Recent Report in Science

Free access to our Science paper on fluorine-atom reactions

The research, lead by Greg Dunning and Dave Glowacki, combines time-resolved vibrational spectroscopy and molecular dynamics simulations to explore fundamental reaction processes, including molecular rearrangement, hydrogen-bond formation, and solvent restructuring around the new molecular species.

Most of us are familiar with the sketch of a ‘reaction profile’ where ‘energy’ is plotted versus ‘reaction progress,’ as in the image on the left. But we want to know in more detail, “What does this reaction coordinate mean?’ Explaining the x-axis takes a combination of chemical knowledge, chemical intuition, and a whole lot of investigation. Furthermore, a lot of information cannot be displayed in these one-dimensional graphs, and we need a better description about the other degrees of freedom. The new research we present in Science, available free of charge through this link, is a further extension of getting at this problem, building up atomistic descriptions of reaction dynamics in liquids.

Figure 1

Even chemists need to simplify the x axis – here we call it ‘Reaction Progress.’ We’ve tried to indicate a few steps along the way, showing what’s actually happening throughout the course of this very fast reaction.

Vibrational spectroscopy, a sensitive probe of molecular structure, provides a method of following bond breaking and forming during chemical reactions. The experiments we report in the article follow the reaction of F + CD3CN → DF + CD2CN with about 1-ps time resolution. (We use deuterium instead of hydrogen for spectroscopic regions, but the chemistry of hydrogen-2 is similar to the more familiar hydrogen-1 isotope.) One picosecond may sound fast, but it’s a bit unnerving to realise that during this interval the D-F molecule will be struck by the solvent about 10 times and it will oscillate about 100 times. In addition, the transfer of the D atom from acetonitrile to the F atom and the initial hydrogen bonding of the newly formed, polar DF molecule have already passed in that initial picosecond.

Molecular dynamics simulation

Chaos or patterned beauty? The blue squiggles show the randomised movement of the solvent molecules during the reaction. The atoms involved in the reaction, deuterium (in white) and fluorine (in green), take much more patterned trajectories.

Enter molecular dynamics simulations. We use a computer to simulate the movement of the atoms and molecules, meaning we can answer all kinds of detailed questions that we have a hard time accessing with spectroscopy. Many of us try to think about chemistry on the level of ‘atoms bumping into molecules’, but even systems of seven atoms are fascinatingly complex. Watching enough movies of a real reaction gives us a better feeling for the rules that govern real chemistry.  Holding these pictures in our brain, we can ask such hypothetical questions as ‘What role does the hydrogen bonding play in the reaction?’ or simply ‘How fast is fast?’ The simulations let us perform a new set of experiments that even the best spectroscopy will never handle.

This combined approach of experiment and theory allows us to map the various chemical traits  onto new, more complex reactive systems. Read the news report from the University of Bristol and access the article in Science.