Simulation of transient infrared spectra of a photoswitchable peptide

Abstract

In transient infrared (IR) experiments, a molecular system may be photoexcited in a nonstationary conformational state, whose time evolution is monitored via IR spectroscopy with high temporal and structural resolution. As a theoretical formulation of these experiments, this work derives explicit expressions for transient one- and two-dimensional IR spectra and discusses various levels of approximation and sampling strategies. Adopting a photoswitchable octapeptide in water as a representative example, nonequilibrium molecular dynamics simulations are performed and the photoinduced conformational dynamics and associated IR spectra are discussed in detail. Interestingly, it is found that the time scales of dynamics and spectra may differ from residue to residue by up to an order of magnitude. Considering merely the cumulative spectrum of all residues, the contributions of the individual residues largely compensate each other, which may explain the surprisingly small frequency shifts and short photoproduct rise times found in experiment. Even when a localized amide I mode is probed (e.g., via isotope labeling), the vibrational frequency shift is shown to depend in a complicated way on the conformation of the entire peptide as well as on the interaction with the solvent. In this context, various issues concerning the interpretation of transient IR spectra and conformational dynamics in terms of a few exponential time scales are discussed.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis

“…It is reasonable to assume that this energy is dissipated rapidly in the macrocycle and is the key factor for the acceleration of the bond rupture in cyclobutene, although this view has been discussed controversially. , The scissile bond in cyclobutene is thermally labile by nature, and depending on the substitution pattern, only moderate heating is needed for rupture. − The significant influence of thermal oscillations in this reaction has also been acknowledged in previous literature . We speculate that the rapid heating upon absorption of a photon is a general working principle of photoswitches and a determining factor in the initiation of various processes like structural changes in proteins − and DNA. , …”

“…With this setup, the authors were able to exert a force of 200 pN to the AFM tip. Other groups exploited the mechanical work performed by azobenzene to induce structural changes in peptides, − DNA, − and synthetic foldamers. − Photoswitches from the spiropyran family were also shown to be applicable in this context. , Quantum mechanochemistry can make a key contribution to our understanding of the mechanical effects during photoswitching by calculating the efficiency of energy conversion and transmission processes. With the use of computational methods, it has been possible, for example, to juxtapose purely mechanical, photochemical, and combined photomechanochemical switching of the azobenzene photoswitch. − This knowledge paves the way for an optimization of molecular machines by increasing the amount of mechanical work they can perform.…”

Time-resolved observation of protein allosteric communication

“…3A. As a note of caution, we mention that only explicit calculations of the transient infrared spectra (which are quite ambitious) would prove that these motions are directly linked to the observed spectral features (61).…”

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

“…2. That experimental observable evolves on roughly the same timescale as the C α (21)-C α (76) distance in the MD simulation and in a similar non-exponential fashion (it would be desirable to link the MD simulations more closely to the IR observable, as recently done for comparable protein systems, [53][54][55][56] which would be an interesting avenue for a future investigation). Fig.…”