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.

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.

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.

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.

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.

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.

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.

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 Triphenylene (C18 H12 ).

For the last decades, the hydrogen-abstraction-acetylene-addition (HACA) mechanism has been widely invoked to rationalize the high-temperature synthesis of PAHs as detected in carbonaceous meteorites (CM) and proposed to exist in the interstellar medium (ISM). By unravelling the chemistry of the 9-phenanthrenyl radical ([C14 H9 ]. ) with vinylacetylene (C4 H4 ), we present the first compelling evidence of a barrier-less pathway leading to a prototype tetracyclic PAH - triphenylene (C18 H12 ) - via an unconventional hydrogen abstraction-vinylacetylene addition (HAVA) mechanism operational at temperatures as low as 10 K. The barrier-less, exoergic nature of the reaction reveals HAVA as a versatile reaction mechanism that may drive molecular mass growth processes to PAHs and even two-dimensional, graphene-type nanostructures in cold environments in deep space thus leading to a better understanding of the carbon chemistry in our universe through the untangling of elementary reactions on the most fundamental level.

Fluorescent 5-Pyrimidine and 8-Purine Nucleosides Modified with an N-Unsubstituted 1,2,3-Triazol-4-yl Moiety.

The Cu(I)- or Ag(I)-catalyzed cycloaddition between 8-ethynyladenine or guanine nucleosides and TMSN3 gave 8-(1- H-1,2,3-triazol-4-yl) nucleosides in good yields. On the other hand, reactions of 5-ethynyluracil or cytosine nucleosides with TMSN3 led to the chemoselective formation of triazoles via Cu(I)-catalyzed cycloaddition or vinyl azides via Ag(I)-catalyzed hydroazidation. These nucleosides with a minimalistic triazolyl modification showed excellent fluorescent properties with 8-(1- H-1,2,3-triazol-4-yl)-2'-deoxyadenosine (8-TrzdA), exhibiting a quantum yield of 44%. The 8-TrzdA 5'-triphosphate was incorporated into duplex DNA containing a one-nucleotide gap by DNA polymerase ß.

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.

4-N-Alkanoyl and 4-N-alkyl gemcitabine analogues with NOTA chelators for 68-gallium labelling.

The conjugation of 4-N-(3-aminopropanyl)-2'-deoxy-2',2'-difluorocytidine with 2-(p-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid (SCN-Bn-NOTA) ligand in 0.1 M Na2CO3 buffer (pH 11) at ambient temperature provided 4-N-alkylgemcitabine-NOTA chelator. Incubation of latter with excess of gallium(III) chloride (GaCl3) (0.6 N AcONa/H2O, pH = 9.3) over 15 min gave gallium 4-N-alkylgemcitabine-NOTA complex which was characterized by HRMS. Analogous [68Ga]-complexation of 4-N-alkylgemcitabine-NOTA conjugate proceeded with high labeling efficiency (94%-96%) with the radioligand almost exclusively found in the aqueous layer (∼95%). The high polarity of the gallium 4-N-alkylgemctiabine-NOTA complex resulted in rapid renal clearance of the 68Ga-labelled radioligand in BALB/c mice.

Antiviral and Cytostatic Evaluation of 5-(1-Halo-2-sulfonylvinyl)- and 5-(2-Furyl)uracil Nucleosides.

Transition metal-catalyzed halosulfonylation of 5-ethynyl uracil nucleosides provided (E)-5-(1-chloro-2-tosylvinyl)uridines. Tetrabutylammonium fluoride-mediated direct CH arylation of 5-iodouracil nucleosides with furan or 2-heptylfuran gave 5-furyl-substituted nucleosides without the necessity of using the organometallic substrates. These two classes of 5-substituted uracil nucleosides as well their corresponding ester derivatives were tested against a broad range of DNA and RNA viruses and the human immunodeficiency virus (HIV). The 3',5'-di-O-acetyl-5-(E)-(1-chloro-2-tosylvinyl)-2'-deoxyuridine (24) inhibited the growth of L1210, CEM and HeLa cancer cells in the lower micromolar range. The (ß-chloro)vinyl sulfone 24 and 5-(5-heptylfur-2-yl)-2'-deoxyuridine (10) displayed micromolar activity against varicella zoster virus (VZV). The 5-(5-heptylfur-2-yl) analog 10 and its 3',5'-di-O-acetyl-protected derivative showed similar activity against the cytomegalovirus (CMV). The 5-(fur-2-yl) derivatives of 2'-deoxyuridine and arabino-uridine inhibited the replication of herpes simplex virus (HSV) TK+ strains while the 5-(5-heptylfur-2-yl) derivative 10 displayed antiviral activity against the parainfluenza virus.

