Simulation of transient infrared spectra of a photoswitchable peptide

Modus Operandi of a Pedalo-Type Molecular Switch: Insight from Dynamics and Theoretical Spectroscopy

Molecular switches which can be triggered by light to interconvert between two or more well-defined conformation differing in their chemical or physical properties are fundamental for the development of materials with on-demand functionalities. Recently, a novel molecular switch based on a the azodicarboxamide core has been reported. It exhibits a volume-conserving conformational change upon excitation, making it a promising candidate for embedding in confined environments. In order to rationally implement and efficiently utilize the azodicarboxamide molecular switch, detailed insight into the coordinates governing the excited-state dynamics is needed. Here, we report a detailed comparative picture of the molecular motion at the atomic level in the presence and absence of explicit solvent. Our hybrid quantum mechanics/molecular mechanics (QM/MM) excited state simulations reveal that, although the energy landscape is slightly modulated by the solvation, the light-induced motion is dominated by a bending-assisted pedalo-type motion independent of the solvation. To support the predicted mechanism, we simulate time-resolved IR spectroscopy from first principles, thereby resolving fingerprints of the light-induced switching process. Our calculated time-resolved data are in good agreement with previously reported measured spectra.

Time-resolved observation of protein allosteric communication

Allostery represents a fundamental mechanism of biological regulation that is mediated via long-range communication between distant protein sites. Although little is known about the underlying dynamical process, recent time-resolved infrared spectroscopy experiments on a photoswitchable PDZ domain (PDZ2S) have indicated that the allosteric transition occurs on multiple timescales. Here, using extensive nonequilibrium molecular dynamics simulations, a time-dependent picture of the allosteric communication in PDZ2S is developed. The simulations reveal that allostery amounts to the propagation of structural and dynamical changes that are genuinely nonlinear and can occur in a nonlocal fashion. A dynamic network model is constructed that illustrates the hierarchy and exceeding structural heterogeneity of the process. In compelling agreement with experiment, three physically distinct phases of the time evolution are identified, describing elastic response ([Formula: see text] ns), inelastic reorganization ([Formula: see text] ns), and structural relaxation ([Formula: see text]s). Issues such as the similarity to downhill folding as well as the interpretation of allosteric pathways are discussed.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Stiff-stilbene photoswitch ruptures bonds not by pulling but by local heating

The forces generated by stiff-stilbene during photoswitching are too low to cause bond rupture, which is instead initiated by heating.

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

By covalently binding a photoswitchable linker across the binding groove of the PDZ2 domain, a small conformational change can be photo-initiated that mimics the allosteric transition of the protein. The response of its binding groove is investigated with the help of ultrafast pump-probe IR spectroscopy from picoseconds to tens of microseconds. The temperature dependence of that response is compatible with diffusive dynamics on a rugged energy landscape without any prominent energy barrier. Furthermore, the dependence of the kinetics on the concentration of certain viscogens, sucrose, and glycerol, has been investigated. A pronounced viscosity dependence is observed that can be best fit by a power law, i.e., a fractional viscosity dependence. The change of kinetics when comparing sucrose with glycerol as viscogen, however, provides strong evidence that direct interactions of the viscogen molecule with the protein do play a role as well. This conclusion is supported by accompanying molecular dynamics simulations.