Nitrogen-Centered Radicals Derived from Azidonucleosides.

Azido-modified nucleosides have been extensively explored as substrates for click chemistry and the metabolic labeling of DNA and RNA. These compounds are also of interest as precursors for further synthetic elaboration and as therapeutic agents. This review discusses the chemistry of azidonucleosides related to the generation of nitrogen-centered radicals (NCRs) from the azido groups that are selectively inserted into the nucleoside frame along with the subsequent chemistry and biological implications of NCRs. For instance, the critical role of the sulfinylimine radical generated during inhibition of ribonucleotide reductases by 2'-azido-2'-deoxy pyrimidine nucleotides as well as the NCRs generated from azidonucleosides by radiation-produced (prehydrated and aqueous) electrons are discussed. Regio and stereoselectivity of incorporation of an azido group ("radical arm") into the frame of nucleoside and selective generation of NCRs under reductive conditions, which often produce the same radical species that are observed upon ionization events due to radiation and/or other oxidative conditions that are emphasized. NCRs generated from nucleoside-modified precursors other than azidonucleosides are also discussed but only with the direct relation to the same/similar NCRs derived from azidonucleosides.

6-azido and 6-azidomethyl uracil nucleosides.

Azido nucleosides have been utilized for click reactions, metabolic incorporation into cellular DNA, and fluorescent imaging of live cells. Two classes of 6-azido modified uracil nucleosides; one with azido group directly attached to uracil ring and second with azido group attached via methylene linker are described. The 6-azido-2'-deoxyuridine (6-AdU) was prepared in 55% overall yield by lithiation-based regioselective C6-iodination of silyl protected 2'-deoxyuridine followed by treatment with sodium azide and deprotection with TBAF. Lithiation-based C6-alkylation of the protected uridine with methyl iodide followed by the oxidation of the 6-methyl product with selenium dioxide and the subsequent mesylation and azidation of the resulting 6-hydroxymethyl group gave after deprotection 6-azidomethyluridine (6-AmU) in 61% overall yield. Direct lithiation-based C6-hydroxymethylation followed by mesylation/azidation sequence and deprotection provided 6-AmU or 6-azidomethyl-2'-deoxyuridine (6-AmdU). Yields for the lithiation-based regioselective C6-iodination and alkylation were higher for uridine than 2'-deoxyuridine derivatives and they appear to be less dependent on the sugar protection group used. Strain promoted click reactions of 6-AdU and 6-AmdU with symmetrically fused cyclopropyl cyclooctyne (OCT) provided fluorescent triazoles. DFT-calculated dihedral angles and energy differences for the favored anti and syn conformation of 6-AdU and 6-AmdU versus their C5 azido counterparts are discussed.

Gas-Phase Synthesis of Coronene through Stepwise Directed Ring Annulation.

Molecular beam experiments together with electronic structure calculations provide the first evidence of a complex network of elementary gas-phase reactions culminating in the bottom-up preparation of the 24π aromatic coronene (C24H12) molecule─a representative peri-fused polycyclic aromatic hydrocarbon (PAH) central to the complex chemistry of combustion systems and circumstellar envelopes of carbon stars. The gas-phase synthesis of coronene proceeds via aryl radical-mediated ring annulations through benzo[e]pyrene (C20H12) and benzo[ghi]perylene (C22H12) involving armchair-, zigzag-, and arm-zig-edged aromatic intermediates, highlighting the chemical diversity of molecular mass growth processes to polycyclic aromatic hydrocarbons. The isomer-selective identification of five- to six-ringed aromatics culminating with the detection of coronene is accomplished through photoionization and is based upon photoionization efficiency curves along with photoion mass-selected threshold photoelectron spectra, providing a versatile concept of molecular mass growth processes via aromatic and resonantly stabilized free radical intermediates to two-dimensional carbonaceous nanostructures.

Construction of quaternary stereocenters at carbon 2' of nucleosides.

