Theoretical study of the interaction between X (H,F) and graphene

This study investigates the interaction between X (X = H and F) and graphene C₅₄H₁₈ (D_6 h), and the potential energy surface of the graphene radical. The calculations on the structures and energies are further discussed thermodynamically and kinetically using the density function theory method at the B3LYP/6-31G (d) level. Our findings show that there are four distinct isomers of C₅₄H₁₈–X. C₅₄H₁₈–H² and C₅₄H₁₈–F⁴ are the most stable isomers in their own systems. In addition, the transition states, as well as reaction pathways of H transferring between different key points on representative patch, are given to explore the possible reaction mechanism. Finally, the stability of C₅₄H₁₈–X₂ is discussed through the density functional theory.     

Computational investigation of double nitrogen doping on graphene

Density functional theory (DFT) calculations were performed to study doping of two nitrogen atoms at different positions on a finite-sized graphene model of C₈₂H₂₄. We examined 21 structures of double nitrogen doped graphene to calculate their relative stabilities. The structure with two nitrogen atoms located apart is the most stable among the positional isomers considered in this study. For double nitrogen doping within a six-membered ring, the 1,4-position is more preferred than 1,3- or 1,2-positions for the finite-sized single layer graphene sheet. Our computational study supports the experimental observation of two nitrogen atoms at the 1,3- and 1,4-positions in a single six-membered ring of graphene. Furthermore, the structures with N-N bond are the least stable among two nitrogen doped graphene structures. The effects of nitrogen doping and the positions of two nitrogen atoms on the HOMO-LUMO energy gap of pristine graphene were analyzed.     

Chemical Structure of Piericidin A

Ozonolysis of Hydropiericidin A diacetate gave an acetylated monohydroxy acid, C₁₇H_32-34 (OCOCH₈)·COOH and its N-methoxycarbonyl amide, C₁₇H_32-34 (OCOCH₃)·CONHCOOCH₃. On the other hand, by ozonolysis of Piericidin A diacetate, an acid C₉H₁₂NO₃·C00H was obtained. On the basis of ultraviolet, infrared and NMR spectra and of chemical evidences, the structure (VI) or (VI′) was presented to this acid. Thus, the structure (VII) or (VII′) was proposed to Piericidin A.     

Theoretical study of the electronic properties of fluorographene

First-principles calculations were performed for fluorine-decorated graphene (fluorographene). Three different hexagonal clusters were used—circular (C₂₄H₁₂), triangular (C₂₃H₁₀) and rectangular (C₂₄H₁₂)—and the fluorine atoms were randomly distributed in the mesh. Graphene is structurally stable in the three geometries, but fluorographene stability is only attained for the circular and triangular clusters. Gaps of the circular graphene and the corresponding fluorographene are 2.94 and 1.13 eV, respectively; in the triangular case, the values are zero and 0.47 eV. Both the circular and triangular structures show a transition from ionic to covalent character.     

Energy gaps of graphene clusters: the first-principles calculations based on high-throughput screening

Abstract

With the enumeration of the triangular lattice fragments, we have systematically investigated the graphene clusters (C_nH_m, n = 14 – 24) with various sizes and shapes, whose structural stabilities and electronic properties are studied by the Hückel molecular orbital (HMO) method and the first-principles calculation. According to the formation energies, we show the structural stabilities of the clusters are closely related to the shape and size, as well as the chemical potential of hydrogen. The energy gaps obtained from the HMO method are in the same trend with the ones calculated by the first-principles calculations, indicating the effective screening of the gap minimum and maximum in a fast speed. There is a general decreasing of the energy gaps with the size increment due to the quantum confinement, meanwhile, the gaps are also highly dependent on the shape of the clusters for those with the same number of carbon atom.     

Studies on reactions of metallic iron with mixtures of aryl carboxylic acids (ArCOOH) and organic halides relevant to corrosion of steel. Preparation of [FeX(OCOAr)]n (X = Cl,Br, I) and its characterization

Crystalline, multinuclear [FeX(OCOAr)]_n (X = Cl, Br, I; Ar = C₆H₅, C₆H₅CHCH, C₆H₅CH₂) is produced by reactions acids (ArCOOH) and alkyl halides (RX). The reactions proceed smoothly above 180 °C, and the formation of [FeX(OCOAr)]_n is accompanished by formation of ester (ArCOOR), and H₂; the stoichiometry of the reaction is expressed by an equation, Fe + 2 ArCOOH + RX → (1/n)[FeX(OCOAr)]_n + ArCOOR + H₂. [FeX(OCOAr)]_n has been characterized by elemental analysis, its chemical reactivities with basic ligands, IR spectroscopy, powder X-ray diffraction pattern, thermogravimetric analysis, and magnetic susceptibility. A reaction mechanism involving a successive reaction of ArCOOH and RX with iron is proposed to elucidate the formation of [FeX(OCOAr)]_n. A reaction of metallic iron with a mixture of C₆H₅COOH and CCl₄ gives C₆H₅COCl in a good yield.     

