Tomáš Šolomek

Photoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and Efficacy

The review covers the knowledge on photoremovable protecting groups and includes all relevant chromophores studied in the time period of 2000–2012; the most relevant earlier works are also discussed.

Fluorescein analogue xanthene-9-carboxylic acid: a transition-metal-free CO releasing molecule activated by green light.

6-Hydroxy-3-oxo-3H-xanthene-9-carboxylic acid is introduced as the first transition-metal-free carbon monoxide releasing molecule activated by visible light (photoCORM). This water-soluble fluorescein analogue releases carbon monoxide in both water and methanol upon irradiation at 500 nm. When selectively irradiated in the presence of hemoglobin (Hb) under physiological conditions, released CO is quantitatively trapped to form carboxyhemoglobin (COHb). The reaction progress can be accurately monitored by characteristic absorption and emission properties of the reactants and products.

The Pyrolysis of Isoxazole Revisited: A New Primary Product and the Pivotal Role of the Vinylnitrene. A Low-Temperature Matrix Isolation and Computational Study

This paper describes the pyrolysis of parent isoxazole and of its 5-methyl and 3,5-dimethyl derivatives by the high-pressure pulsed pyrolysis method, where activation of the precursor molecules occurs predominantly by collisions with the host gas (Ar in our case), rather than with the walls of the pyrolysis tube, where catalyzed processes may occur. The products were trapped at 15 K in Ar matrices and were characterized by vibrational spectroscopy. Thereby, hitherto unobserved primary products of pyrolysis of isoxazole and of its 5-methyl derivative, 3-hydroxypropenenitrile or 3-hydroxybutenenitrile, respectively, were observed. E-Z photoisomerization could be induced in the above hydroxynitriles. On pyrolysis of isoxazole, ketenimine and CO were observed as decomposition products, but this process did not occur when the 5-methyl derivative was pyrolyzed. Instead, the corresponding ketonitrile was formed. In the case of 3,5-dimethylisoxazole, 2-acetyl-3-methyl-2H-azirine was detected at moderate pyrolysis temperatures, whereas at higher temperatures, 2,5-dimethyloxazole was the only observed rearrangement product (next to products of dissociation). These findings are rationalized on the basis of quantum chemical calculations. Thereby it becomes evident that carbonyl-vinylnitrenes play a pivotal role in the observed rearrangements, a role that had not been recognized in previous theoretical studies because it had been assumed that vinylnitrenes are closed-shell singlet species, whereas they are in fact open-shell singlet biradicaloids. Thus, the primary processes had to be modeled by the multiconfigurational CASSCF method, followed by single-point MR-CISD calculations. The picture that emerges from these calculations is in excellent accord with the experimental findings; that is, they explain why some possible products are observed while others are not.

Small-Molecule Fluorophores with Large Stokes Shifts: 9-Iminopyronin Analogues as Clickable Tags

The design, synthesis, and both experimental and theoretical studies of several novel 9-(acylimino)- and 9-(sulfonylimino)pyronin derivatives containing either an oxygen or a silicon atom at position 10 are reported. These compounds, especially the Si analogues, exhibit remarkably large Stokes shifts (around 200 nm) while still possessing a high fluorophore brightness, absorption bands in the near-UV and visible part of the spectrum, and high thermal and photochemical stabilities in protic solvents. The reason for the observed large Stokes shifts is an intramolecular charge-transfer excitation of an electron from the HOMO to the LUMO of the chromophore, accompanied by elongation of the C9-N bond and considerable solvent reorganization due to hydrogen bonding to the solvent. Due to the photophysical properties of the studied compounds and their facile and high-yielding synthesis, as well as a simple protocol for their bioorthogonal ligation to a model saccharide using a Huisgen alkyne-azide cycloaddition, they represent excellent candidates for biochemical and biological applications as fluorescent tags and indicators for multichannel imaging. 9-(Acylimino)pyronins alter their optical properties upon protonation and may also be used as pH sensors.

Searching for Improved Photoreleasing Abilities of Organic Molecules

Photoremovable protecting groups (PPGs) are chemical auxiliaries that provide spatial and temporal control over the release of various molecules: bioagents (neurotransmitters and cell-signaling molecules, Ca(2+) ions), acids, bases, oxidants, insecticides, pheromones, fragrances, etc. A major challenge for the improvement of PPGs lies in the development of organic chromophores that release the desired bioagents upon continuous irradiation at wavelengths above 650 nm, that is, in the tissue-transparent window. Understanding of the photorelease reaction mechanisms, investigated by laser flash photolysis and rationalized with the aid of quantum chemical calculations, allows for achieving this goal. In particular, simple Hückel calculations provide useful guidelines for designing new PPGs, because both the lowest excited singlet and triplet states of conjugated systems can be reasonably well described by a single electronic configuration formed by promotion of a single electron from the highest occupied molecular orbital (HOMO) to the lowest unoccupied MO (LUMO) of the ground state configuration. Here we show that Hückel calculations permit rapid identification of common features in the nodal properties of the frontier orbitals of various chromophores that can be classified into distinct chromophore families. If the electronic excitation involves a substantial electron density transfer to an sp(2) carbon atom at which HOMO and LUMO are nearly disjoint, for example, by virtue of symmetry, favorable photoheterolysis can be expected when the corresponding atom carries a leaving group at the α-position. We show examples of photoheterolytic reactions that indicate that the efficiency of photoheterolysis diminishes for chromophores absorbing in the NIR region. We provide a rationale for more efficient photoheterolytic reactions occurring via the triplet state, and we demonstrate the advantages of this mechanistic pathway. Analogies in the structure-reactivity relationships of PPGs can therefore lead to new strategies for the development of more efficient NIR-absorbing photoremovable protecting groups.

