Noble gas inserted compounds of borazine and its derivative B<Subscript>3</Subscript>N<Subscript>3</Subscript>R<Subscript>6</Subscript>: structures and bonding

Quantum chemistry computations were performed at the MP2 and B3LYP levels of theory using the basis sets aug-cc-pVDZ and def2-TZVPPD to study the noble gas (Ng) compounds formed by insertion of a Ng atom (Kr, Xe, Rn) into the B–H/F and N–H/F bonds of inorganic benzene B₃N₃H₆ and its fluorine derivative B₃N₃F₆. The geometrical structures were optimized and vibrational analysis was carried out to demonstrate these structures being local minima on the potential energy surface. The thermodynamic properties of the formation process of Ng compounds were calculated. A series of theoretical methods based on the wavefunction analysis, including NBO, AIM and ELF methods and energy decomposition analysis, was used to investigate the bonding nature of the noble gas atoms and the properties of the Ng compounds. The N–Ng bond was found to be stronger than the B–Ng bond, but the B–Ng bond is of typical covalent character and σ-donation from the Ng atom to the ring B atom makes the predominant contribution towards stability of the B-Ng bond. NICS calculation shows that these Ng-containing compounds are of weak π-aromaticity.     

Calculations of the C<Subscript>2</Subscript> fragmentation energies of higher fullerenes C<Subscript>80</Subscript> and C<Subscript>82</Subscript>

The C₂ fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C₈₀ and C₈₂ fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C₂ corrections were included in the calculation of fragmentation energies for comparison with experimental C₂ fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C₂ fragmentation of C₈₀, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{80}}}} ^{ + } } \right)}\) agree well with experimental data, whereas in the case of C₈₂ fragmentation, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{82}}}} ^{ + } } \right)}\) exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C₂ fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.

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Figure C₂ fragmentation energies of C₈₀ and C₈₂ fullerenes have been calculated with B3LYP/6-31G* model chemistry, with semiempirical self-consistent-charge density-functional tight-binding (SCC-DFTB) method and with the more rigorous MP2 method. The influence of basis set extension and level of theory on the resulting fragmentation energies is discussed

     

Theoretical investigation of reactivities of amines in the <Emphasis Type="Italic">N</Emphasis>-nitrosation reactions by N<Subscript>2</Subscript>O<Subscript>3</Subscript>

N-nitrosamine is a class of carcinogenic, mutagenic, and teratogenic compounds, which can be produced from N-nitrosation of amine by nitrosating agents. N-nitrosation of 19 amines (eight acyclic amines, five heterocyclic amines, and six amines with unsaturated groups) by N₂O₃ was investigated at the CBS-QB3 level of theory. The results indicate that generally the heterocyclic amines have the highest reactivities among the three kinds of amines, whereas the reactivities of the amines with unsaturated and electron-withdrawing groups are relatively low. Frontier molecular orbital analysis indicates that the energy gap between the HOMO of an amine and the LUMO of N₂O₃ has a close connection with the reactivity of an amine. A structure-reactivity relationship of amines in the N-nitrosation reactions by N₂O₃ was established using the stepwise multivariate linear regression. The results indicate that the reactivity of an amine has a definite relationship (R_adj² = 0.947) with the heterolytic bond dissociation energy of R₁R₂N-H bond, energy of HOMO, NBO occupancy of the natural lone pair orbital of N atom, the NBO charge of the N atom, and the pyramidalization angle of an amine. This work will be helpful to gain more insight into the N-nitrosation reactions.     

DFT study of isomers of the ruthenium dihydride complex RuH<Subscript>2</Subscript>(CO)<Subscript>2</Subscript>(AsMe<Subscript>2</Subscript>Ph)<Subscript>2</Subscript>

A density functional theory (DFT) study of cct-As, ccc, and cct-CO isomers of the ruthenium dihydride complex RuH₂(CO)₂(AsMe₂Ph)₂ is reported (see Scheme for the labeling isomer 34 structures of RuH₂(CO)₂(AsMe₂Ph)₂). Complex geometries and relative energies of different isomers have been calculated with both B3LYP and M06-2X functionals. The results show that the B3LYP calculated Boltzmann populations of cct-As, ccc, and cct-CO isomers are 65.5, 34.2, and 0.3%, respectively. These are in better agreement with the experimental data than those calculated at the M06-2X level. However, the calculations of ¹H NMR chemical shifts were found to be better described with M06-2X than with B3LYP or with HF level of theories. In addition, a transition state between the two most stable isomers was determined through DFT/(B3LYP or M06-2X) calculations.

