A DFT study of hydride transfers to the carbonyl oxygen of DDQ

Hydride‐transfer reactions between benzylic substrates and 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ) were investigated by DFT (density functional theory) calculations. The lowest unoccupied molecular orbital of DDQ has the largest extension on two carbonyl oxygens, which comes from two‐step mixing of antisymmetric orbitals of fragment π MOs. Transition‐state (TS) geometries and activation energies of reactions of four benzylic substrates R²? CH₂‐para‐C₆H₄? R¹ (R¹, R² = H and/or OCH₃) with DDQ were calculated. M06‐2X/6‐311(+*)G* was found to be a practical computational method, giving energies and geometries similar to those of M06‐2X/6‐311++G(3df,2pd) and wB97xD/6‐311++G(3df,2pd). For toluene (R¹ = R² = H), an initiation‐propagation model was suggested, and the calculated kinetic isotope effect k(H)/k(D) = 5.0 with the tunnel correction at the propagating step is in good agreement with the experimental value 5.2. A reaction of para‐MeO? C₆H₄? CH₂(OMe) + DDQ + (H₂O)₁₄ → para‐MeO? C₆H₄? C(?O)H + HOMe + DDQH₂ + (H₂O)₁₃ was investigated by M06‐2X/6‐311(+*)G*. Four elementary processes were found and the hydride transfer (TS1) is the rate‐determining step. The hydride transfer was promoted by association with the water cluster. The size of the water cluster, (H₂O)_n, at TS1 was examined. Three models of n = 14, 20, and 26 were found to give similar activation energies. Metal‐free neutral hydride transfers from activated benzylic substrates to DDQ were proposed to be ready processes both kinetically and thermodynamically. © 2015 Wiley Periodicals, Inc.     

DFT study of oxygen adsorption on modified nanostructured gold pyramids

Periodic DFT calculations are used to predict and investigate the adsorption behavior of molecular oxygen on Au, Au/Pt, and Pt surfaces. To obtain an array of pyramids containing surface atoms with the lowest possible coordination number, a nano-modified surface consisting of a symmetrically "modified" (100) surface was used. The effect of atom substitution (organized alloying) is investigated. The adsorption of molecular oxygen on a pure gold pyramid is exothermic by 0.77 eV for the end-on adsorption mode. In the case of a pure platinum pyramid, the end-on adsorption mode was found to dissociate; however, a side-on geometry was encountered with an energy of adsorption of 2.3 eV. This value is in line with the fact that the adsorption energy of small molecules does not vary much on Pt surfaces with different indices. Additionally, some geometrically related trends of the surface deformation in relation to its composition and after adsorption of molecular oxygen are highlighted.     

A comparative DFT study of oxygen reduction reaction on mononuclear and binuclear cobalt and iron phthalocyanines

The oxygen reduction reaction (ORR) catalyzed by mononuclear and planar binuclear cobalt (CoPc) and iron phthalocyanine (FePc) catalysts is investigated in detail by density functional theory (DFT) methods. The calculation results indicate that the ORR activity of Fe-based Pcs is much higher than that of Co-based Pcs, which is due to the fact that the former could catalyze 4e^- ORRs, while the latter could catalyze only 2e^- ORRs from O₂ to H₂O₂. The original high activities of Fe-based Pcs could be attributed to their high energy level of the highest occupied molecular orbital (HOMO), which could lead to the stronger adsorption energy between catalysts and ORR species. Nevertheless, the HOMO of Co-based Pcs is the ring orbital, not the 3d Co orbital, thereby inhibiting the electron transfer from metal to adsorbates. Furthermore, compared with mononuclear FePc, the planar binuclear FePc has more stable structure in acidic medium and more suitable adsorption energy of ORR species, making it a promising non-precious electrocatalyst for ORR.     

基态氧(3^O2)氧化硅烯的密度泛函计算研究

采用密度泛函[B3LYP(full)/6-311+G^*]方法研究了基态氧(3^O2)氧化硅烯(Si2H4)的机理。计算了三重态初始中间体(IM(T1)到单重态中间体IM2(S0)反应交叉势能面,报道了各反应中间体、产物和过渡态的构型和能量,用频率分析方法对各过渡态进行了验证,进一步用IRC方法对主要的基元反应进行了考察,确定了历经生成1,2-二氧环氧硅烷中间体的氧化过程的主要反应通道。     

