Alkyne-Functionalized Cyclooctyne on Si(001): Reactivity Studies and Surface Bonding from an Energy Decomposition Analysis Perspective

Abstract

The reactivity and bonding of an ethinyl-functionalized cyclooctyne on Si(001) is studied by means of density functional theory. This system is promising for the organic functionalization of semiconductors. Singly bonded adsorption structures are obtained by [2 + 2] cycloaddition reactions of the cyclooctyne or ethinyl group with the Si(001) surface. A thermodynamic preference for adsorption with the cyclooctyne group in the on-top position is found and traced back to minimal structural deformation of the adsorbate and surface with the help of energy decomposition analysis for extended systems (pEDA). Starting from singly bonded structures, a plethora of reaction paths describing conformer changes and consecutive reactions with the surface are discussed. Strongly exothermic and exergonic reactions to doubly bonded structures are presented, while small reaction barriers highlight the high reactivity of the studied organic molecule on the Si(001) surface. Dynamic aspects of the competitive bonding of the functional groups are addressed by ab initio molecular dynamics calculations. Several trajectories for the doubly bonded structures are obtained in agreement with calculations using the nudged elastic band approach. However, our findings disagree with the experimental observations of selective adsorption by the cyclooctyne moiety, which is critically discussed.

An Atomistic Picture of Buildup and Degradation Reactions in Area-Selective Atomic Layer Deposition with a Small Molecule Inhibitor

“…In the pEDA, Δ E int (elec) is decomposed into three well-defined terms Δ E int false( elec false) = Δ E elstat + Δ E Pauli + Δ E orb where Δ E elstat represents the quasiclassical electrostatic energy of the fragments, Pauli term Δ E Pauli accounts for the destabilization due to the Pauli exclusion principle, and Δ E orb signifies the energy gain through charge transfer and polarization due to relaxation of the wave function in the final step of the analysis. For a detailed derivation and discussion of the terms, see ref .…”