This paper describes a simple strategy for DNA immobilization on chemically modified and patterned silicon surfaces. The photochemical modification of hydrogen-terminated Si(111) with undecylenic acid leads to the formation of an organic monolayer covalently attached to the surface through Si-C bonds without detectable reaction of the carboxylic acid group, providing indirect support of a free radical mechanism. Chemical activation of the acid function was achieved by a simple chemical route using N-hydroxysuccinimide (NHS) in the presence of N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide hydrochloride. Single strand DNA with a 5'-dodecylamine group was then coupled to the NHS-activated surface by amide bond formation. Using a previously reported chemical patterning approach, we have shown that DNA can be immobilized on silicon surfaces in spatially well-resolved domains. Methoxytetraethyleneglycolamine was used to inhibit nonspecific adsorption. The resulting DNA-modified surfaces have shown good specificity and chemical and thermal stability under hybridization conditions. The sequential reactions on the surface were monitored by ATR-FTIR, X-ray Photoelectron Spectroscopy, and fluorescence spectroscopy.

The thermal reaction of undecylenic acid with a hydrogen-terminated porous silicon surface takes place at 95°C to yield an organic monolayer covalently attached to the surface through Si-C bonds. The acid terminal group remains intact and is not affected by the chemical process. Under the same conditions, alcohols break the Si-Si back bonds of the PSi matrix. In contrast, the acid function does not react with either the Si-H or the Si-Si bonds of the PSi surface and the reaction takes place at the terminal CvC double bond of the molecule. When the reaction was carried out with decanoic acid, under the same conditions, the reaction was not complete. The functionalized surfaces were characterized using transmission infrared and X-ray photoelectron spectroscopies. The effect of the chemical process on the photoluminescence has been studied, and the stability against corrosion in 100% humidity was verified using chemography. We have demonstrated that the derivatized surface with undecylenic acid can be activated by a simple chemical route using N-hydroxysuccimide in the presence of N-ethyl-NЈ-͑3-dimethylaminopropyl͒ carbodiimide hydrochloride.

The thermal and photochemical processes associated with the acid-induced conversions of 6-nitroBIPS, SP-1, to form the protonated merocyanine (MC-OH+) were investigated via UV/vis spectrophotometric studies in acetone. It was found that the mechanism of trifluoroacetic acid (TFA)-induced ring-opening of the SP and the rate of MC-OH+ formation follows a general acid catalysis mechanism. In accord with this mechanism, the thermal growth of the acid-induced ring-opened form (MC-OH+) was retarded as the concentration of TFA in the medium was increased. The N-protonated SP, i.e., SP-NH+, is formed in a competing side-equilibrium process as an unreactive "sink", with the nitrogen lone-pair no longer available to drive the ring-opening process and resulting in the inverse rate dependence as a linear 1/kobs vs [HA] plot. Addition of a tertiary amine to MC-OH+ regenerated MC which underwent thermal ring closure to the SP, thus restoring its function as a molecular switch. NMR titration of SP samples showed a downfield shift of the N-substituent peak upon increasing the TFA concentration. However, a saturation behavior could not be observed with SP-1 up to 1 M acid, unlike the model compound, N,N-dimethylaniline (N,N-DMA), which indicates a base strength order of N,N-DMA > SP-1. Further, we have demonstrated that in solvent acetone, on acidification, the normal photo- and thermochromic behavior is reversed; now MC-OH+ is photochemically transformed into SP-H+, which undergoes thermal ring-opening to MC-OH+.