Neighboring Carbon Atoms Research Articles

Theoretical analysis on the aromaticity of uracil: Important electronic configurations and solvent effect on the aromaticity

Aromaticity and the important electronic configurations of uracil are studied by index of deviation from aromaticity (IDA) and CiLC (CI/LMO/CASSCF) analysis. The calculated IDA values of uracil are 5.256 and 4.998 in gas phase and in solvent model, respectively. These large IDA values indicate that uracil is almost completely non-aromatic even in solvent. The CiLC analysis has revealed that main ionic electronic configurations of uracil involve charge transfer from endocyclic neighboring carbon atom to exocyclic oxygen atom.

Effects of non-rotationally symmetric aberrations on the quantitative measurement of lattice positions in a graphene monolayer using high-resolution transmission electron microscopy.

It is crucial to determine the position of lattice atoms in a monolayer specimen with high precision using high-resolution transmission electron microscopy (HRTEM). Image simulations indicate that the intensity centers of periodic lattice atoms in graphene may deviate from their intrinsic positions if non-rotationally symmetric aberrations (except for three-fold and six-fold aberrations) exist in the HRTEM imaging system. In this letter, we quantitatively compared the deviations caused by non-rotationally symmetric aberrations, which are equivalent to individually produce a π/4 phase shift in the wave aberration function at a given frequency of 7.2 nm(-1). A two-fold aberration caused a maximum shift of 0.3 Å, and in the images affected by the axial coma, graphene still maintained its hexagonal structure while all of the measured atomic positions deviated. Furthermore, we discovered that atoms on each sublattice tended to shift by similar distances in the image. Based on this rule, we retrieved the intrinsic bond length between neighboring carbon atoms by 'shifting' the measured atom positions in an experimental HRTEM image affected by residual aberrations.

Thermal stability of 3,4,5-trinitropyrazole and its ammonium salt

The thermal decomposition of trinitropyrazole (I) and its ammonium salt proceeds with a very strong self-acceleration, caused mainly by the catalytic action of the condensed products. The first-order rate constant for the initial stage k 1 describes the decomposition to a depth of conversion of 0.5% and is characterized by the following kinetic parameters E (kJ/mol) and log(A, s−1): 131.8 and 9.60 for the liquid phase and 116.0 and 8.57 for the solid state. The rate constant k 1 is smaller if the reaction occurs in nonpolar solvents and if I is methylated at position 1. All these data are interpreted in the framework of a mechanism according to which the reaction involves the oxidation by a nitro group of a neighboring carbon atom and proceeds through a highly polar cyclic transition state. Evaluation of the thermal stability of I is conducted using the method of a reference series composed of well-known regular HEs, which for the first time was implemented in terms of k 1. In the temperature range 20–80°C, the stability of trinitropyrazole is close to that of nitroglycerin. Trinitropyrazole ammonium salt is severalfold more stable than trinitropyrazole itself.

Facile Synthesis of Boron-doped Graphene Nanosheets with Hierarchical Microstructure at Atmosphere Pressure for Metal-free Electrochemical Detection of Hydrogen Peroxide

Hydrogen peroxide (H2O2) is an essential mediator for most of the oxidative biological reactions in enzyme-based biosensor systems, such as glucose oxidase, cholesterol oxidase, and alcohol oxidase. Synthesis of new catalysts to detect the concentration of H2O2 more precisely is indispensable for enzyme-based electrochemical biosensors. In this study, boron-doped graphene nanosheets (BGNs) with 2.2 atomic percentage (at%) boron doping level and a hierarchical microstructure were synthesized by an atmospheric-pressure carbothermal reaction as a noble-metal free catalyst for sensing H2O2. The isolated boron atoms on the BGNs surface act as the electrocatalytic sites by transferring charges to neighbor carbon atoms, and the hierarchical microstructure provides multidimensional electron transport pathways for charge transfer and therefore enhances the electrocatalytic ability. BGNs possess a higher reduction current in the cyclic voltammetry (CV) measurement than that of pristine graphene nanosheets (GNs) over the detection range of 0.0 to 10.0mM at −0.4V (vs. Ag/AgCl). The BGNs modified electrochemical sensor shows a linear range from 1.0 to 20.0mM of H2O2 with a sensitivity of 266.7±3.8μAmM−1cm−2 and limit of detection (LOD) of 3.8μM at a signal-to-noise (S/N) ratio of 3. The beneficial hierarchical microstructure and the synergetic effects arising from doping boron in GNs accomplish the better performance of the BGNs modified electrochemical sensor.

