Direct growth of comet-like superstructures of Au-ZnO submicron rod arrays by solvothermal soft chemistry process

The synthesis, characterization and proposed growth process of a new kind of comet-like Au-ZnO superstructures are described here. This Au-ZnO superstructure was directly created by a simple and mild solvothermal reaction, dissolving the reactants of zinc acetate dihydrate and hydrogen tetrachloroaurate tetrahydrate (HAuCl₄·4H₂O) in ethylenediamine and taking advantage of the lattice matching growth between definitized ZnO plane and Au plane and the natural growth habit of the ZnO rods along [001] direction in solutions. For a typical comet-like Au-ZnO superstructure, its comet head consists of one hemispherical end of a central thick ZnO rod and an outer Au-ZnO thin layer, and its comet tail consists of radially standing ZnO submicron rod arrays growing on the Au-ZnO thin layer. These ZnO rods have diameters in range of 0.2-0.5 μm, an average aspect ratio of about 10, and lengths of up to about 4 μm. The morphology, size and structure of the ZnO superstructures are dependent on the concentration of reactants and the reaction time. The HAuCl₄·4H₂O plays a key role for the solvothermal growth of the comet-like superstructure, and only are ZnO fibers obtained in absence of the HAuCl₄·4H₂O. The UV-vis absorption spectrum shows two absorptions at 365-390 nm and 480-600 nm, respectively attributing to the characteristic of the ZnO wide-band semiconductor material and the surface plasmon resonance of the Au particles.     

A theoretical study on the mechanism of camphor hydroxylation by compound I of cytochrome p450

Mechanistic and energetic aspects for the conversion of camphor to 5-exo-hydroxycamphor by the compound I iron-oxo species of cytochrome P450 are discussed from B3LYP DFT calculations. This reaction occurs in a two-step manner along the lines that the oxygen rebound mechanism suggests. The activation energy for the first transition state of the H atom abstraction at the C5 atom of camphor is computed to be more than 20 kcal/mol. This H atom abstraction is the rate-determining step in this hydroxylation reaction, leading to a reaction intermediate that involves a carbon radical species and the iron-hydroxo species. The second transition state of the rebound step that connects the reaction intermediate and the product alcohol complex lies a few kcal/mol below that for the H atom abstraction on the doublet and quartet potential energy surfaces. This energetic feature allows the virtually barrierless recombination in both spin states, being consistent with experimentally observed high stereoselectivity and brief lifetimes of the reaction intermediate. The overall energetic profile of the catalytic mechanism of camphor hydroxylation particularly with respect to why the high activation energy for the H atom abstraction is accessible under physiological conditions is also considered and calculated. According to a proton source model involving Thr252, Asp251, and two solvent water molecules (Biochemistry 1998, 37, 9211), the energetics for the conversion of the iron-peroxo species to compound I is studied. A significant energy over 50 kcal/mol is released in the course of this dioxygen activation process. The energy released in this chemical process is an important driving force in alkane hydroxylation by cytochrome P450. This energy is used for the access to the high activation energy for the H atom abstraction.     

The first and second derivative matrices in the random phase approximation scheme by using the Lagrangian technique

We have presented the explicit formulas for first and second derivatives of A and B matrices, appearing in the random phase approximation (RPA), with the aid of Lagrangian technique. Owing to the 2n + 1 rule, the Lagrangian approach is more efficient than the conventional approach to evaluate the higher‐order matrix elements. We have confirmed the validity of our formulation by demonstrating the geometry optimization of the first‐excited singlet states of formaldehyde, ethylene, and 1‐amino‐3‐propenal molecules. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

IR observation of adsorption and initial reactions of olefins on Brønsted acid sites of a deuterated ZSM-5

Adsorption of linear olefins (C₂?C₄) on a deuterated H-ZSM-5 (D-ZSM-5) was studied by infrared (IR) spectroscopy. The initial interaction of the olefins with Brønsted acidic OD groups was hydrogen-bonding to form π-complexes at low temperatures. The adsorbed ethene and propene desorbed by heating under evacuation, while various reactions took place for adsorbed 1-butene; double bond migration (DBM) to 2-butene below 230 K followed by dimerization at room temperature. An unusual reaction path was deduced for DBM of 1-butene, where proton transfer from Brønsted acid sites (BAS) to the adsorbed 1-butene was not essential.     

Direct observation of unstable intermediate species in the reaction of trans-2-butene on ferrierite zeolite by picosecond infrared laser spectroscopy

The reaction dynamics of trans-2-butene adsorbed to acidic hydroxyl groups on the surface of ferrierite zeolite is examined by time-resolved spectroscopy using a tunable infrared picosecond pulse laser system. The transient absorption spectra measured by a two-color pump-probe technique at 188-243 K reveal bleaching and hot bands of the OD stretching mode 2 ps after excitation. This vibrationally excited state relaxes within 20 ps at 188 K, while the bleaching band includes a long-lifetime component that lasts for more than 100 ps at 243 K. Thus, the OD (isotope-exchanged hydroxy groups) stretching band does not entirely recover in this period and is mirrored by an analogous weakening of the CH bending band of the adsorbed trans-2-butene. Simultaneously, three new bands in CH stretching region were observed at 3045, 3095, and 3130 cm(-1). This result suggests the presence of a short-lived intermediate formed by reaction between the acidic hydroxyl groups and adsorbed trans-2-butene.     

