Table 1.
Conformations available to aliphatic foldamers
| Backbone structure type | Amino acid substitution patterna | Number of atoms per H-bond ringb | Residues involved in hydrogen bonding (i) | Helix polarityc | References |
|---|---|---|---|---|---|
| αn (310-helix) | Cα | 10 | 3 | N | |
| αn (α-helix) | Cα | 13 | 4 | N | |
| αβ (11-helix) | Cα/C3 or Cα/cyclic C2,3 cyclopentane ring | 11 | 3 | N | 67,69,73 |
| αβ (14,15-helix) | Cα/C3 or Cα/cyclic C2,3 cyclopentane ring | 14, 15 | 4 | N | 69 |
| α2β | Cα/C3 or Cα/cyclic C2,3 cyclopentane ring | 10, 11, 11 | 3 | N | 137 |
| α2β | Cα/C3 | 14 | 4 | N | 67 |
| αβ2 | Cα/C3 or Cα/cyclic C2,3 cyclopentane ring | 11, 11, 12 | 3 | N | 137 |
| αβ2 | Cα/C3 or Cα/cyclic C2,3 cyclopentane ring | 15 | 4 | N | 67,137 |
| βn (12-helix) | Cyclic C2,3 cyclopentane ring | 12 | 3 | N | 132 |
| βn (14-helix) | C2, C3 or C2,3 cyclohexane ring | 14 | 4 | C | 49,132 |
| βn | C2,3d | 8 | 1 | N | 51,52 |
| βn (10/12-helix) | Mixed C2/C3 | 10, 12 | 1/2 | Mixed | 25,28,52,99 |
| βn | C2,3 (cis-oxetane residues) | 10 | 1 | C | 138,139 |
| γn | C4 | 9 | 2 | N | 29 |
| αγ | Cα/C3 | 9 | 1 | N | 140 |
Cα corresponds to Cα-substituted α-amino acids (normal substitution pattern), or disubstituted amino acids (as in α-amino-isobutyric acid). C2 and C3 correspond to the carbon that bears a substituent in β-amino acids.
The number of atoms in the hydrogen bonded rings corresponds to the number of atoms, including the hydrogen of the amide. Note that for some mixed α/β-amino acids, there is more than one ring type that repeats throughout the helix. For example, in α2β the hydrogen bonding occurs between each amide carbonyl at position i and an amide at i + 3. If the ring is formed between the carbonyl of a β-amino acid (at i), then the ring includes two subsequent α-amino acids (at i + 1 and i + 2) before coming to the hydrogen bonded amide proton. Hence there are 10 atoms, as in the 310-helix for this case. The subsequent two hydrogen bonded rings will include an α-amino acid and a β-amino acid, resulting in 11-atom rings.
Direction that the carbonyl group points, toward either the C terminus or the N terminus. A ‘mixed’ entry indicates that the carbonyl group points in both directions, at different points in the helix.
This hydrogen bonding pattern is observed when the C2 position is substituted with a hydroxyl group, when the C2 position is a part of a cyclopropane ring, or when C2 and C3 are part of an oxo-norbonene ring system.