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Molecular Movie Shows Chemistry in Motion

X-ray laser reveals how ring-shaped gas molecules break open and unravel
An overview of the process the molecular movie has revealed

A group of scientists including Dr Adam Kirrander have, for the first time, tracked ultrafast structural changes, captured in quadrillionths-of-a-second steps, as ring-shaped gas molecules burst open and unravel.

Ring-shaped molecules are abundant in biochemistry and also form the basis for many drug compounds. The study points the way to a wide range of real-time X-ray studies of gas-based chemical reactions that are vital to biological processes.

The team of researchers, working at the SLAC National Accelerator Laboratory, Brown, Stanford, and Edinburgh, compiled the full sequence of steps in this basic ring-opening reaction into computerized animations that provide a ???molecular movie??? of the structural changes.

Conducted at SLAC???s Linac Coherent Light Source in California, the pioneering study marks an important milestone in precisely tracking how gas-phase molecules transform during chemical reactions on the scale of femtoseconds. A femtosecond is a 10-15 of a second. These are the fundamental time-scales of chemical reactions, and it is therefore possible to see exactly how the reaction unfolds, down to the motion of individual atoms.

The results are featured in the June 22 edition of Physical Review Letters.

New Views of Chemistry in Action

The study focused on the gas form of 1,3-cyclohexadiene (CHD), a small, ring-shaped organic molecule derived from pine oil. Ring-shaped molecules play key roles in many biological and chemical processes that are driven by the formation and breaking of chemical bonds. The experiment tracked how the ringed molecule unfurls after a bond between two of its atoms is broken, transforming into a nearly linear molecule called hexatriene.

The Making of a Molecular Movie

In the experiment, researchers excited CHD vapor with ultrafast ultraviolet laser pulses to begin the ring-opening reaction. Then they fired LCLS X-ray laser pulses at different time intervals to measure how the molecules changed their shape.

Researchers compiled and sorted over 100,000 strobe-like measurements of scattered X-rays. Then, they matched these measurements to computer simulations that show the most likely ways the molecule unravels in the first 200 quadrillionths of a second after it opens. The simulations, performed by the group of Adam Kirrander, at the University of Edinburgh, show the changing motion and position of its atoms.

Each interval in the animations represent 25 quadrillionths of a second ??-- about 1.3 trillion times faster than the typical 30-frames-per-second rate used to display TV shows.

???It is a remarkable achievement to watch molecular motions with such incredible time resolution,??? said Peter Weber, a Professor at Brown who led the experiment in collaboration with Mike Minitti at SLAC.    

A gas sample was considered ideal for this study because interference from any neighboring CHD molecules would be minimized, making it easier to identify and track the transformation of individual molecules. The LCLS X-ray pulses were like cue balls in a game of billiards, scattering off the electrons of the molecules and onto a position sensitive detector that projected the locations of the atoms within the molecules.

A Successful Test Case for More Complex Studies

 ???This study can serve as a benchmark and springboard for larger molecules that can help us explore and understand even more complex and important chemistry,??? Minitti said.

The work was supported by the DOE Office of Basic Energy Sciences, the Leverhulme Trust, and the European Union.

More Information

The research has also been highlighted elsewhere:

Tuesday, June 23, 2015