Type I and II β-turns prediction using NMR chemical shifts

A method for predicting type I and II β-turns using nuclear magnetic resonance (NMR) chemical shifts is proposed. Isolated β-turn chemical-shift data were collected from 1,798 protein chains. One-dimensional statistical analyses on chemical-shift data of three classes β-turn (type I, II, and VIII) showed different distributions at four positions, (i) to (i + 3). Considering the central two residues of type I β-turns, the mean values of C_ο, C_α, H_N, and N_H chemical shifts were generally (i + 1) > (i + 2). The mean values of C_β and H_α chemical shifts were (i + 1) < (i + 2). The distributions of the central two residues in type II and VIII β-turns were also distinguishable by trends of chemical shift values. Two-dimensional cluster analyses on chemical-shift data show positional distributions more clearly. Based on these propensities of chemical shift classified as a function of position, rules were derived using scoring matrices for four consecutive residues to predict type I and II β-turns. The proposed method achieves an overall prediction accuracy of 83.2 and 84.2 % with the Matthews correlation coefficient values of 0.317 and 0.632 for type I and II β-turns, indicating that its higher accuracy for type II turn prediction. The results show that it is feasible to use NMR chemical shifts to predict the β-turn types in proteins. The proposed method can be incorporated into other chemical-shift based protein secondary structure prediction methods.     

The average local ionization energy as a tool for identifying reactive sites on defect-containing model graphene systems

In a continuing effort to further explore the use of the average local ionization energy $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ as a computational tool, we have investigated how well $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ computed on molecular surfaces serves as a predictive tool for identifying the sites of the more reactive electrons in several nonplanar defect-containing model graphene systems, each containing one or more pentagons. They include corannulene (C₂₀H₁₀), two inverse Stone-Thrower-Wales defect-containing structures C₂₆H₁₂ and C₄₂H₁₆, and a nanotube cap model C₂₂H₆, whose end is formed by three fused pentagons. Coronene (C₂₄H₁₂) has been included as a reference planar defect-free graphene model. We have optimized the structures of these systems as well as several monohydrogenated derivatives at the B3PW91/6-31G* level, and have computed their $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ on molecular surfaces corresponding to the 0.001 au, 0.003 au and 0.005 au contours of the electronic density. We find that (1) the convex sides of the interior carbons of the nonplanar models are more reactive than the concave sides, and (2) the magnitudes of the lowest $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ surface minima (the $ {{\overline{\mathrm{I}}}_{{\mathrm{S}\text{,}\min }}} $ ) correlate well with the interaction energies for hydrogenation at these sites. These $ {{\overline{\mathrm{I}}}_{{\mathrm{S}\text{,}\min }}} $ values decrease in magnitude as the nonplanarity of the site increases, consistent with earlier studies. A practical benefit of the use of $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ is that a single calculation suffices to characterize the numerous sites on a large molecular system, such as graphene and defect-containing graphene models.

Absorption and circular dichroism spectra of CuCl2 complexed with poly(S-carboxymethyl-L-cysteine) and poly(S-carboxyethyl-L-cysteine)

The interaction of CuCl₂ with poly(S-carboxymethyl-L -cysteine) (poly[Cys(CH₂COOH)]) and poly(S-carboxyethyl-L -cysteine) (poly[Cys(C₂H₄COOH)]) were studied by absorption spectra and circular dichroism (CD). On mixing CuCl₂ with polypeptide solutions, absorption bands appeared at 320–325 nm in both polypeptides, and at 255–260 nm in the case of poly[Cys(CH₂COOH)]. A stable bound species was formed in the case of poly[Cys(CH₂COOH)], since the apparent molar absorption coefficient of the bound species did not depend on the mixing ratio. From the absorption data, it was inferred that Cu²⁺ ions were complexed with the side chains, most probably with sulfur atoms and carboxyl groups. Induced optical activities were observed for the two polypeptides. The CD spectra of poly[Cys(CH₂COOH)] + CuCl₂ gave simpler aspects than those of poly[Cys(C₂H₄COOH)] + CuCl₂.     