The electronic states of a double carbon vacancy defect in pyrene: a model study for graphene.

The electronic states occurring in a double vacancy defect for graphene nanoribbons have been calculated in detail based on a pyrene model. Extended ab initio calculations using the MR configuration interaction (MRCI) method have been performed to describe in a balanced way the manifold of electronic states derived from the dangling bonds created by initial removal of two neighboring carbon atoms from the graphene network. In total, this study took into account the characterization of 16 electronic states (eight singlets and eight triplets) considering unrelaxed and relaxed defect structures. The ground state was found to be of (1)Ag character with around 50% closed shell character. The geometry optimization process leads to the formation of two five-membered rings in a pentagon-octagon-pentagon (5-8-5) structure. The closed shell character increases thereby to ∼70%; the analysis of unpaired density shows only small contributions confirming the chemical stability of that entity. For the unrelaxed structure the first five excited states ((3)B3g, (3)B2u, (3)B1u, (3)Au and (1)Au) are separated from the ground state by less than 2.5 eV. For comparison, unrestricted density functional theory (DFT) calculations using several types of functionals have been performed within different symmetry subspaces defined by the open shell orbitals. Comparison with the MRCI results gave good agreement in terms of finding the (1)Ag state as a ground state and in assigning the lowest excited states. Linear interpolation curves between the unrelaxed and relaxed defect structures also showed good agreement between the two classes of methods opening up the possibilities of using extended nanoflakes for multistate investigations at the DFT level.

Negative differential resistance induced by SiNx co-dopant in armchair graphene nanoribbon

By adopting density functional theory in combination with nonequilibrium Green's functions, we investigated the electronic structure and transport properties of silicon/nitrogen ( Si / N ) co-doping armchair graphene nanoribbons (AGNRs) with SiN x co-dopant incorporated in neighboring carbon atoms. The results demonstrate that the electronic structure can be modulated by introducing SiN x co-dopants in AGNRs. The striking negative differential resistance behaviors in the range of low bias can be observed in Si / N co-doped AGNR devices. These remarkable properties suggest the potential application of Si / N co-doping AGNRs in molectronics.

Direct Synthesis of Graphene with Tunable Work Function on Insulators via In Situ Boron Doping by Nickel-Assisted Growth

Work function engineering, a precise tuning of the work function, is essential to achieve devices with the best performance. In this study, we demonstrate a simple technique to deposit graphene on insulators with in situ controlled boron doping to tune the work function. At a temperature higher than 1000 °C, the boron atoms substitute carbon sites in the graphene lattice with neighboring carbon atoms, leading to the graphene with a p-type doping behavior. Interestingly, the involvement of boron vapor into the system can effectively accelerate the reaction between nickel vapor and methane, achieving a fast graphene deposition. The changes in surface potential and work function at different doping levels were verified by Kelvin probe force microscopy, for which the work function at different doping levels was shifted between 20 and 180 meV. Finally, the transport mechanism followed by the Mott variable-range hopping model was found due to the strong disorder nature of the system with localized charge-carrie...

Study of the Influence of Transition Metal Atoms on Electronic and Magnetic Properties of Graphyne Nanotubes Using Density Functional Theory

Density functional theory calculations were used to study the adsorption of three transition metal atoms (Fe, Co, and Ni) on the external surface of two zigzag and two armchair graphyne nanotubes. The most stable position for the adsorption of all three metal atoms on all nanotubes is on the acetylenic ring. The metal atom remains in the plane of the acetylenic ring and makes six bonds with neighboring carbon atoms. Fe and Co complexes are magnetic and show different properties such as metal, semimetal, half-semimetal, and half-semiconductor. Ni complexes are nonmagnetic and semiconductive, with a narrower bandgap in comparison to bare tubes. The results of these calculations are relevant for spintronics and the design of future electronic devices.

