N-Methylformamide, a Hyperplectic Model for Peptides in Thin Film Infrared Spectroscopy on Planar AgX

Photo-stability of peptide-bond aggregates: N-methylformamide dimers

The formation of weakly-bound dimers of N-methylformamide (NMF) and the photochemistry of these dimers after irradiation at 248 nm were explored using matrix-isolation spectroscopy. Calculations were used to characterize the diverse isomers and assign their IR spectra; non-adiabatic dynamics was simulated to understand their photo-deactivation mechanism. The most stable dimers, and , were obtained by trans-trans aggregation (N-HO[double bond, length as m-dash]C interactions) and could be identified in the matrix. The main products formed after irradiation are the trans-cis dimers ( and ), also stabilized by N-HO[double bond, length as m-dash]C interactions. In contrast to the photochemistry of the monomers, no dissociative products were observed after 248 nm irradiation of the dimers. The absence of dissociative products can be explained by a proton-transfer mechanism in the excited state that is faster than the photo-dissociative mechanism. The fact that hydrogen bonding has such a significant effect on the photochemical stability of NMF has important implications to understand the stability of peptide-bonded systems to UV irradiation.

N-alkylacylamides in thin films display infrared spectra of 3₁₀-, α-, and π-helices with visible static and dynamic growth phases

A peptide model is a physical system containing a CONH group, the simplest being HCONHCH3 , N-methylformamide (NMF). We have discovered that NMF and N-methylacetamide (NMA), which form hydrogen-bonded oligomers in thin films on a planar AgX fiber, display infrared (IR) spectra with peaks like those of polypeptide helices. Structures can be assigned by their amide I maxima near 1672 (3(10)), 1655 (3(10)), 1653 (α), 1655 (π), and 1635 cm(-1) (π), which are the first IR data for the π-helix. Sharp peaks are an outcome of immobilization of polar species on the polar surface of silver halides. We report the first use of expanded thin-film IR spectroscopy, in which plots of every spectrum over the amide I-II range show pauses or slow stages in the increase or decrease of absorption. These are identified as static phases followed by dynamic phases, with the incremental gain or loss of a helix turn. A general theory can be stated for such processes. Density functional calculations show that the NMA α-helix pentamer (crystal structure geometry) is transformed into a π-helix-like form. For the first time, an entire sequence (3(10)-helix, α-helix, π-helix, quasiplanar species) of spectra has been recorded for NMA.

N-methyl-trimethylacetamide in thin films displays infrared spectra of π-helices, with visible static and dynamic growth phases, and then a β-sheet

The simplest (minimal) peptide model is HCONHCH3. An increase in the π-helix content with increased substitution in the acyl portion suggested the examination of N-methyl-trimethylacetamide) (NMT). NMT displays spectra, in which there is evolution of a set of helices defined by their amide I maxima near 1686 (3(10)), 1655 (first π), and, most importantly, at 1637 cm(-1) (π). Expanded thin-film infrared spectroscopy (XTFIS) shows pauses or slow stages, which are identified as static phases followed by dynamic phases with the incremental gain or loss of a helix turn. In addition, absorbance at 1637 cm(-1) suddenly increases at 82.1 s (30% over 0.3 s), indicating a phase change and crystallization of the π-helix, along with a coincidental decrease in the absorbance for the first π-helix. A sharp peak occurs at the maximum of the phase change at 82.5 s, representing a pure NMT π-helix. The spectra then undergo a decreasing general absorption loss over 150 s, with the π-helix evolving further to an antiparallel β-sheet fragment. The spectral quality arises from the immobilization of polar molecules on polar surfaces. The crystal structure is that of an antiparallel β-sheet.

Surface electrostatic immobilization of thin layers of water on silver halide. Experimental and calculated infrared spectrum of cyclic trimer of water and a ponderal isotope effect

Evaporation of water on a planar AgX surface leads to a strongly bound monolayer for which IR spectra display the marker peaks for modest numbers of oligomers. From 700-1800 spectra for each isotopomer, H(2)O(16) and H(2)O(18), a pair was selected with moderate intensity at 1616 cm(-1) (a peak reported for the cyclic trimer of water) from the monolayer portion of the experiment. Every selected spectrum had lesser peaks for other oligomers. The sum of a spectroscopic pair reveals the vibrational spectra of the cyclic trimers of H(2)O(16) and H(2)O(18). All fundamentals in the mid-IR are seen including the bending, OH stretching, and intramolecular H-bonding regions, the last never previously recognized. The relative prevalence of cyclic trimer can be attributed to the "low" water concentration on the surface. In addition, a ponderal effect leads to higher concentrations of cyclic trimer in the H(2)O(18) spectra than in the H(2)O(16) spectra and allows observation of combination bands in the H(2)O(18) spectra, representing a new type of isotope effect. The spectroscopic results for the two water isotopomers are much more extensive than those obtained through matrix isolation. Remarkably complete spectra of the cyclic trimer are obtained for the first time, especially for H(2)O(18). DFT calculations with the cyclic trimer on a simplified model for the AgCl surface yield spectra consistent with the experimental spectrum. The technique can be extended to other oligomers of water and many other OH compounds.