Reaction mechanism of CH3M≡MCH3 (M=C, Si, Ge) with C2H4: [2+1] or [2+2] cycloaddition?

The mechanism of the cycloaddition reaction CH₃M≡MCH₃ (M=C, Si, Ge) with C₂H₄ has been studied at the CCSD(T)/6-311++G(d,p)//MP2/6-311++G(d,p) level. Vibrational analysis and intrinsic reaction coordinate (IRC), calculated at the same level, have been applied to validate the connection of the stationary points. The breakage and formation of the chemical bonds of the titled reactions are discussed by the topological analysis of electron density. The calculated results show that, of the three titled reactions, the CH₃Si≡SiCH₃+C₂H₄ reaction has the highest reaction activity because it has the lowest energy barriers and the products with the lowest energy. The CH₃C≡CCH₃+C₂H₄ reaction occurs only with difficulty since it has the highest energy barriers. The reaction mechanisms of the title reactions are similar. A three-membered-ring is initially formed, and then it changed to a four-membered-ring structure. This means that these reactions involve a [2+1] cycloaddition as the initial step, instead of a direct [2+2] cycloaddition.     

Effect of silver ion, carbon dioxide, and oxygen on ethylene action and metabolism

The relationship between ethylene action and metabolism was investigated in the etiolated pea seedling (Pisum sativum L. cv. Alaska) by inhibiting ethylene action with Ag⁺, high CO₂, and low O₂ and then determining if ethylene metabolism was inhibited in a similar manner. Ag⁺ (100 milligrams per liter) was clearly the most potent antiethylene treatment. Ag⁺ pretreatment inhibited the growth retarding action of 0.2 microliters per liter ethylene by 48% and it also inhibited the incorporation of 0.2 microliters per liter ¹⁴C₂H₄ into pea tips by the same amount. As the ethylene concentration was increased from 0.2 to 30 microliters per liter, the effectiveness of Ag⁺ in reducing ethylene action and metabolism declined in a similar fashion. Although Ag⁺ significantly inhibited the incorporation of ¹⁴C₂H₄ into tissue metabolites, the oxidation of ¹⁴C₂H₄ to ¹⁴CO₂ was unaffected in the same tissue.     

Boron- and nitrogen-doped carbon nanotubes and graphene

Multi-walled, single-walled and double-walled carbon nanotubes as well as graphene can be doped with boron and nitrogen. B₂H₆ has been generally used as the boron source while NH₃ or pyridine is employed as the nitrogen source. Doping carbon nanotubes and graphene with boron and nitrogen brings about significant changes in the electronic structure and properties. Such doping not only results in desirable properties but also allows manipulation of properties for specific purposes. Doping with boron- and nitrogen-causes marked changes in the Raman spectra of the carbon nanostructures. In this article, we present the synthesis, characterization and properties of boron- and nitrogen-doped carbon nanotubes and graphene.     

Odd-electron molecular theory of graphene hydrogenation

This paper highlights the molecular essence of graphene and presents its hydrogenation from the viewpoint of the odd-electron molecular theory. This chemical transformation was performed computationally, using a particular algorithm, through the stepwise addition of either hydrogen molecules or hydrogen atoms to a pristine graphene molecule. The graphene was considered to be a membrane, such that either both sides or just one side of the membrane was accessible to adsorbate, and the atoms on the perimeter of the membrane were either fixed (fixed membrane) or free to move (free-standing membrane). The algorithm explored the spatial distribution of the number of effectively unpaired electrons N (DA) over the carbon skeleton of the molecule. The highest ranked N (DA) values were considered to indicate the target atoms at each reaction step. The dependence of the hydrogenation itself and the final graphene hydrides on external factors such as whether the membrane was fixed, if both sides or only one side of the membrane were accessible to hydrogen, and whether the hydrogen was in the molecular or atomic state. Complete hydrogenation followed by the formation of a regular chairlike graphane structure (CH)(n) was only found to be possible for a fixed pristine graphene membrane for which the basal plane is accessible to hydrogen atoms from both sides.     

