Acidity of a Cu-bound histidine in the binuclear center of cytochrome C oxidase

Cytochrome c oxidase (CcO) is a crucial enzyme in the respiratory chain. Its function is to couple the reduction of molecular oxygen, which takes place in the Fea3-CuB binuclear center, to proton translocation across the mitochondrial membrane. Although several high-resolution structures of the enzyme are known, the molecular basis of proton pumping activation and its mechanism remain to be elucidated. We examine a recently proposed scheme (J. Am. Chem. Soc. 2004, 126, 1858; FEBS Lett. 2004, 566, 126) that involves the deprotonation of the CuB-bound imidazole ring of a histidine (H291 in mammalian CcO) as a key element in the proton pumping mechanism. The central feature of that proposed mechanism is that the pKa values of the imidazole vary significantly depending on the redox state of the metals in the binuclear center. We use density functional theory in combination with continuum electrostatics to calculate the pKa values, successively in bulk water and within the protein, of the Cu-bound imidazole in various Cu- and Cu-Fe complexes. From pKas in bulk water, we derived a value of -266.34 kcal.mol(-1) for the proton solvation free energy (Delta). This estimate is in close agreement with the experimental value of -264.61 kcal.mol(-1) (J. Am. Chem. Soc. 2001, 123, 7314), which reinforces the conclusion that Delta is more negative than previous values used for pKa calculations. Our approach, on the basis of the study of increasingly more detailed models of the CcO binuclear center at different stages of the catalysis, allows us to examine successively the effect of each of the two metals' redox states and of solvation on the acidity of imidazole, whose pKa is approximately 14 in bulk water. This analysis leads to the following conclusions: first, the effect of Cu ligation on the imidazole acidity is negligible regardless of the redox state of the metal. Second, results obtained for Cu-Fe complexes in bulk water indicate that Cu-bound imidazole pKa values lie within the range of 14.8-16.6 throughout binuclear redox states corresponding to the catalytic cycle, demonstrating that the effect of the Fe oxidation states is also negligible. Finally, the low-dielectric CcO proteic environment shifts the acid-base equilibrium toward a neutral imidazole, further increasing the corresponding pKa values. These results are inconsistent with the proposed role of the Cu-bound histidine as a key element in the pumping mechanism. Limitations of continuum solvation models in pKa calculations are discussed.     

Interesting periodic variations in physical and chemical properties of homonuclear diatomic molecules

We carry out a systematic study of various ground state and response properties of homonuclear diatomic molecules (from hydrogen to rubidium, including transition metals) as a function of atomic number of constituent atoms. We perform the ground state and response property calculations by using state of the art density functional theory/time dependent density functional theory. We observe that several properties of homonuclear diatomic molecules show periodic variations along rows and columns of the periodic table. The periodic variations in the ground state properties of diatomic molecules may be explained by the nature and type of the bond that exists between the constituent atoms. Similarly, the periodic variations in the response properties such as static dipole polarizability and strength of the van der Waals interaction between diatomic molecules have been correlated with the variations in metallic/nonmetallic character of the elements along the periodic table. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

End-to-end single cyanato and thiocyanato bridged Cu(II) polymers with a new tridentate Schiff base ligand: crystal structure and magnetic properties

A new tridentate Schiff base ligand HL (L = C14H19N2O), derived from the condensation of benzoylacetone and 2-dimethylaminoethylamine in a 1:1 ratio, reacts with copper(ii) acetate and cyanate, thiocyanate or azide, to give rise to several end-to-end polymeric complexes of formulae [CuL(mu(1,3)-NCO)]n 1, [CuL(mu(1,3)-NCS)]n 2 and the complex 3 has two crystallographically independent units of formula [CuL(N3)] in the asymmetric unit cell. Complex 3 exists in dimeric form rather than as a polymeric chain. Compound 1 is the first report of a singly end-to-end cyanate bridged polymeric chain of Cu(II) with a Schiff base as a co-ligand. There are many examples of double NCS bridged polymeric chains, but fewer singly bridged ones such as compound 2. We have characterized these complexes by analytical, spectroscopic, structural and variable temperature magnetic susceptibility measurements. The coordination geometry around the Cu(II) centers is distorted square pyramidal for 1 and 2 and square planar for complex 3. The magnetic susceptibility data show slight antiferromagnetic coupling for the polymers having J values -0.19 and -0.57 cm(-1) for complexes 1 and 2 respectively. The low values of J are consistent with the equatorial-axial disposition of the bridges in the polymers.     

