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

Abstract

N-methylformamide (NMF), the simplest model for peptides, exhibits hyperplectic (both simple and complex) behavior as revealed by thin film infrared spectroscopy on planar AgX [AgCl:AgBr] fiber. IR spectra (0.1 s scans) of 10 microg NMF/dichloromethane(DCM) under N(2) flow first show NMF monomer, dimers, and trimers, which then form surface-organized NMF oligomers as pseudocrystals (P(n)) of increasing length and intensity to P(12). After 4 s, P(12) decays in 1.5 to 4 s steps via P(11), P(10), P(9), P(8), P(7), P(6), and P(5) to P(4) and P(3). The nature of P(n) (n = 5-12) is explained using a model based on the crystal structure of NMF and consisting of a matrix of 7 x 7 helices, alternating R(ight) and L(eft) with TDC (transition dipole coupling) in groups with 2, 3, or 4 neighbors. The total (10) dipolar couplings are matched to the 10 maxima of P(n) and prove the value of the model. P(4) (spectrum 325) fits a 5 x 5 matrix without corners. P(3) is transformed into the very weakly absorbing cyclic hexamer, shown to be very stable and swelling in DCM with increased intensity but without wavelength changes.

N‐Alkylacylamides in Thin Films Display Infrared Spectra of 310‐, α‐, and π‐Helices with Visible Static and Dynamic Growth Phases

“…Our previous study [6] emphasized the disappearance of the IR absorption of the NMF at 1653 cm À1 with the formation of, what we now recognize as, a mixture of 3 10 -and a-quasiplanar forms at Sg 1000. Stimulated by the results for NMA described earlier, we made a plot of the absorbance at wavelengths corresponding to the 3 10 -, a-, and p-helices maxima versus time, which is shown in Figure S3.…”

“…The second is that simple peptide models form Hbonded helices in liquid solution, at least in the electrostatically immobilized thin film on AgX. [6] The third discovery is that each turn of the helix has enough stability, so that its growth pauses for 0.2-0.4 s and, thus, becomes visible as a dark line in a series of spectra. We will develop an explanation for this new mesoscopic phenomenon below.…”

“…[6] TFIS has been used to make a spectroscopic identification of the oligomers of water [cyclic trimer, cyclic pentamer, cyclic hexamers (boat and chair), and bicyclic hexamers]. [7,8] TFIS utilizes a short acquisition time (revealing transient structures), limited IR energy (low signal, Sg, avoiding disruption of transient species), [5,6] and multiple reflections on planar AgX as the substrate for Fourier transform IR spectroscopy-attenuated total internal reflectance (FTIR-ATR), with limited penetration depth and molecular motion restricted by electrostatic immobilization. [8] .…”

N‐Methyl‐trimethylacetamide in Thin Films Displays Infrared Spectra of π‐Helices, with Visible Static and Dynamic Growth Phases, and then a β‐Sheet

“…[ [1][2][3][4] N-Methylpivalamide (4 mg, 98 %, Sigma-Aldrich) was placed in a test tube (10 mL) and pentane (60 mL, HPLC grade, 98 %, SigmaAldrich) was added. A perforated polypropylene cap with drying agent (granular silica gel, Sigma-Aldrich) was used to close the tube.…”

“…It is important to note that the quality of the spectra arises from the immobilization of polar molecules on polar surfaces, such as the AgX element used for the attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopic measurements. [2][3][4] …”