Within: heteroaromatic ring.

Definition

Matched by any of these 2 patterns; the occurrences of all of them are pooled (an atom set found by two patterns counts once).

anchor: one occurrence is one distinct set of these atoms. Unhighlighted atoms must be present but are not part of the group. Atoms are written as the pattern requires them: OH, NH2 and O− mean exactly those hydrogens and that charge. The note beside each atom gives its number in the table and, for a carbon, what its letter alone does not: sp3, sp2 or sp from the number of its connections, or aromatic / aliphatic where the pattern requires one (no note: either will do). Lower-case letters are aromatic atoms; * is any atom, a any aromatic atom.

Pattern 1

#	Atom	Conditions
1 anchor	any aromatic atom	not carbon
2 anchor	any aromatic atom
3 anchor	any aromatic atom
4 anchor	any aromatic atom
5 anchor	any aromatic atom

Bonds: 1–2 single or aromatic; 2–3 single or aromatic; 3–4 single or aromatic; 4–5 single or aromatic; 1–5 single or aromatic.

Anchor atoms: 1, 2, 3, 4, 5. An environment is a SMARTS pattern that must (or must not) match around the atom, beginning at it; it is shown as written.

SMARTS: [a;!#6]1aaaa1 Copy

anchor: one occurrence is one distinct set of these atoms. Unhighlighted atoms must be present but are not part of the group. Atoms are written as the pattern requires them: OH, NH2 and O− mean exactly those hydrogens and that charge. The note beside each atom gives its number in the table and, for a carbon, what its letter alone does not: sp3, sp2 or sp from the number of its connections, or aromatic / aliphatic where the pattern requires one (no note: either will do). Lower-case letters are aromatic atoms; * is any atom, a any aromatic atom.

Pattern 2

#	Atom	Conditions
1 anchor	any aromatic atom	not carbon
2 anchor	any aromatic atom
3 anchor	any aromatic atom
4 anchor	any aromatic atom
5 anchor	any aromatic atom
6 anchor	any aromatic atom

Bonds: 1–2 single or aromatic; 2–3 single or aromatic; 3–4 single or aromatic; 4–5 single or aromatic; 5–6 single or aromatic; 1–6 single or aromatic.

Anchor atoms: 1, 2, 3, 4, 5, 6. An environment is a SMARTS pattern that must (or must not) match around the atom, beginning at it; it is shown as written.

SMARTS: [a;!#6]1aaaaa1 Copy

Ring condition: the matched atoms must form one of the molecule’s smallest rings (its smallest set of smallest rings); the outer envelope of a fused or bridged system does not count.

Matched with RDKit’s substructure matcher on the molecule with implicit hydrogens and RDKit’s default aromaticity model, in the most aromatic resonance form.

Precedence

Not counted where its anchor atoms lie inside a match of: pyridine, pyrimidine, pyridinone (2-/4-pyridone), pyrimidinone (uracil/cytosine type), pyrazine, pyridazine, 1,3,5-triazine, 1,2,3-/1,2,4-triazine, tetrazine, pyrrole, indole, imidazole, pyrazole, 1,2,3-triazole, 1,2,4-triazole, tetrazole, furan, thiophene, oxazole, isoxazole, thiazole, isothiazole, oxadiazole, thiadiazole, purine, pyranone (2-/4-pyrone, coumarin).

The comparison is with every match of the other group before any precedence is applied, so the result does not depend on the order in which groups are tried.

Examples

Each is a test of the definition, checked on every change to it: the stated count must be found exactly. Each counted occurrence is highlighted in its own colour.

n = 1 c1cc[o+]cc1

n = 1 c1cc[s+]cc1

n = 1 c1ccc2[o+]cccc2c1

Near misses

Molecules this group must not be found in (n = 0), also tested on every change. “Matched instead” names a group that takes precedence over this one there: this group’s pattern fits, at the grey atoms, but those lie inside the other group’s match. “Groups found” are simply the groups this molecule has; they did not replace this one.

n = 0 c1ccncc1

Matched instead as: pyridine

n = 0 c1ccccc1

Groups found: benzene ring

n = 0 c1ccc2[nH]ccc2c1

Matched instead as: pyrrole, indole

n = 0 O=c1cccco1

Matched instead as: pyranone (2-/4-pyrone, coumarin)

n = 0 Cc1noc(C)n1

Matched instead as: oxadiazole

n = 0 c1ncc2nc[nH]c2n1

Matched instead as: pyrimidine, imidazole, purine

In the ATB

• 2,849 annotated compounds have it;
• 0 of them have experimental reference data;
• 506 are monofunctional: this is their only group, once (rings count as groups, so a phenol is not).

The annotated compounds are those with experimental reference data plus small, neutral organic compounds (up to 12 heavy atoms), not every ATB molecule. Through the API: GET /api/v1/molecules?functional_group=heteroaromatic_other.

Annotation scheme 2.