Isolation and structure of higher diamondoids, nanometer-sized diamond molecules

Partitioned-formula periodic tables for diamond hydrocarbons (diamondoids)

Isomeric diamond hydrocarbons (diamondoids or polymantanes) with the same number n of adamantane units share the same molecular formula C(Q)(CH)(T)(CH(2))(S) and can be divided into valence isomers (denoted as Q-T-S) by partitioning the number C = Q + T + S of their carbon atoms according to whether they are quaternary, tertiary, or secondary. Vertices of dualists are the centers of adamantane units, and dualist edges connect vertices of adjacent adamantane units (sharing a chair-shaped hexagon). Dualists of diamondoids are hydrogen-depleted skeletons of staggered alkane or cycloalkane rotamers. Diamondoids with acyclic dualists can be classified as catamantanes, those having dualists with chair-shaped six-membered rings as perimantanes, and those having dualists with higher-membered rings that are not perimeters of hexagon-aggregates as coronamantanes. Diamondoids with n adamantane units may be classified into regular catamantanes when the molecular formula is C(4n+6)H(4n+12), and irregular polymantanes (catamantanes or perimantanes) when the number of carbon atoms is lower than 4n + 6. The derivation is presented of formula-periodic tables of regular and irregular diamondoids that allow a better understanding of the shapes and properties of these hydrocarbons for which many applications are predicted.

Synthesis and transformation of linear adamantane assemblies inside carbon nanotubes

We report the assembly and thermal transformation of linear diamondoid assemblies inside carbon nanotubes. Our calculations and observations indicate that these molecules undergo selective reactions within the narrow confining space of a carbon nanotube. Upon vacuum annealing of adamantane molecules encapsulated in a carbon nanotube, we observe a sharp Raman feature at 1857 cm(-1), which we interpret as a stretching mode of carbon chains formed by thermal conversion of adamantane inside a carbon nanotube. Introduction of pure hydrogen during thermal annealing, however, suppresses the formation of carbon chains and seems to keep adamantane intact.

Exploring chemical space for drug discovery using the chemical universe database

Herein we review our recent efforts in searching for bioactive ligands by enumeration and virtual screening of the unknown chemical space of small molecules. Enumeration from first principles shows that almost all small molecules (>99.9%) have never been synthesized and are still available to be prepared and tested. We discuss open access sources of molecules, the classification and representation of chemical space using molecular quantum numbers (MQN), its exhaustive enumeration in form of the chemical universe generated databases (GDB), and examples of using these databases for prospective drug discovery. MQN-searchable GDB, PubChem, and DrugBank are freely accessible at www.gdb.unibe.ch.

Stable alkanes containing very long carbon-carbon bonds

The metal-induced coupling of tertiary diamondoid bromides gave highly sterically congested hydrocarbon (hetero)dimers with exceptionally long central C-C bonds of up to 1.71 Å in 2-(1-diamantyl)[121]tetramantane. Yet, these dimers are thermally very stable even at temperatures above 200 °C, which is not in line with common C-C bond length versus bond strengths correlations. We suggest that the extraordinary stabilization arises from numerous intramolecular van der Waals attractions between the neighboring H-terminated diamond-like surfaces. The C-C bond rotational dynamics of 1-(1-adamantyl)diamantane, 1-(1-diamantyl)diamantane, 2-(1-adamantyl)triamantane, 2-(1-diamantyl)triamantane, and 2-(1-diamantyl)[121]tetramantane were studied through variable-temperature (1)H- and (13)C NMR spectroscopies. The shapes of the inward (endo) CH surfaces determine the dynamic behavior, changing the central C-C bond rotation barriers from 7 to 33 kcal mol(-1). We probe the ability of popular density functional theory (DFT) approaches (including BLYP, B3LYP, B98, B3LYP-Dn, B97D, B3PW91, BHandHLYP, B3P86, PBE1PBE, wB97XD, and M06-2X) with 6-31G(d,p) and cc-pVDZ basis sets to describe such an unusual bonding situation. Only functionals accounting for dispersion are able to reproduce the experimental geometries, while most DFT functionals are able to reproduce the experimental rotational barriers due to error cancellations. Computations on larger diamondoids reveal that the interplay between the shapes and the sizes of the CH surfaces may even allow the preparation of open-shell alkyl radical dimers (and possibly polymers) that are strongly held together exclusively by dispersion forces.

