Ultrafast pump-probe study of the primary photoreaction process in pharaonis halorhodopsin: halide ion dependence and isomerization dynamics

Halorhodopsin is a retinal protein that acts as a light-driven chloride pump in the Haloarchaeal cell membrane. A chloride ion is bound near the retinal chromophore, and light-induced all- trans --> 13- cis isomerization triggers the unidirectional chloride ion pump. We investigated the primary ultrafast dynamics of Natronomonas pharaonis halorhodopsin that contains Cl (-), Br (-), or I (-) ( pHR-Cl (-), pHR-Br (-), or pHR-I (-)) using ultrafast pump-probe spectroscopy with approximately 30 fs time resolution. All of the temporal behaviors of the S n <-- S 1 absorption, ground-state bleaching, K intermediate (13- cis form) absorption, and stimulated emission were observed. In agreement with previous reports, the primary process exhibited three dynamics. The first dynamics corresponds to the population branching process from the Franck-Condon (FC) region to the reactive (S 1 (r)) and nonreactive (S 1 (nr)) S 1 states. With the improved time resolution, it was revealed that the time constant of this branching process (tau 1) is as short as 50 fs. The second dynamics was the isomerization process of the S 1 (r) state to generate the ground-state 13- cis form, and the time constant (tau 2) exhibited significant halide ion dependence (1.4, 1.6, and 2.2 ps for pHR-Cl (-), pHR-Br (-), and pHR-I (-), respectively). The relative quantum yield of the isomerization, which was evaluated from the pump-probe signal after 20 ps, also showed halide ion dependence (1.00, 1.14, and 1.35 for pHR-Cl (-), pHR-Br (-), and pHR-I (-), respectively). It was revealed that the halide ion that accelerates isomerization dynamics provides the lower isomerization yield. This finding suggests that there is an activation barrier along the isomerization coordinate on the S 1 potential energy surface, meaning that the three-state model, which is now accepted for bacteriorhodopsin, is more relevant than the two-state model for the isomerization process of halorhodopsin. We concluded that, with the three-state model, the isomerization rate is controlled by the height of the activation barrier on the S 1 potential energy surface while the overall isomerization yield is determined by the branching ratios at the FC region and the conical intersection. The third dynamics attributable to the internal conversion of the S 1 (nr) state also showed notable halide ion dependence (tau 3 = 4.5, 4.6, and 6.3 ps for pHR-Cl (-), pHR-Br (-), and pHR-I (-)). This suggests that some geometrical change may be involved in the relaxation process of the S 1 (nr) state.     

Production of a positron microprobe using a transmission remoderator.

A production method for a positron microprobe using a beta+-decay radioisotope (22Na) source has been investigated. When a magnetically guided positron beam was extracted from the magnetic field, the combination of an extraction coil and a magnetic lens enabled us to focus the positron beam by a factor of 10 and to achieve a high transport efficiency (71%). A 150-nm-thick Ni(100) thin film was mounted at the focal point of the magnetic lens and was used as a remoderator for brightness enhancement in a transmission geometry. The remoderated positrons were accelerated by an electrostatic lens and focused on the target by an objective magnetic lens. As a result, a 4-mm-diameter positron beam could be transformed into a microprobe of 60 microm or less with 4.2% total efficiency. The S parameter profile obtained by a single-line scan of a test specimen coincided well with the defect distribution. This technique for a positron microprobe is available to an accelerator-based high-intensity positron source and allows 3-dimensional vacancy-type defect analysis and a positron source for a transmission positron microscope.     

In situ observation of the formation of Si clathrate Ba8Si46 at high pressures and high temperatures

X-ray diffraction measurements at high pressures and high temperatures revealed that Si clathrate Ba 8Si 46 is formed by a solid-phase reaction of an 8:30 molar mixture of SrSi 2-phase BaSi 2 and Si after BaSi 2 undergoes the BaSi 2-to-EuGe 2 and the EuGe 2-to-SrSi 2 transitions. The volume reduction during the formation of Ba 8Si 46 is the largest, 7.6%, among the observed transitions. On the other hand, an 8:30 molar mixture of SrSi 2-phase SrSi 2 and Si does not result in the formation of Sr 8Si 46 at high pressures and high temperatures; only SrSi 2 transforms from the SrSi 2 phase into the alpha-ThSi 2 phase, and Si remains in the diamond phase.     