Influences of ribonucleotide on a duplex conformation and its thermal stability: study with the chimeric RNA-DNA strands

To understand the influences of the ribonucleotide on a duplex conformation and its stability, we systematically studied the CD spectra and the thermodynamics of nucleic acid duplexes formed by the chimeric RNA-DNA strand in which ribonucleotides and deoxyribonucleotides were covalently attached. It was found that the duplex stability was context-dependent and independent of the number of ribonucleotides in the chimeric strand, whereas the CD spectra showed less overall structural perturbation by the chimeric junctions. Combining the results of the CD and the thermodynamic data revealed a stability-structure relationship for the duplexes. Importantly, DeltaG(o)37 values estimated for the chimeric junction formation in the RNA-DNA/DNA and the RNA-DNA/RNA duplexes were close to those of RNA/DNA and RNA/RNA interactions, respectively. Furthermore, DeltaG(o)37s of the DNA-RNA/DNA and DNA-RNA/DNA-RNA junctions were similar to those of the DNA duplex, and the values of DNA-RNA/RNA-DNA were similar to those of the DNA/RNA. The thermodynamic analyses suggest that the 5'-nucleotide may be the crucial factor that determines the stability at the chimeric junction. Our results not only suggest influences of the ribonucleotide on a duplex conformation and its stability but also are useful for the design of RNA-DNA chimeric strands applicable to biotechnology.     

Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes

We have studied the interaction between metal ions and the metal ion-binding motif in hammerhead ribozymes, as well as the functions of the metal ion at the motif, with heteronuclear NMR spectroscopy. In this study, we employed model RNA systems which mimic the metal ion-binding motif and the altered motif. In Co(NH3)6(III) titrations, we observed large 1H and 31P chemical shift perturbations for the motif and found that outer-sphere complexation of Co(NH3)6(III) is possible for this motif. From the reinvestigation of our previous 15N chemical shift data for Cd(II) binding, in comparison with those of organometallic compounds, we conclude that Cd(II) can form an inner-sphere complex with the nucleobase in the motif. Therefore, the A9/G10.1 site was found to accept both inner-sphere and outer-sphere complexations. The Mg(II) titration for a slightly different motif from the A9/G10.1 site (G10.1-C11.1 to A10.1-U11.1) revealed that its affinity to Mg(II) was drastically reduced, although the ribozyme with this altered motif is known to retain enzymatic activities. This observation suggests that the metal ion at these motifs is not a catalytic center of hammerhead ribozymes.     

Electrostatic Interactions That Determine the Rate of Pseudorotation Processes in Oxyphosphorane Intermediates: Implications with Respect to the Roles of Metal Ions in the Enzymatic Cleavage of RNA

The enzymatic cleavage of RNA takes place via a cyclic pentacoordinate oxyphosphorane intermediate/transition state. We carried out ab initio investigations on the neutral cyclic oxyphosphorane, which exists as a stable intermediate. As a consequence of the conformational preferences of the pentacoordinate trigonal bipyramidal intermediates, the rotation of the P-OH bonds is strongly coupled with the reaction coordinate for the pseudorotation process. In addition, the neutral PF(4)OH species has a higher barrier to pseudorotation than the corresponding anionic species PF(4)O(-). These findings are related to the positive charge of the hydrogen atoms on the equatorial oxygens in the trigonal bipyramidal structures: the hydrogen atoms preferably adopt eclipsed positions relative to the axial ligands. Fixing the cationic species in these regions causes an increase in the barrier heights for pseudorotation processes and, thus, prevents isomerization by pseudorotation. Consequently, metal coordination in the double-metal ion mechanism for enzymatic cleavage of RNA should serve to exclusively stabilize the trigonal bipyramidal intermediate/transition state for the in-line attack and departure process.     

A non-radical mechanism for methane hydroxylation at the diiron active site of soluble methane monooxygenase

We propose a non‐radical mechanism for the conversion of methane into methanol by soluble methane monooxygenase (sMMO), the active site of which involves a diiron active center. We assume the active site of the MMOH_Q intermediate, exhibiting direct reactivity with the methane substrate, to be a bis(μ‐oxo)diiron(IV ) complex in which one of the iron atoms is coordinatively unsaturated (five‐coordinate). Is it reasonable for such a diiron complex to be formed in the catalytic reaction of sMMO? The answer to this important question is positive from the viewpoint of energetics in density functional theory (DFT) calculations. Our model thus has a vacant coordination site for substrate methane. If MMOH_Q involves a coordinatively unsaturated iron atom at the active center, methane is effectively converted into methanol in the broken‐symmetry singlet state by a non‐radical mechanism; in the first step a methane C? H bond is dissociated via a four‐centered transition state (TS1) resulting in an important intermediate involving a hydroxo ligand and a methyl ligand, and in the second step the binding of the methyl ligand and the hydroxo ligand through a three‐centered transition state (TS2) results in the formation of a methanol complex. This mechanism is essentially identical to that of the methane–methanol conversion by the bare FeO⁺ complex and relevant transition metal–oxo complexes in the gas phase. Neither radical species nor ionic species are involved in this mechanism. We look in detail at kinetic isotope effects (KIEs) for H atom abstraction from methane on the basis of transition state theory with Wigner tunneling corrections.     

RuO2-loaded beta-Ge3N4 as a non-oxide photocatalyst for overall water splitting

Germanium nitride beta-Ge3N4 dispersed with RuO2 nanoparticles is presented as the first example of a non-oxide photocatalyst for the stoichiometric decomposition of H2O into H2 and O2. All of the successful photocatalysts developed for overall water splitting over the past 30 years have been based on oxides of metals. The discovery of a non-oxide photocatalyst, such as nitrides and oxynitrides, achieving the same function is therefore expected to stimulate research on non-oxide photocatalysts. New opportunities for progress in the development of visible light-driven photocatalysis can thus be expected, as the higher valence band positions of metal nitrides compared to the corresponding metal oxides provide narrower band gaps, which are suitable for visible light activity.