Transition-Metal-Free Cross-Coupling of Aryl Halides with Arylstannanes.

Transition-metal-free LiCl-promoted cross-coupling reactions of tetraphenyltin, trichlorophenyl-, dichlorodiphenyl-, and chlorotriphenylstannanes with aryl halides in DMF provided access to biaryls in good to high yields. Up to four phenyl groups were transferred from the organostannanes substrates. The aryls bearing electron-withdrawing groups in either halides or organotin substrates gave coupling products in higher yields. The methodology has been applied for the efficient synthesis of ipriflavones.

Studies toward the oxidative and reductive activation of C-S bonds in 2'-S-aryl-2'-thiouridine derivatives.

Studies directed toward the oxidative and reductive desulfurization of readily available 2'-S-aryl-2'-thiouridine derivatives were investigated with the prospect to functionalize the C2'-position of nucleosides. The oxidative desulfurization-difluorination strategy was successful on 2-(arylthio)alkanoate surrogates, while extension of the combination of oxidants and fluoride sources was not an efficient fluorination protocol when applied to 2'-S-aryl-2'-thiouridine derivatives, resulting mainly in C5-halogenation of the pyrimidine ring and C2'-monofluorination without desulfurization. Cyclic voltammetry of 2'-arylsulfonyl-2'-deoxyuridines and their 2'-fluorinated analogues showed that cleavage of the arylsulfone moiety could occur, although at relatively high cathodic potentials. While reductive-desulfonylation of 2'-arylsulfonyl-2'-deoxyuridines with organic electron donors (OEDs) gave predominantly base-induced furan type products, chemical (OED) and electrochemical reductive-desulfonylation of the α-fluorosulfone derivatives yielded the 2'-deoxy-2'-fluorouridine and 2',3'-didehydro-2',3'-dideoxy-2'-fluorouridine derivatives. These results provided good evidence of the generation of a C2'-anion through carbon-sulfur bond cleavage, opening new horizons for the reductive-functionalization approaches in nucleosides.

Synthesis of 8-(1,2,3-triazol-1-yl)-7-deazapurine nucleosides by azide-alkyne click reactions and direct C-H bond functionalization.

Treatment of toyocamycin or sangivamycin with 1,3-dibromo-5,5-dimethylhydantoin in MeOH (r.t./30 min) gave 8-bromotoyocamycin and 8-bromosangivamycin in good yields. Nucleophilic aromatic substitution of 8-bromotoyocamycin with sodium azide provided novel 8-azidotoyocamycin. Strain promoted click reactions of the latter with cyclooctynes resulted in the formation of the 1,2,3-triazole products. Iodine-mediated direct C8-H bond functionalization of tubercidin with benzotriazoles in the presence of tert-butyl hydroperoxide gave the corresponding 8-benzotriazolyltubercidin derivatives. The 8-(1,2,3-triazol-1-yl)-7-deazapurine derivatives showed moderate quantum yields and a large Stokes shifts of ~ 100 nm.

S-Ribosylhomocysteine Analogues Modified at the Ribosyl C-4 Position.

4-C-Alkyl/aryl-S-ribosylhomocysteine (SRH) analogues were prepared by coupling of homocysteine with 4-substituted ribofuranose derivatives. The diastereoselective incorporation of the methyl substituent into the 4 position of the ribose ring was accomplished by addition of methylmagnesium bromide to the protected ribitol-4-ulose yielding the 4-C-methylribitol in 85% yield as single 4R diastereomer. The 4-C hexyl, octyl, vinyl, and aryl ribitols were prepared analogously. Chelation controlled addition of a carbanion to ketones from the (Si-face) was responsible for the observed stereochemical outcome. Oxidation of the primary alcohol of the 4-C ribitols with the catalytic amount of tetrapropylammonium perruthenate in the presence of N-methylmorpholine N-oxide produced 4-C-alkylribono-1,4-lactones in high yields. Mesylation of the latter compounds at the 5-hydroxyl position and treatment with a protected homocysteine thiolate afforded protected 4-C-alkyl/aryl-SRH analogues as the lactones. Reduction with lithium triethylborohydride and successive global deprotections with TFA afforded 4-C-alkyl/aryl SRH analogues. These analogues might impede the S-ribosylhomocysteinase(LuxS)-catalyzed reaction by preventing ß-elimination of a homocysteine molecule, and thus depleting the production of quorum sensing signaling molecule AI-2.