Pairs Of Carbon Atoms Research Articles

Boron–nitrogen- and boron-substituted anthracenes and -phenanthrenes as models for doped carbon-based materials

The aim of this theoretical study is the investigation of hydrocarbon stability as a function of BN- and B-substitution degree. The targets are anthracene and phenanthrene because they resemble the zig-zag and armchair peripheries of graphene sheets. The computations are made at the RHF and MP2 level with various basis sets. The conclusions drawn are based on the results from calculations for more than 600 different structures created in a systematic way where pairs of carbon atoms are replaced by the respective number of B and N, or solely B-atoms. A common feature of all stable substituted molecules is the tendency for least fragmentation of the carbon skeleton, particularly, for preservation of maximum number of intact carbon aromatic cycles. The major dissimilarity between the BN- and B-substituted molecules are the preferred doping patterns and positions: the favorable structures feature alternation of B and N in the BN-derivatives and disjoint borons separated by C 2 fragments in the B-ones; the nitrogen atoms substitute predominantly secondary carbons, while borons prefer tertiary sites in the BN-substituted hydrocarbons and secondary positions in the B-modified structures. Overall, the anthracene isomers are more stable. The energy and AO contributions to the LUMOs of the studied species are rationalized in terms of electron-accepting properties of the latter, estimating their potential performance as oxidants. Energy depression of LUMOs is achieved mainly in B-substituted hydrocarbons due to large coefficients on the borons causing pronounced delocalization of the orbital. The findings can be used for directed synthesis of novel modified carbon-based materials for practical purposes.

Resonating Valence Bond and σ-Charge Density Wave Phases in a Benzannulated Phenalenyl Radical

We report the preparation of the first benzannulated phenalenyl neutral radical conductor (18), and we show that the compound displays unprecedented solid state behavior: the structure is dominated by two sets of intermolecular interactions: (1) a pi-chain structure with superimposed pi-overlap of the benzannulated phenalenyls along [0 0 1], and (2) an interchain overlap involving a pair of carbon atoms (C4) along [0 1 0]. The pi-chain-type stacking motif is reminiscent of previously reported phenalenyl radicals and the room temperature structure (space group P2/c) together with the conductivity of sigma(RT) = 0.03 S/cm and the Pauli-like magnetic susceptibility are best described by the resonating valence bond (RVB) model. The interchain interaction is unstable with respect to the formation of a sigma-charge density wave (sigma-CDW) involving pairs of C4 carbon atoms between adjacent radicals and this phase is characterized by the P2(1)/c space group which involves a doubling of the unit cell along the [0 1 0] direction. The RVB and CDW phases compete for structural occupancy throughout the whole temperature range (15-293 K) with the RVB phase predominating at 15 and 293 K and the sigma-CDW phase achieving a maximum structural occupancy of about 60% at 150 K where it produces clearly discernible effects on the magnetism and conductivity.

Molecular Dynamics Study on the Effect of Lattice Mismatch on Adhesion Strength between Ceramics and Organic Materials

This paper describes a molecular-dynamics study on the relationship between lattice mismatch and adhesion strength of interfaces between organic materials and ceramics. Aromatic resins with benzene-ring (phenyl-ring) connected structures are used as examples of organic materials. A lattice constant of the aromatic resins is defined as the distance between the second-nearest-neighbor carbon atom pairs of a benzene ring (phenyl ring). The value of the lattice constant of a wholly aromatic polyester resin is about 0.24 nm. On the other hand, a lattice constant of ceramics is defined as the distance between the nearest neighbor atoms in the crystal plane connected with the resin. The lattice constants of the SiO2(111) and TiO2(111) planes are about 0.253 nm and 0.295 nm, respectively. The adhesion of aromatic polyester resin with the SiO2(111) plane is stronger than that with the TiO2(111) plane because the lattice mismatch of the resin with the SiO2(111) plane is smaller than that with the TiO2(111) plane. Reducing the lattice mismatch is found to be effective in strengthening the adhesion.

Beyond the wonder material

When nature had to choose an element as the basis for life, it chose carbon. If I had to guess why, I would say the reason was carbon's extraordinary versatility. Bonding between carbon atoms is exceptionally strong; indeed, the strongest materials on Earth are all made of carbon. However, bonding between carbon and other elements, though stable, can easily be changed by chemical reactions. The resulting compounds are often surprisingly different from one another. For example, a pair of carbon atoms bonded together can accept one, two or three hydrogen atoms, forming ethyne, ethene and ethane – chemicals used in welding, anaesthesia and vodka-making, respectively.