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Graphical Abstract Scheme: Labeling structure of RuH₂(CO)₂(AsMe₂Ph)₂

     

Theoretical study of the reaction mechanism of CH<Subscript>3</Subscript>NO<Subscript>2</Subscript> with NO<Subscript>2</Subscript>, NO and CO: the bimolecular reactions that cannot be ignored

The intriguing decompositions of nitro-containing explosives have been attracting interest. While theoretical investigations have long been concentrated mainly on unimolecular decompositions, bimolecular reactions have received little theoretical attention. In this paper, we investigate theoretically the bimolecular reactions between nitromethane (CH₃NO₂)—the simplest nitro-containing explosive—and its decomposition products, such as NO₂, NO and CO, that are abundant during the decomposition process of CH₃NO₂. The structures and potential energy surface (PES) were explored at B3LYP/6-31G(d), B3P86/6-31G(d) and MP2/6-311?+?G(d,p) levels, and energies were refined using CCSD(T)/cc-pVTZ methods. Quantum chemistry calculations revealed that the title reactions possess small barriers that can be comparable to, or smaller than, that of the initial decomposition reactions of CH₃NO₂. Considering that their reactants are abundant in the decomposition process of CH₃NO₂, we consider bimolecular reactions also to be of great importance, and worthy of further investigation. Moreover, our calculations show that NO₂ can be oxidized by CH₃NO₂ to NO₃ radical, which confirms the conclusion reached formerly by Irikura and Johnson [(2006) J Phys Chem A 110:13974–13978] that NO₃ radical can be formed during the decomposition of nitramine explosives.     

The addition reactions of germylenoid H<Subscript>2</Subscript>GeAlCl<Subscript>3</Subscript> with ethylene: a theoretical investigation

Theoretical calculations using the M062X and QCISD methods were performed on the addition reactions of the aluminum germylenoid H₂GeAlCl₃ with ethylene. The most two stable structures of germylenoid H₂GeAlCl₃, i.e., the p-complex and three-membered ring structures, respectively, were employed as reactants. The calculated results indicate that, for the p-complex, H₂GeAlCl₃ there are two pathways, I and II, of which path I involves just one transition state, while path II involves two transition states between reactants and products. Comparing the reaction barrier heights of path I (44.6 kJ mol^?1) and II (37.6 kJ mol^?1), the two pathways are competitive, with similar barriers under the same conditions, while for the three-membered ring structure, another two pathways, III and IV, also exist. Path III has one transition state; however, in path IV, two transition states exist. By comparing their barrier heights, path III (barrier height 39.2 kJ mol^?1) could occur more easily than path IV (barrier height 92.8 kJ mol^?1). Considering solvent effects on these addition reactions, the PCM model and CH₂Cl₂ solvent were used in calculations, and the calculated results demonstrate that CH₂Cl₂ solvent is unfavorable for the reactions, except for path II. In CH₂Cl₂ solvent, paths II and III are more favorable than paths I and IV.     

