Conformational investigation of α,β-dehydropeptides VII*. Conformation of Ac-Pro-ΔAla-NHCH3 and Ac-Pro-(E)-ΔAbu-NHCH3: comparison with (Z)-substituted α,β-dehydropeptides†

Nanotubes and water-channels from self-assembling dipeptides

Dipeptides are attractive building blocks for biomaterials in light of their inherent biocompatibility, biodegradability, and simplicity of preparation. Since the discovery of diphenylalanine (Phe-Phe) self-assembling ability into nanotubes, research efforts have been devoted towards the identification of other dipeptide sequences capable of forming these interesting nanomorphologies, although design rules towards nanotube formation are still elusive. In this review, we analyze the dipeptide sequences reported thus far for their ability to form nanotubes, which often feature water-filled supramolecular channels as revealed by single-crystal X-ray diffraction, as well as their properties, and their potential biological applications, which span from drug delivery and regenerative medicine, to bioelectronics and bioimaging.

The conformation cis of N-acetyl-N-methyl-α,β-dehydroalanine N′-methylamide and saturated analogues

A series of three homologous amino acids derivatives: N-acetyl-N-methyl-α,β–dehydroalanine N′-methylamide (1), N-acetyl-N-methyl-L-alanine N′-methylamide (2), and N-acetyl-N-methyl-DL-alanine N′-methylamide have been synthesised. The racemic species undergoes spontaneous separation into L and D-enantiomers. From these two chiral forms, the structure of L-enantiomer (3) was analysed. The molecules of 1 – 3 adopt the cis arrangement of the N-terminal amide bond. The molecular conformations are similar for 1 (φ, ψ = 94.6(1)°, −1.7(1)°) and 3 (φ, ψ = 111.5(1)°, −23.8(1)°), and also 2 (φ, ψ = −114.8(2)°, 29.5(2)°), if inversion through the chiral C2 carbon is considered. They are stabilised by intramolecular N—H…N hydrogen bond. In the case of 1, the π—electron conjugation resulting from the planar arrangement of the C2—C21 double bond and C-terminal amide group is another stabilising force of this conformation. Thus, the N-methyldehydroalanine residue should promotes trans-cis isomerisation to a greater extend than the saturated analogue. The compounds 1 – 3 reveal similar associative pattern and form centrosymmetric dimers linked by the intermolecular N—H…O hydrogen bonds.

Conformational investigation of α,β-dehydropeptides. XVI. β-turn tendency in Ac-Pro-ΔXaa-NHMe: crystallographic and theoretical studies

The crystal structures of two diastereomeric alpha,beta-dehydrobutyrine peptides Ac-Pro-(Z)-DeltaAbu-NHMe (I) and Ac-Pro-(E)-DeltaAbu-NHMe (II) have been determined. Both dehydropeptides adopt betaI-turn conformation characterized by the pairs of (phi(i+1), psi(i+1)) and (phi(i+2), psi(i+2)) angles as -66, -19, -97, 11 degrees for I and -59, -27, -119, 29 degrees for II. In each peptide, the betaI turn is stabilized by (i + 3) --> i intramolecular hydrogen bonds with N...O distance of 3.12 A for I and 2.93 A for II. These structures have been compared to the crystal structures of homologous peptides Ac-Pro-DeltaVal-NHMe and Ac-Pro-DeltaAla-NHMe. Theoretical analyses by DFT/B3LYP/6-31 + G** method of conformers formed by these four peptides and by the saturated peptide Ac-Pro-Ala-NHMe revealed that peptides with a (Z) substituent at the C(beta) (i+2) atom of dehydroamino acid, i.e. Ac-Pro-DeltaVal-NHMe and Ac-Pro-(Z)-DeltaAbu-NHMe, predominantly form beta turns, both in vacuo and in polar environment. The tendency to adopt beta-turn conformation is much weaker for the peptides lacking the (Z) substituent, Ac-Pro-(E)-DeltaAbu-NHMe and Ac-Pro-DeltaAla-NHMe. The latter adopts a semi-extended or an extended conformation in every polar environment, including a weakly polar solvent. The saturated peptide Ac-Pro-Ala-NHMe in vacuo prefers a beta-turn conformation, but in polar environment the differences between various conformers are small. The role of pi-electron correlation and intramolecular hydrogen bonds interaction in stabilizing the hairpin structures are discussed.

