Confined linear carbon chains as a route to bulk carbyne.

Strong chemical activity and extreme instability in ambient conditions characterize carbyne, an infinite sp(1) hybridized carbon chain. As a result, much less has been explored about carbyne as compared to other carbon allotropes such as fullerenes, nanotubes and graphene. Although end-capping groups can be used to stabilize carbon chains, length limitations are still a barrier for production, and even more so for application. We report a method for the bulk production of long acetylenic linear carbon chains protected by thin double-walled carbon nanotubes. The synthesis of very long arrangements is confirmed by a combination of transmission electron microscopy, X-ray diffraction and (near-field) resonance Raman spectroscopy. Our results establish a route for the bulk production of exceptionally long and stable chains composed of more than 6,000 carbon atoms, representing an elegant forerunner towards the final goal of carbyne's bulk production.

Conformational analysis of single perfluoroalkyl chains by single-molecule real-time transmission electron microscopic imaging.

Whereas a statistical average of molecular ensembles has been the conventional source of information on molecular structures, atomic resolution movies of single organic molecules obtained by single-molecule real-time transmission electron microscopy have recently emerged as a new tool to study the time evolution of the structures of individual molecules. The present work describes a proof-of-principle study of the determination of the conformation of each C-C bond in single perfluoroalkyl fullerene molecules encapsulated in a single-walled carbon nanotube (CNT) as well as those attached to the outer surface of a carbon nanohorn (CNH). Analysis of 82 individual molecules in CNTs under a 120 kV electron beam indicated that 6% of the CF2-CF2 bonds and about 20% of the CH2-CH2 bonds in the corresponding hydrocarbon analogue are in the gauche conformation. This comparison qualitatively matches the known conformational data based on time- and molecular-average as determined for ensembles. The transmission electron microscopy images also showed that the molecules entered the CNTs predominantly in one orientation. The molecules attached on a CNH surface moved more freely and exhibited more diverse conformation than those in a CNT, suggesting the potential applicability of this method for the determination of the dynamic shape of flexible molecules and of detailed conformations. We observed little sign of any decomposition of the specimen molecules, at least up to 10(7) e·nm(-2) (electrons/nm(2)) at 120 kV acceleration voltage. Decomposition of CNHs under irradiation with a 300 kV electron beam was suppressed by cooling to 77 K, suggesting that the decomposition is a chemical process. Several lines of evidence suggest that the graphitic substrate and the attached molecules are very cold.

Heterogeneous nucleation of organic crystals mediated by single-molecule templates.

Fundamental understanding of how crystals of organic molecules nucleate on a surface remains limited because of the difficulty of probing rare events at the molecular scale. Here we show that single-molecule templates on the surface of carbon nanohorns can nucleate the crystallization of two organic compounds from a supersaturated solution by mediating the formation of disordered and mobile molecular nanoclusters on the templates. Single-molecule real-time transmission electron microscopy indicates that each nanocluster consists of a maximum of approximately 15 molecules, that there are fewer nanoclusters than crystals in solution, and that in the absence of templates physisorption, but not crystal formation, occurs. Our findings suggest that template-induced heterogeneous nucleation mechanistically resembles two-step homogeneous nucleation.

Atomic imaging and spectroscopy of low-dimensional materials with interrupted periodicities.

Identification of individual atoms and examination of their electronic properties in materials are the ultimate goal of all microscopy-based analytical techniques. Here, we demonstrate successful single-atom imaging and spectroscopy in low-dimensional materials using (scanning) transmission electron microscopy together with electron energy-loss spectroscopy (EELS). Edges and point defects in single-layered materials such as graphene, hexagonal boron nitride and WS(2) nanoribbons are investigated by annular dark-field imaging and EELS fine-structure analysis. Individual dopant atoms are unambiguously identified in nano-peapods. It is noteworthy that irradiation damage and specimen contamination even at the single-atom level are crucial issues in these experiments.

Electron microscopic imaging of a single Group 8 metal atom catalyzing C-C bond reorganization of fullerenes.

