Linking theory and experiment - the benzene mystery

Nuts representing benzene dimer structure
Two years ago some colleagues and I did calculations which could, in principle, make the connection between the spectroscopic data and the advanced calculations for van der Waals forces between benzene molecules. As it turned out, we couldn’t make the link at that time. Now I have developed a new model – actually a limited version of the old model – which means that the link can be made.
Professor Ad van der Avoird
Research published last week in the journal Angewandte Chemie International Edition finally provides a solution to one of the questions chemists have been puzzling over for the last 20 years. In an interview with ScienceOmega.com, Professor Ad van der Avoird from the Institute of Theoretical Chemistry at Radboud University Nijmegen explained how, along with Professor Gerard Meijer and colleagues at the Fritz Haber Institute in Berlin, he came up with a theory to perfectly describe the dynamics between the two molecules of the benzene dimer.

In chemistry, covalent bonds form single molecules from individual atoms, but non-covalent interactions also play a very important part. Molecules can interact through hydrogen bonding and by van der Waals forces, for example. Over the years, Professor van der Avoird and his co-authors have looked at other systems involving hydrogen bonding, producing papers on – among other things – the water dimer and liquid water simulations.

"Water is typically hydrogen bonding, but benzene is typically non-hydrogen bonding," Professor van der Avoird said. "As it’s a non-polar molecule the main interactions are van der Waals forces. Consequently, in aromatic molecules with ring systems, these forces are quite important. However, they are quite difficult to calculate accurately."

The benzene dimer is the model system for studying van der Waals forces between molecules, particularly between larger molecules such as proteins because many have side chains containing aromatic groups. Benzene is a molecule in the shape of a hexagonal ring. The dimer – made up of two benzene molecules – does occur in the gas phase if the pressure and temperature are just above the point where it becomes a liquid, but the usual way to study it is in molecular beams, which was done for the first time in 1975. Since then many groups have taken spectra of benzene dimers in molecular beams. However, a number of the features of the spectra produced were not understood.

Attempts to better understand the structure and dynamics of the relationship between the two molecules of the benzene dimer were thwarted by four spectral peaks. No-one has been able to decipher the relationship between the patterns observed in the spectra and the dynamics of the dimer for 20 years.

"On the one hand there were better and better calculations of the interactions between benzene dimers, and on the other there was a lot of spectroscopic data, but a connection could not be made between the two," related Professor van der Avoird.

"Two years ago some colleagues and I did calculations which could, in principle, make the connection between the spectroscopic data and the advanced calculations for van der Waals forces between benzene molecules. As it turned out, we couldn’t make the link at that time. Now I have developed a new model – actually a limited version of the old model – which means that the link can be made."

In combination with the adapted model, the chemists used experimental data gathered in Berlin. The relative position and orientation of two molecules can be specified with six coordinates, and calculations have to be made that can handle motion in all six coordinates quantum mechanically, by rather advanced methods.

"That was possible a few years ago, but the accuracy of the final result was not sufficient that we could make a comparison with the low-frequency spectra. I designed a new model that includes two of the six dimensions, but much more accurately, and a coupling between those two. With that, I could calculate practically the spectra they had been measuring and we could quantitatively compare what was measured and what was calculated."

By restricting the model from six dimensions to two it was able to do the calculations much more precisely, both because it was easier to handle on a computer and because it enabled better converged calculations. The rings rotate in synchronisation, switching rapidly between multiple energy minima. The quantum tunnelling effect which is generated, Professor van der Avoird’s calculations show, is responsible for the distinctive pattern of spectral peaks that have proven so difficult to explain. Now that an explanation has been found, it is bound to have implications for biochemistry and related disciplines.

"Benzene groups – and other kinds of aromatic groups – occur in protein side chains," said Professor van der Avoird. "In some, but not all, amino acids in naturally occurring proteins there are aromatic side chains. In DNA, of course, the base pairs are aromatic molecules and are stacked on top of each other. Researchers interested in protein folding, for example, want to be able to predict how a protein folds from its chemical formula."

The way that proteins are able to fold depends on how the aromatic molecules they contain can stack and interact. Benzene rings can lay one atop the other in the ‘stack’ form, or they can be arranged edge-to-face in a perpendicular fashion (as illustrated by the image above). These are both stable structures for the benzene dimer.

"Both structures occur in nature, and it depends very much on which is more stable for a given system," elucidated Professor van der Avoird. "This appears to determine how proteins fold and how molecules such as DNA interact. It’s been known for a few years that the perpendicular form of the benzene dimer is very slightly more stable than the parallel form, by three per cent or so."

The results will certainly find applications in the large scale simulations used to develop new drugs and locate new drug targets, for example, where an understanding of the van der Waals interactions between receptors and drugs molecules is essential.

COMMENTS


(NOT DISPLAYED)




YOUR COMMENT WILL BE APPROVED BY A MODERATOR
HTML CODE IS NOT PERMITTED.
Add comment
RELATED CONTENT
It's not just the danger of something going wrong at the plant itself. What about nuclear waste? Only recently barrels of radioactive waste have been found dumped in the English Channel. And a greater target for terrorist attacks is a nuclear plant.

Governments need to stop pandering to the energy demand. We need to reduce our consumption. Even if energy is green the waste product is still heat, so we'll always be contributing to global warming.


Commented Julius on
How I learned to stop worrying and love nuclear power

publicservice.co.uk Ltd, Ebenezer House, Ryecroft, Newcastle-under-Lyme, Staffordshire ST5 2UB
Tel: +44 (0)1782 630200, Fax: +44 (0)1782 625533, www.publicservice.co.uk
Registered in England and Wales  Co. Reg No. 4521155   Vat Reg No. 902 1814 62