Theoretical study of the novel sandwich compound [Au<Subscript>3</Subscript>Cl<Subscript>3</Subscript>Tr<Subscript>2</Subscript>]<Superscript>2+</Superscript>

A theoretical study of a sandwich compound with a metal monolayer sheet between two aromatic ligands is presented. A full geometry optimization of the [Au₃Cl₃Tr₂]²⁺ (1) compound, which is a triangular gold(I) monolayer sheet capped by chlorines and bounded to two cycloheptatrienyl (Tr) ligands was carried out using perturbation theory at the MP2 computational level and DFT. Compound (1) is in agreement with the 18–electron rule, the bonding nature in the complex may be interpreted from the donation interaction coming from the Tr rings to the Au array, and from the back-donation from the latter to the former. NICS calculations show a strong aromatic character in the gold monolayer sheet and Tr ligands; calculations done with HOMA, also report the same aromatic behavior on the cycloheptatrienyl fragments giving us an insight on the stability of (1). The Au –Au bond lengths indicate that an intramolecular aurophilic interaction among the Au(I) cations plays an important role in the bonding of the central metal sheet. Figure (a) Ground state geometry of complex 1; (b) Top view of compound 1 and Wiberg bond orders computed with the MP2/B1 computational method; (c) Lateral view of compound 1 and NICS values calculated with the MP2/B1 method; the values in parenthesis were obtained at the VWN/TZP level     

Ab initio studies on the decomposition kinetics of CF<Subscript>3</Subscript>OCF<Subscript>2</Subscript>O radical

The present study deals with the decomposition of CF₃OCF₂O radical formed from a hydrofluoroether, CF₃OCHF₂ (HFE-125), in the atmosphere. The study is performed using ab initio quantum mechanical methods. Two plausible pathways of decomposition of the titled species have been considered, one involving C-O bond scission and the other occurring via F atom elimination. The geometries of the reactant, products and transition states involved in the decomposition pathways are optimized and characterized at DFT (B3LYP) level of theory using 6-311G(d,p) basis set. Single point energy calculations have been performed at G2M(CC,MP2) level of theory. Out of the two prominent decomposition channels considered, the C-O bond scission is found to be dominant involving a barrier height of 15.3 kcal mol⁻¹ whereas the F-elimination path proceeds with a barrier of 26.1 kcal mol⁻¹. The thermal rate constants for the above two decomposition pathways are evaluated using canonical transition state theory (CTST) and these are found to be 1.78 × 10⁶ s⁻¹ and 2.83 × 10⁻⁷ s⁻¹ for C-O bond scission and F-elimination respectively at 298 K and 1 atm pressure. Transition states are searched on the potential energy surfaces involved during the decomposition channels and each of the transition states is characterized. The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate (IRC) calculation.     

Noble gas supported boron-pentagonal clusters B<Subscript>5</Subscript>Ng<Subscript>n</Subscript><Superscript>3+</Superscript>: exploring the structures and bonding

A novel type of trivalent BNg five-membered cational species B₅Ng_n³⁺(Ng = He~Rn, n = 1~5) has been found and investigated theoretically using the B3LYP and MP2 methods with the def2-QZVPPD and def2-TZVPPD basis sets. The geometry, harmonic vibrational frequencies, bond energies, charge distribution, bond nature, aromaticity, and energy decomposition analysis of these structures were reported. The calculated B?Ng bond energy is quite large (the averaged bond energy is in the range of 209.2~585.76 kJ mol^-1) for heavy rare gases and increases with the Ng atomic number. The analyses of the molecular wavefunction show that in the BNg compounds of heavy Ng atoms Ar~Rn, the B?Ng bonds are of typical covalent character. Nuclear independent chemical shifts display that both B₅³⁺ and B₅Ng_n³⁺(n=1~5) have obvious aromaticity. Energy decomposition analysis shows that these BNg compounds are mainly stabilized by the σ-donation from the Ng valence p orbital to the B₅³⁺ LUMO. These findings offer valuable clues toward the design and synthesis of new stable Ng-containing compounds.     

