Defect formation on surfaces bombarded by energetic multiply charged proteins: Implications for the conformation of gas-phase electrosprayed ions

Indirect information on the conformation of highly charged molecular ions may be obtained by monitoring their collisional cross sections and the course of simple gas-phase reactions such as hydrogen-deuterium exchange. In this work, another indirect but more visually oriented approach is explored: electrosprayed protein ions are accelerated toward a highly oriented pyrolytic graphite surface and the resulting single-ion defects are imaged by scanning force and tunneling microscopy. All protein impacts generated shallow hillocks: the shapes depended on the identity and charge state of the incident protein. Lysozyme and myoglobin, both compact, globular proteins in the native state, produced compact, almost circular hillocks. However, hillocks generated by myoglobin that had been denatured in the solution phase were elongated, and the elongation was positively correlated with the charge state of the ion. It appears that structural information about gas-phase multiply charged proteins can be derived from imprints generated by energetic protein impacts on surfaces.     

Superporous agarose beads as a hydrophobic interaction chromatography support

Superporous agarose beads were used as a support for hydrophobic interaction chromatography. These beads have large connecting flow pores in addition to their normal diffusion pores. The flow pores, which are approximately one fifth of the overall diameter of the superporous agarose beads, were earlier shown to give the beads improved mass transfer properties relative to homogeneous agarose beads (Gustavsson and Larsson, J. Chromatogr. A, 734 (1996) 231–240). Superporous agarose beads and homogeneous agarose beads of the same particle size range (106–180 μm) were derivatized with phenyl groups. The properties of the superporous beads were then compared with the homogeneous beads in the separation of a mixture of three model proteins (ribonuclease A, lysozyme and bovine serum albumin) at various superficial flow velocities from 30 to 600 cm/h. The superporous beads gave satisfactory separation at flow velocities five times higher than was possible for homogeneous beads. The performance of the two types of beads was also compared in the purification of lactate dehydrogenase from a beef heart extract at a superficial flow velocity of 150 cm/h. The superporous beads performed considerably better, leading to twice the purification factor and twice the concentration of the desired product. The results were interpreted using the theoretical treatment given by Carta and Rodrigues (Carta and Rodrigues, Chem. Eng. Sci., 48 (1993) 3927).     

Aromatic allylation via diazotization: metal-free C-C bond formation

A new method for the synthesis of allyl aromatic compounds not involving any metal-containing reagent or catalyst has been developed. Arylamines substituted with a large number of different substituents were converted via diazotizative deamination with tert-butyl nitrite in allyl bromide and acetonitrile to the corresponding allyl aromatic compounds. The allylation reaction was found to be suitable for larger scale synthesis due to short reaction times, a nonextractive workup, and robustness toward moisture, air, and type of solvent.     

Electron capture dissociation of substance P using a commercially available Fourier transform ion cyclotron resonance mass spectrometer

Electron capture dissociation of the peptide Substance P is reported for the first time, with an unmodified, commercially available Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. The fragmentation pattern is compared with that obtained with collisionally induced dissociation of the ions in the electrospray ion source, and note that electron capture dissociation gives a more easily interpreted spectrum, showing mainly C-fragments. With the exception of the proline residues, which require cleavage of two chemical bonds, we observe all C-fragmental we find the bias voltage of the electron gun not to be very critical.     

An improved palladium(II)-catalyzed method for the synthesis of aryl ketones from aryl carboxylic acids and organonitriles

A palladium(II)-catalyzed decarboxylative protocol for the synthesis of aryl ketones has been developed. The addition of TFA was shown to improve the reaction yield and employing THF as solvent enabled the use of solid nitriles and in only a small excess. Using this method, five different benzoic acids reacted with a wide range of nitriles to produce 29 diverse (hetero)aryl ketone derivatives in up to 94% yield.     

Effect of hindered diffusion on the adsorption of proteins in agarose gel using a pore model

The hindered diffusion and binding of proteins of different sizes (lysozyme, BSA and IgG) in an agarose gel is described using adsorption kinetic and diffusional data together with an experimentally determined pore size distribution in the gel. The validity of the pore model, including variable diffusion coefficients and porosities is tested against experimental confocal microscopy data. No fitting parameters were used in the present model. The importance of knowing the gel structure is demonstrated especially for large proteins such as IgG. Experimental confocal microscopy data can be explained by the present model.     

On the numerical radius of matrices and its application to iterative solution methods

Uses of the numerical radius in the analysis of basic iterative solution methods, of the SOR method for quasi-Hermitian positive definite matrices (not being consistently ordered) and of maximal eigenvalues of symmetric positive definite matrices using incomplete block-matrix factorizations are presented.     

Equivalent operator preconditioning for elliptic problems

The numerical solution of linear elliptic partial differential equations most often involves a finite element or finite difference discretization. To preserve sparsity, the arising system is normally solved using an iterative solution method, commonly a preconditioned conjugate gradient method. Preconditioning is a crucial part of such a solution process. In order to enable the solution of very large-scale systems, it is desirable that the total computational cost will be of optimal order, i.e. proportional to the degrees of freedom of the approximation used, which also induces mesh independent convergence of the iteration. This paper surveys the equivalent operator approach, which has proven to provide an efficient general framework to construct such preconditioners. Hereby one first approximates the given differential operator by some simpler differential operator, and then chooses as preconditioner the discretization of this operator for the same mesh. In this survey we give a uniform presentation of this approach, including theoretical foundation and several practically important applications for both symmetric and nonsymmetric equations and systems, and some nonlinear examples in the context of Newton linearization. Dedicated to the memory of Gene Golub for his friendly manner and for his broad interest and significant impact on numerical analysis.     

Comparison of preconditioned Krylov subspace iteration methods for PDE-constrained optimization problems

The governing dynamics of fluid flow is stated as a system of partial differential equations referred to as the Navier-Stokes system. In industrial and scientific applications, fluid flow control becomes an optimization problem where the governing partial differential equations of the fluid flow are stated as constraints. When discretized, the optimal control of the Navier-Stokes equations leads to large sparse saddle point systems in two levels. In this paper, we consider distributed optimal control for the Stokes system and test the particular case when the arising linear system can be compressed after eliminating the control function. In that case, a system arises in a form which enables the application of an efficient block matrix preconditioner that previously has been applied to solve complex-valued systems in real arithmetic. Under certain conditions, the condition number of the so preconditioned matrix is bounded by 2. The numerical and computational efficiency of the method in terms of number of iterations and execution time is favorably compared with other published methods.     

Weighted maximal regularity estimates and solvability of non-smooth elliptic systems I

We develop new solvability methods for divergence form second order, real and complex, elliptic systems above Lipschitz graphs, with L ₂ boundary data. The coefficients A may depend on all variables, but are assumed to be close to coefficients A ₀ that are independent of the coordinate transversal to the boundary, in the Carleson sense ‖A−A ₀‖ _C defined by Dahlberg. We obtain a number of a priori estimates and boundary behaviour results under finiteness of ‖A−A ₀‖ _C . Our methods yield full characterization of weak solutions, whose gradients have L ₂ estimates of a non-tangential maximal function or of the square function, via an integral representation acting on the conormal gradient, with a singular operator-valued kernel. Also, the non-tangential maximal function of a weak solution is controlled in L ₂ by the square function of its gradient. This estimate is new for systems in such generality, and even for real non-symmetric equations in dimension 3 or higher. The existence of a proof a priori to well-posedness, is also a new fact.