Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase

Two molecular dynamics (MD) simulations totaling 25 ns of simulation time of monomeric scytalone dehydratase (SD) were performed. The enzyme has a ligand-binding pocket containing a cone-shaped alpha+beta barrel, and the C-terminal region covers the binding pocket. Our simulations clarified the difference in protein dynamics and conformation between the liganded protein and the unliganded protein. The liganded protein held the ligand molecule tightly and the initial structure was maintained during the simulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changed largely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by opening of the C-terminal region, and the protein dynamics was connected with hydration water molecules entry into and release from the binding pocket. In addition, the cooperative motions of the unliganded protein and the hydration water molecules produced the path through the protein interior for ligand binding.     

Regulation of geometry around the ruthenium center of bis(2-pyridinecarboxylato) complexes by the nitrosyl moiety: syntheses, structures, and theoretical studies

cis-[Ru(NO)Cl(pyca)(2)] (pyca = 2-pyridinecarboxylato), in which the two pyridyl nitrogen atoms of the two pyca ligands coordinate at the trans position to each other and the two carboxylic oxygen atoms at the trans position to the nitrosyl ligand and the chloro ligand, respectively (type I shown as in Chart 1), reacted with NaOCH(3) to generate cis-[Ru(NO)(OCH(3))(pyca)(2)] (type I). The geometry of this complex was confirmed to be the same as the starting complex by X-ray crystallography: C(13.5)H(13)N(3)O(6.5)Ru; monoclinic, P2(1)/n; a = 8.120(1), b = 16.650(1), c = 11.510(1) A; beta = 99.07(1) degrees; V = 1536.7(2) A(3); Z = 4. The cis-trans geometrical change reaction occurred in the reactions of cis-[Ru(NO)(OCH(3))(pyca)(2)] (type I) in water and alcohol (ROH, R = CH(3), C(2)H(5)) to form [[trans-Ru(NO)(pyca)(2)](2)(H(3)O(2))](+) (type V) and trans-[Ru(NO)(OR)(pyca)(2)] (type V). The reactions of the trans-form complexes, trans-[Ru(NO)(H(2)O)(pyca)(2)](+) (type V) and trans-[Ru(NO)(OCH(3))(pyca)(2)] (type V), with Cl(-) in hydrochloric acid solution afforded the cis-form complex, cis-[Ru(NO)Cl(pyca)(2)] (type I). The favorable geometry of [Ru(NO)X(pyca)(2)](n)(+) depended on the nature of the coexisting ligand X. This conclusion was confirmed by theoretical, synthetic, and structural studies. The mono-pyca-containing nitrosylruthenium complex (C(2)H(5))(4)N[Ru(NO)Cl(3)(pyca)] was synthesized by the reaction of [Ru(NO)Cl(5)](2)(-) with Hpyca and characterized by X-ray structural analysis: C(14)H(24)N(3)O(3)Cl(3)Ru; triclinic, Ponemacr;, a = 7.631(1), b = 9.669(1), c = 13.627(1) A; alpha = 83.05(2), beta = 82.23(1), gamma = 81.94(1) degrees; V = 981.1(1) A(3); Z = 2. The type II complex of cis-[Ru(NO)Cl(pyca)(2)] was synthesized by the reaction of [Ru(NO)Cl(3)(pyca)](-) or [Ru(NO)Cl(5)](2)(-) with Hpyca and isolated by column chromatography. The structure was determined by X-ray structural analysis: C(12)H(8)N(3)O(5)ClRu; monoclinic, P2(1)/n; a = 10.010(1), b = 13.280(1), c = 11.335(1) A; beta = 113.45(1) degrees; V = 1382.4(2) A(3); Z = 4.     

Participation of lipid peroxidation in rat pertussis vaccine pleurisy. III. Thiobarbituric acid (TBA) reactant and lysosomal enzyme

Activity of lysosomal enzymes, such as N-acetyl-beta-D-glucosaminidase (NAG), was assayed in exudate on a rat model of Bordetella pertussis vaccine pleurisy. Thiobarbituric acid (TBA)-reactive substances (TBA.R) and superoxide dismutase (SOD) activity were then monitored in the exudate on the acute phase response in this inflammatory model. Retention of the exudate in the pleural space increased rapidly after the challenge, and the exudate volume at 24 h reached about three times the volume at 6 h. The activity of SOD at 6 h was shown to be higher than that at 24 h after the challenge, thus showing negative correlations with TBA-R levels and exudate volume. The levels of TBA.R rapidly increased and reached maximum values at 24 h. It was concluded that the above three parameters correlated to the acute phase response in this inflammatory model.     

Triethylborane-induced radical allylation reaction with zirconocene-olefin complex

[reaction: see text] Allylzirconium reagents are effective for radical allylation of alpha-halo carbonyl compounds. The key steps would be homolytic cleavage of the zirconium-carbon bond and halogen abstraction by the resulting Cp(2)ZrCl(III). Zirconocene-olefin complex can be also utilized for the allylation of alpha-halo compounds.     