Theoretical <Emphasis Type="Italic">ab initio </Emphasis>Study of TiCl<Subscript>4</Subscript> Ammonolysis: Gas Phase Reactions of TiN Chemical Vapor Deposition

The mechanism of TiCl₄ ammonolysis has been studied theoretically at ab initio Hartree-Fock, B3LYP, MP2 and CCSD(T)//B3LYP levels using effective core potentials for Ti and Cl and 6-31G* basis sets for N and H. TiCl₄ and products of its ammonolysis form five- and six-coordinated complexes with ammonia, which intermediate substitution of Cl atoms by NH₂ groups. Transition state energies for the subsequent steps of ammonolysis decrease with increasing number of NH₂ groups bound to Ti. The energy of the transition state for the first step of ammonolysis is 19 kcal mol^-1 above the energy of the reactants (TiCl₄+NH₃) and 8 kcal mol^-1 above the products (TiCl₃NH₂ + HCl). The following steps have transition states energetically located below the products, indicating weak hydrogen bonded complex formation as intermediate between transition state and product. A thermodynamic estimation shows the last step of ammonolysis to be endothermic, while the first three steps are exothermic if the adduct formation energy is taken into account.     

The influence of Sc doping on structural,electronic and optical properties of Be<Subscript>12</Subscript>O<Subscript>12</Subscript>, Mg<Subscript>12</Subscript>O<Subscript>12</Subscript> and Ca<Subscript>12</Subscript>O<Subscript>12</Subscript> nanocages: a DFT study

Density functional theory (DFT) calculations were used to study the effect of scandium doping on the structural, energetic, electronic, linear and nonlinear optical (NLO) properties of Be₁₂O₁₂, Mg₁₂O₁₂ and Ca₁₂O₁₂ nanoclusters. Scandium (Sc) doping on nanoclusters leads to narrowing of their E _g, which enhances their conductance greatly. Also, the polarizability (α) and first hyperpolarizability (β₀) of nanoclusters were dramatically increased as Be, Mg or Ca atoms are substituted with a Sc atom. Among all clusters, α and β₀ values for Sc-doped Ca₁₂O₁₂ were the largest. Consequently, the effect of the doping atom, as well as of cluster size, on electronic and optical properties was explored. Time dependent (TD)-DFT calculations were also carried out to confirm the β₀ values; the results show that the higher value of first hyperpolarizability belongs to Sc-doped Ca₁₂O₁₂, which has the smallest transition energy (ΔEgn). The results obtained show that these clusters can be candidates for using in electronic devices and NLO materials in industry.     

Mechanism leading to N<Subscript>2</Subscript>O production in wastewater treating biofilm systems

Wastewater treatment plants are known to be important point sources for nitrous oxide (N₂O) in the anthropogenic N cycle. Biofilm based treatment systems have gained increasing popularity in the treatment of wastewater, but the mechanisms and controls of N₂O formation are not fully understood. Here, we review functional groups of microorganism involved in nitrogen (N) transformations during wastewater treatment, with emphasis on potential mechanism of N₂O production in biofilms. Biofilms used in wastewater treatment typically harbour aerobic and anaerobic zones, mediating close interactions between different groups of N transforming organisms. Current models of mass transfer and biomass interactions in biofilms are discussed to illustrate the complex regulation of N₂O production. Ammonia oxidizing bacteria (AOB) are the prime source for N₂O in aerobic zones, while heterotrophic denitrifiers dominate N₂O production in anoxic zones. Nitrosative stress ensuing from accumulation of NO₂ ^? during partial nitrification or denitrification seems to be one of the most critical factors for enhanced N₂O formation. In AOB, N₂O production is coupled to nitrifier denitrification triggered by nitrosative stress, low O₂ tension or low pH. Chemical N₂O production from AOB intermediates (NH₂OH, HNO, NO) released during high NH₃ turnover seems to be limited to surface-near AOB clusters, since diffusive mass transport resistance for O₂ slows down NH₃ oxidation rates in deeper biofilm layers. The proportion of N₂O among gaseous intermediates (NO, N₂O, N₂) in heterotrophic denitrification increases when NO or nitrous acid (HNO₂) accumulates because of increasing NO₂ ^?, or when transient oxygen intrusion impairs complete denitrification. Limited electron donor availability due to mass transport limitation of organic substrates into anoxic biofilm zones is another important factor supporting high N₂O/N₂ ratios in heterotrophic denitrifiers. Biofilms accommodating Anammox bacteria release less N₂O, because Anammox bacteria have no known N₂O producing metabolism and reduce NO₂ ^? to N₂, thereby lowering nitrosative stress to AOB and heterotrophs.     