Growth of chiral single-walled carbon nanotube caps in the presence of a cobaltcluster

Density functional theory is used to simulate nanotube growth by addition of a pair ofcarbon atoms to a composite chiral nanotube cap/cobalt cluster system, with capscorresponding to near-armchair (6, 5), (7, 5) and near-zigzag (9, 1) nanotubes. Two differentcarbon addition processes are evaluated: in the first, the new carbon atoms are located inthe vicinity of the armchair site of the cap rim, and thus this process provides insight intothe root-growth mechanism; in the second the carbon atoms are initially located under thecobalt cluster, and thus this process helps one to evaluate the dissolution of carbon insidethe metal cluster. The geometric evolution and energetics of the system are used toexplain features of the mechanism of nanotube growth. The root-growth reaction isshown to occur by displacement of a cobalt atom initially interacting with thearmchair site while the added carbon atoms bond to each other forming a newhexagonal ring, whereas the carbon dissolution process shows formation of dimersinside the cluster only for the (6, 5) system. The energetics for both steps revealsthat the dissolution stage is probably controlling the overall nanotube growthrate.

On the stability of non‐conventional π‐complexes between Ni+and toluene, phenyl‐silane and phenyl‐germane

AbstractThe complexes between Ni+and toluene, phenylsilane, and phenylgermane were investigated through the use of high‐level density functional theory (DFT) methods. Both harmonic vibrational frequencies and optimized geometries were obtained at the B3LYP/6‐311G(d,p) and B3LYP/6‐311+G(2df,2p) levels of theory. These results show that at the highest level considered in this work, and in contrast with what was found before for Cu+, the complexes in which Ni+interacts specifically with only one pair of carbon atoms of the aromatic ring collapse to theconventional π‐complexes. However, similarly to Cu+, non‐conventional complex in which the metal ion interacts with theorthocarbon of the aromatic ring and with one of the hydrogen atoms of the XH3(X = Si, Ge) substituent group, through a typical agostic‐type interaction are very stable. Nevertheless, whereas for Cu+these agostic‐type complexes are not only the global minima of the potential energy surface but the dominant species in the gas phase, for Ni+they are slightly less stable than the conventional π‐complexes. Agostic‐type complexes exhibit infrared spectra that are markedly different from those of the conventional π‐complexes, and therefore they could be easily identified using this spectroscopic technique. Copyright © 2006 John Wiley & Sons, Ltd.

Resonance Assignments and Secondary Structure Analysis of E. coli Thioredoxin by Magic Angle Spinning Solid-State NMR Spectroscopy

De novo site-specific 13C and 15N backbone and sidechain resonance assignments are presented for uniformly enriched E. coli thioredoxin, established using two-dimensional homo- and heteronuclear solid-state magic angle spinning NMR correlation spectroscopy. Backbone dihedral angles and secondary structure were derived from the statistical analysis of the secondary chemical shifts, and are in good agreement with solution values for the intact full-length thioredoxin, with the exception of a small number of residues located at the termini of the individual secondary structure elements. A large number of cross-peaks observed in the DARR spectra with long mixing times correspond to the pairs of carbon atoms separated by 4-6 angstroms, suggesting that DARR could be efficiently employed for observation of medium- and long-range correlations. The 108 amino acid residue E. coli thioredoxin is the largest uniformly enriched protein assigned to this degree of completeness by solid-state NMR spectroscopy to date. It is anticipated that with a combination of two-dimensional correlation experiments and high magnetic fields, resonance assignments and secondary structure can be generally derived for other noncrystalline proteins.

Hydrogenation effect on the structural transition of C 60

The effects of hydrogenation on the structural transitions in C 60 and its isomers are investigated from first principles. C 60H 2 and C 60H 60 are used as paradigmatic examples. We find that hydrogenation enhances the stability of the isomers and it reduces the barriers for structural transitions through Stone–Wales bond rotations. The reduction is due to sp 2 bonding of the rotating pair of carbon atoms at the transition state. The calculated barriers for the in-plane Stone–Wales process are 6.03 and 5.30 eV for C 60H 2 and C 60H 60, respectively.