The non-natural nucleosides with a quaternary stereogenic center at C2' are crucial to drug discovery. They have become a cornerstone for the treatment of cancer and various viral infections as exemplified by gemcitabine and sofosbuvir. Major research effort has been expended to gain synthetic access to these nucleoside analogues with a significant steric bulk at C2' in the furanoside ring. The 2'-ketonucleosides and 2'-deoxy-2'-methylenenucleosides emerged as key intermediates in these synthetic strategies. For example, α-face addition of methyl lithium to the 2'-ketonucleosides followed by fluorination of resulting tertiary arabino alcohol with DAST provided 2'-fluoro-2'-C-methyluridine - a core nucleoside component of sofosbuvir. The α-face addition of HCN or HN3 to the 2'-deoxy-2'-methylene nucleosides gave access to the synthetically versatile 2'-cyano-2'-C-methyl and 2'-azido-2'-C-methyl nucleosides. Likewise, the addition of diazomethane to the 2'-exomethylene group gave access to the 2'-spirocyclopropyl analogue. This review primarily discusses synthetic strategies which employs natural nucleosides as substrates but selected approaches involving coupling of the preelaborated sugar precursors with nucleobases are also examined.

Gas phase synthesis of the C40 nano bowl C40H10.

Nanobowls represent vital molecular building blocks of end-capped nanotubes and fullerenes detected in combustion systems and in deep space such as toward the planetary nebula TC-1, but their fundamental formation mechanisms have remained elusive. By merging molecular beam experiments with electronic structure calculations, we reveal a complex chain of reactions initiated through the gas-phase preparation of benzocorannulene (C24H12) via ring annulation of the corannulenyl radical (C20H9•) by vinylacetylene (C4H4) as identified isomer-selectively in situ via photoionization efficiency curves and photoion mass-selected threshold photoelectron spectra. In silico studies provided compelling evidence that the benzannulation mechanism can be expanded to pentabenzocorannulene (C40H20) followed by successive cyclodehydrogenation to the C40 nanobowl (C40H10) - a fundamental building block of buckminsterfullerene (C60). This high-temperature pathway opens up isomer-selective routes to nanobowls via resonantly stabilized free-radical intermediates and ring annulation in circumstellar envelopes of carbon stars and planetary nebulae as their descendants eventually altering our insights of the complex chemistry of carbon in our Galaxy.

Pathways of the Dissociative Electron Attachment Observed in 5- and 6-Azidomethyluracil Nucleosides: Nitrogen (N2) Elimination vs Azide Anion (N3-) Elimination.

5-Azidomethyl-2'-deoxyuridine (5-AmdU, 1) has been successfully employed for the metabolic labeling of DNA and fluorescent imaging of live cells. 5-AmdU also demonstrated significant radiosensitization in breast cancer cells via site-specific nitrogen-centered radical (π-aminyl (U-5-CH2-NH•), 2, and σ-iminyl (U-5-CH═N•), 3) formation. This work shows that these nitrogen-centered radicals are not formed via the reduction of the azido group in 6-azidomethyluridine (6-AmU, 4). Radical assignments were performed using electron spin resonance (ESR) in supercooled solutions, pulse radiolysis in aqueous solutions, and theoretical (DFT) calculations. Radiation-produced electron addition to 4 leads to the facile N3- loss, forming a stable neutral C-centered allylic radical (U-6-CH2•, 5) through dissociative electron attachment (DEA) via the transient negative ion, TNI (U-6-CH2-N3•-), in agreement with DFT calculations. In contrast, TNI (U-5-CH2-N3•-) of 1, via facile N2 loss (DEA) and protonation from the surrounding water, forms radical 2. Subsequently, 2 undergoes rapid H-atom abstraction from 1 and produces the metastable intermediate α-azidoalkyl radical (U-5-CH•-N3). U-5-CH•-N3 converts facilely to radical 3. N3- loss from U-6-CH2-N3•- is thermodynamically controlled, whereas N2 loss from U-5-CH2-N3•- is dictated by protonation from the surrounding waters and resonance conjugation of the azidomethyl side chain at C5 with the pyrimidine ring.