Heating a bulk sample of [60]fullerene complexes, (η(5)-C(5)H(5))MC(60)R(5) (M = Fe, Ru, R = Me, Ph), produces small hydrocarbons because of coupling of R and C(5)H(5) via C-C and C-H bond activation. Upon observation by transmission electron microscopy, these complexes, encapsulated in single-walled carbon nanotubes, underwent C-C bond reorganization reactions to form new C-C bond networks, including a structure reminiscent of [70]fullerene. Quantitative comparison of the electron dose required to effect the C-C bond reorganization of fullerenes and organofullerenes in the presence of a single atom of Ru, Fe, or Ln and in the the absence of metal atoms indicated high catalytic activity of Ru and Fe atoms, as opposed to no catalytic activity of Ln. Organic molecules such as hydrocarbons and amides as well as pristine [60]fullerene maintain their structural integrity upon irradiation by ca. 100 times higher electron dose compared to the Ru and Fe organometallics. The results not only represent a rare example of direct observation of a single-metal catalysis but also have implications for the use of single metal atom catalysis in Group 8 metal heterogeneous catalysis.

Imaging of conformational changes of biotinylated triamide molecules covalently bonded to a carbon nanotube surface.

A diamide molecule bearing a biotin terminus was bonded via an amide linkage to the surface of an aminated single-walled carbon nanotube and examined by a high-resolution transmission electron microscope. The still and movie images allowed us to study not only the conformation of the molecule but also its time evolution. An iterative sequence of modeling and simulation allowed us to assign one plausible conformation out of >10(8) possibilities. The images also provide direct support for the accepted wisdom that the curved regions of pristine carbon nanotubes are chemically reactive.

Properties of individual dopant atoms in single-layer MoS2: atomic structure, migration, and enhanced reactivity.

Single-layered MoS2 doped with Re (n-type) and Au (p-type) are investigated by in situ scanning transmission electron microscopy. Re atoms substituting Mo sites enhance the local chemical affinity, evidenced by agglomeration of other dopant/impurity atoms. Au atoms exist as adatoms and show larger mobility under the electron beam. These behaviors are consistent with density functional theory calculations.

Analysis of the reactivity and selectivity of fullerene dimerization reactions at the atomic level.

High-resolution transmission electron microscopy has proved useful for its ability to provide time-resolved images of small molecules and their movements. One of the next challenges in this area is to visualize chemical reactions by monitoring time-dependent changes in the atomic positions of reacting molecules. Such images may provide information that is not available with other experimental methods. Here we report a study on bimolecular reactions of fullerene and metallofullerene molecules inside carbon nanotubes as a function of electron dose. Images of how the fullerenes move during the dimerization process reveal the specific orientations in which two molecules interact, as well as how bond reorganization occurs after their initial contact. Studies on the concentration, specimen temperature, effect of catalyst and accelerating voltage indicate that the reactions can be imaged under a variety of conditions.

Nucleotide sequences and organization of the genes for carotovoricin (Ctv) from Erwinia carotovora indicate that Ctv evolved from the same ancestor as Salmonella typhi prophage.

Carotovoricin Er (CtvEr), which is produced by a plant soft rot disease causative agent, Erwinia carotovora subsp. carotovora Er, is a high-molecular-weight bacteriocin showing Myoviridae phage-tail-like morphology with contractile sheath and plural tail fibers. We determined the complete nucleotide sequences of CtvEr genes on the E. carotovora Er chromosome and report that CtvEr genes consist of lysis cassette, major and minor structural protein gene clusters. Four promoters were identified. The lysis gene cassette, which is composed of the genes for lysis enzyme and holin, was also identified and characterized. The nucleotide sequences and organization of the genes for CtvCGE, which is produced by E. carotovora strain CGE234-M403 with the morphology similar to CtvEr, were also determined and compared to that of CtvEr, and it was found that CtvCGE is almost identical to CtvEr except for tail fibers which are involved in the killing spectra of both bacteriocins. We also explain that the gene organization and the deduced amino acid sequences of both carotovoricins are very close to those of prophage, which is lysogenized in the chromosome on Salmonella enterica serovar Typhi CT18. These findings strongly suggest that Ctv evolved as a phage tail-like bacteriocin from a common ancestor with Salmonella typhi prophage.