Li+ vs Cu+ Association to Toluene, Phenylsilane and Phenylgermane. Conventional vs Non-Conventional π-Complexes

The complexes between Li+ and Cu+ with toluene, phenylsilane and phenylgermane were investigated through the use of high-level density functional theory (DFT) methods. Both harmonic vibrational frequencies and optimized geometries were obtained at the B3LYP/6-311G(d,p) and B3LYP/6-311+G(2df,2p) levels of theory. Cu+ interactions have a non-negligible covalent character, which clearly differentiate them from Li+ interactions. As a consequence, the topology of the potential energy surfaces (PES) is richer for Cu+ than for Li+ complexes and Cu+ binding energies are 1.4 times higher than Li+ binding energies. For Li+, only conventional π-complexes should be expected in the gas-phase, while for Cu+, other complexes, in which the metal cation interacts specifically with only one pair of carbon atoms of the aromatic ring, are found to be as stable as the conventional π-complexes. Furthermore, for the particular cases of phenylsilane and phenylgermane, the global minima of the PES correspond to a non-conventional complex in which the metal ion interacts with the ortho carbon of the aromatic ring and with one of the hydrogen atoms of the XH3 (X=Si, Ge) substituent group, through a typical agostic-type interaction. This specific interaction is followed by a large activation of the corresponding X–H bond, whose stretching frequency is significantly shifted to the red. Accordingly, the predicted infrared spectra for these non-conventional complexes markedly differ from those of the conventional π-complexes. Toluene is more basic than phenylsilane and phenylgermane when the reference acid is Li+, whereas the basicity of phenylgermane towards Cu+ metal cations is slightly higher than those of phenylsilane and toluene.

Carbon–carbon interactions in iron

Carbon atoms occupy interstitial sites in iron so that the configurations of any solid-solution at constant composition depend solely on the distribution of carbon atoms on the interstitial sub-lattice, this in turn being influenced by interactions between carbon atoms in close proximity. The carbon–carbon interaction energy, which influences the distribution of carbon atoms, is reviewed with a view to understanding the nature of the interaction and to highlight some recent developments in the subject. It appears that the C–C interaction energy for ferrite cannot be deduced from the thermodynamic data currently available, primarily because of the very low solubility of carbon in ferrite. On the other hand, there is ample evidence to support the view that the corresponding energy for austenite is consistent with a strong repulsion between near neighbour pairs of carbon atoms.

Quantum chemistry study on the open end of single-walled carbon nanotubes

Geometrical and electronic structures of open-ended single-walled carbon nanotubes (SWCNTs) are calculated using density functional theory (DFT) with hybrid functional (B3LYP) approximation. Due to different distances between carbon atoms along the edge, reconstruction occurs at the open end of the (4,4) armchair SWCNT, i.e., triple bonds are formed in the carbon atom pairs at the mouth; however, for the (6,0) zigzag SWCNT, electrons in dangling bonds still remain at ‘no-bonding’ states. The ionization potential (IP) of both (4,4) and (6,0) SWCNTs is increased by their negative intrinsic dipole moments, and localized electronic states existed at both of their open ends.

Glass formability of ferrous- and aluminum-based structural metallic alloys

Synthesis of ferrous- and aluminum-based amorphous metals as prospective structural materials is presented and discussed in light of atomic size–composition interaction effects. The search of prospective bulk metallic glasses (BMGs) may benefit from noting that current BMG alloys can be broadly categorized into two atom size-composition classes, distinctly different from ordinary metallic glasses which can exist over a much wider atom size-composition range. The high formability of one class of BMGs is suggested to be due to the presence of a structure-reinforced network or backbone formed by tightly bound components in the undercooled liquid. For the ferrous-based BMG alloys investigated, it is proposed that zirconium-boron and molybdenum–carbon atom pairs constitute the strong backbone structures. Although aluminum-based BMG has not been reported, the good formability of some current aluminum-glasses is suggested to be due to the presence of backbone structures formed by transition metal–lanthanide and magnesium–copper pairs. The ferrous-based bulk metallic glasses obtained have a high reduced glass transition temperature reaching 0.63 and large supercooled liquid region up to 100 K. These bulk metallic glasses are found to be non-ferromagnetic above 160 K as well as having Vickers hardness and specific tensile strengths that far exceed those reported for steel alloys. Magnetization and susceptibility results are presented and compared with ab initio magnetic-structure calculations [D.M. Nicholson, M. Widom, Y. Wang, unpublished results]. Relevant factors on forming bulk metallic glasses are discussed.

Amino acid type-selective backbone 1H-15N-correlations for Arg and Lys.

