Exploring the Growth Dynamics of Size-Selected Carbon Atomic Wires with In Situ UV Resonance Raman Spectroscopy.

Short carbon atomic wires, the prototypes of the lacking carbon allotrope carbyne, represent the fundamental 1D system and the first stage in carbon nanostructure growth, which still exhibits many open points regarding their growth and stability. An in situ UV resonance Raman approach is introduced for real-time monitoring of the growth of carbon atomic wires during pulsed laser ablation in liquid without perturbing the synthesis environment. Single-chain species' growth dynamics are tracked, achieving size selectivity by exploiting the peculiar optoelectronic properties of carbon wires and the tunability of synchrotron radiation. Diverse solvents are systematically explored, finding size- and solvent-dependent production rates linked to the solvent's C/H ratio and carbonization tendency. Carbon atomic wires' growth dynamics reveal a complex interplay between formation and degradation, leading to an equilibrium. Water, lacking in carbon atoms and reduced polyynes solubility, yields fewer wires with rapid saturation. Organic solvents exhibit enhanced productivity and near-linear growth, attributed to additional carbon from solvent dissociation and low relative polarity. Exploring the dynamics of the saturation regime provides new insights into advancing carbon atomic wires synthesis via PLAL. Understanding carbon atomic wires' growth dynamics can contribute to optimizing PLAL processes for nanomaterial synthesis.

Encapsulation and Evolution of Polyynes Inside Single-Walled Carbon Nanotubes.

Polyyne is an sp-hybridized linear carbon chain (LCC) with alternating single and triple carbon-carbon bonds. Polyyne is very reactive; thus, its structure can be easily damaged through a cross-linking reaction between the molecules. The longer the polyyne is, the more unstable it becomes. Therefore, it is difficult to directly synthesize long polyynes in a solvent. The encapsulation of polyynes inside carbon nanotubes not only stabilizes the molecules to avoid cross-linking reactions, but also allows a restriction reaction to occur solely at the ends of the polyynes, resulting in long LCCs. Here, by controlling the diameter of single-walled carbon nanotubes (SWCNTs), polyynes were filled with high yield below room temperature. Subsequent annealing of the filled samples promoted the reaction between the polyynes, leading to the formation of long LCCs. More importantly, single chiral (6,5) SWCNTs with high purity were used for the successful encapsulation of polyynes for the first time, and LCCs were synthesized by coalescing the polyynes in the (6,5) SWCNTs. This method holds promise for further exploration of the synthesis of property-tailored LCCs through encapsulation inside different chiral SWCNTs.

Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea).

Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent. Graphical Abstract.

A DFT Study on the Excited Electronic States of Cyanopolyynes: Benchmarks and Applications.

Highly unsaturated chain molecules are interesting due to their potential application as nanowires and occurrence in interstellar space. Here, we focus on predicting the electronic spectra of polyynic nitriles HC2m+1N (m = 0-13) and dinitriles NC2n+2N (n = 0-14). The results of time-dependent density functional theory (TD-DFT) calculations are compared with the available gas-phase and noble gas matrix experimental data. We assessed the performance of fifteen functionals and five basis sets for reproducing (i) vibrationless electronic excitation energies and (ii) vibrational frequencies in the singlet excited states. We found that the basis sets of at least triple-ζ quality were necessary to describe the long molecules with alternate single and triple bonds. Vibrational frequency scaling factors are similar for the ground and excited states. The benchmarked spectroscopic parameters were shown to be acceptably reproduced with adequately chosen functionals, in particular ωB97X, CAM-B3LYP, B3LYP, B971, and B972. Select functionals were applied to study the electronic excitation of molecules up to HC27N and C30N2. It is demonstrated that optical excitation leads to a shift from the polyyne- to a cumulene-like electronic structure.

Thiotemplated Biosynthesis of Bacterial Polyyne Fatty Acids by a Designated Desaturase Triad.