Tuning the optical gap of nanometer-size diamond cages by sulfurization: a time-dependent density functional study

The optical gap of nanometer sized diamond cages, i.e., diamondoids, lies in the ultraviolet spectral region. Here we show by hybrid functional based time-dependent density-functional calculations that, by varying the number of C=S double bonds at the surface of diamondoids, the absorption onset can be tuned toward the infrared spectral region. Our finding has an important implication for in vivo biological applications where toxic and unstable dye molecules may be substituted by the luminescent sulfurized diamondoids.

Theoretical design of a shallow donor in diamond by lithium-nitrogen codoping

We propose a new substitutional impurity complex in diamond composed of a lithium atom that is tetrahedrally coordinated by four nitrogen atoms (LiN(4)). Density functional calculations are consistent with the hydrogenic impurity model, both supporting the prediction that this complex is a shallow donor with an activation energy of 0.27±0.06 eV. Three paths to the experimental realization of the LiN(4) complex in diamond are proposed and theoretically analyzed.

The properties and applications of nanodiamonds

Nanodiamonds have excellent mechanical and optical properties, high surface areas and tunable surface structures. They are also non-toxic, which makes them well suited to biomedical applications. Here we review the synthesis, structure, properties, surface chemistry and phase transformations of individual nanodiamonds and clusters of nanodiamonds. In particular we discuss the rational control of the mechanical, chemical, electronic and optical properties of nanodiamonds through surface doping, interior doping and the introduction of functional groups. These little gems have a wide range of potential applications in tribology, drug delivery, bioimaging and tissue engineering, and also as protein mimics and a filler material for nanocomposites.

Diamondoid-modified DNA

We prepared novel C5-modified triphosphates and phosphoramidites with a diamondoid functionally linked to the nucleobase. Using primer extension experiments with different length templates we investigated whether the modified triphosphates were enzymatically incorporated into DNA and whether they were further extended. We found that all three modified nucleotides can be incorporated into DNA using a single-nucleotide incorporation experiment, but only partially using two templates that demand for multiple incorporation of the modified nucleotides. The modified phosphoramidites were introduced into oligonucleotides utilizing DNA synthesizer technology. The occurring oligonucleotide structures were examined by circular dichroism (CD) and melting temperature (T(m)) measurements and were found to adapt similar helix conformations as their unmodified counterparts.

Ordered phases of encapsulated diamondoids into carbon nanotubes

Diamondoids are hydrogen-terminated nanosized diamond fragments that are present in petroleum crude oil at low concentrations. These fragments are found as oligomers of the smallest diamondoid, adamantane (C(10)H(16)). Due to their small size, diamondoids can be encapsulated into carbon nanotubes to form linear arrangements. We have investigated the encapsulation of diamondoids into single walled carbon nanotubes with diameters between 1.0 and 2.2 nm using fully atomistic simulations. We performed classical molecular dynamics and energy minimizations calculations to determine the most stable configurations. We observed molecular ordered phases (e.g. double, triple, 4- and 5-stranded helices) for the encapsulation of adamantane, diamantane, and dihydroxy diamantane. Our results also indicate that the functionalization of diamantane with hydroxyl groups can lead to an improvement on the molecular packing factor when compared to non-functionalized compounds. Comparisons to hard-sphere models revealed differences, especially when more asymmetrical diamondoids were considered. For larger diamondoids (i.e., adamantane tetramers), we have not observed long-range ordering but only a tendency to form incomplete helical structures. Our calculations predict that thermally stable (at least up to room temperature) complex ordered phases of diamondoids can be formed through encapsulation into carbon nanotubes.