Exotic Reaction Dynamics in the Gas-Phase Preparation of Anthracene (C14H10) via Spiroaromatic Radical Transients in the Indenyl-Cyclopentadienyl Radical-Radical Reaction.

The gas-phase reaction between the 1-indenyl (C9H7•) radical and the cyclopentadienyl (C5H5•) radical has been investigated for the first time using synchrotron-based mass spectrometry coupled with a pyrolytic reactor. Soft photoionization with tunable vacuum ultraviolet photons afforded for the isomer-selective identification of the production of phenanthrene, anthracene, and benzofulvalene (C14H10). The classical theory prevalent in the literature proposing that radicals combine only at their specific radical centers is challenged by our discovery of an unusual reaction pathway that involves a barrierless combination of a resonantly stabilized hydrocarbon radical with an aromatic radical at the carbon atom adjacent to the traditional C1 radical center; this unconventional addition is followed by substantial isomerization into phenanthrene and anthracene via a category of exotic spiroaromatic intermediates. This result leads to a deeper understanding of the evolution of the cosmic carbon budget and provides new methodologies for the bottom-up synthesis of unique spiroaromatics that may be relevant for the synthesis of more complex aromatic carbon skeletons in deep space.

A molecular beam and computational study on the barrierless gas phase formation of (iso)quinoline in low temperature extraterrestrial environments.

Despite remarkable progress toward the understanding of the formation pathways leading to polycyclic aromatic hydrocarbons (PAHs) in combustion systems and in deep space, the complex reaction pathways leading to nitrogen-substituted PAHs (NPAHs) at low temperatures of molecular clouds and hydrocarbon-rich, nitrogen-containing atmospheres of planets and their moons like Titan have remained largely obscure. Here, we demonstrate through laboratory experiments and computations that the simplest prototype of NPAHs - quinoline and isoquinoline (C9H7N) - can be synthesized via rapid and de-facto barrier-less reactions involving o-, m- and p-pyridinyl radicals (C5H4N˙) with vinylacetylene (C4H4) under low-temperature conditions.

Gas-phase synthesis of corannulene - a molecular building block of fullerenes.

Fullerenes (C60, C70) detected in planetary nebulae and carbonaceous chondrites have been implicated to play a key role in the astrochemical evolution of the interstellar medium. However, the formation mechanism of even their simplest molecular building block-the corannulene molecule (C20H10)-has remained elusive. Here we demonstrate via a combined molecular beams and ab initio investigation that corannulene can be synthesized in the gas phase through the reactions of 7-fluoranthenyl (C16H9˙) and benzo[ghi]fluoranthen-5-yl (C18H9˙) radicals with acetylene (C2H2) mimicking conditions in carbon-rich circumstellar envelopes. This reaction sequence reveals a reaction class in which a polycyclic aromatic hydrocarbon (PAH) radical undergoes ring expansion while simultaneously forming an out-of-plane carbon backbone central to 3D nanostructures such as buckybowls and buckyballs. These fundamental reaction mechanisms are critical in facilitating an intimate understanding of the origin and evolution of the molecular universe and, in particular, of carbon in our galaxy.

Chemical synthesis of the organoarsenical antibiotic arsinothricin.

We report two routes of chemical synthesis of arsinothricin (AST), the novel organoarsenical antibiotic. One is by condensation of the 2-chloroethyl(methyl)arsinic acid with acetamidomalonate, and the second involves reduction of the N-acetyl protected derivative of hydroxyarsinothricin (AST-OH) and subsequent methylation of a trivalent arsenic intermediate with methyl iodide. The enzyme AST N-acetyltransferase (ArsN1) was utilized to purify l-AST from racemic AST. This chemical synthesis provides a source of this novel antibiotic for future drug development.

Site of Azido Substitution in the Sugar Moiety of Azidopyrimidine Nucleosides Influences the Reactivity of Aminyl Radicals Formed by Dissociative Electron Attachment.

