A new approach towards peptidosulfonamides: synthesis of potential inhibitors of bacterial peptidoglycan biosynthesis enzymes MurD and MurE

Peptidosulfonamides are an emerging group of peptidomimetics with a variety of applications in medicinal chemistry. We present a novel approach to the synthesis of peptidosulfonamides, and apply it to a series of new potential inhibitors of the bacterial peptidoglycan biosynthesis enzymes MurD and MurE. The synthesis was conducted via N-phthalimido β-aminoethanesulfonyl chlorides, which are new building blocks for the synthesis of peptidosulfonamides. In the most crucial step, sulfonic acids or their sodium salts were converted into the corresponding sulfonyl chlorides using an excess of either SOCl₂ or SOCl₂/DMF, and then coupled to the C-protected amino acid. None of the compounds significantly inhibited MurD, however, some inhibited MurE; one had an IC₅₀ below 200 μM, which constitutes a promising starting point for further development. Molecular modelling simulations were performed on two analogues to investigate the absence of inhibitory activity of the sulfonamide compounds on MurD.     

Converged properties of clean metal surfaces by all-electron first-principles calculations

All-electron full-potential linearized augmented plane-wave calculations of the surface energy, work function, and interlayer spacings of close-packed metal surfaces are presented, in particular, for the free-electron-like metal surfaces, Mg(0 0 0 1) and Al(1 1 1), and for the transition metal surfaces, Ti(0 0 0 1), Cu(1 1 1), Pd(1 1 1), and Pt(1 1 1). We investigate the convergence of the surface energy as a function of the number of layers in the slab, using the Cu(1 1 1) surface as an example. The results show that the surface energy, as obtained using total energies of the slab and bulk from separate calculations, converges well with respect to the number of layers in the slab. Obviously, it is necessary that bulk and surface calculations are performed with the same high accuracy. Furthermore, we discuss the performance of the local-density and generalized gradient approximations for the exchange-correlation functional in describing the various surface properties.     

Regioselectivity in the ene-reaction of singlet oxygen with cyclic alkenes: photooxygenation of methyl-substituted 1,4-cyclohexadiene derivatives

The photooxygenation of the 1-methyl-, 2,3-dimethyl-, and 1,4-dimethylcyclohexa-1,4-dienes, which are readily available through Birch reduction, yielded the corresponding ene-products. The formed endocyclic dienes were trapped by the addition of singlet oxygen to give the corresponding bicyclic endoperoxy hydroperoxides. In the case of 1-methylcyclohexa-1,4-diene and 1,4-dimethylcyclohexa-1,4,-diene, the cis-effect determined the product distribution. Photooxygenation of 2,3-dimethylcyclohexa-1,4-dienes gave mainly exocyclic olefin, which was attributed to the lowered rotational barrier of the methyl group and increased reactivity of the methyl groups.     

Structural studies of Cr-doped mullite derived from single-phase precursors

Cr-doped mullites were prepared from single-phase precursors containing up to 9.60 wt% Cr₂O₃ using a sol-gel technique followed by thermal treatment. Particle induced X-ray emission spectroscopy and X-ray powder diffraction were used to characterize the samples. Mullites were orthorhombic, space group Pbam. Cr doping caused the increase of unit-cell parameters. Strongest expansion was noticed along c-axis followed by a and b (Δc/c=0.089, Δa/a=0.061, Δb/b=0.045% per mole Cr₂O₃). A second phase, namely θ-(Al,Cr)₂O₃, was revealed by XRD in the sample containing 9.60 wt% Cr₂O₃. The structure of mullites was refined by the Rietveld method, location of Cr³⁺ was performed by the EPR spectroscopy. At low chromium doping level (Cr₂O₃ content less than ∼5 wt%) Cr³⁺ ions were substituted for Al³⁺ in the AlO₆ octahedra of the mullite structure (M1 site). For higher doping level, Cr³⁺ ions were additionally substituted for Al³⁺ in the AlO₆ octahedra of the second phase [θ-(Al,Cr)₂O₃ at 1400 °C, or α-(Al,Cr)₂O₃ at 1600 °C] which segregated in the system. Substitution of Cr³⁺ for Al³⁺ on M1 site in the mullite structure resulted in increase of average distances in (M1)O₆ octahedron and decrease of average distances in T*O₄ tetrahedron, while average distances in TO₄ tetrahedron stayed almost constant.     

