Estimation of dye configuration from conventional chiroptical spectra of porphyrin integrates: combination of exciton theory with Monte Carlo molecular structural simulation

Dye integrates (arrays and aggregates) are the subject of current interest in photochemical devices. However, they are in general not suitable for X-ray crystallography because of their poor crystallinity. Here, we improved a simple method of estimating dye configurations in porphyrin integrates from their visible absorption (AB) and circular dichroism (CD) spectra. For this purpose, we calculate the dipolar and optical rotatory strengths of an integrate on the basis of the exciton theory for a given porphyrin configuration, generate the theoretical AB and CD spectra of the dye integrate using a phenomenological line shape function, a Voigt function with an adjustable line width, and optimize the configuration by minimizing the square sum (S) of the difference between the observed and calculated spectra. We adopted two optimization methods to achieve a least-squares fit between the calculated and observed spectra: the Metropolis Monte Carlo (MC) method, which incorporates S into the molecular force-field energy as a constraint, and the quasi-Newton (QN) method, which numerically minimizes S and uses no molecular force field. To check the feasibility of these methods, we simulated the AB and CD spectra of Tr?ger's base and meso-meso-linked porphyrins using the QN program, then compared the dye configurations with their X-ray structures. The calculated dye configuration of Tr?ger's base porphyrin is sufficiently in agreement with that of the X-ray structure (RMSD=0.21 A for the ZnS4 center), whereas that of meso-meso-linked porphyrin was not. These results were discussed in terms of charge transfer between two porphyrins. Finally, we applied the QN and MC methods to the structural estimation of a newly prepared peptide-linked bis(porphyrin) Boc-(PorZn,S)2-OBut. The best configurations estimated by these two methods were sufficiently in agreement with each other.     

Effects of the supporting electrolyte on the kinetics of the removal of proteins adsorbed on a stainless steel surface by H2O2-electrolysis

The effects of different types of supporting electrolytes on the removal of beta-lactoglobulin (beta-Lg) after being adsorbed to a stainless steel surface by a H2O2-electrolysis treatment was investigated. In this process, hydroxyl radicals (*OH), generated by the electrolysis of hydrogen peroxide, decompose the substances adhering to the surface. The removal of the adsorbed protein from the stainless steel surface during the treatment was monitored in situ by ellipsometry. The apparent first-order removal rate constants, k(cl), for 17 types of supporting electrolytes were determined, as well as the current corresponding to the rate of generation of *OH. The k(cl) and generated current values for LiCl, NaCl, KCl, KNO(3), K(2)SO(4), CH(3)COOK, and K(2)CO(3) were all similar. Ca(2+) and Mg(2+) strongly suppressed the removal of the adsorbed protein. The presence of ammonium compounds led to an increase in k(cl) and current values. In H2O2-electrolysis in the presence of potassium phosphate, the removal was extremely rapid, and an apparent increase in the thickness of the adsorbed layer was observed. The mechanisms responsible for the peculiar effects of calcium, magnesium, phosphate, and ammonium compounds were investigated by means of a Fourier transform infrared (FTIR) spectroscopic analysis, as well as by the characteristics of the removal under different treatment conditions.     

Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods

All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca(2+)-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.     

Monte Carlo Shell Model Mass Predictions

The nuclear mass calculation is discussed in terms of large-scale shell model calculations. First, the development and limitations of the conventional shell model calculations are mentioned. In order to overcome the limitations, the Quantum Monte Carlo Diagonalization (QMCD) method has been proposed. The basic formulation and features of the QMCD method are presented as well as its application to the nuclear shell model, referred to as Monte Carlo Shell Model (MCSM). The MCSM provides us with a breakthrough in shell model calculations: the structure of low-lying states can be studied with realistic interactions for a nearly unlimited variety of nuclei. Thus, the MCSM can contribute significantly to the study of nuclear masses. An application to N∼20 unstable nuclei far from the β-stability line is mentioned. This revised version was published online in July 2006 with corrections to the Cover Date.     

