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Junji Nakamura

Publications and source records attributed to Junji Nakamura.

14 recordsLinked to original sources

Why is formate synthesis insensitive to copper surface structures?

Experiments have revealed that formate synthesis from carbon dioxide and hydrogen is structure insensitive to copper catalyst surfaces, while the reverse formate decomposition reaction is structure sensitive. The present ab initio density functional theory (DFT) calculations show that the reaction of CO2 with surface atomic hydrogen initially leads to the formation of unstable monodentate formate, which has similar adsorption energies on Cu(111), Cu(100), and Cu(110). The structure of the transition state is similar to that of monodentate formate. It is also shown that gaseous CO2 is directly reacted with surface hydrogen, as suggested by previous experiments. The position of the similar transition state and the direct reaction mechanism well explain the similar energetic pathways, that is, the structure insensitivity.

Journal Article↗

Cluster and periodic DFT calculations: the adsorption of atomic nitrogen on M(111) (M = Cu, Ag, Au) surfaces.

First-principle density functional calculations with cluster and slab models have been performed to investigate adsorption and thermally activated atomic nitrogen on M(111) (M = Cu, Ag, Au) surfaces. Optimized results indicate that the basis set of the N atom has a distinct effect on the adsorption energy but an indistinct one on the equilibrium distance. For the N/M(111) adsorption systems studied here, the threefold face centered cubic (fcc) hollow site is found to be the most stable adsorption site. The reason for the fcc site is that the perfected adsorption site has been explained by the density of states (DOS) analysis, that is, that N(2p) has the smallest DOS population near the Fermi level on the fcc site as compared with other adsorption sites. The variations of the adsorption energy as a function of adsorption site are similar and in the following order of N-M(111) binding strengths on a given site: Cu(111) > Ag(111) > Au(111). It is found that the N atom forms essentially an ionic bond for the most stable site. Large contributions between the M(ns) and N(2p) orbitals (n = 4, 5, and 6 for Cu, Ag, and Au, respectively) are found for the cluster model at the B3LYP/LANL2DZ-6-31G(d,p) level and also found in the slab DFT-GGA calculation results, which are the main characteristics of M-N bonds. At last, the dissociation of N2 on Cu(111) and Au(111) has also been obtained in this work, and the results showed that the dissociation of N2 on Cu(111) is more active than that on the Au(111) surface.

Journal Article↗

The relationship between adsorption energies of methyl on metals and the metallic electronic properties: a first-principles DFT study.

A theoretical study of CH3 adsorbed on the (111) surface of some transition and noble metal surfaces M (M = Cu, Ni, Rh, Pt, Pd, Ag, Au) and on the Fe(100) is presented. We find that the hollow site is preferred more than the top one for Fe, Ni, Rh, and Cu, but it is the other way for Pt, Pd, Au, and Ag. In addition, a good linear relationship was observed between the chemisorption energy and d-band center for Group VIII metals or the square of the coupling matrix element for Group IB metals at the hollow site. Interestingly, with a detailed comparison of the adsorption energies at the top and hollow sites, we find that the adsorption energies among each group are very similar on the top site, which supports the theoretical model of Hammer and Norskov that the coupling between the HOMO of adsorbate and sp states of the metal is dominant and almost equal, and that the second coupling to the d-band contributes less but reflects the change of the adsorption energy. It confirms that the coupling to the d band comprises two opposite factors, that is, the d-band center was attractive and the square of the coupling matrix element was repulsive, such that the contributions from the two factors can counteract each other at the top site.

Journal Article↗

Kinetic mechanism of methanol decomposition on Ni(111) surface: a theoretical study.

The decomposition of methanol on the Ni(111) surface has been studied with the pseudopotential method of density functional theory-generalized gradient approximation (DFT-GGA) and with the repeated slab models. The adsorption energies of possible species and the activation energy barriers of the possible elementary reactions involved are obtained in the present work. The major reaction path on Ni surfaces involves the O-H bond breaking in CH(3)OH and the further decomposition of the resulting methoxy species to CO and H via stepwise hydrogen abstractions from CH(3)O. The abstraction of hydrogen from methoxy itself is the rate-limiting step. We also confirm that the C-O and C-H bond-breaking paths, which lead to the formation of surface methyl and hydroxyl and hydroxymethyl and atom hydrogen, respectively, have higher energy barriers. Therefore, the final products are the adsorbed CO and H atom.