Dissipation of the Membrane Potential in Susceptible Corn Mitochondria by the Toxin of Helminthosporium maydis, Race T, and Toxin Analogs

We have tested directly the effect of Helminthosporium maydis T (Hmt) toxin and various analogs on the membrane potential formed in mitochondria isolated from a Texas (T) cytoplasmic male-sterile and a normal (N) corn. ATP, malate or succinate generated a membrane potential (negative inside) as monitored by the absorbance change of a cationic dye, safranine. The relative membrane potential (Δψ) could also be detected indirectly as ⁴⁵Ca²⁺ uptake. Hmt toxin added to T mitochondria dissipated the steady state Δψ similar to addition of a protonophore, carbonyl cyanide m-chlorophenylhydrazone (CCCP). Toxin analogs (Cpd XIII: C₄₁H₆₈O₁₂ and Cpd IV: C₂₅H₄₄O₆), reduced native toxin (RT2C: C₄₁H₈₄O₁₃) and Pm toxin (band A: C₃₃H₆₀O₈, produced by the fungus, Phyllosticta maydis) were effective in dissipating Δψ and decreasing Ca²⁺ uptake with the following order: Pm (100) » HmT (23-30) > Cpd XIII (11-25) » RT2C (0-4−1.8) > Cpd IV (0.2−1.0). In contrast, the toxins and analogs had no effect on Δψ formed in N mitochondria. The striking similarities of the HmT toxin (band 1: C₄₁H₆₈O₁₃) and Cpd XIII on T mitochondrial activities provide strong evidence supporting the correctness of the polyketol structure assigned to the native toxin. Since the Δψ in energized mitochondria is caused mainly by the electrogenic extrusion of H⁺, the results support the idea that HmT toxin increases membrane permeability of T mitochondria to H⁺. The host specificity of the toxin suggests that an interaction with unique target site(s) on the inner mitochondrial membrane of T corn causes H⁺ leakage.     

Coordination properties of α-hydroxy carboxylic acids. Part I. Binuclear niobium (V) complex acids and some salts

The conditions of dissolution of freshly precipitated niobium (V) oxide in α-hydroxy carboxylic acids glycolic, lactic, malic and tartaric were investigated. The dissolution is a function of the molar ratio α-hydroxy carboxylic acid/hydrated niobium(V) oxide, pH of the solution, temperature and time. From solutions of α-hydroxy monocarboxylic acids at 2 < pH < 3 the binuclear complexes H₃O[Nb₂O₄(C₂H₂O₃)(C₂H₃O₃)]·H₂O and H₃O[Nb₂O₄(C₃H₄O₃)(C₃H₅O₃)]·H₂O were isolated. Colourless, poorly-crystalline complexes are 1:1 electrolytes and, according to i.r. spectral evidence, the binuclearity in their structures is achieved through oxygen bridges. With α-hydroxy dicarboxylic acids crystalline M[Nb₂O₃(C₄H₃O₅)(C₄H₄O₅)]·nH₂O and poorly crystalline complexes, M₂[Nb₂O₂(C₄H₂O₆)₂]·nH₂O, M = H₃O⁺, NH₄⁺ were prepared as 1:1 electrolytes for the former and 1:2 electrolytes for the latter. Analytical, spectral, conductometric and potentiometric titration data give evidence for binuclear malatoniobate(V) and tartratoniobate(V) anions with bridging complex-forming agents.     

DFT studies of acrolein molecule adsorption on pristine and Al- doped graphenes

The ability of pristine graphene (PG) and Al-doped graphene (AlG) to detect toxic acrolein (C₃H₄O) was investigated by using density functional calculations. It was found that C₃H₄O molecule can be adsorbed on the PG and AlG with adsorption energies about ?50.43 and – v30.92 kcal mol^?1 corresponding to the most stable configurations, respectively. Despite the fact that interaction of C₃H₄O has no obvious effects on the of electronic properties of PG, the interaction between C₃H₄O and AlG can induce significant changes in the HOMO/LUMO energy gap of the sheet, altering its electrical conductivity which is beneficial to sensor designing. Thus, the AlG may be sensitive in the presence of C₃H₄O molecule and might be used in its sensor devices. Also, applying an external electric filed in an appropriate orientation (almost stronger than 0.01 a.u.) can energetically facilitate the adsorption of C₃H₄O molecule on the AlG.     

