Dedicated with best wishes to Prof. Edgar Heilbronner on the occasion of his 80th birthdayThe photochemistry of several 2-(2-nitrophenyl)ethyl-caged compounds including caged thymidine nucleosides was studied by nanosecond laser flash photolysis and stationary illumination experiments with quantitative HPLC analysis for quantum yields and product distribution. Effects of solvent basicity and acidity were investigated by varying the H 2 O content and HCl concentration, respectively, in MeCN/H 2 O mixtures. For all compounds 1 ± 7 investigated, intramolecular H abstraction by the nitro group from the exocyclic a-position with respect to the aryl moiety was found to be the primary process. The protolytic dissociation equilibrium of the resulting aci-nitro compound was kinetically characterized in the 0.1 ± 10 ms time region. In general, two reaction channels compete for the aci-nitro compound and its anion: b-elimination of the caged compound occurs from the anion, while from the undissociated aci-nitro compound, a nitrosobenzene derivative is formed with no release of the caged compound. The yield ratio of these two reaction channels can be controlled through shifts in the protolytic dissociation equilibrium of the aci-nitro compound. In solutions with either low basicity (H 2 O-free MeCN) or high acidity (higher concentration of HCl in H 2 O/MeCN), two as yet unidentified products are formed, each one specifically for one of the mentioned conditions. Introduction. ± Photolabile protecting groups play an important role in synthetic organic chemistry [1], for caging of biologically active molecules [2], and for lightdirected, combinatorial solid-phase syntheses of biopolymers [3]. A particularly attractive application is the generation of so-called high-density DNA chips [4] [5] which are needed in various types to perform the sequencing by hybridisation (SBH) method for oligonucleotide and gene sequencing [6]. The o-nitrobenzyl (oNB) type of protecting groups has been commonly used since 1901 when the photoreaction was discovered [7], and its reaction mechanism has been investigated in detail [8]. So far, the [(a-methyl-2-nitropiperonyl)oxy]carbonyl ([1-(6-nitro-1,3-benzodioxol-5-yl)-ethoxy]carbonyl; MeNPOC) group has been the preferred choice in DNA-chip production [4].The photochemical cleavage mechanism of the (o-nitrobenzyl)oxy function is triggered by the abstraction of a benzylic H-atom by the excited nitro group [9]. Recently, a new type of photolabile protecting group was developed on the basis of the [2-(2-nitrophenyl)ethoxy]carbonyl functionality [10] [11] which is cleaved by a lightinduced b-elimination process with formation of o-nitrostyrene, CO 2 , and the corresponding alcohol. It was suggested [10] that, in analogy to the o-nitrobenzyl groups, the cleavage of the [2-(2-nitrophenyl)ethoxy]carbonyl moiety, too, should start with the formation of an aci-nitro intermediate, through H abstraction by the nitro group at the exocyclic a-position with respect to the aryl moiety. Based on results from laser f...
Conditions and kinetics of triplet sensitization as a method for increasing the light sensitivity of photolabile protecting groups used for the photolithographic synthesis of oligonucleotide microarrays were quantitatively studied with the photolabile 2-(2-nitrophenyl)propyl protecting group in homogeneous solutions and on glass substrates by using laser flash photolysis, continuous illumination with HPLC analysis, fluorescence dye labelling, and hybridization. In terms of efficiency and avoidance of chemical side reactions, 9H-thioxanthen-9-one was the most-suitable sensitizer. Both in solution and on a glass substrate, the photostationary kinetics were quantitatively modelled and the relevant kinetic parameters determined. While the sensitization kinetics was diffusion-controlled both in solution and on the chip, the photostationary kinetics was essentially of zero order only on the chip because here the triplet-quenching effect of the released photoproduct 2-(2-nitrophenyl)propene was suppressed as a consequence of the inhomogeneous reaction that took place in a narrow diffusion zone above the surface from where the photoproducts could quickly escape. The kinetic simulation allowed quantitative estimate of the density of reactive groups on the surface. It was further demonstrated that, with 9H-thioxanthen-9-one as a sensitizer, high-density oligonucleotide microarrays of high quality can be produced with one-third of the normal exposure time.
The influence of ionic strength variation and of exciplex formation between silver ions and triplet excited RuL
Light-induced release of photolabile protecting groups is a key step in the photolithographic in-situ synthesis of oligonucleotides in the production of high-density DNA-chips. [1,2] Protecting groups of the o-nitrophenyl type that are preferentially used for this purpose have rather low absorption coefficients at 366 nm, the wavelength of the most conveniently used mercury line. The weak absorptivity of these compounds leads to principal limitations of their light sensitivity. Since they have photoreactive triplet states, however, this problem can be overcome by introducing a triplet sensitizer that efficiently absorbs the light and transfers the electronic energy to the reactive protecting group.The sensitized photodeprotection was studied in detail for the o-nitrophenyl-2-propoxycarbonyl (NPPOC) group [3] where the photo cleavage occurs via b-elimination of the corresponding nitrostyrene derivative as shown in the scheme. The first step of this reaction is photochemically initiated intramolecular H-atom transfer from the a-position to the nitro group whereby an aci-nitro compound is formed [3] . Protolytic dissociation of the aci-nitro compound is followed by the b-elimination from the aci-nitro anion. As an example of the time-resolved
Light-induced release of photolabile protecting groups is a key step in the photolithographic in-situ synthesis of oligonucleotides in the production of high-density DNA-chips. [1,2] Protecting groups of the o-nitrophenyl type that are preferentially used for this purpose have rather low absorption coefficients at 366 nm, the wavelength of the most conveniently used mercury line. The weak absorptivity of these compounds leads to principal limitations of their light sensitivity. Since they have photoreactive triplet states, however, this problem can be overcome by introducing a triplet sensitizer that efficiently absorbs the light and transfers the electronic energy to the reactive protecting group.The sensitized photodeprotection was studied in detail for the o-nitrophenyl-2-propoxycarbonyl (NPPOC) group [3] where the photo cleavage occurs via b-elimination of the corresponding nitrostyrene derivative as shown in the scheme. The first step of this reaction is photochemically initiated intramolecular H-atom transfer from the a-position to the nitro group whereby an aci-nitro compound is formed [3] . Protolytic dissociation of the aci-nitro compound is followed by the b-elimination from the aci-nitro anion. As an example of the time-resolved
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