Computer simulation of selective aggregation in binary colloids

The morphology of clusters formed by selective aggregation of binary colloids is studied in a two-dimensional Monte Carlo simulation for a large range of number fractions (200:1, 100:1, 10:1, 2:1). We find remarkable similarity in morphology to those observed in experiments, from the formation of closed "micelles" to large branched clusters. Quantitative studies of the fractal dimension, kinetics, and cluster size distribution are also carried out and compared with diffusion-limited cluster aggregation and reaction-limited cluster aggregation models.     

Universal occurrence of soot superaggregates with a fractal dimension of 2.6 in heavily sooting laminar diffusion flames

Using small-angle light scattering we show that a new phase of soot with size ca. 10 microm and a fractal dimension of D approximately equal to 2.6 exists in laminar diffusion flames for a wide range of heavily sooting fuels. This new phase appears to be a supramicrometer extension of the well-known submicrometer, D approximately equal to 1.8 phase of soot formed via diffusion-limited cluster aggregation (DLCA). The occurrence of this new soot phase correlates with an empirical sooting index for fuels. This supports a creation scenario in which these supramicrometer aggregates are created via a percolation of the submicrometer, D approximately equal to 1.8 aggregates.     

On the adsorption and diffusion of Methylene Blue in glass fibers

The adsorption and diffusion phenomena of Methylene Blue dye on glass fiber have been explored. Both isotherm and kinetics have been studied. Effect of process parameters such as pH, adsorbent loading, and initial dye concentration was investigated. Temperature had a little effect on adsorption. A diffusion model was developed to estimate the diffusivity of the dye in glass fiber. The diffusivity was found to be varying exponentially with the dye concentration.     

Measurement of the Diffusivity of Cesium Ion in Aqueous Rubidium Chloride Solution

For the first time cesium diffusivity in aqueous solutions of rubidium chloride is being reported here in the concentration range from 0.001 to 4.00 mol⋅dm⁻³. The measurement use a radioactive tracer technique employing a sliding cell mechanism. These diffusivity values were utilized to understand the transport mechanism of Cs ion in the RbCl–H₂O system using the Onsager-Gosting-Harned equation and the extended Debye-Hückel equation. The observed deviation between the theoretical and experimental diffusivities are explained by introducing the concept of Field-Dielectric-Gradient forces and energies that exist around an ion, which takes care of the finite size of the ion, ion-water interaction and the ion-ion interaction in a continuum basis.     

Molecular interaction of organic dyes in bulk and confined media

Molecular interactions of five thiazine dyes with increasing alkyl substitution have been studied in aqueous and microemulsion media at 303 K within a concentration range of (1.35–7.00) × 10^?4 M. The dimerization constant (K_d) values for the five dyes are ranged between 1.761 and 6.258 × 10³ l mol^?1 in bulk water media, where as in microemulsion media, K_d's are ranged between 1.760 and 4.110 × 10³ l mol^?1. Thionine (with no methyl substitution) and azure A (with two methyl substitution) displayed slightly larger K_d values in microemulsion water pools compared to bulk water while other dyes recorded significant drop in K_d values. The influence of microemulsion media on the molecular interaction of dyes has been explained in terms of electrostatic and hydrophobic factors. The monomer and the dimer spectra are explained in terms of molecular exciton model and the optical absorption parameters of both the species are reported in bulk and confined media.