Ultrafast Electron Diffraction of Isolated Molecules | Ultrafast Electron Crystallography of Surfaces and Crystals Ultrafast Electron Diffraction of Isolated Molecules* Beginning with x-rays at the turn of the 20th century, diffraction techniques have allowed determination of equilibrium three-dimensional structures with atomic resolution, in systems ranging from diatoms (NaCl) to DNA, proteins and complex assemblies such as viruses. For dynamics, the time resolution has similarly reached the fundamental atomic scale of motion. With the advent of femtosecond time resolution nearly two decades ago, it has become possible to study—in real time—the dynamics of non-equilibrium molecular systems, also from the very small (NaI) to the very large (DNA, proteins and their complexes). Armed with this ability to capture both the static architecture as well as the temporal behavior of the chemical bond, a tantalizing goal that now stimulates researchers the world over is the potential to map out, in real time, the coordinates of all individual atoms in a reaction, as, for example, when a molecule unfolds to form selective conformations or when a protein docks onto the cell surface. These transient structures provide important insights into the function of chemical and biological molecules. As function is intimately associated with intrinsic conformational dynamics, knowing a molecule’s static structure is often only the first step toward unraveling how the molecule functions, especially in the world of biology. Thus, elucidating the real-time ‘structural dynamics’ of far-from-equilibrium conformations at atomic scale resolution is vital to understanding the fundamental mechanisms of complex chemical and biological systems. The method of choice in our laboratory has been ultrafast electron diffraction (UED), which has unique advantages. With properly timed sequences of ultrafast electron pulses, it is now possible to image complex molecular structures in the four dimensions of space and time with resolutions of ~0.01 Å and 1 ps, respectively. The new limits of ultrafast electron diffraction (UED) provide the means for the determination of transient molecular structures, including reactive intermediates and non-equilibrium structures of complex energy landscapes. By freezing structures on the ultrafast timescale, we are able to develop concepts that correlate structure with dynamics. Examples include structure-driven radiationless processes, dynamics-driven reaction stereochemistry, pseudorotary transition-state structures, and non-equilibrium structures exhibiting negative temperature, bifurcation, or selective energy localization in bonds. These successes in the studies of complex molecular systems, even without heavy atoms, and the recent development of a new machine devoted to structures in the condensed phase, establish UED as a powerful method for mapping out temporally changing molecular structures in chemistry, and potentially, in biology. The UED technique employs properly timed sequences of ultrafast pulses—a femtosecond laser pulse to initiate the reaction and ultrashort electron pulses to probe the ensuing structural change in the molecular sample. The resulting electron diffraction patterns are then recorded on a CCD camera. This sequence of pulses is repeated, timing the electron pulse to arrive before or after the laser pulse; in effect, a series of snapshots of the evolving molecular structure are taken. Each time-resolved diffraction pattern can then, in principle, be inverted to reveal the three-dimensional molecular structure that gave rise to the pattern at that specific time delay. However, in practice, a key challenge lies in recovering the molecular structural information that is embedded in the as-acquired diffraction images. To access the small population of changing structures embedded in the large background signal, we have developed the Diffraction-Difference Method in our laboratory. The method consists of timing the electron pulses so as to establish an in situ reference signal (usually the ground-state structure obtained at negative time). The digital nature of our processing methodology then allows us to obtain the difference of each time-resolved diffraction pattern from this reference signal, thus revealing the change from the reference structure in the form of difference rings. Ultrafast electron diffraction combines several disparate fields of study: femtosecond pulse generation, electron beam optics, CCD detection systems, and GED. Output from a femtosecond laser is split into a pump path and an electron-generation path. The pump laser proceeds directly into the vacuum chamber and excites a beam of molecules. The probe laser is directed toward a back-illuminated photocathode, where the laser generates electron pulses via the photoelectric effect; the electrons are accelerated, collimated, focused, and scattered by the isolated molecules. The time delay between the arrival of the pump laser pulse and the probe electron pulse is controlled with a computer-driven translation stage. The resulting diffraction patterns are detected with a CCD camera, and the images are stored on a computer for later analysis. The UED-3 apparatus is also equipped with a time-of-flight mass spectrometer (MS-TOF) to aid in the identification of species generated during the course of chemical reactions. In 1999, Philip Ball of Nature observed, ‘Diffraction on the ‘molecular’ timescale of femtoseconds is an infant discipline which promises wonders once perfected, but which is capable right now of only the crudest of impressionistic sketches: blurred images of lattice dynamics, showing evidence of rapid change but without a single molecule (let alone an atom) in focus. The static photography of the Braggs has yet to produce its first movie.’ UED has not only succeeded in bringing isolated molecules into sharp focus but has also captured the crucial ‘freeze frames’ in these movies—generating much excitement for the burgeoning field of ‘structural dynamics’. *The text above has been adapted from the following publications. Selected Publications Dark Structures in Molecular Radiationless Transitions Determined by Ultrafast Diffraction, R. Srinivasan, J. S. Feenstra, S. T. Park, S. Xu, A. H. Zewail, Science 2005, 307, 558. Ultrafast Electron Diffraction (UED) — A New Development for the 4D Determination of Transient Molecular Structures, R. Srinivasan, V. A. Lobastov, C.-Y. Ruan, A. H. Zewail, Helv. Chim. Acta 2003, 86, 1763. Ultrafast Diffraction of Transient Molecular Structures in Radiationless Transitions, V. A. Lobastov, R. Srinivasan, B. M. Goodson, C.-Y. Ruan, J. S. Feenstra, A. H. Zewail, J. Phys. Chem. A 2001, 105, 11159. Ultrafast Diffraction and Structural Dynamics: The Nature of Complex Molecules Far from Equilibrium, C.-Y. Ruan, V. A. Lobastov, R. Srinivasan, B. M. Goodson, H. Ihee, A. H. Zewail, Proc. Natl. Acad. Sci. USA 2001, 98, 7117. Direct Imaging of Transient Molecular Structures with Ultrafast Diffraction, H. Ihee, V. A. Lobastov, U. M. Gomez, B. M. Goodson, R. Srinivasan, C.-Y. Ruan, A. H. Zewail, Science 2001, 291, 458.