Photoenolization-Induced Oxirane Ring Opening in 2,5-Dimethylbenzoyl Oxiranes To Form Pharmaceutically Promising Indanone Derivatives

Irradiation of 2,5-dimethylbenzoyl oxiranes results in a relatively efficient and high-yielding formation of β-hydroxy functionalized indanones that structurally resemble biologically active pterosines. Nanosecond laser flash photolysis and quantum-chemical calculations based on density functional theory provided evidence that this photochemical transformation proceeds primarily via a photoenolization mechanism. Our study revealed considerable complexity of the mechanism and that structural modifications can significantly alter the reaction pathway and yield different products. The scope of this photochemical transformation for the synthesis of some pharmaceutically important compounds was investigated.

Orthogonal Photocleavage of a Monochromophoric Linker

The 4-acetyl-2-nitrobenzyl moiety, substituted in both benzylic and phenacyl positions with leaving groups, has been proposed as a monochromophoric photocleavable linker. The attached groups can be disconnected selectively and orthogonally upon irradiation.

Photochemistry of S-Phenacyl Xanthates

Various synthetically readily accessible S-phenacyl xanthates are shown to undergo photoinitiated homolytic scission of the C-S bond in the primary step. The resultant fragments, phenacyl and xanthic acid radicals, recombine to form symmetrical 1,4-diketones and xanthogen disulfides, respectively, in high to moderate chemical yields in chemically inert solvents. They can also be efficiently trapped by a hydrogen-atom-donating solvent to give acetophenone and xanthic acid derivatives. The latter compound is in situ thermally converted to the corresponding alcohol in high chemical yields. S-Phenacyl xanthates could thus be utilized as synthetic precursors to the above-mentioned compounds or as photoremovable protecting groups for alcohols in which the xanthate moiety represents a photolabile linker. The photochemically released phenacyl radical fragments efficiently but reversibly add to the thiocarbonyl group of the parent xanthate molecule. The kinetics of this degenerative reversible addition-fragmentation transfer (RAFT)/macromolecular design via the interchange of xanthates (MADIX) mechanism was studied using laser flash photolysis (LFP) and density functional theory (DFT) calculations. The rate constants of the RAFT addition step, k(add) ∼ 7 × 10(8) M(-1) s(-1), and phenacyl radical addition to a double bond of 1,1-diphenylethylene, k(add) ∼ 10(8) M(-1) s(-1), in acetonitrile were experimentally determined by LFP. In addition, photoinitiation of the methyl methacrylate polymerization by S-phenacyl xanthate is demonstrated. The polydispersity index of the resulting poly(methyl methacrylate) was found to be ∼1.4. We conclude that S-phenacyl xanthates can serve simultaneously as photoinitiators as well as RAFT/MADIX agents in polymerization reactions.

Photochemistry of 2-nitrobenzylidene acetals.

Photolysis of dihydroxy compounds (diols) protected as 2-nitrobenzylidene acetals (ONBA) and subsequent acid- or base-catalyzed hydrolysis of the 2-nitrosobenzoic acid ester intermediates result in an efficient and high-yielding release of the substrates. We investigated the scope and limitations of ONBA photochemistry and expanded upon earlier described two-step procedures to show that the protected diols of many structural varieties can also be liberated in a one-pot procedure. In view of the fact that the acetals of nonsymmetrically substituted diols are converted into one of the corresponding 2-nitrosobenzoic acid ester isomers with moderate to high regioselectivity, the mechanism of their formation was studied using various experimental techniques. The experimental data were found to be in agreement with DFT-based quantum chemical calculations that showed the preferential cleavage occurs on the acetal C-O bond in the vicinity of more electron-withdrawing (or less electron-donating) groups. The study also revealed considerable complexity in the cleavage mechanism and that the structural variations in the substrate can significantly alter the reaction pathway. This deprotection strategy was found to be also applicable for 2-thioethanol when released from the corresponding monothioacetal in the presence of a reducing agent, such as ascorbic acid.

Adiabatic triplet state tautomerization of p-hydroxyacetophenone in aqueous solution.

The primary photophysical processes of p-hydroxyacetophenone (HA) and the ensuing proton transfer reactions in aqueous solution were investigated by picosecond pump-probe spectroscopy and nanosecond laser flash photolysis. Previous studies have led to mutually inconsistent conclusions. The combined data allow us to rationalize the excited-state proton transfer processes of HA in terms of a comprehensive, well-established reaction scheme. Following fast and quantitative ISC to the triplet state, (3)HA*, adiabatic proton transfer through solvent water simultaneously forms both the anion, (3)A(-)*, and the quinoid triplet enol tautomer, (3)Q*. The latter subsequently equilibrates with its anion (3)A(-)*. Ionization and tautomerization are likely to compete with the desired release reactions of p-hydroxyphenacyl photoremovable protecting groups.