Quenching of tryptophan fluorescence in various proteins by a series of small nickel complexes

A series of twelve anionic, cationic, and neutral nickel(II) complexes have been synthesized and characterized. The interaction of these complexes with bovine serum albumin (BSA), human serum albumin (HSA), lysozyme (Lyso), and tryptophan (Trp) has been studied using steady-state fluorescence spectroscopy. Dynamic and static quenching constants have been calculated, and the role played in quenching by the ligand and complex charge investigated. The nickel complexes showed selectivity towards the different proteins based on the environment surrounding the Trp residue(s). Only small neutral complexes with hydrophobic ligands effectively quenched protein fluorescence via static quenching, with association constants ranging from 10(2) M(-1) (free Trp) to 10(10) M(-1) (lysozyme), indicating a spontaneous and thermodynamically favorable interaction. The number of binding sites, on average, was determined to be one in BSA, HSA and free Trp, and two in lysozyme.     

Encapsulating zinc(II) within a hydrophobic cavity

A new macrobicyclic ligand has been prepared, and it is shown to bind Zn(2+) on the inside. The ligand consists of a triamido(amine) motif to coordinate the metal ion and a narrow, hydrophobic channel above the metal binding site.     

Spectral editing in MAS NMR of aprotic solids P---Cd cross-polarization and heteronuclear double-quantum filtering studies in II-IV-V2 semiconductor alloys

Magic-angle-spinning NMR spectra of aprotic solids, ceramics and glasses frequently suffer from poor site resolution due to wide chemical shift distribution effects. In such cases, cross-polarization and heteronuclear double-quantum filtering experiments involving nuclei other than ¹H offer unique spectral editing capabilities. The utility of such assignment techniques for examining site populations in semiconductor alloys is demonstrated for the chalcopyrite systems CdGeAs_2−xP_x, CdSiAs_2−xP_x and Zn_xCd_1−xGeP₂. The results permit a distinction between local and non-local effects on experimental chemical shift trends and reveal that compositional dependences observed in these alloys are dominated by non-local chemical shift contributions.     

High‐order stable interpolations for immersed boundary methods

The analysis and improvement of an immersed boundary method (IBM) for simulating turbulent flows over complex geometries are presented. Direct forcing is employed. It consists in interpolating boundary conditions from the solid body to the Cartesian mesh on which the computation is performed. Lagrange and least squares high‐order interpolations are considered. The direct forcing IBM is implemented in an incompressible finite volume Navier–Stokes solver for direct numerical simulations (DNS) and large eddy simulations (LES) on staggered grids. An algorithm to identify the body and construct the interpolation schemes for arbitrarily complex geometries consisting of triangular elements is presented. A matrix stability analysis of both interpolation schemes demonstrates the superiority of least squares interpolation over Lagrange interpolation in terms of stability. Preservation of time and space accuracy of the original solver is proven with the laminar two‐dimensional Taylor–Couette flow. Finally, practicability of the method for simulating complex flows is demonstrated with the computation of the fully turbulent three‐dimensional flow in an air‐conditioning exhaust pipe. Copyright © 2006 John Wiley & Sons, Ltd.     

Verification and validation of impinging round jet simulations using an adaptive FEM

This paper illustrates the use of an adaptive finite element method as a means of achieving verification of codes and simulations of impinging round jets, that is obtaining numerical predictions with controlled accuracy. Validation of these grid‐independent solution is then performed by comparing predictions to measurements. We adopt the standard and accepted definitions of verification and validation (Technical Report AIAA‐G‐077‐1998, American Institute of Aeronautics and Astronautics, 1998; Verification and Validation in Computational Science and Engineering. Hermosa Publishers: Albuquerque, NM, 1998). Mesh adaptation is used to perform the systematic and rigorous grid refinement studies required for both verification and validation in CFD. This ensures that discrepancies observed between predictions and measurements are due to deficiencies in the mathematical model of the flow. Issues in verification and validation are discussed. The paper presents an example of code verification by the method of manufactured solution. Examples of successful and unsuccessful validation for laminar and turbulent impinging jets show that agreement with experiments is achieved only with a good mathematical model of the flow physics combined with accurate numerical solution of the differential equations. The paper emphasizes good CFD practice to systematically achieve verification so that validation studies are always performed on solid grounds. Copyright © 2004 John Wiley & Sons, Ltd.     

