Conformer-specific photochemistry imaged in real space and time

The journal of physical chemistry. B, 2011

Employing nonequilibrium molecular dynamics (MD) simulations and transient infrared (IR) spectroscopy, a joint theoretical/experimental study on a water-soluble photoswitchable octapeptide designed by Renner et al. [Biopolymers 2002, 63, 382] is presented. The simulations predict the cooling of the hot photoproducts on a time scale of 7 ps and complex conformational rearrangements ranging from a few picoseconds to several nanoseconds. The experiments yield a dominant fast relaxation time of 5 ps, which is identified as the cooling time of the peptide in water and also accounts for initial conformational changes of the system. Moreover, a weaker component of 300 ps is found, which reflects the overall conformational relaxation of the system. The virtues and the limitations of the joint MD/IR approach to describe biomolecular conformational rearrangements are discussed.

The Journal of Physical Chemistry B, 2013

The photoinduced ring-closing reaction in diarylethene, which serves as a model system for understanding reactive crossings through conical intersections, was directly observed with atomic resolution using femtosecond electron diffraction. Complementary ab initio calculations were also performed. Immediately following photoexcitation, subpicosecond structural changes associated with the formation of an open-ring excited-state intermediate were resolved. The key motion is the rotation of the thiophene rings, which significantly decreases the distance between the reactive carbon atoms prior to ring closing. Subsequently, on the few picosecond time scale, localized torsional motions of the carbon atoms lead to the formation of the closed-ring photoproduct. These direct observations of the molecular motions driving an organic chemical reaction were only made possible through the development of an ultrabright electron source to capture the atomic motions within the limited number of sampling frames and the low data acquisition rate dictated by the intrinsically poor thermal conductivity and limited photoreversibility of organic materials.

Biophysical Journal, 2006

Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates reveals that the conformational rearrangement of the peptide is rather complex and occurs on at least four timescales: 1) After photoexcitation, the azobenzene unit of the molecule undergoes nonadiabatic photoisomerization within 0.2 ps. 2) On the picosecond timescale, the cooling (13 ps) and the stretching (14 ps) of the photoexcited peptide is observed. 3) Most reaction coordinates exhibit a 50-100 ps component reflecting a fast conformational rearrangement. 4) The 500-1000 ps component observed in the simulation accounts for the slow diffusion-controlled conformational equilibration of the system. The simulation of the photoinduced molecular processes is in remarkable agreement with time-resolved optical and infrared experiments, although the calculated cooling as well as the initial conformational rearrangements of the peptide appear to be somewhat too slow. Based on an ab initio parameterized vibrational Hamiltonian, the time-dependent amide I frequency shift is calculated. Both intramolecular and solvent-induced contributions to the frequency shift were found to change by &2cm ÿ1 , in reasonable agreement with experiment. The potential of transient infrared spectra to characterize the conformational dynamics of peptides is discussed in some detail.

ChemPhysChem, 2009

Structural changes on a broad range of length and time scales are closely connected to biochemical function. The high relevance of conformational dynamics to macromolecular processes has long been hidden to structural characterization methods like X-ray crystallography and NMR. However, more recently, increasing focus is put on biomolecular dynamics [1] for example, in the context of intrinsically disordered proteins, [2] conformational selection in protein-ligand binding, [3] and protein folding. [4] The ability of polypeptide chains and nucleic acids to spontaneously adopt unique three-dimensional structures in aqueous solution is one of the most fundamental examples of biological self-assembly. A missing but crucial part in the current picture of protein folding is the characterisation of the denatured state, the conformational ensemble of unfolded protein chains. The initial event of folding is thought to be intramolecular contact formation of amino acid residues, a process that is mediated by chain diffusion. [5] Similar conformational events are thought to be crucial for functionality of intrinsically disordered protein domains. Fluorescence spectroscopy provides means to follow conformational dynamics on timescales down to those of fluorescence lifetimes of reporter fluorophores, typically a few nanoseconds. [6, 7] Fçrster resonance energy transfer (FRET) [8-10] and photoinduced electron transfer (PET) [11] are two mechanisms that lead to variation of fluorescence emission by distance-dependent fluorescence quenching between a fluorophore and a quenching moiety. Whereas FRET from a donor (D) to an acceptor (A) fluorophore scales with 1/[1+A C H T U N G T R E N N U N G (R/R 0) 6 ], where R 0 is typically between 2 and 8 nm, PET requires contact formation (van der Waals contact) for efficient quenching with a separation between D and A on the sub-nanometre length scale. PET-quenching can occur transiently through molecular collisions, a process called "dynamic quenching", or in molecular complexes that are stable for multiple excitation-emission