On the functional properties of the confluent hypergeometric zeta-function

A zeta-function associated with Kummer’s confluent hypergeometric function is introduced as a classical Dirichlet series. An integral representation, a transformation formula, and relation formulas between contiguous functions and one generalization of Ramanujan’s formula are given. The inverse Laplace transform of confluent hypergeometric functions is essentially used to derive the integral representation.     

Metallosupramolecular Structures Derived from a Series of Diphosphine‐bridged Digold(I) Metalloligands with Terminal d‐Penicillamine

In this report, we describe our recent work on the development of a new family of chiral heteroleptic digold(I) metalloligands with mixed diphosphine and d ‐penicillaminate (d ‐pen), [Au₂(dppx)(d ‐pen‐S)₂]^2– (dppx = PPh₂(CH₂)_nPPh₂, n = 1–5) and their application for the construction of chiral multinuclear and metallosupramolecular structures. The reactions of the metalloligands with 3d metal ions produce a variety of chiral heterobimetallic structures retaining the digold(I) metalloligand structure, ranging from discrete trinuclear to infinite helix structures that depend on the type of dppx. In addition, monophosphine and triphosphine analogues of the metalloligands were designed, and their coordination behavior is discussed to show the essential properties and potential extensibility of this class of metalloligands.     

Catalytic enantioselective amination of silyl enol ethers using chiral dirhodium(II) carboxylates: asymmetric formal synthesis of (-)-metazocine

Dirhodium(II) tetrakis[N-tetrafluorophthaloyl-(S)-tert-leucinate], Rh2(S-TFPTTL)4, is an exceptionally efficient catalyst for enantioselective aminations of silyl enol ethers derived from acyclic ketones or alpha,beta-enones with [N-(2-nitrophenylsulfonyl)imino]phenyliodinane (NsN=IPh), providing N-(2-nitrophenylsulfonyl)-alpha-amino ketones in high yields and with enantioselectivities of up to 95% ee. The effectiveness of the present catalytic protocol has been demonstrated by an asymmetric formal synthesis of (-)-metazocine.     

Criteria for determining the hydrogen-bond structures of a tyrosine side chain by fourier transform infrared spectroscopy: density functional theory analyses of model hydrogen-bonded complexes of p-cresol

Fourier transform infrared (FTIR) spectroscopy is a powerful method to investigate the structures of key Tyr residues involved in various protein reactions. In this study, we have performed density functional theory (DFT) calculations for various hydrogen-bonded complexes of p-cresol, a simple model of a Tyr side chain, in different hydrogen-bond forms to develop explicit criteria for determining the hydrogen-bond structures of Tyr using FTIR spectroscopy. The CO stretching (nuCO) and COH bending (deltaCOH) vibrations were focused as markers and calculated results were compared with experimental data of p-cresol and Tyr. The calculated and experimental nuCO frequencies appeared at 1280-1260, 1260-1250, 1255-1235, and 1240-1220 cm-(1) in the hydrogen-bond donor, free, donor-acceptor, and acceptor forms, respectively. These frequencies, which showed little overlap between the individual hydrogen-bond forms, had a negative linear correlation with the CO lengths in optimized geometries. The deltaCOH frequencies were found at 1255-1210 cm-(1) in the donor form, while the free and acceptor forms showed relatively low deltaCOH frequencies at 1185-1165 and 1190-1160 cm-(1), respectively. In the donor-acceptor form, the vibrational mode with a considerable deltaCOH contribution was found at 1280-1255 cm-(1) with a weak IR intensity. This frequency and the nuCO frequency in the donor-acceptor form are similar to the nuCO and deltaCOH frequencies, respectively, of the donor form, making it difficult to discriminate the two forms. These two forms can be clearly distinguished by detecting a strong nuCO(D) band in p-cresol-OD or Tyr-OD, in which the deltaCOD vibration largely downshifts to approximately 1000 cm-(1). The nuCO(D) frequency of the donor-acceptor form was found at 1260-1240 cm-(1), while that of the donor form was at 1270-1255 cm-(1). Practically, plotting the frequency of the lower-frequency strong IR band (nuCO of the donor-acceptor form or deltaCOH of the donor form) of undeuterated species against the nuCO(D) frequency is convenient for accurate discrimination. Because the donor form shows a positive linear correlation between deltaCOH and nuCO(D) frequencies, the two forms exhibited distinct areas in this plot. The effects of hydrogen-bond interactions on other potential IR and Raman markers are also discussed.     

