Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation

Reversible phosphorylation of proteins is a post‐translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes remains a subject of active debate. In particular, the nature of transition state (TS), whether it has an associative or dissociative character, has been one of the most controversial issues. Structural evidence supports associative TS, whereas physical organic studies point to a dissociative character. Here we perform hybrid quantum mechanics/molecular mechanics simulations for the reversible phosphorylation of phosphoserine phosphatase (PSP) to study the nature of the TS. Both phosphorylation and dephosphorylation reactions are investigated based on the two‐dimensional energy surfaces along phosphoryl and proton transfer coordinates. The structures of the active site at TS in both reactions reveal compact geometries, consistent with crystal structures of PSP with phosphate analogues. However, the electron density of the phosphoryl group in both TS structures slightly decreases compared with that in the reactant states. These findings suggest that the TS of PSP has a geometrically associative yet electronically dissociative character and strongly depends on proton transfer being coupled with phosphoryl transfer. Structure and literature database, which searches on phosphotransferases, suggest that such a hybrid TS is consistent with many structures and physical organic studies and likely holds for most enzymes catalyzing phosphoryl transfer. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

17,17-Dialkyltetrabenzo[a,c,g,i]fluorenes with extremely high solid-state fluorescent quantum yields: relationship between crystal structure and fluorescent properties

Six 17,17-dialkyltetrabenzo[a,c,g,i]fluorenes (dialkylTBFs) 2–7 (methyl to n-hexyl) were prepared by treatment of 17H-tetrabenzo[a,c,g,i]fluorene (TBF) 1 with n-alkyl halides under basic conditions in moderate yields upon column chromatography and recrystallization. All the compounds show intense blue fluorescence in solutions. On the other hand, in the solid state, the fluorescent spectra and the quantum yields (Φ_p) vary with their alkyl chains. In particular, the Φ_p values of 4–7 bearing n-propyl to n-hexyl groups are close to unity, while the fluorescence of 1 is almost quenched. Crystallographic analyses of 2–7 revealed that the TBF moieties have helicene-like chiral structures in the crystals, and that the alkyl groups basically take an all-trans planar conformation. Because the longer alkyl substituents can serve as a spacer to prevent TBF nuclei from aggregation, π–π interactions of the TBF moieties probably play an important role in quenching the solid-state fluorescence. The relationship between the optical properties and molecular arrangements in the crystals are discussed.     

An Extremely Simple Dibenzopentalene Synthesis from 2‐Bromo‐1‐ethynylbenzenes Using Nickel(0) Complexes: Construction of Its Derivatives with Various Functionalities

Nice and easy : A very simple synthesis for dibenzopentalenes, which starts from 1‐bromo‐2‐ethynylbenzenes, has been developed. It uses Ni⁰ complexes (see scheme), from which a relatively stable Ni^II complex as an important intermediate has been isolated. Dibenzopentalenes with various functional groups can be prepared by the procedure, and their electronic properties are consistent with theoretical calculations.

     

Measurements of binary diffusion coefficients for metal complexes in organic solvents by the Taylor dispersion method

Infinite dilution binary diffusion coefficients, D₁₂, of ferrocene, 1,1′-dimethylferrocene and ethylferrocene in hexane, cyclohexane and ethanol at 313.2 K and pressures from 0.2 to 19 MPa, in acetonitrile at 298.2–333.2 K and 0.2 MPa, and various metallic acetylacetonate, acac, complexes such as Co(acac)₃, Ru(acac)₃, Rh(acac)₃, Pd(acac)₂ and Pt(acac)₂ mainly in ethanol at 313.2 K and 0.2 MPa were measured by the Taylor dispersion method. The D₁₂ values in m² s⁻¹ for the three ferrocenes in the present study and those of ferrocene and 1,1′-dimethylferrocene in supercritical carbon dioxide in our previous studies were represented by the modified hydrodynamic equation over a wide range of viscosity: M^0.5D₁₂/T = 1.435 × 10⁻¹³η^−0.8446 with average absolute relative deviation of 2.40% for 316 data points, where M is the solute molecular weight, T is the temperature in K, η is the solvent viscosity in Pa s. Although the D₁₂ values for the acac complexes were roughly represented by the above hydrodynamic equation, the accuracies were lower because they were dependent on not solute molecular weight but the number of acac ligand in the complex molecules.     

