Solution-Phase Conformations of N-Acetyl-N‘-methyl-l-alaninamide from Vibrational Raman Optical Activity

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.

Secondary structure formation in N-substituted peptides

A systematic conformational analysis on several model peptides with N-substituted amino acids was performed on the basis of ab initio MO theory at the HF/6-31G* and HF/3-21G levels with inclusion of solvation effects to study the influence of N-substitution on the formation of typically secondary structural elements, e.g. beta sheets, helices and turns. The conformational flexibility of some structures was examined by means of molecular dynamics simulations in the gas phase and in solution. The results show a restriction of the conformational flexibility of the peptide chain after introduction of an N-substituted amino acid. N-substitution makes beta sheet formation more difficult. Several consecutive N-substituted amino acids in a sequence lead to conformers different from those found on the energy hypersurface of the corresponding N-unsubstituted peptides. There is a strong tendency to form periodically helical conformations, e.g. the polyglycine II or the alpha helix, which can be extended over several N-substituted amino acid residues. As long as 1<--4 hydrogen bond formation remains possible, the major types of beta turns can be formed with a distinct preference for the betaII and betaVIa turns. The betaI turn in particular is considerably destabilized.

Infrared and Raman vibrational optical activity: theoretical and experimental aspects

Advances in the field of vibrational optical activity (VOA) are reviewed over the past decade. Topics are surveyed with an emphasis on the theoretical and instrumental progress in both vibrational circular dichroism (VCD) and Raman optical activity (ROA). Applications of VOA to stereochemical and biological problems are reviewed, with a bias toward new kinds of experiments made possible by theoretical and instrumental advances. In the field of VCD, the most notable advances have taken place in the quality and size of ab initio calculations of VOA intensities and in the quality of step-scan Fourier transform instrumentation. For ROA, the most dramatic progress has occurred in the areas of theoretical formulation and high-throughput instrumentation. Applications of VOA now include all major classes of biological and pharmaceutical molecules. VOA's importance as a diagnostic tool will likely grow as the control of molecular chirality increases in research and industrial areas.

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.