In this work, electron-induced site-specific formation of neutral π-type aminyl radicals (RNH·) and their reactions with pyrimidine nucleoside analogs azidolabeled at various positions in the sugar moiety, e.g., at 2'-, 3'-, 4'-, and 5'- sites along with a model compound 3-azido-1-propanol (3AZPrOH), were investigated. Electron paramagnetic resonance (EPR) studies confirmed the site and mechanism of RNH· formation via dissociative electron attachment-mediated loss of N2 and subsequent facile protonation from the solvent employing the 15N-labeled azido group, deuterations at specific sites in the sugar and base, and changing the solvent from H2O to D2O. Reactions of RNH· were investigated employing EPR by warming these samples from 77 K to ca. 170 K. RNH· at a primary carbon site (5'-azido-2',5'-dideoxyuridine, 3AZPrOH) facilely converted to a σ-type iminyl radical (R═N·) via a bimolecular H-atom abstraction forming an α-azidoalkyl radical. RNH· when at a secondary carbon site (e.g., 2'-azido-2'-deoxyuridine) underwent bimolecular electrophilic addition to the C5═C6 double bond of a proximate pyrimidine base. Finally, RNH· at tertiary alkyl carbon (4'-azidocytidine) underwent little reaction. These results show the influence of the stereochemical and electronic environment on RNH· reactivity and allow the selection of those azidonucleosides that would be most effective in augmenting cellular radiation damage.

Gas phase formation of cyclopentanaphthalene (benzindene) isomers via reactions of 5- and 6-indenyl radicals with vinylacetylene.

The tricyclic polycyclic aromatic hydrocarbons (PAHs) 3H-cyclopenta[a]naphthalene (C13H10), 1H-cyclopenta[b]naphthalene (C13H10) and 1H-cyclopenta[a]naphthalene (C13H10) along with their indene-based bicyclic isomers (E)-5-(but-1-en-3-yn-1-yl)-1H-indene, (E)-6-(but-1-en-3-yn-1-yl)-1H-indene, 5-(but-3-ene-1-yn-1-yl)-1H-in-dene, and 6-(but-3-ene-1-yn-1-yl)-1H-indene were formed via a "directed synthesis" in a high-temperature chemical micro reactor at the temperature of 1300 ± 10 K through the reactions of the 5- and 6-indenyl radicals (C9H7˙) with vinylacetylene (C4H4). The isomer distributions were probed utilizing tunable vacuum ultraviolet light by recording the photoionization efficiency curves at mass-to-charge of m/z = 166 (C13H10) and 167 (13CC12H10) of the products in a supersonic molecular beam. The underlying reaction mechanisms involve the initial formation of van-der-Waals complexes followed by addition of the 5- and 6-indenyl radicals to vinylacetylene via submerged barriers, followed by isomerization (hydrogen shifts, ring closures), and termination via atomic hydrogen elimination accompanied by aromatization. All the barriers involved in the formation of 3H-cyclopenta[a]naphthalene, 1H-cyclopenta[b]naphthalene and 1H-cyclopenta[a]naphthalene are submerged with respect to the reactants indicating that the mechanisms are in fact barrierless, potentially forming PAHs via the hydrogen abstraction - vinylacetylene addition (HAVA) pathway in the cold molecular clouds such as Taurus Molecular Cloud-1 (TMC-1) at temperatures as low as 10 K.

Semisynthesis of the Organoarsenical Antibiotic Arsinothricin.

Arsinothricin [AST (1)], a new broad-spectrum organoarsenical antibiotic, is a nonproteinogenic analogue of glutamate that effectively inhibits glutamine synthetase. We report the chemical synthesis of an intermediate in the pathway to 1, hydroxyarsinothricin [AST-OH (2)], which can be converted to 1 by enzymatic methylation catalyzed by the ArsM As(III) S-adenosylmethionine methyltransferase. This is the first report of semisynthesis of 1, providing a source of this novel antibiotic that will be required for future clinical trials.

Gas phase formation of phenalene via 10π-aromatic, resonantly stabilized free radical intermediates.