ChemPhysChem

The ability of nonlinear electronic spectroscopy to track folding/unfolding processes of proteins in solution by monitoring aromatic interactions is investigated by first-principles simulations of two-dimensional (2D) electronic spectra of a model peptide. A dominant reaction pathway approach is employed to determine the unfolding pathway of a tetrapeptide, which connects the initial folded configuration with stacked aromatic side chains and the final unfolded state with distant noninteracting aromatic residues. The π-stacking and excitonic coupling effects are included through ab initio simulations based on multiconfigurational methods within a hybrid quantum mechanics/molecular mechanics scheme. It is shown that linear absorption spectroscopy in the ultraviolet (UV) region is unable to resolve the unstacking dynamics characterized by the three-step process: T-shapedtwisted offset stackingunstacking. Conversely, pump–probe spectroscopy can be used to resolve aromatic interactions b...

Nature Chemistry

Photochemical & Photobiological Sciences, 2007

When polychromatic X-rays are shined onto crystalline material, they generate a Laue diffraction pattern. At third generation synchrotron radiation sources, a single X-ray pulse of ∼100 ps duration is enough to produce interpretable Laue data from biomolecular crystals. Thus, by initiating biological turnover in a crystalline protein, structural changes along the reaction pathway may be filmed by ultra-fast Laue diffraction. Using laser-light as a trigger, transient species in photosensitive macromolecules can be captured at near atomic resolution with sub-nanosecond time-resolution. Such pump-probe Laue experiments have now reached an outstanding level of sophistication and have found a domain of excellence in the investigation of light-sensitive proteins undergoing cyclic photo-reactions and producing stiff crystals. The main theoretical concepts of Laue diffraction and the challenges associated with time-resolved experiments on biological crystals are recalled. The recent advances in the design of experiments are presented in terms of instrumental choices, data collection strategy and data processing, and some of the inherent difficulties of the method are highlighted. The discussion is based on the example of myoglobin, a protein that has traversed the whole history of pump-probe Laue diffraction, and for which a massive amount of data have provided considerable insight into the understanding of protein dynamics.

Journal of the American Chemical Society

The function of proteins is linked to their conformations that can be resolved with several high-resolution methods. However, only a few methods can provide the temporal order of intermediates and conformational changes, with each having its limitations. Here, we combine pulsed electron−electron double resonance spectroscopy with a microsecond freeze-hyperquenching setup to achieve spatiotemporal resolution in the angstrom range and lower microsecond time scale. We show that the conformational change of the C α-helix in the cyclic nucleotide-binding domain of the Mesorhizobium loti potassium channel occurs within about 150 μs and can be resolved with angstrom precision. Thus, this approach holds great promise for obtaining 4D landscapes of conformational changes in biomolecules.

Physical chemistry chemical physics : PCCP, 2016

In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure element...

Physical Review X, 2020

Pump-probe measurements aim to capture the motion of electrons and nuclei on their natural timescales (femtoseconds to attoseconds) as chemical and physical transformations take place, effectively making "molecular movies" with short light pulses. However, the quantum dynamics of interest are filtered by the coordinate-dependent matrix elements of the chosen experimental observable. Thus, it is only through a combination of experimental measurements and theoretical calculations that one can gain insight into the internal dynamics. Here, we report on a combination of structural (relativistic ultrafast electron diffraction, or UED) and spectroscopic (time-resolved photoelectron spectroscopy, or TRPES) measurements to follow the coupled electronic and nuclear dynamics involved in the internal conversion and photodissociation of the polyatomic molecule, diiodomethane (CH 2 I 2). While UED directly probes the 3D nuclear dynamics, TRPES only serves as an indirect probe of nuclear dynamics via Franck-Condon factors, but it is sensitive to electronic energies and configurations, via Koopmans' correlations and photoelectron angular distributions. These two measurements are interpreted with trajectory surface hopping calculations, which are capable of simulating the observables for both measurements from the same dynamics calculations. The measurements highlight the nonlocal dynamics captured by different groups of trajectories in the calculations. For the first time, both UED and TRPES are combined with theory capable of calculating the observables in both cases, yielding a direct view of the structural and nonadiabatic dynamics involved.