Conformational investigation of alpha,beta-dehydropeptides. IX. N-Acetyl-(E)-alpha,beta-methylamide: stereoelectronic properties from infrared and theoretical studies

The Fourier transform infrared spectra of Ac-(E)-deltaAbu-NHMe were analyzed to determine the predominant solution conformation(s) of this (E)-alpha,beta-dehydropeptide-related compound and the electron density perturbation in its amide groups. The measurements were performed in dichloromethane and acetonitrile in the region of mode vs (N-H), amide I, amide II and vs (C(alpha)=Cbeta). The equilibrium geometrical parameters, calculated by a method based on the density functional theory with the B3LYP functional and the 6-31G* basis set, were used to support spectroscopic interpretation and gain some deeper insight into the molecule. The experimental and theoretical data were compared with those of three previously described molecules: isomeric Ac-(Z)-deltaAbu-NHMe, Ac-deltaAla-NHMe, which is deprived of any beta-substituent, and saturated species Ac-Abu-NHMe. The titled compound assumes two conformational states in equilibrium in the DCM solution. One conformer is extended almost fully and like Ac-deltaAla-NHMe is C5 hydrogen-bonded. The other adopts a warped C5 structure similar to that of Ac-(Z)-deltaAbu-NHMe. The C5 hydrogen bond, unlike the H-bond in Ac-deltaAla-NHMe, is disrupted by acetonitrile. The resonance within the N-terminal amide groups in either of the (E)-deltaAbu conformers is not as well developed as the resonance in Ac-Abu-NHMe. However, these N-terminal groups, compared with the other unsaturated compounds, constitute better resonance systems in each conformationally related couple: the C5 hydrogen-bonded Ac-(E)-deltaAbu-NHMe/Ac-deltaAla-NHMe and the warped C5 Ac-(E)-deltaAbu-NHMe/Ac-(Z)-deltaAbu-NHMe. The resonance within the C-terminal groups of the latter couple apparently is similar, but less developed than the resonance in Ac-Abu-NHMe. The electron distribution within the C-terminal group of the hydrogen-bonded C5 (E)-deltaAbu conformer apparently is determined mainly by the electron influx from the C(alpha)=Cbeta double bond.

Conformational investigation of alpha,beta-dehydropeptides. VIII. N-acetyl-alpha,beta-dehydroamino acid N'-methylamides: conformation and electron density perturbation from infrared and theoretical studies

The Fourier transform infrared spectra are analyzed in the regions of Vs(N-H), amide I, amide II and Vs(C alpha = C beta) bands for a series of Ac-delta Xaa-NHMe, where delta Xaa = delta Ala, (Z)-delta Abu, (Z)-delta Leu, (Z)-delta Phe and delta Val, to determine the predominant solution conformation of these alpha,beta-dehydropeptide-related molecules and the electron distribution perturbation in their amide bonds. The measurements were performed in dichloromethane (DCM). To confirm and rationalize the assignments, the spectra of the respective series of saturated Ac-Xaa-NHMe, recorded in DCM, and the spectra of these two series of unsaturated and saturated compounds, recorded in acetonitrile, were examined. To help interpret the spectroscopic results, the equilibrium geometrical parameters for some selected amides were used. These were optimized with ab initio methods in the 6-31G** basis set. Each of the dehydroamides studied adopted a C5 structure, which in Ac-delta Ala-NHMe is fully extended and accompanied by the strong C5 hydrogen bond. Interaction with the C alpha = C beta bond lessened the amidic resonance within each of the flanking amide groups. The N-terminal C = O bond was noticeably shorter, both amide bonds were longer than the corresponding bonds in the saturated entities and the N-terminal amide system was distorted. Ac-delta Ala-NHMe constituted an exception. Its C-terminal amide bond was shorter than the standard one and both amide systems were prototypically planar.