Electron and X‐Ray Methods of Ultrafast Structural Dynamics: Advances and Applications

In this contribution, we highlight the state of the art in the determination of structures with ultrafast electrons and X‐rays. We provide our perspectives and reflections on the principles, techniques and methods, and on applications from different disciplines, with some focus on physical, chemical and biological structures. Although this article is not a survey of all the work done with these techniques, it provides a comprehensive referencing to current research.     

Structural dynamics of surfaces by ultrafast electron crystallography: experimental and multiple scattering theory

Recent studies in ultrafast electron crystallography (UEC) using a reflection diffraction geometry have enabled the investigation of a wide range of phenomena on the femtosecond and picosecond time scales. In all these studies, the analysis of the diffraction patterns and their temporal change after excitation was performed within the kinematical scattering theory. In this contribution, we address the question, to what extent dynamical scattering effects have to be included in order to obtain quantitative information about structural dynamics. We discuss different scattering regimes and provide diffraction maps that describe all essential features of scatterings and observables. The effects are quantified by dynamical scattering simulations and examined by direct comparison to the results of ultrafast electron diffraction experiments on an in situ prepared Ni(100) surface, for which structural dynamics can be well described by a two-temperature model. We also report calculations for graphite surfaces. The theoretical framework provided here allows for further UEC studies of surfaces especially at larger penetration depths and for those of heavy-atom materials.     

Irreversible chemical reactions visualized in space and time with 4D electron microscopy

We report direct visualization of irreversible chemical reactions in space and time with 4D electron microscopy. Specifically, transient structures are imaged following electron transfer in copper-tetracyanoquinodimethane [Cu(TCNQ)] crystals, and the oxidation/reduction process, which is irreversible, is elucidated using the single-shot operation mode of the microscope. We observed the fast, initial structural rearrangement due to Cu(+) reduction and the slower growth of metallic Cu(0) nanocrystals (Ostwald ripening) following initiation of the reaction with a pulse of visible light. The mechanism involves electron transfer from TCNQ anion-radical to Cu(+), morphological changes, and thermally driven growth of discrete Cu(0) nanocrystals embedded in an amorphous carbon skeleton of TCNQ. This in situ visualization of structures during reactions should be extendable to other classes of reactive systems.     

Ultrafast solvation dynamics of human serum albumin: correlations with conformational transitions and site-selected recognition

Human serum albumin, the most abundant protein found in blood plasma, transports a great variety of ligands in the circulatory system and undergoes reversible conformational transitions over a wide range of pH values. We report here our systematic studies of solvation dynamics and local rigidity in these conformations using a single intrinsic tryptophan (W214) residue as a local molecular probe. With femtosecond resolution, we observed a robust bimodal distribution of time scales for all conformational isomers. The initial solvation occurs in several picoseconds, representing the local librational/rotational motions, followed by the dynamics, in the tens to hundreds of picoseconds, which result from the more bonded water in the tryptophan crevice. Under the physiological condition of neutral pH, we measured approximately 100 ps for the decay of the solvation correlation function and observed a large wobbling motion at the binding site that is deeply buried in a crevice, revealing the softness of the binding pocket and the large plasticity of the native structure. At acidic pH, the albumin molecule transforms to an extended conformation with a large charge distribution at the surface, and a similar temporal behavior was observed. However, at the basic pH, the protein opens the crevice and tightens its globular structure, and we observed significantly faster dynamics, 25-45 ps. These changes in the solvation dynamics are correlated with the conformational transitions and related to their structural integrity.     

Dynamics of Electrons in Ammonia Cages: The Discovery System of Solvation

Two centuries ago solvated electrons were discovered in liquid ammonia and a century later the concept of the solvent cage was introduced. Here, we report a real time study of the dynamics of size‐selected clusters, n=20 to 60, of electrons in ammonia, and, for comparison, that of electrons in water cages. Unlike the water case, the observed dynamics for ammonia indicates the formation, through a 100 fs temperature jump, of a solvent collective motion in a 500 fs relaxation process. The agreement of the experimental results—obtained for a well‐defined n, gated electron kinetic energy, and time delay—with molecular dynamics theory suggests the critical and different role of the kinetic energy and the librational motions involved in solvation.     

Direct observation of the primary bond-twisting dynamics of stilbene anion radical

The anion radicals of stilbenes in the collisionless isolated phase were synthesized by electron attachment, and their dynamics were observed in real time on the femtosecond time scale. The observed coherent vibrational motion (approximately 42 cm(-1)) and the primary bond-twisting dynamics (approximately 650 fs) for the D2 state are on a vastly different time scale from that reported (approximately 10 ns) in solution.     

1,1-dioxonaphtho[1,2-b]thiophene-2-methyloxycarbonyl (alpha-Nsmoc) and 3,3-dioxonaphtho[2,1-b]thiophene-2-methyloxycarbonyl (beta-Nsmoc) amino-protecting groups

Of the three theoretically possible, Bsmoc-related, naphthothiophene sulfone-based amino-protecting groups, the two most readily available derivatives, the alpha- and beta-Nsmoc analogues, have been examined as substitutes for the Bsmoc residue in cases where the latter lead to oily protected amino acids or amino acid fluorides. All of the naphtho systems gave easily handled solid amino acid derivatives. The intermediate sulfone alcohol 11 used as the key reagent for introduction of the alpha-Nsmoc protecting group was readily made from alpha-tetralone (Scheme 1). The corresponding beta-analogue 17 was made similarly on a small scale, but due to the high cost of beta-tetralone, an alternate route involving reaction of rhodanine with alpha-naphthaldehyde was used for large-scale work (Scheme 2). All proteinogenic amino acids were converted to their alpha- and beta-Nsmoc derivatives. Deblocking studies showed that the reactivity toward deblocking by piperidine followed the order alpha-Nsmoc > Bsmoc > beta-Nsmoc. 1H NMR experiments showed that deblocking of the two new systems was mechanistically similar to that previously established for the Bsmoc derivative in that the reaction is initiated by Michael addition to the beta-carbon atom of the alpha,beta-unsaturated sulfone system. Application of alpha- and beta-Nsmoc amino acids to the solid-phase synthesis of two model peptides was examined. An advantage of the alpha-Nsmoc system over the long-known Bsmoc system proved to be the milder conditions needed for the deblocking step relative to the Bsmoc case, which is itself more readily deblocked than the classic Fmoc analogue.