Stereocontrolled synthesis of phosphinyl dipeptide isosteres using an asymmetric center at the phosphorus atom

Phosphinyl dipeptide isosteres (PDIs) are important compounds for the development of potent and selective inhibitors of various aspartic proteases and Zn metalloproteases. The stereochemistry of PDIs affects their biological activity. PDIs were prepared successfully using the concept of asymmetric induction from the chiral phosphorus atom of the phosphinate moiety to the neighboring carbon atom. This methodology involves diastereoselective α-alkylation and β'-alkylation of P-chiral phosphinate derivatives, prepared through lipase-catalyzed kinetic resolution, which produces Phe-Ala type and Pro-Phe type PDIs. The synthesis of Leu-Pro type PDIs in a protected form was achieved through a cross-coupling reaction of stereodefined α-amino-H-phosphinate with alkenyl triflate, followed by diastereoselective hydrogenation of the alkene moiety.

Point defect weakened thermal contraction in monolayer graphene.

We investigate the thermal expansion behaviors of monolayer graphene and three configurations of graphene with point defects, namely the replacement of one carbon atom with a boron or nitrogen atom, or of two neighboring carbon atoms by boron-nitrogen atoms, based on calculations using first-principles density functional theory. It is found that the thermal contraction of monolayer graphene is significantly decreased by point defects. Moreover, the corresponding temperature for negative linear thermal expansion coefficient with the maximum absolute value is reduced. The cause is determined to be point defects that enhance the mechanical strength of graphene and then reduce the amplitude and phonon frequency of the out-of-plane acoustic vibration mode. Such defect weakening of graphene thermal contraction will be useful in nanotechnology to diminish the mismatching or strain between the graphene and its substrate.

Perdeuteration: Vital to visualising solvent in neutron crystallography?

Early neutron crystallography studies replaced hydrogen with deuterium by soaking the crystal in heavy water prior to data collection, which exchanged labile hydrogen atoms (OH, NH, and SH) and solvent molecules only. Carbon bonded hydrogen atoms were not replaced, and their negative scattering density resulted in cancellation in nuclear density maps with resolution worse than 1.8 Å. Furthermore complications arise due to partial exchange, where deuterium is present in some unit cells and hydrogen in others. More recently it has become possible to completely replace hydrogen with deuterium through expression in a deuterated medium, using facilities such as the Deuteration Laboratory (DLAB) in Grenoble. As this is a complex and expensive task, the question arises as to the importance of its use. As well as allowing the study of radically smaller crystals (<0.05mm3), it also has the possibility to avoid the cancellation problems discussed above. We have obtained data from high quality crystals of partially hydrogenated type III antifreeze protein, where methyl protonated valine and leucine residues were incorporated into the perdeuterated protein. This provides an excellent opportunity to assess the effects of negative scattering from hydrogen atoms not only on the visibility of neighbouring carbon atoms but also on water molecules in close vicinity. The observation of these cancellation effects gives a further reason to use full deuteration in neutron protein crystallography.

Rectification induced in N2AA-doped armchair graphene nanoribbon device

By using non-equilibrium Green function formalism in combination with density functional theory, we investigated the electronic transport properties of armchair graphene nanoribbon devices in which one lead is undoped and the other is N2AA-doped with two quasi-adjacent substitutional nitrogen atoms incorporating pairs of neighboring carbon atoms in the same sublattice A. Two kinds of N2AA-doped style are considered, for N dopants substitute the center or the edge carbon atoms. Our results show that the rectification behavior with a large rectifying ratio can be found in these devices and the rectifying characteristics can be modulated by changing the width of graphene nanoribbons or the position of the N2AA dopant. The mechanisms are revealed to explain the rectifying behaviors.

