The infrared driven cis-trans isomerization reaction of nitrous acid (HONO) and energy transport in peptide helices

Abstract

This thesis contains the results of two distinct scientific inquiries. The first part investigates a model system for ground state chemical reactions whereas the second part examines the energy transport in peptide helices. The cis-trans isomerization of nitrous acid (HONO) in solid matrices is a model system of a chemical reaction in the electronic ground state. The isomerization reaction is reversible and can be triggered by the photo-excitation of the OH stretch. Exciting OHcis in an IR pump - IR probe experiment, we observed vibrationally hot trans molecules on an ultrafast time scale (20-50 ps) with the isomerization following a two step process. The first step corresponds to the direct coupling of the vibrational excited state with the reaction channel state(s), whereas the second step represents the energy that is re-fed in the reaction channel from intermediate states (states that get populated by the OHcis). The quantum yield of the cis!trans isomerization reaction after exciting OHcis increases by 30% when cooling the matrix from 30 K to 15 K, being (at the low temperature) 50-70%. We also estimated that the quantum yield of the backward reaction decreases by approximatively 40% in the same temperature range. This behavior is explained in the framework of Marcus theory of electron and proton transfer in the barrierless regime. In this regime, the theory predicts a 40% increase in quantum yield of the forward reaction, in agreement with the 30% from experiment. Hence, quantum yield could go up to 100% at sufficiently low temperatures. A wealth of information about the dynamics of the isomerization reaction and the cooling process following excitation was obtained by performing two color experiments, in which OH stretch, N=O stretch and HON bend were excited and probed in different combinations. The rotational dynamics of the cis and trans isomers were investigated in the Kr matrix at 30 K. We observed that the central atoms of the molecule rotate in a hula hoop motion upon the H isomerization. With these series of experiments, we were the first to study the ultrafast dynamics of a ground state reaction in the low excitation regime. To investigate the mechanism of heat transport in peptide helices, we designed an eight amino acid peptide helix to which we attached an azobenzene chromophore. After exciting the azobenzene with a UV pulse, we followed the heat propagation through the helix using the shifts in the amide I band in the IR. With the help of isotope labeling, we were able to spectroscopically isolate specific amino acids in the sequence at different positions along the helix. We found that the heat does not propagate through the hydrogen bonds, as it was theoretically suggested, but rather through the backbone of the helix. Furthermore, fitting our data to a rate equation system, we estimated a heat diffusion coefficient D=2 Å2/ps. Exciting the molecule with IR light, we calculated a heat diffusivity coefficient four times higher than the one when UV excitation was used. Below 270 K, the heat transport is inefficient and mostly ballistic whereas above this temperature it is more efficient and diffusive in character. These studies are the first steps towards the investigation of vibrational energy transport in large bio-polymers and proteins