Identification of individual tetra- and pentacyclic naphthenic acids in oil sands process water by comprehensive two-dimensional gas chromatography/mass spectrometry

The oils sands industry of Canada produces large volumes of process water (OSPW) which is stored in large lagoons. The OSPW contains complex mixtures of somewhat toxic, water-soluble, acid-extractable organic matter sometimes called 'naphthenic acids' (NA). Concerns have been raised over the possible environmental impacts of leakage of OSPW and a need has therefore arisen for better characterisation of the NA. Recently, we reported the first identification of numerous individual tricyclic NA in OSPW by comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GCxGC/ToF-MS) of the methyl esters. The acids were diamondoid adamantane acids, resulting, it was proposed, from biotransformation of the corresponding alkyladamantane hydrocarbons, which is a known process. Biotransformation of higher alkylated diamondoid hydrocarbons was, until now, unknown but here we describe the identification of numerous pentacyclic NA as diamantane and alkyldiamantane acids, using the same methods. Further, we suggest tentative structures for some of the tetracyclic acids formed, we propose, by ring-opening of alkyldiamantanes. We suggest that this is further evidence that some of the acid-extractable organic matter in the OSPW originates from extensive biodegradation of the oil, whether in-reservoir or environmental, although other oxidative routes (e.g. processing) may also be possible. The results may be important for helping to better focus reclamation and remediation strategies for NA and for facilitating the identification of the sources of NA in contaminated environmental samples.

Crystal engineering using functionalized adamantane

We performed a first-principles investigation on the structural, electronic and optical properties of crystals made of chemically functionalized adamantane molecules. Several molecular building blocks, formed by boron and nitrogen substitutional functionalizations, were considered to build zinc blende and wurtzite crystals, and the resulting structures presented large bulk moduli and cohesive energies, wide and direct bandgaps, and low dielectric constants (low-κ materials). Those properties provide stability for such structures up to room temperature, superior to those of typical molecular crystals. This indicates a possible road map for crystal engineering using functionalized diamondoids, with potential applications ranging from space filling between conducting wires in nanodevices to nano-electromechanical systems.

Optical excitation energies, Stokes shift, and spin-splitting of C24H72Si14

As an initial step toward the synthesis and characterization of sila-diamondoids, such as sila-adamantane (Si(10)H(16),T(d)), the synthesis of a fourfold silylated sila-adamantane molecule (C(24)H(72)Si(14),T(d)) has been reported in literature [Fischer et al., Science 310, 825 (2005)]. We present the electronic structure, ionization energies, quasiparticle gap, and the excitation energies for the Si(14)(CH(3))(24) and the exact silicon analog of adamantane Si(10)H(16) obtained at the all-electron level using the delta-self-consistent-field and transitional state methods within two different density functional models: (i) Perdew-Burke-Ernzerhof generalized gradient approximation and (ii) fully analytic density functional (ADFT) implementation with atom dependent potential. The ADFT is designed so that molecules separate into atoms having exact atomic energies. The calculations within the two models agree well, to within 0.25 eV for optical excitations. The effect of structural relaxation in the presence of electron-hole-pair excitations is examined to obtain its contribution to the luminescence Stokes shift. The spin-influence on exciton energies is also determined. Our calculations indicate overall decrease in the absorption, emission, quasiparticle, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps, ionization energies, Stokes shift, and exciton binding energy when passivating hydrogens in the Si(10)H(16) are replaced with electron donating groups such as methyl (Me) and trimehylsilyl (-Si(Me)(3)).

Synthesis and characterization of diamond-coated CNTs and their reinforcement in Nylon-6 single fiber

Diamond nanoparticle (DN)-coated CNTs were synthesized using a cationic surfactant-assisted sonochemical method. The as-prepared DN coated CNTs were characterized using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and transmission electron microscopy (TEM). The results show that the DNs were coated on the outer wall surface of CNTs. The DN-coated CNTs were infused in Nylon-6 polymer through a melt extrusion process to form nanocomposite fibers that were tested for their tensile properties. The ultimate tensile strength is found to be 363 MPa for DN/CNTs/Nylon-6 single fibers as compared to 240 MPa for neat Nylon-6 single fibers. These results were also compared with Nylon-6 fibers infused with pristine CNTs and pristine DNs.

