A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures.

Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.

Effects of Entangled IR Radiation and Tunneling on the Conformational Interconversion of 2-Cyanophenol.

The conformers of 2-cyanophenol (2CP) and their interconversions were studied by infrared (IR) spectroscopy after trapping the monomers of the gaseous compound into low-temperature (15 K) argon (Ar) and nitrogen (N2) matrixes. To assist in the interpretation of the experimental results, B3LYP, MP2, and QCISD electronic structure calculations were carried out for the 2CP molecule. Two planar conformers, cis and trans (orientation of OH with respect to the cyano group), are predicted with gas-phase populations at the sublimation temperature of ∼98 and ∼2%, respectively. The most stable form (cis) was experimentally identified in both cryomatrixes, whereas the less stable one (trans) was not detected in Ar but could be observed in the N2 matrix with an abundance of ∼15%. Selective and bidirectional conversion between the two identified conformers was achieved upon irradiating the compound trapped in N2 matrix with near-infrared (NIR) laser light tuned at the wavenumbers of the 2ν(OH) transitions of the respective conformers. The conformational composition of 2CP was also found to be affected by the broad-band IR radiation emitted by the spectrometer source. This effect could be suppressed, partially or completely, by using different long-pass IR filters, with cutoff values of approximately 2200, 1590, and 1170 cm-1. The observed conformational changes are rationalized in terms of a competition between the over-the-barrier (light-induced) and through-the-barrier (hydrogen atom tunneling) effects. Very interestingly, both effects occur on the same time scale.