Carbon↗

Catalytic functions of Mo/Ni/MgO in the synthesis of thin carbon nanotubes.

The functions and structures of Mo/Ni/MgO catalysts in the synthesis of carbon nanotubes (CNTs) have been investigated by transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and Raman spectroscopy. Thin 2-5-walled CNTs with high purities (over 90%) have been successfully synthesized by catalytic decomposition of CH(4) over Mo/Ni/MgO catalysts at 1073 K. It has been found that the yield of CNTs as well as the outer diameter or thickness correlates well with the contents of these three elements. The three components Mo, Ni, and MgO are all necessary to synthesize the thin CNTs at high yields since no catalytic activity was observed for CNT synthesis when one of these components was not present. The outer diameter of the CNTs increases from 4 to 13 nm and the thickness of graphene layers also increases with increasing Mo content at a fixed Ni content, while the inner diameter stays at 2-3 nm regardless of their contents. Furthermore, the average outer diameter is in good agreement with the average particle size of metal catalyst. That is, the thickness or the outer diameter can be controlled by selecting the composition of the Mo/Ni/MgO catalysts. XRD analyses have shown that Mo and Ni form a Mo-Ni alloy before CNT synthesis, while the Mo-Ni alloy phase is separated into Mo carbide and Ni. These alloy particles are supported on MgO cubic particles 15-20 nm in width. It has been found that only small Mo-Ni alloy particles 2-16 nm in size catalyze CNT synthesis, with larger particles over 15 nm exhibiting no activity. Mo carbide and Ni should play different roles in the synthesis of the thin CNTs, in which Ni is responsible for the dissociation of CH(4) into carbon and Mo(2)C works as a carbon reservoir.

Journal Article↗

Characterization of methoxy adsorption on some transition metals: a first principles density functional theory study.

Based on the gradient-density functional theory, calculation results of methoxy adsorption on Au(111), Ag(111), Cu(111), Pt(111), Pd(111), Ni(111), Rh(111), and Fe(100) surfaces are presented, and a consistent picture for some key physical properties determining the reactivity of metals appears. These eight metals belong to two groups: either with filled d electrons (group IB) or with unfilled but more than half filled d electrons (group VIII). The calculated adsorption energies are quite in agreement with the experimental data as well as the previous theoretical calculation results. Importantly, using the analysis of B. Hammer and J. K. Norskov, Nature (London) 376, 232 (1995) and in Chemisorption and Reactivity on Supported Clusters and Thin Films, edited by R. M. Lambert and G. Pacchioni (Kluwer Academic, Dordrecht, 1997), pp. 285-351, the binding energies have selectively been linearly correlated to the d-band center and to the size of the metal d-band orbital overlapping with the adsorbate (coupling matrix element) for these two groups of metals. And by analyzing the nature of the adsorption bonding, the possible reason of this difference is suggested.

Journal Article↗

Association of interleukin-10 promoter single nucleotide polymorphisms -819 T/C and -592 A/C with aging.

Increased inflammatory activity is known to accompany aging. Single nucleotide polymorphisms of inflammatory mediator genes might therefore affect the aging process. Relation of eight SNPs (tumor necrosis factor-alpha [TNF-alpha] -1031 T/C, interleukin-10 [IL-10] -819 T/C, IL-1beta -511 C/T, IL-6 -634 C/G, IL-18 -607 A/C, transforming growth factor-beta [TGF-beta] +869 C/T, matrix metalloproteinase-1 [MMP-1] -1607 1G/2G, and MMP-3 -1171 5A/6A) with age or gender was evaluated in 500 Japanese persons (mean age: 56.7 years old, range: 19-100) by the chi-square test. There was a significant association of IL-10 -819 T/C with age (p =.0026). The association remained significant after multivariate logistic regression analysis (odds ratio for an age interval for 1 year, 1.009; 95% CI, 1.002-1.016). Furthermore, the genotype distribution of IL-10 -819 T/C was completely consistent with that of -592 A/C. These data suggest that IL-10 -819 T/C and -592 A/C may be a promising candidate for an aging-related gene in a Japanese population.