Surface-Enhanced Raman Spectroscopy of Self-Assembled Monolayer Conformation and Spatial Uniformity on Silver Surfaces

We apply well-characterized silver nanowire grating (Ag-NWG) plasmonic surfaces as a Raman surface spectroscopy tool, which is based on surface-enhanced Raman scattering (SERS), to study the surface conformation characteristics of amine terminated alkanethiol self-assembled monolayers (SAMs). The surface conformation has implications for amine group availability, which is important when SAMs are used as linking layers for the binding of secondary molecules. Two different alkanethiols with different alkane chain lengths, namely 2-aminoethanethiol (cysteamine, CEA) and 11-aminoundecanethiol (AUT), are investigated. It is shown that both alkanethiols bind to Ag surfaces forming corresponding Ag-thiolates, however surface conformations, which are related to the ordering of the SAM, are different for these two SAM systems. The degree of SAM ordering is assessed by quantifying the integrated intensity ratio of the trans to gauche nu(C-S) vibrational bands from single spectra measurements and from spatially averaged spectra. These vibrational modes occur at different vibrational frequencies depending on the conformation (trans versus gauche) of the neighboring carbon atom. We demonstrate that the CEA SAMs are less ordered than AUT SAMs; thus, the amine terminal group availability differs between both systems.

Electronic and Quantum Transport Properties of Atomically Identified Si Point Defects in Graphene.

We report high-resolution scanning transmission electron microscopy images displaying a range of inclusions of isolated silicon atoms at the edges and inner zones of graphene layers. Whereas the incorporation of Si atoms to a graphene armchair edge involves no reconstruction of the neighboring carbon atoms, the inclusion of a Si atom to a zigzag graphene edge entails the formation of five-membered carbon rings. In all the observed atomic edge terminations, a Si atom is found bridging two C atoms in a 2-fold coordinated configuration. The atomic-scale observations are underpinned by first-principles calculations of the electronic and quantum transport properties of the structural anomalies. Experimental estimations of Si-doped graphene band gaps realized by means of transport measurements may be affected by a low doping rate of 2-fold coordinated Si atoms at the graphene edges, and 4-fold coordinated at inner zones due to the apparition of mobility gaps.

Quantum conductance of zigzag graphene oxide nanoribbons

The electronic properties of zigzag graphene oxide nanoribbons (ZGOR) are presented. The results show interesting behaviors which are considerably different from the properties of the perfect graphene nanoribbons (GNRs). The theoretical methods include a Huckel-tight binding approach, a Green's function methodology, and the Landauer formalism. The presence of oxygen on the edge results in band bending, a noticeable change in density of states and thus the conductance. Consequently, the occupation in the valence bands increase for the next neighboring carbon atom in the unit cell. Conductance drops in both the conduction and valence band regions are due to the reduction of allowed k modes resulting from band bending. The asymmetry of the energy band structure of the ZGOR is due to the energy differences of the atoms. The inclusion of a foreign atom's orbital energies changes the dispersion relation of the eigenvalues in energy space. These novel characteristics are important and valuable in the study of quantum transport of GNRs.

Catalytic Mechanisms of Sulfur-Doped Graphene as Efficient Oxygen Reduction Reaction Catalysts for Fuel Cells

Density functional theory (DFT) was applied to study sulfur-doped graphene clusters as oxygen reduction reaction (ORR) cathode catalysts for fuel cells. Several sulfur-doped graphene clusters with/without Stone–Wales defects were investigated and their electronic structures, reaction free energy, transition states, and energy barriers were calculated to predict their catalytic properties. The results show that sulfur atoms could be adsorbed on the graphene surface, substitute carbon atoms at the graphene edges in the form of sulfur/sulfur oxide, or connect two graphene sheets by forming a sulfur cluster ring. These sulfur-doped graphene clusters with sulfur or sulfur oxide locating at graphene edges show electrocatalytic activity for ORR. Catalytic active sites distribute at the zigzag edge or the neighboring carbon atoms of doped sulfur oxide atoms, which possess large spin or charge density. For those being the active catalytic sites, sulfur atoms with the highest charge density take a two-electron tran...