Structural and Optical Properties of Novel In<Subscript>2</Subscript>O<Subscript>3</Subscript> Nanoparticle-Assembled Nanorods

In₂O₃ nanoparticle-assembled nanorods with distinct surface morphologies have been newly synthesized by a dehydration process of self-assembled In(OH)₃ nanorods obtained from a liquid-based route. The reaction mechanism and the structural transformation between these two one-dimensional nanorods, In₂O₃ and In(OH)₃, were precisely characterized by means of various qualitative and quantitative analyses with X-ray scattering simulations. The broad absorption band in the UV–visible spectrum evidently originates from the nanoparticle-assembling effect within the In₂O₃ nanorods. An intensive photoluminescence emission at 440 nm observed under an excitation wavelength of 325 nm is attributed to the existence of oxygen vacancies within the In₂O₃ nanorods.     

Xylem parenchyma cells deliver the H<Subscript>2</Subscript>O<Subscript>2</Subscript> necessary for lignification in differentiating xylem vessels

Lignification in Zinnia elegans L. stems is characterized by a burst in the production of H₂O₂, the apparent fate of which is to be used by xylem peroxidases for the polymerization of p-hydroxycinnamyl alcohols into lignins. A search for the sites of H₂O₂ production in the differentiating xylem of Z. elegans stems by the simultaneous use of optical (bright field, polarized light and epi-polarization) and electron-microscope tools revealed that H₂O₂ is produced on the outer-face of the plasma membrane of both differentiating (living) thin-walled xylem cells and particular (non-lignifying) xylem parenchyma cells. From the production sites it diffuses to the differentiating (secondary cell wall-forming) and differentiated lignifying xylem vessels. H₂O₂ diffusion occurs mainly through the continuous cell wall space. Both the experimental data and the theoretical calculations suggest that H₂O₂ diffusion from the sites of production might not limit the rate of xylem cell wall lignification. It can be concluded that H₂O₂ is produced at the plasma membrane in differentiating (living) thin-walled xylem cells and xylem parenchyma cells associated to xylem vessels, and that it diffuses to adjacent secondary lignifying xylem vessels. The results strongly indicate that non-lignifying xylem parenchyma cells are the source of the H₂O₂ necessary for the polymerization of cinnamyl alcohols in the secondary cell wall of lignifying xylem vessels.     

Effects of the Oral Administration of K<Subscript>2</Subscript>Cr<Subscript>2</Subscript>O<Subscript>7</Subscript> and Na<Subscript>2</Subscript>SeO<Subscript>3</Subscript> on Ca,Mg, Mn,Fe, Cu,and Zn Contents in the Heart,Liver, Spleen,and Kidney of Chickens

This study aimed to investigate the effects of selenium on the ion profiles in the heart, liver, spleen, and kidney through the oral administration of hexavalent chromium. Approximately 22.14 mg/kg b.w. K₂Cr₂O₇ was added to water to establish a chronic poisoning model. Different selenium levels (0.00, 0.31, 0.63, 1.25, 2.50, and 5.00 mg Na₂SeO₃/kg b.w.) around the safe dose were administered to the experimental group model. Ca, Mg, Mn, Fe, Cu, and Zn were detected in the organs through flame atomic absorption spectrometry after these organs were exposed to K₂Cr₂O₇ and Na₂SeO₃ for 14, 28, and 42 days. Results showed that these elements exhibited various changes. Ca contents declined in the heart, liver, and spleen. Ca contents also decreased on the 28th day and increased on the 42nd day in the kidney. Mn contents declined in the heart and spleen but increased in the kidney. Mn contents also decreased on the 28th day and increased on the 42nd day in the liver. Cu contents declined in the heart and spleen. Cu contents increased on the 28th day and decreased on the 42nd day in the liver and kidney. Zn contents declined in the heart and spleen. Zn contents increased on the 28th day and decreased on the 42nd day in the liver and kidney. Fe contents decreased in the heart and liver. Fe contents increased on the 28th day and decreased on the 42nd day in the spleen and kidney. Mg contents did not significantly change in these organs. Appropriate selenium contents enhanced Mn and Zn contents, which were declined by chromium. Conversely, appropriate selenium contents reduced Ca, Fe, and Cu contents, which were increased by chromium. In conclusion, the exposure of chickens to K₂Cr₂O₇ induced changes in different trace elements, and Na₂SeO₃ supplementation could alleviate this condition.     

