Ultrafast X-ray scattering: structural dynamics from diatomic to protein molecules

Abstract

Recent years have witnessed the birth of picosecond pump-probe X-ray diffraction and scattering techniques, thanks to the technological developments in the third generation synchrotron beamlines and advances in theory and data analysis by combining quantum calculations, molecular dynamics simulations and global fitting analysis. Our laboratories have employed this technique to study structural dynamics and spatiotemporal kinetics of many molecular systems in solution including diatomic molecules, haloalkanes, organometallic complexes and protein molecules over timescales from picoseconds (ps) to milliseconds. The visualising power and unbiased sensitivity of X-ray scattering proved to be instrumental in identifying global reaction pathways and in some cases capturing detailed threedimensional structures of reaction intermediates. Many results have accumulated from which we have selected some interesting examples to be reviewed here. The structural dynamics of Br 2 and I 2 are compared and the reaction pathways for HgBr 2 and HgI 2 are compared. Solvents may affect the reaction pathways as illustrated in the photolysis of CH 2 I 2 in two different solvents. How does the excitation wavelength affect the reaction pathways is another important aspect in photochemistry as shown for Ru 3 (CO) 12 . Applications to the folding of cytochrome-c and the structural dynamics of myoglobin and bacteriorhodopsin are also reviewed. The time resolution is currently limited to about 100 ps, the Xray pulse width available from synchrotron sources. In the near future, X-ray free electron lasers (XFELs) will deliver 100 fs or shorter X-ray pulses. In femtosecond (fs) X-ray scattering experiments with this higher resolution, real-time observation of ultrafast chemical events, such as bond-breaking and bond-making will be possible. So far, gas-phase reactions, which are the main targets for ultrafast electron diffraction due to the high scattering power of electrons, have not yet been studied with time-resolved X-ray scattering, but in principle this discipline will become feasible with the coming XFEL sources. We thus discuss potential fs X-ray scattering experiments for gas phase as well as solution phase reactions. In addition, the high photon flux and the coherence of XFEL-generated X-ray pulses might open up new research areas, such as single-molecule diffraction.

Synchrotron ultrafast techniques for photoactive transition metal complexes

“…In the case of large biomolecules such as proteins, the structural information is contained both in the small-angle (SAXS) and in the wide-angle (WAXS) ranges [176][177][178][179][180][181]. Owing to the inverse relationship between scattering angle and interatomic distance, information on the global protein features (size, shape) can be extracted from analysis of the SAXS region of the scattering curve, while the WAXS region is particularly sensitive to tertiary and quaternary structure [69], and therefore to the folding of helices and sheets.…”

“…However, working in reciprocal space often excludes a straightforward and intuitive interpretation. For this reason, results are often presented in real space, after a sine-Fourier transform operation [43,54,69]. Indeed, a real-space TR-XSS signal represents the differential atom-atom pair distribution function during the course of the reaction [49,51,52,54,70,71].…”

“…Data analysis of such patterns can then reveal the structural evolution of different reaction pathways, limited only by the signal-to-noise ratio of the difference signal between excited and non-excited states. In the last decade, TR-XSS has been successfully employed to monitor light-driven solution-phase structural rearrangements for a variety of systems, from small elementary molecules to proteins and macromolecules of biological relevance [43,65,69].…”

On the calculation of x-ray scattering signals from pairwise radial distribution functions

“…The first work on this formulation is almost a century old [9], and many versions and modifications have been presented [1,5,[10][11][12][13][14][15][16][17][18][19][20][21][22][23]. Much of the work has been based on determining the atomic distributions from scattering signals, not vice versa, and not always with explanations for modifications made, compared to previous publications.…”

“…We aim to provide a full formalism, with the complete set of details behind its derivation, to go hand-in hand with Molecular Dynamics (MD) simulations. These simulations are becoming more and more ubiquitous in -and essential for -the analysis of ultra-fast X-ray scattering experiments of solvated molecules [1][2][3][4]. The motivation for the work is threefold:…”