Synthetic and structural studies of [6]-, [7]- and [10]metacyclophanes

A new preparative sequence from 2,3-polymethylene-2-cyclopentenone 5 to 2,6-polymethylenebromobenzenes 3 (n = 6, 7, 10) and 2,6-polymethylenephenyllithiums 6 has been found. The reaction of 6 with various electrophiles produces a number of new compounds to disclose the unique reactivity of the aryl C-Li moiety surrounded by the polymethylene chain. Photolysis of 3a and 3b provides transannular products 8, 10 and 11, all arising from the proximity between the aromatic bromine and the aliphatic hydrogen intraannularly opposed to be removed as HBr. Spectrometric study gives quantitative data of the dependence of the molecular geometry upon the chain length and the aromatic substituents. The energy barriers ΔG_c^≠ of the conformational flipping are 17·4 kcal/mol (T_c 76·5°) for [6]metacyclophane (7a), 11·5 kcal/mol (T_c ?28°) for [7]metacyclophane (7b), ·8 kcal/mol for [10]metacyclophane (7c). The lower-energy process of the aliphatic chain in [6]metacyclophane derivatives is the pseudorotation with substituent-dependent barrier ΔG_c^≠ 11·1 kcal/mol (T_c ?31·5°) for 7a, 12·4 kcal/mol (T_c ?4·5°) for 3a and 12·7 kcal/mol (T_c 1·0°) for 12a. The rather large rotational barrier is attributed to the compressed structure of each system. The benzene ring distortion of the cyclophanes is deduced from the bathochromic shift of the B-band and the diamagnetic shift of the benzene proton signals in the PMR.     

Effect of Static Magnetic Field on Photocatalytic Degradation of Methylene Blue over ZnO and TiO2 Powders

Magnetic field effects (MFEs) on photocatalytic degradation of methylene blue (MB) solution over ZnO and TiO₂ powders are investigated under static magnetic field up to 0.7 T with light irradiation by ultraviolet (UV) light emitting diode. The UV–visible-near-infrared spectrometer is used to monitor the MB concentrations. The positive MFE is observed for ZnO, while the negative MFE for TiO₂, and both MFEs are increased with the increase in the magnetic field applied. By increasing the settling time (the time interval between the preparation of MB solution and the powder dispersion into the MB solution), the photodegradation abilities under MFEs are decreased for both the catalysts. The cause of MFE is discussed in terms of dissolved oxygen in the MB solution and magnetic adsorption of the constituent molecules.     

Low-temperature growth of high-Tc superconducting films by plasma-enhanced metal-organic chemical vapor deposition

Plasma-enhanced MOCVD in which metal-organic compounds are sublimated directly into the growth chamber is studied for the first time as a new low-temperature process for growing superconducting YBa₂Cu₃O-_-x thin films. Y(THD)₃, Ba(THD)₂, Cu(THD)₂ and oxygen are used as metal sources and oxydizing agent. Emission spectroscopy reveals that activated metal-organic compounds and activated oxygen species are present during film growth. Superconducting YBa₂Cu₃O_7-x films whose zero-resistivity temperature are 50 K and 82 K are grown at 550°C and 600°C.     

Simultaneous Determination of Pyridine-Triphenylborane Anti-Fouling Agent and Its Degradation Products in Artificial Seawater by CZE

We developed a CZE method for simultaneous determination of pyridine-triphenylborane (PTPB) anti-fouling agent and its degradation products such as diphenylborinic acid (DPB), phenylboronic acid (MPB), and phenol in artificial seawater (ASW) with no extraction procedure. The ASW samples, in which 20 % (v/v) acetonitrile was added, were injected directly into the capillary using vacuum injection. As the background electrolyte, 60 mM sodium tetraborate adjusted to pH 9.8 was used. The LODs (S/N = 3) for PTPB, DPB, MPB, and phenol were, respectively, 55, 78, 126, and 30 μg L^?1. The RSDs (n = 4) for analytes listed above were in the respective ranges of 2.7–5.7, 0.68–6.1, and 0.69–1.1 % for the peak area, peak height, and migration time. Simple degradation experiments were conducted to verify the usefulness of the proposed method. The PTPB samples dissolved in ASW were put in the open air, and rooms with and without light. The sample solutions were analyzed over time. We inferred that PTPB in ASW was more degraded by photolysis than by hydrolysis. The proposed CZE method has been demonstrated as a useful tool to elucidate the PTPB degradation process and its degradation products in ASW.     

Synthesis of Seven-Membered Benzolactones by Nickel-Catalyzed C−H Coupling of Benzamides with Oxetanes

A NiCl₂(PEt₃)₂-catalyzed regioselective C−H coupling of 8-aminoquinoline-derived benzamides with oxetanes has been developed. The reaction proceeds with concomitant removal of the 8-aminoquinoline auxiliary to directly form the corresponding seven-membered benzolactones, which frequently occur in natural products and bioactive molecules. Additionally, no stereochemical erosion is observed during the course of the reaction, and the use of enantioenriched and substituted oxetane thus provides a new avenue to the optically active benzolactone.     

Detailed Analysis of the Crystal Structures and Magnetic Properties of a Dysprosium(III) Phthalocyaninato Sextuple-Decker Complex: Weak f–f Interactions Suppress Magnetic Relaxation

In the research field of single-molecule magnets (SMMs), lanthanoid–lanthanoid interactions, so-called f–f interactions, are known to affect the SMM properties, although their magnitudes are small. In this article, an SMM with very weak f–f interactions is reported, and the effects of the interactions on the SMM properties are discussed. X-ray structural analysis of the Dy^III-Cd^II-phthalocyaninato sextuple-decker complex (Dy₂Cd₃) reveals that the intramolecular Dy−Dy length in Dy₂Cd₃ is more than 13 Å, which is longer than the intermolecular Dy−Dy length. Even though the two Dy^III ions are far apart, intermolecular ferromagnetic dipole–dipole interactions are observed in Dy₂Cd₃. From detailed analysis of ac magnetic susceptibilities, quantum tunneling of the magnetization (QTM) in Dy₂Cd₃ is partially suppressed owing to the existence of very weak Dy−Dy interactions. Our results show that even very weak Dy−Dy interactions act as a dipolar bias, suppressing QTM.