For the last few decades, the Hydrogen-Abstraction/aCetylene-Addition (HACA) mechanism has been fundamental in aiding our understanding of the source of polycyclic aromatic hydrocarbons (PAHs) in combustion processes and in circumstellar envelopes of carbon rich stars. However, the reaction mechanisms driving high temperature molecular mass growth beyond triphenylene (C18H12) along with the link between PAHs and graphene-type nanostructures as identified in carbonaceous meteorites such as in Murchison and Allende has remained elusive. By exploring the reaction of the 1-naphthyl radical (C10H7˙) with methylacetylene (CH3CCH) and allene (H2CCCH2) under conditions prevalent in carbon-rich circumstellar environments and combustion systems, we provide compelling evidence on a facile formation of 1H-phenalene (C13H10) - the central molecular building block of graphene-type nanostructures. Beyond PAHs, molecular mass growth processes from 1H-phenalene via ring-annulation through C3 molecular building blocks may ultimately lead to two-dimensional structures such as graphene nano flakes and after condensation of multiple layers to graphitized carbon. These fundamental reaction mechanisms are of crucial significance to facilitate an understanding of the origin and chemical evolution of carbon in our Galaxy.

Model Substrate/Inactivation Reactions for MoaA and Ribonucleotide Reductases: Loss of Bromo, Chloro, or Tosylate Groups from C2 of 1,5-Dideoxyhomoribofuranoses upon Generation of an α-Oxy Radical at C3.

We report studies on radical-initiated fragmentations of model 1,5-dideoxyhomoribofuranose derivatives with bromo, chloro, and tosyloxy substituents on C2. The effects of stereochemical inversion at C2 were probed with the corresponding arabino epimers. In all cases, the elimination of bromide, chloride, and tosylate anions occurred when the 3-hydroxyl group was unprotected. The isolation of deuterium-labeled furanone products established heterolytic cleavage followed by the transfer of deuterium from labeled tributylstannane. In contrast, 3-O-methyl derivatives underwent the elimination of bromine or chlorine radicals to give the 2,3-alkene with no incorporation of label in the methyl vinyl ether. More drastic fragmentation occurred with both of the 3-O-methyl-2-tosyloxy epimers to give an aromatized furan derivative with no deuterium label. Contrasting results observed with the present anhydroalditol models relative to our prior studies with analogously substituted nucleoside models have demonstrated that insights from biomimetic chemical reactions can provide illumination of mechanistic pathways employed by ribonucleotide reductases (RNRs) and the MoaA enzyme involved in the biosynthesis of molybdopterin.

Molecular mass growth through ring expansion in polycyclic aromatic hydrocarbons via radical-radical reactions.

Polycyclic aromatic hydrocarbons (PAHs) represent key molecular building blocks leading to carbonaceous nanoparticles identified in combustion systems and extraterrestrial environments. However, the understanding of their formation and growth in these high temperature environments has remained elusive. We present a mechanism through laboratory experiments and computations revealing how the prototype PAH-naphthalene-can be efficiently formed via a rapid 1-indenyl radical-methyl radical reaction. This versatile route converts five- to six-membered rings and provides a detailed view of high temperature mass growth processes that can eventually lead to graphene-type PAHs and two-dimensional nanostructures providing a radical new view about the transformations of carbon in our universe.

How to add a five-membered ring to polycyclic aromatic hydrocarbons (PAHs) - molecular mass growth of the 2-naphthyl radical (C10H7) to benzindenes (C13H10) as a case study.