A DFT+U study of defect association and oxygen migration in samarium-doped ceria

A specialized genetic algorithm (GA) is used to search the structural space of samarium-doped ceria (SDC) for the most energetically stable configurations which will predominate in low temperature fuel cells. A systematic investigation of all configurations of 3.2% SDC and a GA investigation of 6.6% SDC are presented for the first time at the DFT+U level of theory. It was found that Sm atoms prefer to occupy the nearest neighbor (NN) position relative to the oxygen vacancy at 3.2%, while at 6.6%, a balance exists between various Sm-vacancy interactions and the vacancies prefer to be separated by ～6 ?. Also, the migration barriers for oxygen diffusion are calculated amongst the best structures in 3.2% and 6.6% SDC and are found to be comparable to the barriers in Gd-doped ceria at the DFT+U level of theory. While the migration calculations provide insight on the oxygen diffusion mechanism in this material, the favored configurations from our GA enable future research on concentrated SDC and contribute to the atomistic understanding of the influence of dopant-vacancy and vacancy-vacancy interactions on ionic conductivity.     

Effect of GTP and GDP nucleotides on vinblastine binding affinity to tubulin: a DFT study

Vinblastine (VLB) is an anticancer agent that inhibits microtubule assembly by binding with tubulin. Density functional theory (DFT) calculations are used to examine low-energy minima of the energy surface of vinblastine-tubulin complex. Thermodynamic data of the binding site of vinblastine to tubulin are extracted with the hybrid DFT (B3LYP (Becke, three-parameter, Lee–Yang–Parr)) method, and then the influence of several solvents, such as water, methanol and ethanol, and different temperatures are discussed on infrared parameters by self-consistent reaction field (SCRF = dipole) method. The effect of guanosine triphosphate (GTP) and guanosine diphosphate (GDP) nucleotides on vinblastine binding affinity to tubulin was realised in water solvent by comparing the changes of ?G (Gibbs free energy) of VLB-tubulin and VLB-tubulin bonded to GTP or GDP. The result showed that GDP and GTP increase significantly the binding affinity and the role of GDP is more important than that of GTP.     

A DFT study of the domino inter

The molecular mechanism of the domino inter [4 + 2]/intra [3 + 2] cycloaddition reactions of nitroalkenes with enol ethers to give nitroso acetal adducts has been characterized using density functional theory methods with the B3LYP functional and the 6-31G basis set. The presence of Lewis acid catalyst and solvent effects has been taken into account to model the experimental environment. These domino processes comprise two consecutive cycloaddition reactions: the first one is an intermolecular [4 + 2] cycloaddition of the enol ether to the nitroalkene to give a nitronate intermediate, which then affords the final nitroso acetal adduct through an intramolecular [3 + 2] cycloaddition reaction. The intermolecular [4 + 2] cycloaddition can be considered as a nucleophilic attack of the enol ether to the conjugated position of the nitroalkene, with concomitant ring closure and without intervention of an intermediate. For this cycloaddition process, the presence of the Lewis acid favors the delocalization of the negative charge that is being transferred from the enol ether to the nitroalkene and decreases the activation energy of the first cycloaddition. The [4 + 2] cycloaddition presents a total regioselectivity, while the endo/exo stereoselectivity depends on the bulk of the Lewis acid used as catalyst. Thus, for small Lewis acid catalyst, modeled by BH(3), the addition presents an endo selectivity. The [3 + 2] cycloaddition reactions present an total exo selectivity, due to the constraints imposed by the tether. Inclusion of Lewis acid catalyst and solvent effects decrease clearly the barrier for the first [4 + 2] cycloaddition relative to the second [3 + 2] one. Calculations for the activation parameters along this domino reaction allow to validate the results obtained using the potential energy barriers.     

Electrophoretic purification of the alpha and beta subunits of phosphorylase kinase and evidence in support of the deduced amino acid sequences

A simple, rapid sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) method is presented for isolating the alpha, alpha' and beta subunits of rabbit muscle phosphorylase kinase. The SDS-PAGE procedure can yield milligram amounts of alpha and beta from a single preparative gel and also allows isolation of the alpha' isozyme free of alpha. Notably the method provides the purified subunits in a form amenable to structural analysis. Edman degradation of alpha and alpha' reveal identical NH2-terminal structures. Amino acid analysis of the electrophoretically purified alpha and beta subunits are in good agreement with their deduced primary structures. The amino acid sequence of 488 residues in alpha and 713 residues in beta were determined by gas phase Edman degradation. The data support the recently deduced primary structures of alpha (Zander et al., Proc. Natl. Acad. Sci. USA, 1988, 85, 9381-9385).     

