ATB | Functional Group

carbamate `carbamate` Nitrogen: acyl nitrogen

Definition

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.

#	Atom	Conditions
1 anchor	nitrogen	3 connections (hydrogens included)
2 anchor	carbon	3 connections (hydrogens included)
3 anchor	oxygen	1 connection (hydrogens included)
4 anchor	oxygen	2 connections (hydrogens included); 0 hydrogens
5	carbon, nitrogen

Bonds: 1–2 any; 2–3 double; 2–4 single; 4–5 single.

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

SMARTS: [#7X3]~[#6X3](=[#8X1])-[#8X2;H0]-[#6,#7]

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

No group takes precedence over it.

Takes precedence over: ether (aliphatic), aryl ether, ester.

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 COC(N)=O

n = 1 CCOC(=O)NC

n = 1 O=C1NCCO1

n = 1 CNC(=O)Oc1ccccc1

n = 1 CNC(=O)ON=C(C)SC

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 CC(=O)OC

Groups found: ester

n = 0 NC(N)=O

Groups found: urea

n = 0 CC(N)=O

Groups found: amide I

n = 0 NC(=O)O

Groups found: carbamic acid

In the ATB

1,277 annotated compounds have it;
9 of them have experimental reference data;
137 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=carbamate.

Annotation scheme 2.