Square-planar N2S2NiII complexes with an extended pi-conjugated system

The reaction of a mixture of 2-(1-naphthyl)benzothiazoline (HL1) and 2,6-diphenylbenzo[1,2-d:4,5-d']bisthiazoline (H3L2) with nickel(II) acetate tetrahydrate yielded three kinds of square-planar nickel(II) complexes: one nickel(II) complex with innocent ligands ([Ni(L1)2] (1c)) and two nickel(II) complexes with non-innocent ligands ([Ni(L1-L1)] (1a) and [Ni(L1-L2)] (1b)). The complex 1c has two bidentate-N,S ligands, which are formed via ring opening of HL1. On the other hand, the two complexes 1a and 1b contain a tetradentate-N2S2 ligand, which is created via ring opening of HL1 and H3L2, followed by bond formation between imino carbon atoms. Complexes 1a and 1b show very intense absorptions in the near-infrared (NIR) region, characteristic of square-planar complexes with non-innocent ligands. The third nickel(II) complex having a non-innocent tetradentate-N2S2 ligand ([Ni(L2-L2)] (2)) was prepared from H3L2 and nickel(II) acetate tetrahydrate. The electronic spectrum of 2 exhibits a very intense absorption at 981 nm (epsilon = 3.6 x 10(4) M-1 cm-1), which is significantly red-shifted compared with those of 1a (837 nm and 4.4 x 10(4) M-1 cm-1) and 1b (885 nm and 4.5 x 10(4) M-1 cm-1), indicating the presence of an extended pi delocalization. The reaction of 2,6-bis(3,5-dichlorophenyl)benzo[1,2-d:4,5-d']bisthiazoline (H3L3) with nickel(II) acetate tetrahydrate also led to the formation of a nickel(II) complex with a non-innocent ligand ([Ni(L3-L3)] (3)). While complex 3 is analogous to 2, its electrical conductivity is much higher than that of 2. The molecular structures of 1b, 1c, 2, and 3 were determined by X-ray crystallography.     

A chemiluminescence biochemical oxygen demand measuring method

A new chemiluminescence biochemical oxygen demand (BOD_CL) determining method was studied by employing redox reaction between quinone and Baker's yeast. The measurement was carried out by utilizing luminol chemiluminescence (CL) reaction catalyzed by ferricyanide with oxidized quinone of menadione, and Saccharomyces cerevisiae using a batch-type luminometer. In this study, dimethyl sulfoxide was used as a solvent for menadione. After optimization of the measuring conditions, the CL response to hydrogen peroxide in the incubation mixture had a linear response between 0.1 and 100 μM H₂O₂ (r² = 0.9999, 8 points, n = 3, average of relative standard deviation; R.S.D._av = 4.22%). Next, a practical relationship between the BOD_CL response and the glucose glutamic acid concentration was obtained over a range of 11-220 mg O₂ L⁻¹ (6 points, n = 3, R.S.D._av 3.71%) with a detection limit of 5.5 mg O₂ L⁻¹ when using a reaction mixture and incubating for only 5 min. Subsequently, the characterization of this method was studied. First, the BOD_CL responses to 16 pure organic substances were examined. Second, the influences of chloride ions, artificial seawater, and heavy metal ions on the BOD_CL response were investigated. Real sample measurements using river water were performed. Finally, BOD_CL responses were obtained for at least 8 days when the S. cerevisiae suspension was stored at 4 °C (response reduction, 69.9%; R.S.D. for 5 testing days, 18.7%). BOD_CL responses after 8 days and 24 days were decreased to 69.9% and 35.8%, respectively, from their original values (R.S.D. for 8 days involving 5 testing days, 18.7%).