Adult↗

Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry.

In order to elucidate the thermo-stabilization mechanism of the tryptophan synthase alpha-subunit from the extreme thermophile Thermus thermophilus HB8 (Tt-alpha-subunit), its crystal structure was determined and its stability was examined using DSC. The results were compared to those of other orthologs from mesophilic and hyperthermophilic organisms. The denaturation temperature of the Tt-alpha-subunit was higher than that of the alpha-subunit from S. typhimurium (St-alpha-subunit) but lower than that of the alpha-subunit from P. furiosus (Pf-alpha-subunit). Specific denaturation enthalpy and specific denaturation heat capacity values of the Tt-alpha-subunit were the lowest among the three proteins, suggesting that entropy effects are responsible for the stabilization of the Tt-alpha-subunit. Based on a structural comparison with the St-alpha-subunit, two deletions in loop regions, an increase in the number of ion pairs and a decrease in cavity volume seem to be responsible for the stabilization of the Tt-alpha-subunit. The results of structural comparison suggest that the native structure of the Tt-alpha-subunit is better adapted to an ideally stable structure than that of the St-alpha-subunit, but worse than that of the Pf-alpha-subunit. The results of calorimetry suggest that the residual structure of the Tt-alpha-subunit in the denatured state contributes to the stabilization.

Amino Acid Sequence↗

Evaluation of a new efficient procedure for single-nucleotide polymorphism genotyping: tetra-primer amplification refractory mutation system-polymerase chain reaction.

Tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) is a new efficient method for single-nucleotide polymorphism (SNP) genotyping. To determine the optimal conditions for ARMS-PCR we attempted to genotype ten SNPs. DNA was extracted from the peripheral blood of 168 unrelated healthy Japanese volunteers. Two problems inhibited uniform efficiency of the amplification of three bands. The first problem was the lower amplification efficiency of the shorter and allele-specific products compared with the largest product. This phenomenon was overcome by increasing the relative concentration of the inner primers. The second problem was non-specific amplification of the shorter products. To reduce the amplification of these non-specific bands, adjusting any one of the following PCR conditions was effective: i) reducing the ratio of the inner primer concentration relative to that of the outer primers; ii) increasing the annealing temperature for the initial 5-10 cycles; iii) hot start PCR. With these procedures all ten of the SNPs were successfully genotyped. Our present data may be useful in the further application of tetra-primer ARMS-PCR to SNP genotyping.

Asian People↗

Essential role of rho kinase in the Ca2+ sensitization of prostaglandin F(2alpha)-induced contraction of rabbit aortae.

Inhibition of dephosphorylation of the 20 kDa myosin light chain (MLC(20)) is an important mechanism for the Ca(2+)-induced sensitization of vascular smooth muscle contraction. We investigated whether this mechanism operates in prostaglandin F(2alpha) (PGF(2alpha))-induced contraction of rabbit aortic smooth muscle and, if so, whether protein kinase C (PKC) or rho-associated kinase (rho kinase) contribute to the inhibition of dephosphorylation. In normal medium, PGF(2alpha) (10 microM) increased the phosphorylation of MLC(20) and developed tension. The rho-kinase inhibitors fasudil and hydroxyfasudil inhibited these changes, despite having no effect on a phorbol-ester-induced MLC(20) phosphorylation. After treatment with verapamil or chelation of external Ca(2+) with EGTA, PGF(2alpha) increased the MLC(20) phosphorylation and tension without an increase in [Ca(2+)](i), all of which were sensitive to fasudil and hydroxyfasudil. ML-9, a MLC kinase inhibitor, quickly reversed the KCl-induced MLC(20) phosphorylation and contraction to the resting level. However, fractions of PGF(2alpha)-induced contraction and MLC(20) phosphorylation were resistant to ML-9 but were sensitive to fasudil. Ro31-8220 (10 microM), a PKC inhibitor, did not affect the phosphorylation of MLC(20) and the tension caused by PGF(2alpha), thus excluding the possibility of the involvement of PKC in the PGF(2alpha)-induced MLC(20) phosphorylation. PGF(2alpha) increased phosphorylation at Thr654 of the myosin binding subunit (MBS) of myosin phosphatase, which is a target of rho kinase, and fasudil decreased the phosphorylation. These data suggest that the PGF(2alpha)-induced contraction is accompanied by the inhibition of MLC(20) dephosphorylation through rho kinase-induced MBS phosphorylation, leading to Ca(2+) sensitization of contraction. An actin-associated mechanism may also be involved in the PGF(2alpha)-induced sensitization.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗

