Dependence of Amide Vibrations on Hydrogen Bonding

Abstract

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [-O-C=NH+] structure over the [O=C-NH] structure. However, Triggs and Valentini’s UV-Raman study of solvation and hydrogen bonding effects on ε-caprolactum, N,N-dimethylacetamide (DMA) and N-methylacetamide (NMA) (J .Phys. Chem., 1992; 96, 6922-31) cast doubt on the validity of this model by demonstrating that contrary to the resonance model prediction, carbonyl hydrogen bonding does not impact the AmII’ frequency of DMA. In this study we utilize density functional theory (DFT) calculations to examine the impact of hydrogen bonding on the C=O and N-H functional groups of NMA, which is typically used as a simple model of the peptide bond. Our calculations indicate that, as expected, the hydrogen bonding frequency dependence of the AmI vibration predominantly derives from the C=O group, whereas the hydrogen bonding frequency dependence of the AmII vibration primarily derives from N-H hydrogen bonding. In contrast, the hydrogen bonding dependence of the conformation sensitive AmIII band derives equally from both C=O and N-H groups, and, thus, is equally responsive to hydrogen bonding at the C=O or N-H site. Our work shows that a clear understanding of the normal mode composition of the amide vibrations is crucial for an accurate interpretation of the hydrogen bonding dependence of amide vibrational frequencies.

A mechanistic view of lipid membrane disrupting effect of PAMAM dendrimers

“…Considering the spectra of PAMAM/DPPC mixtures, a shift of the amide I and amide II bands can be observed as a result of the interaction between the dendrimer and the phospholipid bilayers. The downshift of the amide I frequency and the increase in the amide II band position suggest an increased level of hydrogen bonding of the dendrimer molecule [56].…”

Infrared Action Spectroscopy of Low-Temperature Neutral Gas-Phase Molecules of Arbitrary Structure

“…In contrast to the amide I band, the positions of the amide II band for the NMA oligomers are blueshifted with respect to the monomer. The frequency blueshift is due to the combination of the two effects of hydrogen bonding: the geometry change due to the elongation of NH and C-N bonds, and the electron density redistribution on the carbonyl oxygen and amide hydrogen atoms [29,30]. The same factors lead to the blueshift in the frequencies of the amide III bands, which we observed at 1277 and 1298 cm −1 for the NMA dimers and trimers, respectively.…”

“…2(b)]. Its frequency is only slightly redshifted by 6 cm −1 with respect to the monomer frequency due to the NH group being hydrogen bonded [29]. In contrast to the amide I band, the positions of the amide II band for the NMA oligomers are blueshifted with respect to the monomer.…”

“…Amide I corresponds to the CO stretch vibration with some CN and CC stretch, and is located at 1708, 1681, and 1656 cm −1 for the NMA monomers, dimers, and trimers, respectively. The redshift observed for the oligomers with respect to the monomer is attributed to the more delocalized nature of the CO stretch oscillators due to the CO bond length elongation upon hydrogen bonding [29,30]. It is worth noting that the shoulder of the amide I band at 1702 cm −1 in the spectrum of the NMA dimers is due to the non-hydrogen-bonded CO stretch vibration [see Fig.…”

Co-localised Raman and force spectroscopy reveal the roles of hydrogen bonds and π-π interactions in defining the mechanical properties of diphenylalanine nano- and micro-tubes

“…18 Experimental evidence of blue-shifting of the amide III band upon H bonding at the N-H site has been reported, both for a-helical and b-sheet polypeptides. 19 In addition, comparison between experimental and theoretical calculations of the Raman spectra of polypeptides allowed the estimation of the force constants corresponding to H bonds based on the frequency of the amide III band.…”