Observing the intricate chemical transformation of an individual molecule as it undergoes a complex reaction is a long-standing challenge in molecular imaging. Advances in scanning probe microscopy now provide the tools to visualize not only the frontier orbitals of chemical reaction partners and products, but their internal covalent bond configurations as well. We used noncontact atomic force microscopy to investigate reaction-induced changes in the detailed internal bond structure of individual oligo-(phenylene-1,2- ethynylenes) on a (100) oriented silver surface as they underwent a series of cyclization processes. Our images reveal the complex surface reaction mechanisms underlying thermally induced cyclization cascades of enediynes. Calculations using ab initio density functional theory provide additional support for the proposed reaction pathways.

Supported by the Office of Naval Research BRC Program (molecular synthesis, characterization, and STM imaging); the Helios Solar Energy Research Center supported by the Office of Science, Office of Basic Energy Sciences, U.S. Department of Energy under contract DE-AC02-05CH11231 (STM and nc-AFM instrumentation development, AFM operation); NSF grant DMR-1206512 (image analysis); and European Research Council advanced grant DYNamo ERC-2010-AdG-267374 (ab initio calculations). Computing time was provided by the Barcelona Supercomputing Center “Red Española de Supercomputacion.” D.G.d.O. acknowledges fellowship support by the European Union under FP7-PEOPLE-2010-IOF-271909, A.R. by Austrian Science Fund (FWF) grant J3026-N16, and D.J.M. by the Spanish “Juan de la Cierva” program ( JCI-2010-08156).

Peer Reviewed