Improved degradation of lignocellulosic biomass pretreated by Fenton-like reaction using Fe<Subscript>3</Subscript>O<Subscript>4</Subscript> magnetic nanoparticles

The ability of Fe₃O₄ Fenton-like reaction to produce glucose from lignocellulosic biomass was investigated. Fe₃O₄ magnetite nanoparticles were chemically synthesized from iron salts (a mixture of 1 M FeCl₂ and 2M FeCl₃) using an ammonia solution (30% NH₄OH). The synthesized Fe₃O₄ nanoparticles were further characterized by X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy, scanning electron microscopy, and transmission electron microscopy. Reed stems and rice straw biomasses pretreated with optimized Fenton-like reagents (Fe₃O₄ and H₂O₂) increased glucose production by 177 and 87%, respectively, compared to the control without the catalysts.     

Elevated CO<Subscript>2</Subscript> ameliorated oxidative stress induced by elevated O<Subscript>3</Subscript> in <Emphasis Type="Italic">Quercus mongolica</Emphasis>

Using open top chambers, the effects of elevated O₃ (80 nmol mol⁻¹) and elevated CO₂ (700 μmol mol⁻¹), alone and in combination, were studied on young trees of Quercus mongolica. The results showed that elevated O₃ increased malondialdehyde content and decreased photosynthetic rate after 45 days of exposure, and prolonged exposure (105 days) induced significant increase in electrolyte leakage and reduction of chlorophyll content. All these changes were alleviated by elevated CO₂, indicating that oxidative stress on cell membrane and photosynthesis was ameliorated. After 45 days of exposure, elevated O₃ stimulated activities of superoxide dismutase (SOD, EC 1.15.1.1) and ascorbate peroxidase (APX, EC 1.11.1.11), but the stimulation was dampened under elevated CO₂ exposure. Furthermore, ascorbate (AsA) and total phenolics contents were not higher in the combined gas treatment than those in elevated O₃ treatment. It indicates that the protective effect of elevated CO₂ against O₃ stress was achieved hardly by enhancing ROS scavenging ability after 45 days of exposure. After 105 days of exposure, elevated O₃ significantly decreased activities of SOD, catalase (CAT, EC 1.11.1.6) and APX and AsA content. Elevated CO₂ suppressed the O₃-induced decrease, which could ameliorate the oxidative stress in some extent. In addition, elevated CO₂ increased total phenolics content in the leaves both under ambient O₃ and elevated O₃ exposure, which might contribute to the protection against O₃-induced oxidative stress as well.     

QM/MM theoretical study of the pentacoordinate Mn(III) and resting states of manganese-reconstituted cytochrome P450<Subscript>cam</Subscript>

Quantum mechanical/molecular mechanical (QM/MM) theoretical calculations were performed for the pentacoordinate Mn(III) and water-bound resting states of the Mn-reconstituted mutant of cytochrome P450_cam (Mn-P450_cam) in order to obtain insights into their characters, especially, their spin state ordering. The QM/MM study was carried out by use of the B3LYP and BLYP density functional theory (DFT) methods coupled to the CHARMM force field. Although the relative energies of possible spin states for the Mn-P450_cam species varied depending on the functional, this dependence was less significant compared with previous calculations on the corresponding intermediates of wild-type P450_cam. The results suggested that both Mn-P450_cam intermediates have quintet ground states. Additional time-dependent DFT (TDDFT) calculations were carried out for the quintet states of these species using the B3LYP and BP86 functionals with the electrostatic environmental effect included. The TDDFT results enabled us to assign the origins of the peaks observed in optical absorption spectra (Makris et al. in J. Inorg. Biochem. 100:507–518, 2006). Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.