Various bacterial species are capable of producing highly modified fatty acid derivatives with conjugated triple bonds, which play important ecological roles as antifungals and toxins in mutualistic and pathogenic interactions. Furthermore, the terminal polyyne moiety is of interest as pharmacophore and as tag in bioorthogonal chemistry and live imaging. To gain insight into the assembly of these highly reactive natural products, we investigated tetrayne (caryoynencin and protegencin) biosynthesis genes (cay and pgn) from Trinickia caryophylli and Pseudomonas protegens. Pathway dissection and reconstitution in the heterologous host Burkholderia graminis revealed the genes minimally required for polyyne formation. Mutational analyses and biochemical assays demonstrated that polyyne biosynthesis is thiotemplated, involving a fatty acyl-AMP ligase, a designated acyl carrier protein, and a thioesterase. Heterologous expression of point-mutated desaturase genes showed that three desaturases work synergistically to introduce four triple bonds. These findings point to an intricate desaturase complex and provide important information for future bioengineering experiments.

HCnH- Anion Chains with n ≤ 8 Are Nonlinear and Their Permanent Dipole Makes Them Potential Candidates for Astronomical Observation.

To be detectable in space via radio astronomy, molecules should have a permanent dipole moment. This is the plausible reason why HCnH chains are underproportionally represented in the interstellar medium in comparison with the isoelectronically equivalent HCnN chain family, which is the most numerous homologous series astronomically observed so far. In this communication, we present results of quantum chemical calculations for the HCnH family at several levels of theory: density functional theory (DFT/B3LYP), coupled-cluster expansions (ROCCSD(T)), and G4 composite model. Contradicting previous studies, we report here that linear HCnH- anion chains with sizes of astrochemical interest are unstable (i.e., not all calculated frequencies are real). Nonlinear cis and trans HCnH- anion chains turn out to be stable both against molecular vibrations (i.e., all vibrational frequencies are real) and against electron detachment (i.e., positive electroaffinity). The fact that the cis anion conformers possess permanent dipole is the main encouraging message that this study is aiming at conveying to the astrochemical community, as this makes them observable by means of radio astronomy.

Polyyne [3]Rotaxanes: Synthesis via Dicobalt Carbonyl Complexes and Enhanced Stability.

New strategies for synthesizing polyyne polyrotaxanes are being developed as an approach to stable carbyne "insulated molecular wires". Here we report an active metal template route to polyyne [3]rotaxanes, using dicobalt carbonyl masked alkyne equivalents. We synthesized two [3]rotaxanes, both with the same C28 polyyne dumbbell component, one with a phenanthroline-based macrocycle and one using a 2,6-pyridyl cycloparaphenylene nanohoop. The thermal stabilities of the two rotaxanes were compared with that of the naked polyyne dumbbell in decalin at 80 °C, and the nanohoop rotaxane was found to be 4.5 times more stable.

Polyacetylene Glycosides: Isolation, Biological Activities and Synthesis.

Polyacetylene glycosides (PAGs) constitute a relatively small class of secondary metabolites characterized by the presence of a sugar unit anomerically connected to a polyacetylene. These compounds are found in fungi, seaweed, and more often in plants. PAGs exhibit a wide range of biological and pharmacological activities and, as a result, the literature of these compounds has grown exponentially in recent years.

Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity.