Isolation and Structure of Sclerothionine,a Metabolite of Sclerotinia Fungus

A new sulfur-containing imidazole compound, m.p. 218~223°C (decomp.), ${[\alpha ]}_{\text{D}}^{24}+{7.4}^{°}$ in water), C₁₁H₁₉N₃O₃S was isolated from sclerotia of Sclerotinia libertiana and named sclerothionine. The chemical structure of sclerothionine was identified with 2-hydroxyethyl-ergothioneine which was synthesized from ethylene chlorhydrine and ergothioneine.     

Study of the Mechanism of Action of p-Chloromercuribenzoate on Endonuclease from the Bacterium Serratia marcescens

The mechanism of action of p-chloromercuribenzoate (PCMB) on Serratia marcescens nuclease was investigated. The analysis showed that PCMB forms complexes with DNA. Binding of C₇H₅O₂Hg⁺ to DNA changes the secondary structure of the DNA. These changes alter the enzymatic activity of S. marcescens nuclease, which was previously found to be sensitive to the secondary structure of the substrates. The nuclease activity was either suppressed or stimulated in the presence of PCMB depending on the C₇H₅O₂Hg⁺ to nucleotide equivalent ratio. Binding of C₇H₅O₂Hg⁺ to DNA did not form an abortive enzyme–substrate complex. Binding of Mg²⁺ to the C₇H₅O₂Hg–DNA complex caused appropriate changes in secondary structure of the substrate. Since Mg²⁺ and C₇H₅O₂Hg⁺, though differing in the type of metal cation, are similar in their mechanisms of influence on enzymatic activity of S. marcescens nuclease, the identity of other metal-containing effectors in their mechanism of action on Serratia marcescens nuclease is assumed.     

Synthesis and molecular structure of trinuclear mixed-metal cluster cations containing arene and hydrido ligands

The mixed-metal trinuclear cluster cations [H₃Ru₂(C₆Me₆)₂Os(C₆H₆)(O)]⁺ (1), [H₃Ru₂(1,2,4,5-C₆H₂Me₄)₂Os(p-MeC₆H₄ⁱPr)(O)]⁺ (2) and [H₃Ru₂(1,2,4,5-C₆H₂Me₄)₂Os(C₆H₆)(O)]⁺ (3) have been synthesised from the corresponding dinuclear precursors [H₃Ru₂(arene)₂]⁺ and the corresponding mononuclear complexes [Os(arene)(H₂O)₃]²⁺, isolated and characterised as the tetrafluoroborate and hexafluorophosphate salts. The cations 1, 2 and 3 are heteronuclear analogues of the cluster cation [H₃Ru₃(C₆H₆)(C₆Me₆)₂(O)]⁺ that possesses a homonuclear metallic core. The single-crystal X-ray structure analyses of [1][BF₄], [2][PF₆] and [3][PF₆] reveal an equiangular metal triangle despite the presence of an osmium atom in the metallic core.     

The Non-Ionic Detergent Brij 58 Conserves the Structure of the Tonoplast H+-ATPase of Mesembryanthemum crystallinum L. During Solubilization and Partial Purification

The effects of solubilization with Triton X-100 or Brij 58 on the polypeptide composition and the substrate affinity of the tonoplast H⁺-ATPase of plants of Mesembryanthemum crystallinum performing C₃ photosynthesis or crassulacean acid metabolism (CAM) have been compared. Although all known subunits of the tonoplast H⁺-ATPase were present in the fraction of solubilized proteins after treatment with Brij 58 or Triton X-100, with Triton X-100 the apparent K_M value for ATP hydrolysis was increased by a factor of 1.8 and 1.5 in preparations from C₃ and CAM plants, respectively, even at low concentrations in contrast to treatment with Brij 58. This is explained by structural changes of the tonoplast H⁺-ATPase due to the Triton X-100 treatment. After solubilization with Brij 58 the tonoplast H⁺-ATPase was partially purified by Superose-6 size-exclusion FPLC. When Brij 58 was present, addition of lipids to the chromatography buffer was not necessary to conserve enzyme activity in contrast to previously described purification methods using Triton X-100. The substrate affinity of the partial purified H⁺-ATPase was similar to the substrate affinity obtained for ATP-hydrolysis of native tonoplast vesicles, indicating that the enzyme structure during partial purification was conserved by using Brij 58. The results underline that the lipid environment of the tonoplast H⁺-ATPase is important for enzyme structure and function.