Kainic acid induces leukemia inhibitory factor mRNA expression in the rat brain: differences in the time course of mRNA expression between the dentate gyrus and hippocampal CA1/CA3 subfields.

Leukemia inhibitory factor (LIF) is a pluripotent cytokine which affects the survival and differentiation of various types of cells both in the hematopoietic and nervous systems. In this study, the time course and localization of LIF mRNA expression following kainic acid-induced seizures were examined by northern blot analyses and in situ hybridization. Northern blot analyses demonstrated that intraperitoneal injection of kainic acid at a convulsive dose induced LIF mRNA expression intensely in the hippocampus and moderately to weakly in the cerebral cortex, thalamus and hypothalamus. The expression peaked at 8-24 h after the injection in the hippocampus and cerebral cortex and at 8 h in the thalamus and hypothalamus. In situ hybridization revealed different time courses of LIF mRNA expression depending on the area of the hippocampus; that is, the expression peaked at 10 h in the granule cell layer of the dentate gyrus, then at 12 h in the polymorph and molecular layers of the dentate gyrus, and finally at 12-24 h in the strata oriens and radiatum of the CA1 and CA3 subfields. It is worth noting that the expression of LIF mRNA was intense in the dentate gyrus, the region where neurogenesis and aberrant network reorganization have been shown to be induced by seizures. The upregulation of LIF mRNA expression in the dentate granule cell layer followed by that in the dentate polymorph and molecular layers may be involved in activity-dependent neurogenesis in the granule cell layer and ectopic migration of granule cells to the polymorph and molecular layers in the dentate gyrus.

Animals↗

ATP induces leukemia inhibitory factor mRNA in cultured rat astrocytes.

Leukemia inhibitory factor (LIF) is a cytokine involved in the survival and differentiation of the neural cells in the central and peripheral nervous systems. In the present study, we examined the effects of various neurotransmitter receptor agonists on LIF mRNA expression in cultured rat astrocytes, microglia and neurons to elucidate the cell types producing LIF and to clarify the neurotransmitter(s) regulating the mRNA expression. The results demonstrated that the expression of LIF mRNA was intensely induced by ATP in the cultured astrocytes. Experiments using ATP, UTP and related compounds showed the involvement of P2Y2 and P2Y4 purinoceptors in the expression induced by ATP.

Adenosine Diphosphate↗

Photochemical behavior of some p-styrylstilbenes and related compounds: spectral properties and photoisomerization in solution and in solid state.

The spectral properties and Z,E-photoisomerizations of three 4-styrylstilbenes, a 4,4'-bis(P-methylstyryl)benzene and a 4,4'-distyrylstilbene were investigated in solution and in the solid state. Some notable features of the absorption and fluorescence spectra due to the structures and the phases (solution or solid) were observed, especially the Stokes shifts. Interesting photochemical behaviors in solution and in the solid state were also found. While the (E,Z)-4-styrylstilbenes undergo a one-way photoisomerization to their E,E-isomers with almost equal rates in solution, their quantum yields in the solid state decrease with increasing substituent size at the terminal aromatic rings. On the other hand, the 4,4'-bis(beta-methylstyryl)benzene undergoes a mutual photoisomerization in solution, but its E,Z-isomer isomerizes in a one-way manner to the E,E-isomer in the solid state. Additionally, the (Z,E,Z)-4,4'-styrylstilbene was found to undergo a one-way photoisomerization to the E,E,E-isomer via the E,E,Z-isomer in solution and the crystalline E,E,Z-isomer to the E,E,E-isomer in the solid state.

Isomerism↗