Two‐Phase System Utilizing Hydrophobic Metal–Organic Frameworks (MOFs) for Photocatalytic Synthesis of Hydrogen Peroxide

Much effort has been devoted to photocatalytic production of hydrogen peroxide (H₂O₂) as an alternative to fossil fuels. From an economic point of view, reductive synthesis of H₂O₂ from O₂ coupled with the oxidative synthesis of value‐added products is particularly interesting. We herein report application of MIL‐125‐NH₂, a photoactive metal–organic framework (MOF), to a benzylalcohol/water two‐phase system that realized photocatalytic production and spontaneous separation of H₂O₂ and benzaldehyde. Hydrophobization of the MOF enabled its separation from the aqueous phase. This resulted in enhanced photocatalytic efficiency and enabled application of various aqueous solutions including extremely low pH solution which is favorable for H₂O₂ production but fatal to MOF structure. In addition, a highly concentrated H₂O₂ solution was obtained by simply reducing the volume of the aqueous phase.     

MeV- and Sub-MeV-photon Sources Based on Compton Backscattering at Spring-8 and KPSI-JAEA

Recently we have constructed two facilities for generating photon beams in the MeV and sub-MeV energy regions by means of the Compton backscattering with a laser and an electron beam at SPring-8 and at Kansai Photon Science Institute of Japan Atomic Energy Agency(KPSIJAEA).The MeV-photon source at SPring-8 consists of a continuous-wave optically-pumped far infrared laser with a wavelength of 118.8 μm and an 8 GeV stored electron beam.Present MeV-photon flux is estimated to be 1.3×10~3 photons/s.On the other hand,the sub-MeV-photon source at KPSI-JAEA consists of a pulse Nd:YAG laser with a wavelength of 1 064 nm and a 150 MeV electron beam accelerated by microtron.In the first trial of the photon production in this source,backscattered photon flux is estimated to be 20 photons/pulse.Both the Compton backscattered photon sources have possibilities to be used for new tools in various fields such as nuclear physics,materials science,and astronomy.     

Unconventional pairing originating from the disconnected Fermi surfaces of superconducting LaFeAsO1-xFx

For a newly discovered iron-based high T_{c} superconductor LaFeAsO1-xFx, we have constructed a minimal model, where inclusion of all five Fe d bands is found to be necessary. The random-phase approximation is applied to the model to investigate the origin of superconductivity. We conclude that the multiple spin-fluctuation modes arising from the nesting across the disconnected Fermi surfaces realize an extended s-wave pairing, while d-wave pairing can also be another candidate.     

Silica gel assisted reductive cyclization of 2-nitro-β-piperidinostyrenes,derived from 2-nitrotoluenes,to indoles

An efficient modification of the Leimgruber-Batcho method of indole synthesis has been devised that facilitates the synthesis of a variety of 2,3-unsubstituted indoles containing halogen, methoxy and benzyloxy groups, from 2-nitrotoluenes, in high yields. The modified method involves the condensation of 2-nitrotoluenes with tripiperidinomethane followed by the reductive cyclization of the intermediate 2-nitro-β-piperidinostyrenes with iron and acetic acid in refluxing toluene in the presence of silica gel (column chromatography grade, 60–200 mesh).     

Perfusion study of the pulmonary hilar region by SPECT--normal cases

Alveoli in the hilar region comprise the peripheral area containing daughter branches from subsegmental or one more divisional peripheral bronchi. Pulmonary perfusion in hilar region was examined by SPECT (single photon emission CT) in ten normal volunteers. ROI (region of interest) in the axial images were set in the hilar region, the upper, middle and lower lung fields with 10.8 mm thickness. Counts/one pixel (C/P) were calculated in these ROI. There was a tendency of C/P increase from upper to lower lung field. And there were no significant differences in C/P increase between hilar region and other axial fields. In the chronic obstructive pulmonary diseases, however, ventilation studies in the previous reports using Xe dynamic CT or PET (positron emission tomography) showed differences between outer region and hilar region. This method will be expected to evaluate the pulmonary perfusion not only in the whole lung but in different lung areas, including the hilar region in the chronic obstructive pulmonary diseases.