The Reduction of Aromatic Aldehydes and Benzils by Sodium Formaldehyde Sulphoxylate

Sodium formaldehyde sulphoxylate is shown to be an effective reagent for the reduction of some aromatic aldehydes to alcohols. Benzils are also reduced under neutral or basic conditions to give mainly benzoins. Ketones are reduced only slowly.     

Identification of ligands that target the HCV-E2 binding site on CD81

Hepatitis C is a global health problem. While many drug companies have active R&D efforts to develop new drugs for treating Hepatitis C virus (HCV), most target the viral enzymes. The HCV glycoprotein E2 has been shown to play an essential role in hepatocyte invasion by binding to CD81 and other cell surface receptors. This paper describes the use of AutoDock to identify ligand binding sites on the large extracellular loop of the open conformation of CD81 and to perform virtual screening runs to identify sets of small molecule ligands predicted to bind to two of these sites. The best sites selected by AutoLigand were located in regions identified by mutational studies to be the site of E2 binding. Thirty-six ligands predicted by AutoDock to bind to these sites were subsequently tested experimentally to determine if they bound to CD81-LEL. Binding assays conducted using surface Plasmon resonance revealed that 26 out of 36 (72 %) of the ligands bound in vitro to the recombinant CD81-LEL protein. Competition experiments performed using dual polarization interferometry showed that one of the ligands predicted to bind to the large cleft between the C and D helices was also effective in blocking E2 binding to CD81-LEL.     

The Fourier space restricted Hartree-Fock method for the electronic structure calculation of linear poly(tetrafluoroethylene)

Building on the pioneering work of Jean-Marie André and working in the laboratory he founded, the authors have developed a code called FT-1D to make Hartree-Fock electronic structure computations for stereoregular polymers using Ewald-type convergence acceleration methods. That code also takes full advantage of all line-group symmetries to calculate only the minimal set of two-electron integrals and to optimize the computation of the Fock matrix. The present communication reports a benchmark study of the FT-1D code using polytetrafluoroethylene(PTFE) as a test case. Our results not only confirm the algorithmic correctness of the code through agreement with other studies where they are applicable, but also show that the use of convergence acceleration enables accurate results to be obtained in situations where other widely-used codes(e.g., PLH and Crystal) fail. It is also found that full attention to the line-group symmetry of the PTFE polymer leads to an increase of between one and two orders of magnitude in the speed of computation. The new code can therefore be viewed as extending the range of electronic-structure computations for stereoregular polymers beyond the present scope of the successful and valuable code Crystal.     

Intrinsic dispersivity of randomly packed monodisperse spheres

We determine the intrinsic longitudinal dispersivity l(d) of randomly packed monodisperse spheres by separating the intrinsic stochastic dispersivity l(d) from dispersion by unavoidable sample dependent flow heterogeneities. The measured l(d), scaled by the hydrodynamic radius r(h), coincide with theoretical predictions [Saffman, J. Fluid Mech. 7, 194 (1960)] for dispersion in an isotropic random network of identical capillaries of length l and radius a, for l/a=3.82, and with rescaled simulation results [Maier et al., Phys. Fluids 12, 2065 (2000)].     

Simulations of ferrite-dielectric-wire composite negative index materials

We perform extensive finite difference time domain simulations of ferrite based negative index of refraction composites. A wire grid is employed to provide negative permittivity. The ferrite and wire grid interact to provide both negative and positive index of refraction transmission peaks in the vicinity of the ferrite resonance. Notwithstanding the extreme anisotropy in the index of refraction of the composite, negative refraction is seen at the composite air interface allowing the construction of a focusing concave lens with a magnetically tunable focal length.     

Comparative 11A structure of two molluscan hemocyanins from 3D cryo-electron microscopy

Hemocyanins are giant extracellular proteins that transport oxygen in the hemolymph of many molluscs. Molluscan hemocyanins are cylindrical decamers or didecamers of a 350-400 kDa subunit that contains seven or eight different covalently linked globular functional units (FUs), arranged in a linear manner. Each FU carries a single copper active site and reversibly binds one dioxygen molecule. As a consequence, the decamer can carry up to 70 or 80 O(2) molecules. Although complete sequence information is now available from several molluscan hemocyanins, many details of the quaternary structure are still unclear, including the topology of the 10 subunits within the decamer. Here we show 3D reconstructions from cryo-electron micrographs of the hemocyanin decamer of Nautilus pompilius (Cephalopoda) and Haliotis tuberculata (Gastropoda) at a resolution of 11A (FSC(1/2-bit) criterion). The wall structure of both hemocyanins is very similar and shows, as in previous reconstructions, three tiers with 20 functional units each that encircle the cylinder wall, and the 10 oblique minor and major wall grooves. However, the six types of wall FUs of the polypeptide subunit, termed a-b-c-d-e-f, are now for the first time individually discernable by their specific orientation, shape, and connections. Also, the internal collar complex of the decamers shows superior resolution which, in this case, reveals striking differences between the two hemocyanins. The five arcs (FU-g pairs) of the central collar (in both hemocyanins) and the five slabs (FU-h pairs) of the peripheral collar (only present in Haliotis hemocyanin), as well as their connections to the wall and to each other are now more clearly defined. The arc is attached to the wall through a feature termed the anchor, a previously undescribed structural element of the hemocyanin wall.     

Synthesis and Biological Evaluation of a Class of Mitochondrially‐Targeted Gadolinium(III) Agents

A structure–activity relationship study of a library of novel bifunctional Gd^III complexes covalently linked to arylphosphonium cations is reported. Such complexes have been designed for potential application in binary cancer therapies such as neutron capture therapy and photon activation therapy. A positive correlation was found between lipophilicity and cytotoxicity of the complexes. Mitochondria uptake was determined by means of inductively coupled plasma mass spectrometry (ICP‐MS), and Gd uptake was determined by means of quantification using synchrotron X‐ray fluorescence (XRF) imaging. A negative correlation between lipophilicity and tumour selectivity of the Gd^III complexes was demonstrated. This study highlights the delicate balance required to minimise in vitro cytotoxicity and optimise in vitro tumour selectivity and mitochondrial localisation for this new class of mitochondrially‐targeted binary therapy agents. We also report the highest in vitro tumour selectivity for any Gd agent reported to date, with a T/N (tumour/normal cell) ratio of up to 23.5±6.6.     

Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.