Atomistic packing models for experimentally investigated swelling states induced by CO2 in glassy polysulfone and poly(ether sulfone)

Atomistic packing models have been created, which help to better understand the experimentally observed swelling behavior of glassy polysulfone and poly (ether sulfone), under CO₂ gas pressures up to 50 bar at 308 K. The experimental characterization includes the measurement of the time‐dependent volume dilation of the polymer samples after a pressure step and the determination of the corresponding gas concentrations by gravimetric gas‐sorption measurements. The models obtained by force‐field‐based molecular mechanics and molecular dynamics methods allow a detailed atomistic analysis of representative swelling states of polymer/gas systems, with respect to the dilation of the matrix. Also, changes of free volume distribution and backbone mobility are accessible. The behavior of gas molecules in unswollen and swollen polymer matrices is characterized in terms of sorption, diffusion, and plasticization. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1874–1897, 2006     

Conversion of single-stranded oligonucleotides into cloned duplexes and its consecutive application to short artificial genes.

A general method to convert single-stranded, chemically synthesized oligonucleotides into cloned duplexes is described. Oligonucleotides supplied with 3'-terminal extensions that are complementary to 3'-protruding ends obtained by certain restriction enzymes can be cloned either directly or with the help of an adapter molecule into double-stranded vectors. Two methods have also been developed for consecutive cloning applications. According to these methods, the synthetic oligonucleotides (and their enzymatically prepared complementary strands) are joined, one after the other, inside a cloning vector, each joining requiring one cloning step. Synthetic genes are thus built up from oligonucleotides corresponding to only one strand of the DNA. The sequential assembly of the cloned duplex takes place in the 5' to 3' direction. Each oligonucleotide is supplied with a four-nucleotide-long 3'-terminal extension, but this sequence is eliminated when the joining takes place, leaving no limiting sequence between the oligonucleotides. The two consecutive cloning methods, the adapter and the polycloning site methods, are illustrated by the assembly of short artificial genes.     

Dynamic NMR study of the flexibility of 2-amino-3-aroyl-4,6-diaryl-pyrylium salts

Dynamic NMR investigations of a number of 2-amino-3-aroyl-4,6-diaryl-pyrylium salts were carried out. The barrier to rotation of the partial C, N double bond was determined and proved to be in the range of 62 to 63 kJ/mol. Quantum chemical calculations of bond orders and electron densities of the different atoms in the molecules show the distinct double bond character of the exocyclic C, N bond. This is in agreement with the relatively high barrier to rotation. By quantum chemical ab initio 3-21G calculations, the dynamic behaviour of this kind of compounds was simulated; two pairs (image and mirror image) of ground state conformations, in coincidence with the experiment, were obtained. Received: 10 May 1996 / Revised: 1 July 1996 / Accepted: 4 July 1996     

3D molecular imaging SIMS

Thin monolayer and bilayer films of spin cast poly(methyl methacrylate) (PMMA), poly(2-hydroxyethyl methacrylate) (PHEMA), poly(lactic) acid (PLA) and PLA doped with several pharmaceuticals have been analyzed by dynamic SIMS using SF₅⁺ polyatomic primary ion bombardment. Each of these systems exhibited minimal primary beam-induced degradation under cluster ion bombardment allowing molecular depth profiles to be obtained through the film. By combing secondary ion imaging with depth profiling, three-dimensional molecular image depth profiles have been obtained from these systems. In another approach, bevel cross-sections are cut in the samples with the SF₅⁺ primary ion beam to produce a laterally magnified cross-section of the sample that does not contain the beam-induced damage that would be induced by conventional focussed ion beam (FIB) cross-sectioning. The bevel surface can then be examined using cluster SIMS imaging or other appropriate microanalysis technique.     

Theory of Non-Equilibrium Stationary States as a Theory of Resonances

We study a small quantum system (e.g., a simplified model for an atom or molecule) interacting with two bosonic or fermionic reservoirs (say, photon or phonon fields). We show that the combined system has a family of stationary states parametrized by two numbers, T ₁ and T ₂ (‘reservoir temperatures’). If T ₁ ≠ T ₂, then these states are non-equilibrium stationary states (NESS). In the latter case we show that they have nonvanishing heat fluxes and positive entropy production and are dynamically asymptotically stable. The latter means that the evolution with an initial condition, normal with respect to any state where the reservoirs are in equilibria at temperatures T ₁ and T ₂, converges to the corresponding NESS. Our results are valid for the temperatures satisfying the bound min (T ₁,T ₂) > g ^{2 + α}, where g is the coupling constant and 0 < α < 1 is a power related to the infra-red behaviour of the coupling functions. Submitted: March 20, 2006. Revised: March 19, 2007. Accepted: May 11, 2007. Marco Merkli: Partly supported by an NSERC PDF, the Institute of Theoretical Physics of ETH Zürich, Switzerland, the Departments of Mathematics of McGill University and the University of Toronto, Canada. Matthias Mück: Supported by DAAD under grant HSP III. Israel Michael Sigal: Supported by NSERC under grant NA7901.