Theoretical analysis of oxygen reduction reaction and H2O2 formation and the impact of CF3SO3H coverage on Pt (111)

Theoretical analysis of ORR on Pt (111) was carried out with the combined technique of DFT calculation and the UBI-QEP method in order to understand the overall ORR pathways, behavior of H₂O₂ formation, and the impact of trifluoromethane sulfonic acid (CF₃SO₃H and TfOH) coverage, the alternative material of Nafion^®, on the reactivity on the Pt surface. The ORR scheme consisting of elementary reactions was then modeled to determine the dominant path and the limiting step based on their activation energies. The results showed that the dominant ORR path included the H₂O₂ formation step and OOH formation step was limiting. When TfOH covered the Pt surface, it was revealed that the adsorption energy of an O₂ molecule on Pt (111) was decreased due to the lower Fermi level and the d-band center, resulting in decreasing the activation energy of the limiting step. TfOH, however, could suppress the O₂ adsorption on the Pt surface. In addition, with the TfOH coverage, it was indicated that the limiting step of ORR was shifted to H₂O-production step which was after the H₂O₂ production, resulting in the enhancement of the H₂O₂ formation.     

Molecular dynamics study of solubilization of cyclohexane,benzene, and phenol into mixed micelles composed of sodium dodecyl sulfate and octaethylene glycol monododecyl ether

Molecular dynamics calculations of a mixed micelle composed of sodium dodecyl sulfate (SDS) and octaethylene glycol monododecyl ether (C₁₂E₈) were performed for six compositions (SDS/C₁₂E₈ = 100/0, 80/20, 60/40, 40/60, 20/80, and 0/100) to investigate the composition dependence of the mixed micelle structure and solubilization of cyclohexane, benzene, and phenol molecules by the micelle. The radial density distribution of the hydrophilic polyoxyethylene (POE) group of C₁₂E₈ as a function of distance from the micelle center is very sharp for micelles with high SDS content because the POE group captures a Na⁺ ion in solution and wraps around it to form a compact crown-ether-like complex. The hydrophobic dodecyl groups of SDS and C₁₂E₈ were separately distributed in the mixed micelle core. ΔG(r) evaluated for each solute showed that despite the structural changes of the micelle the binding strength of the solute molecules to the micelle did not change significantly. © 2019 Wiley Periodicals, Inc.     

CH/pi hydrogen bonds determine the selectivity of the Src homology 2 domain to tyrosine phosphotyrosyl peptides: an ab initio fragment molecular orbital study

The CH/pi hydrogen bond is a weak molecular force occurring between CH groups (soft acids) and pi-systems (soft bases), and has been recognized to be important in the interaction of proteins with their specific ligands. For instance, it is well known that Src homology-2 protein (SH2) recognizes its specific pTyr peptide in two key regions, pTyr-binding region and specificity-determining region, by the use of attractive molecular forces, including the CH/pi hydrogen bond. We hypothesized that the CH/pi hydrogen bond plays a key role in determining the selectivity of SH2 proteins, and studied this issue by the ab initio fragment molecular orbital (FMO) method. The FMO calculations were carried out, at the HF/6-31G* and MP2/6-31G* level, for SH2 domains of Src, Grb2, P85alpha(N), Syk, and SAP, in complex with corresponding pTyr peptides. CH/pi hydrogen bonds have in fact been found to be important in stabilizing the structure of the complexes. We conclude that the CH/pi hydrogen bond plays an indispensable role in the recognition of SH2 domains with their specific pTyr peptides, thus playing a vital role in the signal transduction system.     

Stable ion and electrophilic chemistry of the sterically crowded stilbene 1,1'-Bi(benzocyclobutenylidene) and its derivatives

Generation and NMR studies of novel carbocations and carboxonium ions are reported from sterically hindered stilbene 1,1'-bi(benzocyclobutenylidene) 1, its dimethoxy derivative 5, and from their skeletally rearranged derivatives, namely, the spirocyclic ketone 6, diastereomeric alcohols 7 and isomeric diols 8. Quenching experiments on the carbocations under various conditions resulted in the formation/isolation of several novel covalent adducts. Acid-catalyzed isomerization of the diols 8 produced a remarkable dimeric molecule, whose structure was confirmed by X-ray analysis. Reactions of hindered stilbenes 1 and 5 with Br 2/CDCl 3 were examined via NMR experiments. The experimentally observed carbocations were also studied computationally by GIAO-DFT and by NICS.     