Natural products that possess alkyne or polyyne moieties have been isolated from a variety of biological sources and possess a broad a range of bioactivities. In bacteria, the basic biosynthesis of polyynes is known, but their biosynthetic gene cluster (BGC) distribution and evolutionary relationship to alkyne biosynthesis have not been addressed. Through comprehensive genomic and phylogenetic analyses, the distribution of alkyne biosynthesis gene cassettes throughout bacteria was explored, revealing evidence of multiple horizontal gene transfer events. After investigation of the evolutionary connection between alkyne and polyyne biosynthesis, a monophyletic clade was identified that possessed a conserved seven-gene cassette for polyyne biosynthesis that built upon the conserved three-gene cassette for alkyne biosynthesis. Further diversity mapping of the conserved polyyne gene cassette revealed a phylogenetic subclade for an uncharacterized polyyne BGC present in several Pseudomonas species, designated pgn. Pathway mutagenesis and high-resolution analytical chemistry showed the Pseudomonas protegens pgn BGC directed the biosynthesis of a novel polyyne, protegencin. Exploration of the biosynthetic logic behind polyyne production, through BGC mutagenesis and analytical chemistry, highlighted the essentiality of a triad of desaturase proteins and a thioesterase in both the P. protegens pgn and Trinickia caryophylli (formerly Burkholderia caryophylli) caryoynencin pathways. We have unified and expanded knowledge of polyyne diversity and uniquely demonstrated that alkyne and polyyne biosynthetic gene clusters are evolutionarily related and widely distributed within bacteria. The systematic mapping of conserved biosynthetic genes across the available bacterial genomic diversity proved to be a fruitful method for discovering new natural products and better understanding polyyne biosynthesis. IMPORTANCE Natural products bearing alkyne (triple carbon bond) or polyyne (multiple alternating single and triple carbon bonds) moieties exhibit a broad range of important biological activities. Polyyne metabolites have been implicated in important ecological roles such as cepacin mediating biological control of plant pathogens and caryoynencin protecting Lagriinae beetle eggs against pathogenic fungi. After further phylogenetic exploration of polyyne diversity, we identified a novel gene cluster in Pseudomonas bacteria with known biological control abilities and proved it was responsible for synthesizing a new polyyne metabolite, protegencin. The evolutionary analysis of polyyne pathways showed that multiple biosynthetic genes were conserved, and using mutagenesis, their essentiality was demonstrated. Our research provides a foundation for the future modification of polyyne metabolites and has identified a novel polyyne, protegencin, with potential bioactive roles of ecological and agricultural importance.

Masked Alkyne Equivalents for the Synthesis of Mechanically Interlocked Polyynes*.

Polyyne polyrotaxanes, encapsulated cyclocarbon catenanes and other fascinating mechanically interlocked carbon-rich architectures should become accessible if masked alkyne equivalents (MAEs) can be developed that are large enough to prevent unthreading of a macrocycle, and that can be cleanly unmasked under mild conditions. Herein, we report the synthesis of a new bulky MAE based on t-butylbicyclo[4.3.1]decatriene. This MAE was used to synthesize a polyyne [2]rotaxane and a masked-polyyne [3]rotaxane by Cadiot-Chodkiewicz coupling. Glaser cyclo-oligomerization of the [2]rotaxane gave masked cyclocarbon catenanes. The unmasking behavior of the catenanes and rotaxanes was tested by photolysis at a range of UV wavelengths. Photochemical unmasking did not proceed cleanly enough to prepare extended encapsulated polyyne polyrotaxanes. We highlight the scope and challenges involved with this approach to interlocked carbon-rich architectures.

Identification of Feldin, an Antifungal Polyyne from the Beefsteak Fungus Fistulina hepatica.

Fruiting body-forming members of the Basidiomycota maintain their ecological fitness against various antagonists like ascomycetous mycoparasites. To achieve that, they produce myriads of bioactive compounds, some of which are now being used as agrochemicals or pharmaceutical lead structures. Here, we screened ethyl acetate crude extracts from cultures of thirty-five mushroom species for antifungal bioactivity, for their effect on the ascomycete Saccharomyces cerevisiae and the basidiomycete Ustilago maydis. One extract that inhibited the growth of S. cerevisiae much stronger than that of U. maydis was further analyzed. For bioactive compound identification, we performed bioactivity-guided HPLC/MS fractionation. Fractions showing inhibition against S. cerevisiae but reduced activity against U. maydis were further analyzed. NMR-based structure elucidation from one such fraction revealed the polyyne we named feldin, which displays prominent antifungal bioactivity. Future studies with additional mushroom-derived eukaryotic toxic compounds or antifungals will show whether U. maydis could be used as a suitable host to shortcut an otherwise laborious production of such mushroom compounds, as could recently be shown for heterologous sesquiterpene production in U. maydis.

Is It Conjugated or Not? The Theoretical and Experimental Electron Density Map of Bonding in p-CH3CH2COC6H4-C≡C-C≡C-p-C6H4COCH3CH2.

The electron density of p-CH3CH2COC6H4-C≡CC≡C-p-C6H4COCH3CH2 has been investigated on the basis of single-crystal X-ray diffraction data collected to high resolution at 100 K and from theoretical calculations. An analysis of the X-ray data of the diyne showed interesting "liquidity" of electron distribution along the carbon chain compared to 1,2-diphenylacetylene. These findings are compatible with the results of topological analysis of Electron Localization Function (ELF), which has also revealed a larger (than expected) concentration of the electron density at the single bonds. Both methods indicate a clear π-type or "banana" character of a single bond and a significant distortion from the typical conjugated structure of the bonding in the diyne with a small contribution of cumulenic structures.

