene a bridged compound any more than indane (which also could be named as 'bicyclo[4.3.0]nona-1,3,5-triene')

Kirill

[Alan McNaught]

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Part of the problem here is that IUPAC defines a subset of bridged compounds for which nomenclature rules require the bridge to be named explicitly. This is the point addressed by P-25.4.1.1. However, I do not think we need to take this into account for the purpose of the ontology. In fact I doubt whether we should include 'bridged fused systems' at all as defined by IUPAC, since the distinction is artificial, depending on whether fusion nomenclature as developed by IUPAC can describe a polycyclic system without need for a bridge prefix. Furthermore, the distinction can depend on what trivially named fused systems are approved by IUPAC for use as fusion components. In other words the distinction does not depend on inherent structural features.

I think the current ChEBI definition of bridged compounds is probably OK; it includes compounds such as bicyclo[3.3.1]nonane, where the two rings have three atoms in common. Your suggestion to have 'fused compounds is_a bridged compounds' seems fine to me. I would say that indane and bicyclo[4.2.0]octa-1,3,5-triene are both bridged compounds and both fused-ring compounds. Also I would have 'CHEBI 33599 spiro-fused compounds is_a CHEBI 35293 fused compounds' (see P-24.1).

Alan

[Kirill Degtyarenko]

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I did

fused compounds (CHEBI:35293) is a bridged compounds (CHEBI:35990);

but I cannot do

spiro compounds (CHEBI:33599) is a fused compounds (CHEBI:35293)

it will mean that spiro compounds is a bridged compounds -- but this is not correct! P-25.0 clearly says that spirofusion is NOT a fusion.

[Alan McNaught]

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You are right: spiro compounds cannot be categorised as bridged compounds.

However I am uncomfortable with the idea that spirofusion is not fusion. Indeed P-25.0 says specifically 'This type of fusion is called spirofusion'. So I suggest that we revert to the position with both 'bridged compounds' and 'fused compounds' as children of 'polycyclic compounds'; then we would have 'ortho-fused compounds' and 'ortho- and peri-fused compounds' as children of both 'fused compounds' and 'bridged compounds', but 'spiro-fused compounds' as a child only of 'fused compounds'. Does this make sense to you?

Alan