Coverage dependence of oxygen decomposition and surface diffusion on rhodium 111: a DFT study

A systematic study of oxygen adsorption, decomposition and diffusion on Rh111 and its dependence on coadsorbed oxygen molecules has been performed using density functional theory calculations. First, the bonding strength between metal surface and adsorbed oxygen molecules has been studied as a function of initial oxygen coverage. The bonding strength decreases with increasing oxygen coverage, which points towards a self-inhibition of the adsorption process. The potential energy hypersurface (PES) for the dissociation of oxygen molecules adsorbed on a threefold fcc position perpendicular to the surface was calculated using a combined linear/quadratic synchronous transit method with conjugate gradient refinements. The results indicate that a minor amount of oxygen on the surface enhances the decomposition of further oxygen molecules, while this process is inhibited at higher coverage. Moreover, PES calculations of a single site jump of atomic oxygen on rhodium 111 indicate that the activation energy increases as well with increasing oxygen coverage. All results are discussed with respect to a rhodium based catalytic NOx reduction/decomposition system proposed by Nakatsuji, which decomposes nitrogen oxides in oxygen excess.     

A DFT study on the thermal decomposition of 2-chloroethylsilane

Structural Chemistry - The thermal decomposition of 2-chloroethylsilane (H3SiCH2CH2Cl) was investigated by density functional theory (DFT) method at the B3LYP/6-311G(d,p) level. The structures of...     

A DFT study on the vibrational spectroscopy of protoporphyrin IX

Infrared and Raman spectra of protoporphyrin IX were recorded. DFT quantum chemical calculations were performed. Optimised molecular geometry, electric charge distribution, vibrational force constants were computed. The normal coordinate analysis and the scaling of the force constants yielded all the necessary data for the simulation of the infrared and Raman spectra and the potential energy distribution calculations. The result was the interpretation of all vibrational modes of the molecule. Conclusions were drawn from the difficulties arisen during the assignment of the vibrational spectra of such large molecules.     

A DFT study of the hydrolysis of hydantoin

Density functional theory (DFT) calculations were made on the hydrolysis of hydantoin (2,4-imidazolidinedione). In the neutral hydrolysis, reacting systems composed of hydantoin and (H₂O)_n with n = 1+3, 2+3, 3+3, and 4+3 were adopted. Three water molecules (“+3”) participate in the in-plane hydrogen-bond circuit, and the n–3 = 1, 2, 3 or 4 water cluster works for the out-of-plane nucleophilic attack onto the carbonyl carbon of hydantoin. Transition states (TSs) involving bond interchanges prompted by proton transfers were determined. The reaction path with n = 3+3 containing N-carbamoyl glycine, N-carboxy glycine and three tetrahedral intermediates was found to be most likely. In the acid-catalyzed hydrolysis, a reacting system composed of hydantoin and H₃O⁺(H₂O)₇ was employed. Ten TSs and nine intermediates were obtained. N-carbamoyl glycine and N-carboxy glycine were confirmed to be detectable stable species. The product consists of glycine, carbonic acid (not CO₂), NH₄⁺, and (H₂O)₅. It has the exothermic energy, whereas the product in the neutral hydrolysis is of the endothermic one for all n values. For both neutral (n = 3+3) and acid-catalyzed hydrolyses, the rate-determining steps were calculated to be for formation of the tetrahedral intermediate, HOOC-CH₂-NH-C(OH)₂NH₂. The pattern of proton transfers along hydrogen bonds was carefully investigated.     

Guidelines for routine measurement of blood hemoglobin oxygen affinity. IFCC Scientific Division, Committee on pH, Blood Gases, and Electrolytes.

Two methods for the routine determination of blood hemoglobin oxygen affinity are described. Both methods use whole blood and do not require special equipment, tonometry, or special gas mixtures. The first method consists of a one-point determination of p 50, and requires only 200 muL to 400 muL of whole blood, therefore making it suitable for the pediatric population. The second method uses multiple points, thereby establishing both the shape and position of the hemoglobin oxygen equilibrium curve between 10 and 99% oxygen saturation. Interpretation of p 50 is discussed in relation to evaluation of patients with hemoglobinopathies and as a parameter in estimating availability of oxygen to the tissues.     

A DFT study on the electronic structure for iridium nitride under high pressure

We present density functionary theory (DFT) calculations on the structural parameters and electronic structure for iridium nitride by using the generalized gradient approximation (GGA) and the Perdew–Burke–Ernserhof (PBE) exchange-correlation functional. The lattice parameters and bulk modulus (B ₀) for the ground state are obtained, and the energy band structure and electron densities of states (DOS) of IrN₂ are presented. It is found that IrN₂ has a very close indirect energy gap. There is a strong covalent bond between the two nearest N atoms. This gives rise to a very high elastic modulus of IrN₂ and reveals the quasimolecular nature of the N₂ in IrN₂ crystal. Lattice parameters, bulk modulus, and the electronic structure of IrN₂ under high pressure have also been investigated based on DFT. The compressibility along three cell vectors is very close to each other. The band gap increases a little with the pressure even when the pressure is up to 100 Gpa.