Hole Transfer in Open Carbynes.

We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT). The nanowire is made of N carbon atoms. We use the functional B3LYP and the basis sets 3-21G, 6-31G*, cc-pVDZ, cc-pVTZ, cc-pVQZ. We also utilize a few Tight-Binding (TB) wire models, a very simple model with all sites equivalent and transfer integrals given by the Harrison ppπ expression (TBI) as well as a model with modified initial and final sites (TBImod) to take into account the presence of one or two or three hydrogen atoms at the edge sites. To achieve similar site occupations in cumulenes with those obtained by converged RT-TDDFT, TBImod is sufficient. However, to achieve similar frequency content of charge and dipole moment oscillations and similar coherent transfer rates, the TBImod transfer integrals have to be multiplied by a factor of four (TBImodt4times). An explanation for this is given. Full geometry optimization at the B3LYP/6-31G* level of theory shows that in cumulenes bond length alternation (BLA) is not strictly zero and is not constant, although it is symmetrical relative to the molecule center. BLA in cumulenic cases is much smaller than in polyynic cases, so, although not strictly, the separation to cumulenes and polyynes, approximately, holds. Vibrational analysis confirms that for N even all cumulenes with coplanar methylene end groups are stable, for N odd all cumulenes with perpendicular methylene end groups are stable, and the number of hydrogen atoms at the end groups is clearly seen in all cumulenic and polyynic cases. We calculate and discuss the Density Functional Theory (DFT) ground state energy of neutral molecules, the CDFT (Constrained DFT) "ground state energy" of molecules with a hole at one end group, energy spectra, density of states, energy gap, charge and dipole moment oscillations, mean over time probabilities to find the hole at each site, coherent transfer rates, and frequency content, in general. We also compare RT-TDDFT with TB results.

Toonapolyynes A-D, new polyynes from Toona ciliata.

Phytochemical investigation on the leaves and twigs of Toona ciliata has led to the isolation of four new polyynes (1-4) and two knowns (5 and 6). Their structures were determined by extensive spectroscopic analysis (MS, UV, IR, and NMR) and Mosher's method. All compounds were evaluated for their inhibitory activities against HepG2 human tumor cell line but were inactive.

Syntheses, Structures, and Spectroscopic Properties of 1,10-Phenanthroline-Based Macrocycles Threaded by PtC8 Pt, PtC12 Pt, and PtC16 Pt Axles: Metal-Capped Rotaxanes as Insulated Molecular Wires.

The platinum polyynyl complexes trans-(C6 F5 )(p-tol3 P)2 Pt(C≡C)n/2 H undergo oxidative homocoupling (O2 , CuCl/TMEDA) to diplatinum polyynediyl complexes trans, trans-(C6 F5 )(p-tol3 P)2 Pt(C≡C)n Pt(Pp-tol3 )2 (C6 F5 ) (n=4, 2; 6, 5; 8, 8; 92-97 %) as reported previously. When related reactions are conducted in the presence of CuI adducts of the 1,10-phenanthroline-based macrocycles 2,9-(1,10-phenanthrolinediyl)(p-C6 H4 O(CH2 )6 O)2 (1,3-C6 H4 ) (10, 33-membered) or 2,9-(1,10-phenanthrolinediyl)(p-C6 H4 O(CH2 )6 O)2 (2,7-naphthalenediyl) (11, 35-membered), excess K2 CO3 , and I2 (oxidant), rotaxanes are isolated that feature a Pt(C≡C)n Pt axle that has been threaded through the macrocycle (2⋅10, 9 %; 5⋅10, 41 %; 5⋅11, 28 %; 8⋅10, 12 %; 8⋅11, 9 %). Their crystal structures are determined and analyzed in detail, particularly with respect to geometric perturbations and the degree of steric sp carbon chain insulation. NMR spectra show a number of shielding effects. UV/Vis spectra do not indicate significant electronic interactions between the Pt(C≡C)n Pt axles and macrocycles, although cyclic voltammetry data suggest rapid reactions following oxidation.

