Kinetic study of nickel(II) complexation by pteroylglutamic acid

The kinetics of the complexation of NiII by pteroylglutamic acid have been studied in the 545 ∘C range, the ionic strength (0.6 M) being regulated with KNO3, in the 5.5–7.0pH range, using the stopped-flow method. Under the experimental conditions two processes were observed. The faster process was detected in the millisecond range and is associated with the reaction between NiII and the ligand. The slower is observed within a few seconds. Complementary equilibrium studies were made at 25 ∘C. The results are consistent with the formation of a 1:1 complex between the reactants, and a mechanism is proposed to account for the observed behaviour. Equilibrium constants for the NiII plus pteroylglutamic acid system, as well as activation parameters, are reported. This revised version was published online in June 2006 with corrections to the Cover Date.     

Steepest Descent, CG, and Iterative Regularization of Ill-Posed Problems

The state of the art iterative method for solving large linear systems is the conjugate gradient (CG) algorithm. Theoretical convergence analysis suggests that CG converges more rapidly than steepest descent. This paper argues that steepest descent may be an attractive alternative to CG when solving linear systems arising from the discretization of ill-posed problems. Specifically, it is shown that, for ill-posed problems, steepest descent has a more stable convergence behavior than CG, which may be explained by the fact that the filter factors for steepest descent behave much less erratically than those for CG. Moreover, it is shown that, with proper preconditioning, the convergence rate of steepest descent is competitive with that of CG.This revised version was published online in October 2005 with corrections to the Cover Date.     

Shallow implantation of "Size-Selected" Ag clusters into graphite

We have investigated the implantation of Ag(N) (N = 20-200) clusters into a graphite substrate over the range of energies (E) 0.75-6 keV using molecular dynamics simulations. We find that after implantation the silver clusters remain coherent, albeit amorphous, and rest at the bottom of an open tunnel in the graphite created by the impact. It is found that the implantation depth of the clusters varies linearly as E/N2/3. We conclude that the cluster is decelerated by a constant force proportional to its cross-sectional area. We also identify a threshold energy for surface penetration associated with elastic compression of the graphite substrate.     

Proton transfer reaction ion trap mass spectrometer

Proton transfer reaction mass spectrometry is a relatively new field that has attracted a great deal of interest in the last few years. This technique uses H(3)O(+) as a chemical ionization (CI) reagent to measure volatile organic compounds (VOCs) in the parts per billion by volume (ppbv) to parts per trillion by volume (pptv) range. Mass spectra acquired with a proton transfer reaction mass spectrometer (PTR-MS) are simple because proton transfer chemical ionization is "soft" and results in little or no fragmentation. Unfortunately, peak identification can still be difficult due to isobaric interferences. A possible solution to this problem is to couple the PTR drift tube to an ion trap mass spectrometer (ITMS). The use of an ITMS is appealing because of its ability to perform MS/MS and possibly distinguish between isomers and other isobars. Additionally, the ITMS duty cycle is much higher than that of a linear quadrupole so faster data acquisition rates are possible that will allow for detection of multiple compounds. Here we present the first results from a proton transfer reaction ion trap mass spectrometer (PTR-ITMS). The aim of this study was to investigate ion injection and storage efficiency of a simple prototype instrument in order to estimate possible detection limits of a second-generation instrument. Using this prototype a detection limit of 100 ppbv was demonstrated. Modifications are suggested that will enable further reduction in detection limits to the low-ppbv to high-pptv range. Furthermore, the applicability of MS/MS in differentiating between isobaric species was determined. MS/MS spectra of the isobaric compounds methyl vinyl ketone (MVK) and methacrolein (MACR) are presented and show fragments of different mass making differentiation possible, even when a mixture of both species is present in the same sample. However, MS/MS spectra of acetone and propanal produce fragments with the same molecular masses but with different intensity ratios. This allows quantitative distinction only if one species is predominant. Fragmentation mechanisms are proposed to explain the results.     

Decay of the peroxide intermediate in laccase: reductive cleavage of the O-O bond.