Semiconductor to metal transition by tuning the location of N2AA in armchair graphene nanoribbons

The electronic band structures and transport properties of N2AA-doped armchair graphene nanoribbons (aGNRs) with two quasi-adjacent substitutional nitrogen atoms incorporated in pairs of neighboring carbon atoms in the same sublattice A are investigated by using non-equilibrium Green function formalism in combination with density functional theory. The results show that the coupling effect between the Pz orbitals of carbon and nitrogen atoms plays an important role in the transition between semiconductor and metal by different locations of N2AA-doped aGNRs. And the striking negative differential resistance behaviors can be found in such devices. These tremendous properties suggest potential application of N2AA-doped aGNRs in graphene-based nanoelectronic devices.

A Catalyst with Two‐Coordinate Nickel: Theoretical and Catalytic Studies

AbstractThe bisadduct (cAAC)2NiIICl2 [1; cAAC = cyclic (alkyl)(amino)carbene] was directly synthesized by treating cAAC with NiCl2. Compound 1 was reduced to (cAAC)2Ni0 (2) by using lithium diisopropylamide or KC8. Crystals of 2 were stable under an inert gas for several months and decomposed upon heating above 165 °C. On the basis of the calculated natural bond orbital charge values of the nickel atom in 2, the oxidation state of nickel was determined to be between NiI and Ni0 (+0.34). Theoretical calculations suggested a closed‐shell singlet electronic configuration of 2 with little biradical character. Ab initio multiconfigurational C(R)ASSCF/CASPT2 calculations predicted a closed‐shell singlet electronic configuration (Ni0), whereas excited spin states possessed NiI character with unpaired electrons on neighboring carbon atoms. The catalytic activity of complex 2 was investigated for the homocoupling of various unactivated aryl chlorides/fluorides. The biaryls were obtained in good yields at moderate temperature. Theoretical studies showed that an intermediate containing NiIII was more favored than one with NiIV.

Supercapacitor performance of nitrogen-doped carbon nanotube arrays

Arrays of nitrogen-doped carbon nanotubes (N-CNTs) have been grown on Si substrates by thermolysis of vapors of acetonitrile and ferrocene. To change the content of incorporating nitrogen, carbonyls of Mo, W, and Cr were added in the reaction mixture. The products were comparatively studied using electron microscopy, Raman scattering, X-ray photoelectron spectroscopy, and charge/discharge cycling in an acidic electrolyte. Electrochemical characteristics of N-CNTs were correlated with nanotube length and chemical state of nitrogen. It is found that pyridinic nitrogen has determining effect on the N-CNT performance at low scan rates of potential. The density functional theory calculations of N-CNT models reveal that protonation of pyridinic nitrogen induces a net of negative charges on the neighboring carbon atoms that could increase the electrode capacitance. Cyclic voltammogram of nitrogen-doped carbon nanotube array at a scan rate of 2 mV s−1 in a 1 M H2SO4 aqueous solution and possible assignment of redox peaks.

Study of interaction between radioactive nuclides and graphite surface by the first-principles and statistic physics

The adsorption and desorption of four kinds of main radioactive productions (cesium, iodine, strontium and silver) on graphite surface in high temperature gas cooled reactors (HTGRs) have been studied. Using the first-principles density-functional theory, adsorptive geometry, energy and electron structure on the perfect and defective graphite surfaces have been calculated. It turns out that the adsorption of Cs, I and Sr atoms belongs to chemisorption while the adsorption of Ag is a pure physisorption. When introducing a vacancy in graphite surface, nuclide adatoms will be trapped by the vacancy and form chemical bonds with three nearest neighbor carbon atoms, leading to significant increase of the adsorption energy. In addition, a model of grand canonical ensemble is employed to deduce the adsorption rate as a function of temperature and partial pressure of nuclides produced. The transition temperate from adsorption to desorption of nuclides on graphite surface is defined as the inflexion point of the adsorption rate and its variation with nuclide density is obtained.