Author:

Abstract:

In semiconductor manufacturing of 3-D nano-transistors, modified kinetics have been encountered for the aqueous chemical etching of thin films in 1-D and 2-D nano-confined volumes, either delayed or accelerated [1,2]. Deviations from kinetics observed on planar substrates were attributed to the overlap of electrostatic double layers (EDL) on opposite walls and the consequent depletion or enrichment of reactive ions in the nano-space. These explanations stem from studies on nanofluidic systems, where however electrostatic effects cannot explain all observations [3]. The study of the mechanisms in play in the etching of thin films is hampered by the complexity of the reaction schemes. On the other hand, biorthogonal click chemistry provides kinetically simple reactions in aqueous solutions, which are also being used in the binding of biological molecules such as DNA to the active surface of biosensors. In this last purpose, the surface is covered with a SAM ending with one of the reactants. Reactions at the surface of highly organized monomolecular layers, such as SAMs, are typically retarded compared to those in solution [4]. In nanofluidic devices, kinetics will be affected by both the confinement in the SAM and in the nano-channels. We studied the cycloaddition of dibenzylcyclooctyne-PEG3-alcohol (DBCO) to a linear azide-terminated SAM in ultra-pure water, a second order strain-promoted azide-alkyne click chemistry reaction with no side reaction when performed in solution. Kinetics were monitored in-situ using ATR-FTIR. For this purpose, double-side polished silicon wafers without and with 320nm deep nanochannels of varying width (32-64nm) were cleaved and polished to make ATR crystals that were mounted in a flow cell [5]. The cycloaddition in presence of an excess DBCO could be described as a pseudo-first-order reaction in all cases, in agreement with literature on similar reactions in solution [6,7]. However, the rate constant for the reaction with the SAM was higher by about 3 orders of magnitude compared to those of similar reactions in solution [6,7]. The interactions of the rather hydrophobic SAM surface (water contact angle of 84°) with the hydrophobic head of the DBCO molecule, together with the orientation of the azide groups at the surface of the SAM were likely responsible for the faster reaction with the DBCO molecule. On the other hand, the rate constant for the SAM in the nanochannels was about 4 times smaller than that for the planar surface. Here an explanation was sought in the overlap of the EDLs of the polarized SAM surfaces and its influence on the orientation of the polar-tailed DBCO molecule inside the channels. In support of this interpretation, changes in electrical potential inside the channels were probed using pH measurements with fluorescein, as described in [8].