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).
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.
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
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
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.
Dark Structures in Molecular Radiationless Transitions
Determined by Ultrafast Diffraction, R. Srinivasan,
Feenstra, S. T. Park, S. Xu, A. H. Zewail, Science 2005, 307,
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.