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The intermediates in a chemical reaction photographed 'red-handed'

May 03, 2016

One of the long-standing goals being pursued by chemists has been to succeed in following and directly visualising how the structures of molecules change when they undergo complex chemical transformations. Reaction intermediates, which are highly unstable substances that form in different steps in a reaction before the products are obtained, are particularly difficult to identify and characterise owing to their short lifetimes. Getting to know the structure of these intermediate species may be very helpful in understanding the reaction mechanisms and, what is more, could have a great impact on the chemical industry, materials science, nanotechnology, biology and medicine.

A leading international team of researchers led by Felix R. Fischer and Michael F. Crommie (University of California at Berkeley and the Lawrence Berkeley National Laboratory), and by Angel Rubio (Professor at the UPV/EHU-University of the Basque Country and leader of the UPV/EHU's Nano-Bio Spectroscopy Research Group, and Director of the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg) has imaged and resolved the bond configuration of the reactants, the intermediates and final products of a complex, organic reaction at the single-molecule level. The prestigious journal Nature Chemistry has published this research in its latest issue.

The team has obtained the images of the chemical structures associated with different steps in the reaction cascade involving multiple steps of enediyne molecules on a silver surface, using non-contact atomic force microscopy (nc-AFM) with a particularly sensitive tip: it uses a very fine needle that can detect the smallest bumps on an atomic scale (in a way not unlike reading in Braille) as it absorbs a carbon monoxide molecule that acts like a "finger" on the text to increase its resolution.

The precise identification of the bond configuration of the intermediate species "has made it possible to determine the intricate sequence of chemical transformations along the reaction mechanism from reactants via intermediates to end products," explained Ángel Rubio, the UPV/EHU professor, "and at the same time unravel the microscopic mechanisms behind that intricate dynamical behaviour".

Stabilizing the intermediates

By combining the latest advances in numerical calculus and the classical analytical models that describe the kinetics of sequential chemical reactions, an area that explores the speed of the reactions and the molecular events taking place in it has been proven. So to explain the stabilization of the intermediates, it is not enough just to consider their potential energy, it is essential to bear in mind the energy dissipation and the changes in molecular entropy, which measures how far a system is organised. The surface, and in particular the interaction of the extremely unstable intermediates with the surface, play a key role for both the entropy and the dissipation of energy, which highlights a fundamental difference between the surface-supported reactions and gas-phase or solution chemistry.

Such detailed understanding achieved though the synergy between the imaging of the chemical reactions of a molecule and the latest advances in computer modelling "constitutes a fundamental milestone in the analysis of chemical reactions," he specified. In fact, as he went on to highlight, with all this "many of the limitations in conventional spectroscopic techniques have been surpassed and an unprecedented image has been obtained on an atomic scale of the reaction mechanisms, driving forces and kinetics". According to Rubio, all this new knowledge may open up countless hitherto unexplored fields: future designs and optimizations of heterogeneous catalytic systems, development of novel synthetic tools applied to carbon-based nanotechnology, as well as biochemical and materials science applications.
Additional information

The research was carried out by the research groups led by Felix R. Fischer and Michael F. Crommie (University of California at Berkeley and Lawrence Berkeley National Laboratory), and by Angel Rubio (Professor at the UPV/EHU, leader of the UPV/EHU's Nano-Bio Spectroscopy Research Group, and Director of the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg). It should be pointed out that the calculations were made by Dr Alejandro Pérez, the post-doctoral researcher in the UPV/EHU's Nano-bio Spectroscopy Research Group, and that the Ikerbasque Research Professors Dimas G. Oteyza (DIPC) and Miguel Moreno Ugeda (CIC Nanogune) played a significant role in the experiments conducted at Berkeley when he was there.

The activity of the Nano-bio Spectroscopy Research Group, led by the UPV/EHU professor Ángel Rubio and which is attached to the Department of Materials Sciences, focusses on the theoretical research and modelling of electronic and structural properties of condensed matter as well as the development of new theoretical tools and computer codes to explore the electronic response of solids and nanostructures when handling external electromagnetic fields.

Bibliographical reference

A. Riss, A. Pérez-Paz, S. Wickenburg, H.-Z. Tsai, D. G. de Oteyza, A. J. Bradley, M. M. Ugeda, P. Gorman, H. S. Jung, M. F. Crommie, A. Rubio & F. R. Fischer. "Imaging Single-Molecule Reaction Intermediates Stabilized by Surface Dissipation and Entropy". Nature Chemistry. 2016. DOI: 10.1038/nchem.2506

University of the Basque Country

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