Carboxy-terminated crystalline silicon surfaces are of fundamental importance for biochip fabrication because of their reactivity toward biological macromolecules. To explore the feasibility of direct attachment of bifunctional molecules (e.g., omega-alkenoic acids) to hydrogen-terminated silicon crystal (H-Si) via Si-C linkages, we have investigated the photoreactivities of the alkene (-CH=CH(2)) and carboxy (-COOH) terminal groups of 1-dodecene, undecanoic acid, and undecylenic acid toward H-Si. The alkene terminus was found to react substantially faster than the carboxy terminus under UV irradiation (at 350 nm). By controlling the reaction time, high-quality carboxy-terminated monolayers, comparable to those formed by ester hydrolysis, can be obtained from a direct, one-step photochemical reaction between H-Si and undecylenic acid.

Nucleic acids possess charged phosphate groups in their backbones, which require counterions to reduce the repulsive Coulombic interactions between the strands. Herein we report how different mono- and divalent metal cations influence the molecular orientations of DNA molecules on silicon surfaces upon immobilization and hybridization. Our sum frequency generation (SFG) spectroscopy studies demonstrated that the degree of conformational variation of DNA self-assembled monolayers on silicon depends on the type of metal cations present. The molecular orientation change of immobilized single-stranded oligonucleotides correlates with DNA-cation affinity (Mg(2+) > Ca(2+) > K(+) approximately Na(+)): metal cations with the strongest affinity disrupt the structure of the underlying linker monolayer the most. Upon hybridization the trend is reversed, which is attributed to the greater ability of divalent cations to mask the negative charges on the DNA backbone. These findings provide useful information for the construction of more sensitive DNA biosensors, particularly the optimization of on-chip hybridization performance.

Carboxylic acid-terminated monolayers on crystalline silicon surfaces can be readily modified with biological macromolecules for the fabrication of semiconductor-based biosensing devices. They were prepared by acidcatalyzed hydrolysis of alkoxycarbonyl (ester)-terminated monolayers and studied by vibrational sum frequency generation (SFG) spectroscopy. The C-H vibration region of the SFG spectra consists of strong methyl bands with significant contributions from methylene stretching modes, indicating that these monolayers are generally ordered but with considerable gauche defects in the alkyl chains in comparison with n-alkyl monolayers. After hydrolysis, the methylene stretching modes prevail, with "residues" of the methyl bands, indicating incomplete hydrolysis and disruption of the monolayer structure. This work demonstrates that SFG is capable of providing quantitative information on structure-reactivity correlations in organic monolayers.