Photolabile Protecting Groups for Nucleosides: Mechanistic Studies of the 2-(2-Nitrophenyl)ethyl Group

Abstract

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...

Highly Efficient Photolabile Protecting Groups with Intramolecular Energy Transfer

“…Transient absorption spectra as well as decay curves of the thioxanthone triplet were recorded. Following the change of the transient absorption spectra in time, the triplet-triplet absorption decay as well as the formation of the aci-nitro form of the NPPOC group, a known intermediate of the deprotection step of NPPOC, [10] could be detected. In N 2 -saturated solution, the thioxanthone triplet lifetimes for all bichromophoric compounds are much shorter than for unmodified thioxanthone (see Figure 2 and Table 1).…”

“…The widely used [(a-methyl-2-nitropiperonyl)oxy]carbonyl (MeNPOC) group [7] has a reasonable absorption coefficient at the wavelengths usually applied (in practice preferentially the mercury line at l = 366 nm, e MeOH,366 nm % 2500 m À1 cm À1 ), but the photochemical deprotection yield is quite small (3 % in MeOH). [8] In contrast, the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) protecting group, [9] the reaction of which is represented in Scheme 1, [10] shows a much higher quantum yield (41 % in MeOH), but has a significantly lower absorptivity (e MeOH,366 nm % 230 m À1 cm À1 ). Thus, for both MeNPOC and NPPOC fairly long irradiation times are required during which undesired photoreactions may take place.…”

Intramolecular Sensitization of Photocleavage of the Photolabile 2‐(2‐Nitrophenyl)propoxycarbonyl (NPPOC) Protecting Group: Photoproducts and Photokinetics of the Release of Nucleosides

“…As observed previously, this peak decreases at longer irradiation times due to subsequent transformations of this product. [22,25,32] The peak at t R = 20.8 min is assigned to a nitroso product that originates from the primary aci-nitro intermediate by a reaction pathway competing with b elimination (Scheme 1). [22] This pathway primarily results in formation of a nitroso product (nitroso product 1 in Scheme 1).…”

“…[22,25,32] The peak at t R = 20.8 min is assigned to a nitroso product that originates from the primary aci-nitro intermediate by a reaction pathway competing with b elimination (Scheme 1). [22] This pathway primarily results in formation of a nitroso product (nitroso product 1 in Scheme 1). As a detailed structural analysis has shown, an intramolecular rearrangement induced by the electrophilic attack of the newly formed benzylic OH group at the carbon center of the carbonate linker gives rise to nitroso product 2 (see Scheme 1).…”

“…[17] In photoremovable protecting groups involving the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) group, which was introduced by Pfleiderer and co-workers, [18][19][20] cleavage is due to b elimination, and formation of the reactive and problematic nitroso byproduct [21] can be suppressed by using suitable reaction conditions (Scheme 1). [22] This is probably the reason why chips of higher quality result when using the NPPOC group. [23,24] At 366 nm, the most commonly used mercury line for irradiation, the light sensitivities ef of MeNPOC (e 366nm,MeOH = 3000 m À1 cm…”