Four novel amino acid type-selective triple resonance experiments to identify the backbone amino proton and nitrogen resonances of Arg and Lys and of their sequential neighbors in (13C,15N)-labeled proteins are presented: the R(i+1)-HSQC and R(i,i+1)-HSQC select signals originating from Arg side chains, the K(i+1)-HSQC and K(i,i+1)-HSQC select signals originating from Lys side chains. The selection is based on exploiting the characteristic chemical shifts of a pair of carbon atoms in Arg and Lys side chains using selective 90 degree pulses. The new experiments are recorded as two-dimensional 1H-15N-correlations and their performance is demonstrated with the application to a protein domain of 83 amino acids.

Gas-Phase Molecular Structure of Corannulene, C20H10. An Electron-Diffraction Study Augmented by ab Initio and Normal Coordinate Calculations

The molecular structure of corannulene has been investigated by gas-phase electron diffraction with help from ab initio calculations at the B3LYP/6−31(d) level and normal coordinate analysis. The structure is closely similar to both that found in the crystal and that predicted from the molecular orbital calculation, but the carbon skeleton differs significantly from a C20 fragment of C60. The molecule of C5v symmetry is skull-cap shaped with five six-membered rings fused to the central five-membered ring and to each other. However, unlike C60 in which the corresponding hexagons are planar, the outermost pairs of carbon atoms with their hydrogens are bent out, tending to flatten the molecule. The bond lengths (rg/A) with uncertainties of 2σ for the four different types of C−C bonds in corannulene are, beginning with that held jointly by the pentagon and hexagon and proceeding around the hexagon, C1−C2 = 1.414(6), C1−C6 = 1.414(20), C6−C7 = 1.447(16), and C7−C8 = 1.380(16). The average C−C bond is about 0.0...

Electronic properties of variably charged defects in crystalline semiconductors

The electronic properties of defects with various spatial configurations are examined in relation to corresponding sets of valence bonds. The examination is based on the analysis of the energy functional, in which the elastic energy in the anharmonic approximation, the variation in the electronic term of the defect quasi-molecule defined by the electron localization, and Hubbard’s interaction energy are taken into account. Two types of such defects are recognized, namely, the defects with strong and weak electron-atom interaction. For defects of the first type, which are characterized by positive effective correlation energy, no variations of the adiabatic potential topology are observed after the electron localization. The pair of carbon atoms (CiCs) and donor-acceptor pairs in the crystalline silicon belong to this type of defect. The effective occupancy is calculated for this type of defects as a function of adiabatic potential parameters. Transformation of the initial double-well potential into the single-well potential after the localization of the carriers is substantial for the properties of the second type defects. In this case, the effective correlation energy can be either positive or negative. The analysis of the known experimental results permits us to assume that the interstitial boron atom in silicon belongs to this type of defect. The adiabatic potential (in which the interstitial boron atom moves), the activation energies for transitions between different charge states of this defect, and the effective occupancy are calculated from the experimental data reported by Watkins.

Biosynthesis and elongation of short- and medium-chain-length fatty acids.

Short- and medium-chain-length fatty acids (FAs) are important constituents of a wide array of natural products. Branched and straight short-chain-length FAs originate from branched chain amino acid metabolism, and serve as primers for elongation in FA synthase-like reactions. However, a recent model proposes that the one-carbon extension reactions that utilize 2-oxo-3-methylbutyric acid in leucine biosynthesis also catalyze a repetitive one-carbon elongation of short-chain primers to medium-chain-length FAs. The existence of such a mechanism would require a novel form of regulation to control carbon flux between amino acid and FA biosynthesis. A critical re-analysis of the data used to support this pathway fails to support the hypothesis for FA elongation by one-carbon extension cycles of alpha-ketoacids. Therefore, we tested the hypothesis experimentally using criteria that distinguish between one- and two-carbon elongation mechanisms: (a) isotopomer patterns in terminal carbon atom pairs of branched and straight FAs resulting from differential labeling with [(13)C]ăcetate; (b)(13)C]threonine labeling patterns in odd- and even chain length FAs; and (c) differential sensitivity of elongation reactions to inhibition by cerulenin. All three criteria indicated that biosynthesis of medium-chain length FAs is mediated primarily by FA synthase-like reactions.