Laccase is a multicopper oxidase that contains four Cu ions, one type 1, one type 2, and a coupled binuclear type 3 Cu pair. The type 2 and type 3 centers form a trinuclear Cu cluster that is the active site for O(2) reduction to H(2)O. To examine the reaction between the type 2/type 3 trinuclear cluster and dioxygen, the type 1 Cu was removed and replaced with Hg(2+), producing the T1Hg derivative. When reduced T1Hg laccase is reacted with dioxygen, a peroxide intermediate (P) is formed. The present study examines the kinetics and mechanism of formation and decay of P in T1HgLc. The formation of P was found to be independent of pH and did not involve a kinetic solvent isotope effect, indicating that no proton is involved in the rate-determining step of formation of P. Alternatively, pH and isotope studies on the decay of P revealed that a proton enhances the rate of decay by 10-fold at low pH. This process shows an inverse k(H)/k(D) kinetic solvent isotope effect and involves protonation of a nearby residue that assists in catalysis, rather than direct protonation of the peroxide. Decay of P also involves a significant oxygen isotope effect (k(16)O(2)/k(18)O(2)) of 1.11 +/- 0.05, indicating that reductive cleavage of the O-O bond is the rate-determining step in the decay of P. The activation energy for this process was found to be approximately 9.0 kcal/mol. The exceptionally slow rate of decay of P is explained by the fact that this process involves a 1e(-) reductive cleavage of the O-O bond and there is a large Franck-Condon barrier associated with this process. Alternatively, the 2e(-) reductive cleavage of the O-O bond has a much larger driving force which minimizes this barrier and accelerates the rate of this reaction by approximately 10(7) in the native enzyme. This large difference in rate for the 2e(-) versus 1e(-) process supports a molecular mechanism for multicopper oxidases in which O(2) is reduced to H(2)O in two 2e(-) steps.     

Dynamics of polydisperse hard-spheres under strong confinement

We use molecular simulation to probe the connection between local structure and the unusual re-entrant dynamics observed for polydisperse hard-sphere liquids confined in thin slit pores. The local structure is characterised by calculating 2-D bond-orientational order parameters associated with square and hexatic order for particles in the layer adjacent to the confining walls. When the wall separation is commensurate with the average particle size, the particles primarily exhibit local hexatic order, whereas local square order increases in prevalence for incommensurate geometries. The relaxation time extracted from the ensemble-averaged mean-square displacement increases exponentially with the static correlation length associated with hexatic local order in strongly confined commensurate geometries, in agreement with theoretical predictions for dynamical slowing. Square order, by contrast, is not associated with a growing length scale for either commensurate or incommensurate geometries, indicating that it is strongly geometrically frustrated. Our results suggest that the influence of bond-orientational order on dynamical slowing may be altered by changing the extent of confinement.     

Chemical kinetics at high pressure

Abstract

Numerous studies have demonstrated the importance to include pressure as a kinetic parameter in the elucidation of inorganic reaction mechanisms. These studies have specially led to a better understanding and a systematic classification of solvent exchange and ligand substitution reactions of octahedral complexes of transition metal elements. The mechanistic picture for substution reactions on square planar complexes is well established and involves a concurrent bimolecular attack by solvent and the nucleophile on the substrate with a considerable discrimination among different entering groups. The search for factor promoting the conversion of the normal associative mode of activation into a dissociative process has then attracted much attention. Two attempts to induce dissociation, as studied by high-pressure NMR, are presented: one is to prevent the formation by means of sterically hindered ligands, the other one is to promote bond weakening at the leaving group.     

Engineering of a two-step purification strategy for a panel of monoclonal immunoglobulin M directed against undifferentiated human embryonic stem cells

A two-step purification strategy comprising of polyethylene glycol (PEG) precipitation and anion-exchange chromatography was developed for a panel of monoclonal immunoglobulin M (IgM) (pI 5.5–7.7) produced from hybridoma cultures. PEG precipitation was optimized with regards to concentration, pH and mixing. For anion-exchange chromatography, different resins were screened of which Fractogel EMD, a polymer grafted porous resin had the highest capacity. Despite its significantly slower mass transfer, the binding capacity was still higher compared to a convection driven resin (monolith). This purification strategy was successfully demonstrated for all 9 IgMs in the panel. In small scale most antibodies could be purified to >95% purity with the exception of two which gave a lower final purity (46% and 85%). The yield was dependent on the different antibodies ranging from 28% to 84%. Further improvement of recovery and purity was obtained by the digestion of DNA present in the hybridoma supernatant using an endonuclease, benzonase. So far this strategy has been applied for the purification of up to 2 l hybridoma supernatants.