Extraction of iridium(IV) from hydrochloric acid media with crown ether in chloroform, and its determination by ICP–AES

A new method for the quantitative extraction and determination of trace amounts of iridium from hydrochloric acid media has been established based on the formation of an ion-association complex of iridium hexachloro anion IrCl₆ ^2– with dicyclohexyl-18-crown-6 (DC18C6) oxonium cation in chloroform, then determination by inductively coupled plasma atomic emission spectrometry (ICP–AES). The effect of various factors (solvent, acid concentration, crown ether, reagent concentration, shaking time, composition of the extracted species, foreign ions, etc.) on the extraction and back-extraction of iridium has been investigated. The procedure was used to determine traces of iridium in palladium chloride and rhodium chloride.     

Adsorbed state of nitrogen on ruthenium catalysts: TPD and isotopic study

The adsorbed state of nitrogen on Ru catalysts was studied by a TPD technique combined with an isotopic technique. (1) A molecular and an atomic species on Ru powder, (2) a molecular and three atomic species on Raney-Ru, and (3) two molecular and probably three atomic species on Raney-Ru/K were identified, respectively. Relations between the adsorbed states and those reactivities for an isotopic equilibration reaction of N₂ were discussed.     

X-Ray Tube Voltage Dependence of Wiener Spectra of Screen Structure Mottle Recorded on Front and Back Emulsions

A low-speed screen/film system was used to investigate structure mottle, i.e., the density fluctuation of an x-ray film due to inhomogeneous screen structure. The tube voltage dependence of the Wiener spectra of the structure mottle was separately determined for front and back film emulsions. The Wiener spectral values of the structure mottle of the front emulsion were greater than those of the back emulsion at lower tube voltages. The spectral values of the structure mottle of the front emulsion decreased with tube voltage, while those of the back emulsion increased. We explain these phenomena by the behavior of the Wiener spectra of the relative spatial fluctuation of fluorescence intensity due to following reasons: (1) spatial thickness fluctuation of the screen produces a relative spatial fluctuation of x-ray energy absorbed in the screen, and (2) as the distance between the emulsion of the film and the average position of the x-ray absorption in the screen lengthens, the number of random scattering and absorption of light photons increase.Presented at the International Commission for Optics Topical Meeting, Kyoto, 1994.     

Improved Quantitative Dynamic Range of Time-of-Flight Mass Spectrometry by Simultaneously Waveform-Averaging and Ion-Counting Data Acquisition

Two different types of data acquisition methods, “averaging mode” and “ion-counting mode”, have been used in a time-of-flight (TOF) mass spectrometry. The most common method is an averaging mode that sums waveform signals obtained from each flight cycle. While it is possible to process many ions arriving at the same TOF in one flight cycle, low-abundance ions are difficult to measure because ion signals are overwhelmed by noises from the detection system. An ion-counting mode is suitable for the detection of such low-concentration ions, but counting loss occurs when two or more ions arrive at the detector within the dead time of the acquisition system. In this study, we introduce a technique that combines two methods to measure target ions with a high concentration difference, i.e., averaging mode and ion-counting mode are used simultaneously for high abundant and trace ions, respectively. By processing waveforms concurrently during data acquisition, one can choose to analyze either or both types of data to achieve a highly quantitative mass spectrum over a wide range of sample concentrations. The result of the argon isotope analysis shows that this method provides a more accurate determination of the isotope ratio compared to averaging mode alone at one-twentieth of the analysis time required by ion-counting alone.

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Acid-catalyzed cyclization of vinylsilanes bearing an amino group. Stereoselective synthesis of pyrrolidines

[reaction: see text] In the presence of an acid catalyst, vinylsilanes 1 bearing an amino group protected by an electron-withdrawing group were smoothly cyclized to 2-(silylmethyl)pyrrolidines 2. This cyclization was utilized for the stereoselective synthesis of 2,n-disubstituted pyrrolidines (n = 3-5). The cyclized products could be converted to the corresponding alcohols by oxidative cleavage of the carbon-silicon bond with TBAF and H2O2.