Distinction among isomeric unsaturated fatty acids as lithiated adducts by electrospray ionization mass spectrometry using low energy collisionally activated dissociation on a triple stage quadrupole instrument

Features of tandem mass spectra of dilithiated adduct ions of unsaturated fatty acids obtained by electrospray ionization mass spectrometry with low-energy collisionally activated dissociation (CAD) on a triple stage quadrupole instrument are described. These spectra distinguish among isomeric unsaturated fatty acids and permit assignment of double-bond location. Informative fragment ions reflect cleavage of bonds remote from the charge site on the dilithiated carboxylate moiety. The spectra contain radical cations reflecting cleavage of bonds between the first and second and between the second and third carbon atoms in the fatty acid chain. These ions are followed by a closed-shell ion series with members separated by 14 m/z units that reflect cleavage of bonds between the third and fourth and then between subsequent adjacent pairs of carbon atoms. This ion series terminates at the member reflecting cleavage of the carbon–carbon single bond vinylic to the first carbon–carbon double bond. Ions reflecting cleavages of bonds distal to the double bond are rarely observed for monounsaturated fatty acids and are not abundant when they occur. For polyunsaturated fatty acids that contain double bonds separated by a single methylene group, ions reflecting cleavage of carbon–carbon single bonds between double bonds are abundant, but ions reflecting cleavages distal to the final double bond are not. Cleavages between double bonds observed in these spectra can be rationalized by a scheme involving a six-membered transition state and subsequent rearrangement of a bis-allylic hydrogen atom to yield a terminally unsaturated charge-carrying fragment and elimination of a neutral alkene. The location of the β-hydroxy-alkene moiety in ricinoleic acid can be demonstrated by similar methods. These observations offer the opportunity for laboratories that have tandem quadrupole instruments but do not have instruments with high energy CAD capabilities to assign double bond location in unsaturated free fatty acids by mass spectrometric methods without derivatization.

1,1,2,2-Tetramethyl-1,2-disilacycloocta-3,7-diyne — structure and bonding properties of a highly strained cyclic diyne

1,1,2,2-Tetramethyl-1,2-disilacycloocta-3,7-diyne (4) could be prepared by reaction of 1,8-dibromo-4,4,5,5-tetramethyl-4,5-disilaocta-2,6-diyne (9) with lithium in the presence of catalytic amounts of biphenyl. X-Ray investigations on single crystals of 4 revealed an almost planar structure adopting C2v symmetry. The transannular distances between the pairs of carbon atoms in the triple bonds are 2.672 and 3.153 A, respectively. The analysis of the He(I) photoelectron spectrum of 4 reveals a strong interaction between the in-plane π-orbitals of the triple bonds and the Si–Si σ-bond.

BN-naphthalene and carbon-containing derivatives: an ab initio study

Ab initio calculations are used to examine the stability of various isomers of benzene and naphthalene after substitution of pairs of carbon atoms by the isoelectronic boron-nitrogen (BN) tandem. It is found that stability is enhanced by keeping the B and N atoms adjacent to one another. When multiple pairs of BN are present, these pairs prefer to be consecutive with one another. The energy is also lowered by maintaining the heteroatoms on the same ring of naphthalene. Another factor is the preference that consecutive carbon atoms be grouped into even numbers. Successively higher degrees of substitution lead to a regular drop in the molecular valency, as well as increased hardness.

Evidence for the Existence of Sulfur-Doped Fullerenes from Elucidation of Their Photophysical Properties

Evidence is presented that carbon atoms of the hollow fullerene cage can be replaced by sulfur atoms, as has been suggested theoretically. S-doped fullerenes are obtained by arc-vaporization of graphite in the presence of thiophene or 3-methylthiophene. Mass spectra indicate the dominant processes are the substitutions of pairs of carbon atoms by sulfur atoms with the predominant ratios of sulfur to replaced carbon pairs being 1, 1/3, or 1/4. Fractions that contain a large group of such compounds with a substantial S enrichment can be collected by column chromatography, but no single pure compound can be isolated. Since the mass spectra can be interpreted in alternate ways involving S incorporation as an adduct, evidence was sought for their existence from a detailed study of the fluorescence of these species. The fluorescence emission spectra are red-shifted from and consistent with absorption spectra and can be attributed to the emission from symmetry-broken distorted S-doped derivatives of fullerenes. An optical bandgap of 2.5 eV is derived for the S-doped fullerenes resulting from the splitting of the hu degenerate state. The fluorescence lifetimes of these molecules are 2−7 ns, considerably larger than those of the undoped fullerenes.