The three-ring polycyclic aromatic hydrocarbons (PAHs) 3H-benz[e]indene (C13H10) and 1H-benz[f]indene (C13H10) along with their naphthalene-based isomers 2-(prop-2-yn-1-yl)naphthalene (C13H10), 2-(prop-1-yn-1-yl)naphthalene (C13H10), and 2-(propa-1,2-dien-1-yl)naphthalene (C13H10) were formed through a "directed synthesis"via a high temperature chemical micro reactor under combustion-like conditions (1300 ± 35 K) through the reactions of the 2-naphthyl isomer (C10H7˙) with allene (C3H4) and methylacetylene (C3H4). The isomer distributions were probed utilizing tunable vacuum ultraviolet radiation from the Advanced Light Source (ALS) by recording the photoionization efficiency curves at mass-to-charge of m/z = 166 (C13H10) and 167 (13CC12H10) of the products in a supersonic molecular beam. Complemented by electronic structure calculations, our study reveals critical mass growth processes via annulation of a five-membered ring from the reaction between aryl radicals and distinct C3H4 isomers at elevated temperatures as present in combustion processes and in circumstellar envelopes of carbon stars. The underlying reaction mechanisms proceed through the initial addition of the 2-naphthyl radical with its radical center to the π-electron density of the allene and methylacetylene reactants via entrance barriers between 8 and 14 kJ mol-1, followed by isomerization (hydrogen shifts, ring closure), and termination via atomic hydrogen losses accompanied by aromatization. The reaction mechanisms reflect the formation of indene - the prototype PAH carrying a single five- and a single six-membered ring - synthesized through the reaction of the phenyl radical (C6H5˙) with allene and methylacetylene. This leads us to predict that aryl radicals - upon reaction with allene/methylacetylene - may undergo molecular mass growth processes via ring annulation and de facto addition of a five-membered ring to form molecular building blocks essential to transit planar PAHs out of the plane.

Reactivity of the Indenyl Radical (C9 H7 ) with Acetylene (C2 H2 ) and Vinylacetylene (C4 H4 ).

The reactions of the indenyl radicals with acetylene (C2 H2 ) and vinylacetylene (C4 H4 ) is studied in a hot chemical reactor coupled to synchrotron based vacuum ultraviolet ionization mass spectrometry. These experimental results are combined with theory to reveal that the resonantly stabilized and thermodynamically most stable 1-indenyl radical (C9 H7. ) is always formed in the pyrolysis of 1-, 2-, 6-, and 7-bromoindenes at 1500 K. The 1-indenyl radical reacts with acetylene yielding 1-ethynylindene plus atomic hydrogen, rather than adding a second acetylene molecule and leading to ring closure and formation of fluorene as observed in other reaction mechanisms such as the hydrogen abstraction acetylene addition or hydrogen abstraction vinylacetylene addition pathways. While this reaction mechanism is analogous to the bimolecular reaction between the phenyl radical (C6 H5. ) and acetylene forming phenylacetylene (C6 H5 CCH), the 1-indenyl+acetylene→1-ethynylindene+hydrogen reaction is highly endoergic (114 kJ mol-1 ) and slow, contrary to the exoergic (-38 kJ mol-1 ) and faster phenyl+acetylene→phenylacetylene+hydrogen reaction. In a similar manner, no ring closure leading to fluorene formation was observed in the reaction of 1-indenyl radical with vinylacetylene. These experimental results are explained through rate constant calculations based on theoretically derived potential energy surfaces.

Gas phase synthesis of [4]-helicene.

A synthetic route to racemic helicenes via a vinylacetylene mediated gas phase chemistry involving elementary reactions with aryl radicals is presented. In contrast to traditional synthetic routes involving solution chemistry and ionic reaction intermediates, the gas phase synthesis involves a targeted ring annulation involving free radical intermediates. Exploiting the simplest helicene as a benchmark, we show that the gas phase reaction of the 4-phenanthrenyl radical ([C14H9]•) with vinylacetylene (C4H4) yields [4]-helicene (C18H12) along with atomic hydrogen via a low-barrier mechanism through a resonance-stabilized free radical intermediate (C18H13). This pathway may represent a versatile mechanism to build up even more complex polycyclic aromatic hydrocarbons such as [5]- and [6]-helicene via stepwise ring annulation through bimolecular gas phase reactions in circumstellar envelopes of carbon-rich stars, whereas secondary reactions involving hydrogen atom assisted isomerization of thermodynamically less stable isomers of [4]-helicene might be important in combustion flames as well.