1,1′-Bis(phosphoranylidenamino)ferrocene palladium(II) complexes: An unusual case of dative Fe → Pd bonding

Subtle differences in the electron-richness of nitrogen atoms in 1,1′-bis(phosphoranylidenamino)ferrocenes can change the coordination geometry of their palladium(II) complexes from cis to trans. Trans complexation results in concomitant formation of a relatively short dative Fe-Pd bond of 2.67 Å.     

Chemical confirmation of a pentavalent phosphorane in complex with beta-phosphoglucomutase

This communication reports the X-ray crystal structure of the alpha-d-galactose-1-phosphate complex with that of Lactococcus lactis beta-phosphoglucomutase (beta-PGM) crystallized in the presence of Mg2+ cofactor and the enzyme-to-phosphorus ratio determined by protein and phosphate analyses of the crystalline complex. The 1:1 ratio determined for this complex was compared to the 1:2 ratio determined for the crystals of beta-PGM grown in the presence of substrate and Mg2+ cofactor. This result verifies the published structure assignment of this latter complex as the phosphorane adduct formed by covalent bonding between the active site Asp8 carboxylate to the C(1)phosphorus of the beta-glucose 1,6-bisphosphate ligand and rules out the proposal of a beta-PGM-glucose-6-phosphate-1-MgF3- complex.     

Exploring the scope of the 29G12 antibody catalyzed 1,3-dipolar cycloaddition reaction

[Chemical reaction: See text] 29G12 is a murine monoclonal antibody programmed to catalyze the regio- and enantioselective 1,3-dipolar cycloaddition reaction between 4-acetamidobenzonitrile N-oxide 1a and N,N-dimethylacrylamide 2a (Toker, J. D.; Wentworth, P., Jr.; Hu, Y.; Houk, K. N.; Janda, K. D. J. Am. Chem. Soc. 2000, 122, 3244). Given the unique nature of 29G12 as a protein biocatalyst for this chemical reaction, we have investigated both the substrate specificity and mechanistic parameters of the 29G12-catalyzed process. These studies have shown that while 29G12 is specific for its dipole substrate 1a, the antibody is highly promiscuous with respect to the dipolarophiles it can process. 29G12 accepts a bulky hydrophobic dipolarophile cosubstrate, with rates of product formation up to 70-fold faster than with the original substrate 2a. In all cases, the respective isoxazoline products are produced with exquisite regio- and stereochemical control (78-98% ee). Comparison between the steady-state kinetic parameters from the 29G12-catalyzed reaction of 1a with the most efficient versus the original dipolarophile cosubstrate (2m and 2a, respectively), reveals that while the effective molarities (EM)s are almost identical (EM(2m)) 26 M; EM((2a)) 23 M), the affinity of 29G12 for the larger dipolarophile 2m is more than 1 order of magnitude higher than for 2a [Km(2m) 0.44 +/- 0.04 mM; Km(2a) 5.8 +/- 0.4 mM]. Furthermore, when 2m is the cosubstrate, the affinity of 29G12 for its dipole 1a is also greatly improved [Km(1a) 0.82 +/- 0.1 mM compared to Km(1a) 3.4 +/- 0.4 mM when 2a is the cosubstrate]. An analysis of the temperature dependence of the 29G12-catalyzed reaction between 1a and 2m reveals that catalysis is achieved via a decrease in enthalpy of activation (DeltaDeltaH 4.4 kcal mol(-1)) and involves a large increase in the entropy of activation (DeltaDeltaS 10.4 eu). The improved affinity of 29G12 for the nitrile oxide 1a in the presence of 2m, coupled with the increase in DeltaDeltaS during the 29G12-catalyzed reaction between 1a and 2m supports the notion of a structural reorganization of the active site to facilitate this antibody-catalyzed reaction.