Bioorganic chemistry of signaling molecules in microbial communication.

Microorganisms produce and secrete a variety of secondary metabolites including fatty acids, polyketides, terpenoids, alkaloids, and peptides. Among them, many molecules act as chemical signals that play important roles in inter-/intra-species microbial communication or the interaction with host organisms. In this review, I focus on our recent reports of the microbial signaling molecules involved in bacterium-fungus, bacterium-plant, and fungus-plant interactions. Their potential contribution to pest management is also discussed.

Pyridyl-Endcapped Polyynes: Stabilized Wire-like Molecules.

A 4-ethynylpyridyl derivative with sterically shielding phenyl groups in the 3- and 5-positions has been synthesized and used to terminate a series of polyynes. This approach allows for the synthesis of stable polyynes up to an octayne, twice as long as previous accessible for "unstabilized" pyridyl-endcapped polyynes. The potential of these polyynes as wire-like linkers to metal centers is demonstrated by axial coordination of pyridyl groups to zinc- and ruthenium-metalloporphyrins.

Pharmacokinetic profiles of falcarindiol and oplopandiol in rats after oral administration of polyynes extract of Oplopanax elatus.

Polyynes, such as facarindiol (FAD) and oplopandiol (OPD), are responsible for anticancer activities of Oplopanax elatus (O. elatus). A novel approach to pharmacokinetics determination of the two natural polyynes in rats was developed and validated using a liquid chromatography-electrospray ionization-mass spectrometry (LC-MS) method. Biosamples were prepared by liquid-liquid extraction using ethyl acetate/n-hexane (V : V = 9 : 1) and the analytes were eluted on an Agilent ZORBAX Eclipse Plus C18 threaded column (4.6 mm × 50 mm, 1.8 µm) with the mobile phase of acetonitrile-0.1% aqueous formic acid at a flow-rate of 0.5 mL·min(-1) within a total run time of 11 min. All analytes were simultaneously monitored in a single-quadrupole mass spectrometer in the selected ion monitoring (SIM) mode using electrospray source in positive mode. The method was demonstrated to be rapid, sensitive, and reliable, and it was successfully applied to the pharmacokinetic studies of the two polyynes in rat plasma after oral administration of polyynes extract of O. elatus.

Pharmacokinetic profiles of falcarindiol and oplopandiol in rats after oral administration of polyynes extract of Oplopanax elatus / 中国天然药物

Polyynes, such as facarindiol (FAD) and oplopandiol (OPD), are responsible for anticancer activities of Oplopanax elatus (O. elatus). A novel approach to pharmacokinetics determination of the two natural polyynes in rats was developed and validated using a liquid chromatography-electrospray ionization-mass spectrometry (LC-MS) method. Biosamples were prepared by liquid-liquid extraction using ethyl acetate/n-hexane (V : V = 9 : 1) and the analytes were eluted on an Agilent ZORBAX Eclipse Plus C18 threaded column (4.6 mm × 50 mm, 1.8 μm) with the mobile phase of acetonitrile-0.1% aqueous formic acid at a flow-rate of 0.5 mL·min(-1) within a total run time of 11 min. All analytes were simultaneously monitored in a single-quadrupole mass spectrometer in the selected ion monitoring (SIM) mode using electrospray source in positive mode. The method was demonstrated to be rapid, sensitive, and reliable, and it was successfully applied to the pharmacokinetic studies of the two polyynes in rat plasma after oral administration of polyynes extract of O. elatus.

Carbyne: The Molecular Approach.

For the last 60+ years, the synthesis and study of cumulenes and polyynes have been the focus of a small, but dedicated, group of researchers. Many of the remarkable electronic, optical, and structural properties of cumulenes and polyynes had already been identified in the earliest reports. The molecular lengths achievable by the initial syntheses were, unfortunately, somewhat limited by synthetic methods available. For the past 15 years, we have worked toward expanding on the synthesis of cumulenes and polyynes through the development of new methods and stabilization motifs. As new compounds have become available, homologous series of cumulenes and polyynes have then been examined as a function of molecular length. While we are not yet there, we would like to eventually provide a general description of the sp-carbon allotrope carbyne, and this account presents some of our efforts toward this goal.