Formation Mechanisms of Covalent Nanostructures from Density Functional Theory
In this chapter, it is demonstrated how electronic structure calculations, with focus on density functional theory, can be used to gain insight about on-surface reactions. I first give a brief introduction to how density functional theory can be used to study reactions. The focus is then shifted to two different types of on-surface reactions, highlighting the theoretical work that has been performed to gain detailed atomistic insight into them. First, the state of the art of the theory behind on-surface Ullmann coupling is described. In this reaction, molecular building blocks dehalogenate, which enables them to covalently couple. The most crucial reaction parameters are identified—the diffusion and coupling barriers of surface-supported radicals—and the potential for theory to optimize these is discussed. We then concentrate on the homo-coupling between terminal alkynes, a rudimentarily different process where molecules initially couple before undergoing a dehydrogenation step. The theory of the mechanism behind this coupling strategy is less developed than that of the on-surface Ullmann coupling, where fundamental questions remain to be unraveled. For example, by the subtle change of substrate from Ag to Au, the on-surface alkyne chemistry is completely altered from the homo-coupling to a cyclodehydrogenation reaction for the same molecular building block, of which origin remains unknown. The main objective of the chapter is to give an impression of what kind of information theory can obtain about reaction on surface, as well as to motivate and inspire for future theoretical studies, which will be needed to turn on-surface synthesis into a more predictive discipline.
KeywordsDensity Functional Theory Reaction Path Reaction Energy Transition State Theory Terminal Alkyne
Without the close collaboration with experimental partners, much of the presented work would not have been possible. In particular, Dr. Yi-Qi Zhang, Dr. habil. Florian Klappenberger, and Prof. Johannes Barth at Technische Universität München are acknowledged for their groundbreaking experiments on the homo-coupling of terminal alkynes. Furthermore, I am grateful to Prof. Sven Stafström at Linköping University for encouraging me to follow this exciting line of research.
- 1.Bieri, M., Treier, M., Cai, J., Aït-Mansour, K., Ruffieux, P., Gröning, O., Gröning, P., Kastler, M., Rieger, R., Feng, X., Müllen, K., Fasel, R.: Porous graphenes: two-dimensional polymer synthesis with atomic precision. Chem. Commun., 6919–6921 (2009)Google Scholar
- 2.Bieri, M., Nguyen, M.-T., Gröning, O., Cai, J., Treier, M., Aït-Mansour, K., Ruffieux, P., Pignedoli, C.A., Passerone, D., Kastler, M., Müllen, K., Fasel, R.: Two-dimensional polymer formation on surfaces: insight into the roles of precursor mobility and reactivity. J. Am. Chem. Soc. 132, 16669–16676 (2010)Google Scholar
- 7.Bürker, C., Ferri, N., Tkatchenko, A., Gerlach, A., Niederhausen, J., Hosokai, T., Duhm, S., Zegenhagen, J., Koch, N., Schreiber, F.: Exploring the bonding of large hydrocarbons on noble metals: diindoperylene on Cu(111), Ag (111), and Au (111). Phys. Rev. B 87, 165443–165447 (2013)CrossRefGoogle Scholar
- 11.Di Giovannantonio, M., El Garah, M., Lipton-Duffin, J., Meunier, V., Cardenas, L., Fagot Revurat, Y., Cossaro, A., Verdini, A., Perepichka, D.F., Rosei, F., Contini, G.: Insight into organometallic intermediate and its evolution to covalent bonding in surface-confined Ullmann polymerization. ACS Nano 7, 8190–8198 (2013)CrossRefGoogle Scholar
- 33.Zhang, Y.-Q., Kepčija, N., Kleinschrodt, M., Diller, K., Fischer, S., Papageorgiou, A.C., Allegretti, F., Björk, J., Klyatskaya, S., Klappenberger, F., Ruben, M., Barth, J.V.: Homo-coupling of terminal alkynes on a noble metal surface. Nat. Commun. 3, 1286 (2012)Google Scholar