Analytical method for determination of disaccharides derived from keratan sulfates in human serum and plasma by high-performance liquid chromatography/turbo-ionspray ionization tandem mass spectrometry

We established a highly sensitive LC/MS/MS method for the analysis of the disaccharides produced from keratan sulfates (KS). It was revealed that the disaccharides produced by keratanase II enzymatic digestion of KS could be determined with high sensitivity by negative ion mode of multiple reaction monitoring. Furthermore, monosulfated and disulfated disaccharides can be separated using a Hypercarb (2.0 mm i.d. x 150 mm, 5 microm) with a gradient elution of acetonitrile-0.01 m ammonium bicarbonate (pH 10). This method was applied to the determination of KS in serum and plasma of control subjects. The intra-day precision expressed as %CV was within 6.8% for five replicate analyses with three different control serum. The inter-day (overall, n = 15) precision was within 7.3% for three days. This method is sensitive, reproducible and would be useful for clinical analysis.     

Formation of Isomeric Tetrathiotungstate Clusters [{Cp*Ru(CO)}2(WS4){W(CO)4}] by the Reaction of [Cp*2Ru2S4] with [W(CO)3(MeCN)3]

Thermal and photochemical interconversion occurs between the isomeric pair of tetrathiotungstate [WS₄]²⁻ clusters 1 and 2 , which were formed by thermolysis of [Cp^*₂Ru₂S₄] and [W(CO)₃(MeCN)₃] [Eq. (1)] and then structurally characterized. During synthesis, a dramatic redistribution of ligands between the Ru and W atoms takes place without the loss of any CO and S ligands.     

Bulk-sensitive spectroscopic studies on noncentrosymmetric superconducting system of Mg–Ir–B

We present the data from ultrahigh-resolution laser-excited photoemission spectroscopy on a newly discovered noncentrosymmetric superconductor Mg₁₀Ir₁₉B₁₆. We observed the evidences for the opening of superconducting gap where numerical fittings show that isotropic s-wave model can satisfactorily explain the behavior of spectra near the Fermi level. We also present the valence band photoemission spectrum and B K fluorescence spectrum to discuss the basic electronic structure of Mg₁₀Ir₁₉B₁₆.     

A surface hopping method for chemical reaction dynamics in solution described by diabatic representation: an analysis of tunneling and thermal activation

We present a surface hopping method for chemical reaction in solution based on diabatic representation, where quantum mechanical time evolution of the vibrational state of the reacting nuclei as well as the reaction-related electronic state of the system are traced simultaneously together with the classical motion of the solvent. The method is effective in describing the system where decoherence between reactant and product states is rapid. The diabatic representation can also give a clear picture for the reaction mechanism, e.g., thermal activation mechanism and a tunneling one. An idea of molecular orbital theory has been applied to evaluate the solvent contribution to the electronic coupling which determines the rate of reactive transition between the reactant and product potential surfaces. We applied the method to a model system which can describe complex chemical reaction of the real system. Two numerical examples are presented in order to demonstrate the applicability of the present method, where the first example traces a chemical reaction proceeded by thermal activation mechanism and the second examines tunneling mechanism mimicking a proton transfer reaction.     

Effect of laser annealing using high repetition rate pulsed laser on optical properties of phosphorus-ion-implanted ZnO nanorods

The effect of high repetition rate pulsed laser annealing with a KrF excimer laser on the optical properties of phosphorus-ion-implanted zinc oxide nanorods has been investigated. The recovery levels of phosphorus-ion-implanted zinc oxide nanorods have been measured by photoluminescence spectra and cathode luminescence images. Cathode luminescence disappeared over 300 nm below the surface due to the damage caused by ion implantation with an acceleration voltage of 25 kV. When the annealing was performed at a low repetition rate of the KrF excimer laser, cathode luminescence was recovered only in a shallow area below the surface. The depth of the annealed area was increased along with the repetition rate of the annealing laser. By optimizing the annealing conditions such as the repetition rate, the irradiation fluence and so on, we have succeeded in annealing the whole damaged area of over 300 nm in depth and in observing cathode luminescence. Thus, the effectiveness of high repetition rate pulsed laser annealing on phosphorus-ion-implanted zinc oxide nanorods was demonstrated.