Vibrational spectroscopy and DFT calculations of di‐amino acid cyclic peptides. Part I: cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) in the solid state and in aqueous solution

Abstract

Investigations of the vibrational spectra of cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid-state and aqueous protonated samples, as well as their corresponding N-deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3-LYP/cc-pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas-phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di-amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C 2 and C 1 symmetries for the six-membered rings of cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L-AlaGly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis-peptide linkage are shown to be significantly different from those of the trans-peptides. For example, deuterium shifts have shown that the cis-amide I vibrations found in cyclo(Gly-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Ala-Gly) have larger N-H contributions compared to their trans-amide counterparts. Compared to trans-amide II vibrations, cis-amide II vibrations show a considerable decrease in N-H character.

Three Types of Induced Tryptophan Optical Activity Compared in Model Dipeptides: Theory and Experiment

“…[83] For example, c-(l-Alal-Ala) in a crystal is puckered, whereas c-(l-Ala-d-Ala) is nearly flat. [83] For example, c-(l-Alal-Ala) in a crystal is puckered, whereas c-(l-Ala-d-Ala) is nearly flat.…”

“…It is known that the cyclic dipeptidic unit is normally quite flexible, and its conformation is very dependent on the amino acid side-chain type and interactions. [83] For example, c-(l-Alal-Ala) in a crystal is puckered, whereas c-(l-Ala-d-Ala) is nearly flat. [84] The peptide ring in the c-(l-Trp-l-Trp) crystal structure is also flat.…”

Differential laser-induced perturbation Raman spectroscopy: a comparison with Raman spectroscopy for analysis and classification of amino acids and dipeptides

“…Accordingly, the most significant vibrational bands identified through the loadings of the PCA analysis of Raman and DLIPS datasets for classification, including their relative intensity in the Raman or DLIPS spectra were tabulated in Table 1 were more prominent in their respective DLIPS spectra, noting that the band assignments for these shifts can be readily found in the literature for the amino acids and dipeptides. [34][35][36][37][38][39][40][41] The relative intensity differences as well as loading differences of the DLIPS spectral bands as compared to the Raman spectral bands are attributed to differences in the coupling of the excimer laser into various amino acids and dipeptides. It should be highlighted that these intensity differences between DLIPS and Raman spectral bands originated from the perturbative role of the UV light on the molecular bonds with DLIPS, as opposed to traditional vibrational response with Raman.…”

Tracking the Amide I and αCOO− Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

“…The amide I vibration has been found to be heavily dependent on the formation of intramolecular hydrogen bonds in proteins, and hydrogen bonds, in turn, are integral in the stabilization of various protein secondary structures [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ]. As a result, vibrational spectroscopy combined with density functional theory (DFT) computations is commonly employed to investigate the molecular geometries, dynamics, and secondary structures of short peptide chains [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ]. Navarette and coworkers reported the Raman and IR vibrational spectra for l -glutamic acid [ 44 ], l -aspartic acid (D) [ 35 ], and the glutamic acid (EE) and aspartic acid (DD) dipeptides [ 35 ] in their seminal works and found that these molecules are zwitterio...…”