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.

Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 dNTPase Activity and Nucleic Acid Binding.

Sterile alpha motif histidine-aspartate domain protein 1 (SAMHD1) is a deoxynucleotide triphosphohydrolase that exists in monomeric, dimeric, and tetrameric forms. It is activated by GTP binding to an A1 allosteric site on each monomer subunit, which induces dimerization, a prerequisite for dNTP-induced tetramerization. SAMHD1 is a validated drug target stemming from its inactivation of many anticancer nucleoside drugs leading to drug resistance. The enzyme also possesses a single-strand nucleic acid binding function that promotes RNA and DNA homeostasis by several mechanisms. To discover small molecule inhibitors of SAMHD1, we screened a custom ∼69 000-compound library for dNTPase inhibitors. Surprisingly, this effort yielded no viable hits and indicated that exceptional barriers for discovery of small molecule inhibitors existed. We then took a rational fragment-based inhibitor design approach using a deoxyguanosine (dG) A1 site targeting fragment. A targeted chemical library was synthesized by coupling a 5'-phosphoryl propylamine dG fragment (dGpC3NH2) to 376 carboxylic acids (RCOOH). Direct screening of the products (dGpC3NHCO-R) yielded nine initial hits, one of which (R = 3-(3'-bromo-[1,1'-biphenyl]), 5a) was investigated extensively. Amide 5a is a competitive inhibitor against GTP binding to the A1 site and induces inactive dimers that are deficient in tetramerization. Surprisingly, 5a also prevented ssDNA and ssRNA binding, demonstrating that the dNTPase and nucleic acid binding functions of SAMHD1 can be disrupted by a single small molecule. A structure of the SAMHD1-5a complex indicates that the biphenyl fragment impedes a conformational change in the C-terminal lobe that is required for tetramerization.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Pyrimidine Nucleosides with a Reactive (ß-Chlorovinyl)sulfone or (ß-Keto)sulfone Group at the C5 Position, Their Reactions with Nucleophiles and Electrophiles, and Their Polymerase-Catalyzed Incorporation into DNA.

Transition-metal-catalyzed chlorosulfonylation of 5-ethynylpyrimidine nucleosides provided (E)-5-(ß-chlorovinyl)sulfones A, which undergo nucleophilic substitution with amines or thiols affording B. The treatment of vinyl sulfones A with ammonia followed by acid-catalyzed hydrolysis of the intermediary ß-sulfonylvinylamines gave 5-(ß-keto)sulfones C. The latter reacts with electrophiles, yielding α-carbon-alkylated or -sulfanylated analogues D. The 5'-triphosphates of A and C were incorporated into double-stranded DNA, using open and one-nucleotide gap substrates, by human or Escherichia coli DNA-polymerase-catalyzed reactions.

VUV Photoionization Study of the Formation of the Simplest Polycyclic Aromatic Hydrocarbon: Naphthalene (C10H8).

The formation of the simplest polycyclic aromatic hydrocarbon (PAH), naphthalene (C10H8), was explored in a high-temperature chemical reactor under combustion-like conditions in the phenyl (C6H5)-vinylacetylene (C4H4) system. The products were probed utilizing tunable vacuum ultraviolet light by scanning the photoionization efficiency (PIE) curve at a mass-to-charge m/ z = 128 (C10H8+) of molecules entrained in a molecular beam. The data fitting with PIE reference curves of naphthalene, 4-phenylvinylacetylene (C6H5CCC2H3), and trans-1-phenylvinylacetylene (C6H5CHCHCCH) indicates that the isomers were generated with branching ratios of 43.5±9.0 : 6.5±1.0 : 50.0±10.0%. Kinetics simulations agree nicely with the experimental findings with naphthalene synthesized via the hydrogen abstraction-vinylacetylene addition (HAVA) pathway and through hydrogen-assisted isomerization of phenylvinylacetylenes. The HAVA route to naphthalene at elevated temperatures represents an alternative pathway to the hydrogen abstraction-acetylene addition (HACA) forming naphthalene in flames and circumstellar envelopes, whereas in cold molecular clouds, HAVA synthesizes naphthalene via a barrierless bimolecular route.