Proton pumping mechanism in cytochrome c oxidase

Two different issues, important for the pumping mechanism of cyctochrome c oxidase, have been addressed in the present study. One of them concerns the nature of two key proton transfer transition states. A simple electrostatic model is used to suggest that the transition state (TS) for transfer to the pump-site should be positively charged, while the one for transfer to the binuclear center should be charge-neutral. The character of the former TS will guarantee that the protons will be pumped to the outside and not return to the inside, while the neutral character of the latter one will allow transfer with a sufficiently low barrier. In the simple electrostatic analysis, leading to this qualitative picture of the pumping process, the results from the kinetic experiments are strictly followed, but it is at least as important to follow the fundamental requirements for pumping. In this perspective, the uncertainties in the quantitative analysis should be rather unimportant for the emerging qualitative picture of the pumping mechanism. The second problem addressed concerns the purpose of the K-channel. It is argued that the reason for the presence of the K-channel could be that protons cannot pass through the binuclear center at some stage of pumping. Barriers and water binding energies were computed using hybrid density functional theory (DFT) to investigate this question.     

The bonding in second row transition metal dihydrides,difluorides and dichlorides

Summary The dihydrides, the difluorides and the dichlorides of the second row transition metal atoms from yttrium to palladium have been studied with methods including electron correlation of all valence electrons. Comparisons are made to the previously studied corresponding diatomic systems. It is found that the general trends of the binding energies of the second hydride and halide remain the same as in the diatomic hydrides and halides. The second ligand binding energies for the dihalides thus vary much more than for the dihydrides. This is due to important attractive effects between the halide lone-pairs and empty 4d-orbitals to the left and strong repulsions towards occupied 4d-orbitals to the right. For some systems the second ligand binds much more than the first ligand, as for RuF₂ where the difference is 34.3 kcal/mol, whereas for other systems the reverse is true, as for PdCl₂ where the first ligand binds more than the second with 20.4 kcal/mol. The results can be explained by strong ligand field effects and differences in the atomic spectra.     

Determination of wear metals in lubrication oils: a comparison study of ICP-OES and FAAS.

Certain wear metals (Fe, Cr, Ni, Cu and Zn) of various lubrication oils were determined by means of ICP-OES and FAAS. The kerosene dilution method, which is used widely together with ICP-OES, was applied with both methods here. Calibration standards were made from a commercial organo-metallic standard. Our aim was to clarify the possibility of using the quick kerosene dilution method together with FAAS for a rapid check for certain indicator metals. Metal determinations with FAAS were accurate enough for quantitative work in machine condition diagnostics and waste oil characterization, when compared with those with ICP-OES.     

The truncatedSVD as a method for regularization

The truncated singular value decomposition (SVD) is considered as a method for regularization of ill-posed linear least squares problems. In particular, the truncated SVD solution is compared with the usual regularized solution. Necessary conditions are defined in which the two methods will yield similar results. This investigation suggests the truncated SVD as a favorable alternative to standard-form regularization in cases of ill-conditioned matrices with well-determined numerical rank.This work was carried out while the author visited the Dept. of Computer Science, Stanford University, California, U.S.A., and was supported in part by National Science Foundation Grant Number DCR 8412314, by a Fulbright Supplementary Grant, and by the Danish Space Board.     

Implicit Solution of Hyperbolic Equations with Space-Time Adaptivity

Adaptivity in space and time is introduced to control the error in the numerical solution of hyperbolic partial differential equations. The equations are discretised by a finite volume method in space and an implicit linear multistep method in time. The computational grid is refined in blocks. At the boundaries of the blocks, there may be jumps in the step size. Special treatment is needed there to ensure second order accuracy and stability. The local truncation error of the discretisation is estimated and is controlled by changing the step size and the time step. The global error is obtained by integration of the error equations. In the implicit scheme, the system of linear equations at each time step is solved iteratively by the GMRES method. Numerical examples executed on a parallel computer illustrate the method.     

Thiophene‐cored 2,2‐bis(methylol)propionic acid dendrimers for optical‐power‐limiting applications

The synthesis and characterization of dendron‐coated 2,5‐bis(phenylethynyl)thiophene chromophores are described. The dendrimers were grown divergently on the arylthiophene core with the versatile anhydride of 2,2‐bis(methylol)propionic acid. The arylthiophene core was synthesized with Sonogashira coupling reactions. Structurally well‐defined dendrimers up to the fourth generation were grown, as confirmed by size exclusion chromatography, NMR, and matrix‐assisted laser desorption/ionization time‐of‐flight analysis. The different dendritic substitution did not influence the absorption spectra of the compounds in or near the visible region. Solutions of arylthiophenes had good transparency at wavelengths greater than 400 nm. The dendritic thiophenes exhibited an optical‐power limit at the laser wavelength of 532 nm. However, the magnitude of the optical‐power limit of these compounds was slightly lower than that of a nondendritic arylthiophene with n‐pentyl substituents. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1177–1187, 2005     

Determination of the atomic-state population in A Kr-Br2 mixture

The atomic-state populations of the 5s[1$\text{1}\text{2}$]° metastable level of Kr and of the 5s²P_{$\text{3}\text{2}$} resonant level of Br in a Kr-Br₂ mixture have been determined as functions of current strength. Occurrence of energy transfer from the Kr-level to the Br-level has been verified.