The influence of a single thiol group on the electronic and optical properties of the smallest diamondoid adamantane

At the nanoscale, the surface becomes pivotal for the properties of semiconductors due to an increased surface-to-bulk ratio. Surface functionalization is a means to include semiconductor nanocrystals into devices. In this comprehensive experimental study we determine in detail the effect of a single thiol functional group on the electronic and optical properties of the hydrogen-passivated nanodiamond adamantane. We find that the optical properties of the diamondoid are strongly affected due to a drastic change in the occupied states. Compared to adamantane, the optical gap in adamantane-1-thiol is lowered by approximately 0.6 eV and UV luminescence is quenched. The lowest unoccupied states remain delocalized at the cluster surface leaving the diamondoid's negative electron affinity intact.

STUDY OF ELECTRONIC STRUCTURE AND NEGATIVE ELECTRON AFFINITY OF NANODIAMONDS PASSIVATED BY CHn SPECIES

A series of diamond nanoparticles with different surface terminations, (I) CH n (n = 1, 2) and (II) CH n (n = 1–3) species, have been investigated by means of density functional theory (DFT) to probe the effects of the terminated CH n species on the geometric and electronic structures and related properties. Our results show that quantum confinement effects of HOMO–LUMO gap occurs for the series I particles with size up to 1.1 nm, in contrast to the much weaker decay of the gap for larger size. With the existence of additional CH3 species, for size larger than 1 nm, the series II particles have larger gaps than the series I counterparts, which may be even larger than that of bulk diamond. The compositions of HOMO and LUMO are responsible for the different behaviors in the quantum confinement, which agrees with the experimentally observed spectral feature in the X-ray absorption measurement. In addition, our results show that the negative electron affinity is strongly dependent on the C/H ratio for the hydrogenated diamond nanoparticles.

Nanographene and nanodiamond; new members in the nanocarbon family

Nanographene and nanodiamond are new members of nanocarbons, which consist of nano-sized hexagonal and tetrahedral networks, respectively. The presence of edges and surfaces distinguishes nanographene and nanodiamond, respectively, from other nanocarbons owing to their structure dependent electronic features. Nanographene has an unconventional nonbonding pi-state (edge state) localized around its edge that is dependent on the edge geometry. The edge states, having localized spins, impart a nanographene-based molecular magnetic character. The structure and electronic/magnetic properties of nanodiamond vary depending on how the surface carbon atoms are terminated. Nanodiamond, with a naked surface, is subjected to structural reconstruction at the expense of sigma-dangling bonds. The hydrogenation of the surface is expected to give an electron reservoir function. The incompletely hydrogenated surface is magnetic with surface-induced spins.

Optical response of diamond nanocrystals as a function of particle size, shape, and symmetry

The optical spectra of hydrogen-passivated diamond clusters (diamondoids) precisely defined in size and shape have been measured in the gas phase, i.e., under an environment similar to boundary conditions typically assumed by theory. Characteristic optical properties evolve for these wide band-gap semiconductor nanocrystals as a function of size, shape, and symmetry in the subnanometer regime. These effects have not previously been theoretically predicted. The optical response of the tetrahedral-shaped C_{26}H_{32} diamond cluster [1(2,3)4] pentamantane is found to be remarkably similar to that of bulk diamond.

Core and valence exciton formation in x-ray absorption, x-ray emission and x-ray excited optical luminescence from passivated Si nanocrystals at the Si L(2,3) edge

Resonant inelastic x-ray scattering (RIXS), x-ray absorption spectroscopy and x-ray excited optical luminescence (XEOL) have been used to measure element specific filled and empty electronic states over the Si L(2,3) edge of passivated Si nanocrystals of narrow size distribution (diameter 2.2 ± 0.4 nm). These techniques have been employed to directly measure absorption and luminescence specific to the local Si nanocrystal core. Profound changes occur in the absorption spectrum of the nanocrystals compared with bulk Si, and new features are observed in the nanocrystal RIXS. Clear signatures of core and valence band exciton formation, promoted by the spatial confinement of electrons and holes within the nanocrystals, are observed, together with band narrowing due to quantum confinement. XEOL at 12 K shows an extremely sharp feature at the threshold of orange luminescence (i.e., at ∼1.56 eV (792 nm)) which we attribute to recombination of valence excitons, providing a lower limit to the nanocrystal band gap.