Direct calculation of trans-hydrogen-bond 13C-15N 3-bond J-couplings in entire polyalanine alpha-helices. A density functional theory study

We present the first trans-H-bond 13C-15N 3-bond J couplings calculated from entire neutral and protonated alpha-helical polyalanines. The neutral helices considered are those of the capped peptides, acetyl(Ala)NNH2, where N = 8, 16, 17, and 18, while the protonated peptides are the uncapped (Ala)17 protonated at three different positions. The calculated J values correlate well with O...H distances and somewhat less well with N...O distances, particularly if the terminal H-bonds are eliminated from the correlation. The J values calculated using the entire helix are about 6% lower in magnitude than those recently reported for H-bonding chains whose geometries were extracted from the same helices. Aqueous solvation favors protonation of the alpha-helix on the terminal COOH. Experimental measurements of the trans-H-bond 13C-15N 3-bond J couplings in acidic solution should be interpreted with this context.     

A Phage Display-Identified Short Peptide Capable of Hydrolyzing Calcium Pyrophosphate Crystals—The Etiological Factor of Chondrocalcinosis

Chondrocalcinosis is a metabolic disease caused by the presence of calcium pyrophosphate dihydrate crystals in the synovial fluid. The goal of our endeavor was to find out whether short peptides could be used as a dissolving factor for such crystals. In order to identify peptides able to dissolve crystals of calcium pyrophosphate, we screened through a random library of peptides using a phage display. The first screening was designed to select phages able to bind the acidic part of alendronic acid (pyrophosphate analog). The second was a catalytic assay in the presence of crystals. The best-performing peptides were subsequently chemically synthesized and rechecked for catalytic properties. One peptide, named R25, turned out to possess some hydrolytic activity toward crystals. Its catalysis is Mg²⁺-dependent and also works against soluble species of pyrophosphate.     

Crystal and molecular structure of diastereomeric 2-diphenylthiophosphinoyl-cis-(4,6-dimethyl)-1,3-dithianes

The crystal and molecular structures of a pair of diastereomeric 2-diphenylthiophosphinoyl-cis-(4,6-dimethyl)-1,3-dithianes 2 have been determined by the X-ray method. The differences in corresponding bond distances in cis-2 and trans-2 are discussed in context of the anomeric effect operating in this heterocyclic system. The comparison of selected structural parameters between diastereomeric cis- and trans-dithianes 2 and their 5-t-butyl analogs 1 is also discussed. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:537–541, 1998     

Crystal and molecular structures of isomeric 2-morpholino-2-thiono-4-methyl-1,3,2-dioxaphosphinane and 2-morpholino-2-oxo-4-methyl-1,3,2-dioxaphosphinane

Two isomeric pairs of compounds, cis- and trans-2-morpholino-2-thiono-4-methyl-1,3,2-dioxaphosphinane ( 1A + 1B ) and 2-morpholino-2-oxo-4-methyl-1,3,2-dioxaphosphinane ( 2A + 2B ) were obtained and separated into the pure compounds by silica gel chromatography. Attempts at crystallization afforded 1A , 1B , and 2B . Each crystalline isomer was studied by the X-ray technique, and each crystal and molecular structures assigned. These studies revealed that 1B and 2B have exocyclic 4-CH₃ and sulfur (for 1B ) or 4-CH₃ and oxygen (for 2B ) in the diequatorial position (cis-geometry), while compound 1A possesses the 4-CH₃ group in equatorial position while sulfur is in an axial position (trans-geometry). For all the examined compounds, all the basic geometrical parameters, such as bond lengths, bond and torsion angles, and the deformation of a chair conformation of the six-membered heterocyclic rings, have been established. Such unambiguous assignment of cis-trans geometry in both pairs of 1 and 2 allowed us to confirm the stereoretentive PS → PO conversion by means of OXONE® and the stereoinvertive mechanism of formic-acid catalyzed hydrolysis of phosphorothiomorpholidates. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:271–279, 1998     

The X-ray crystal and molecular structure of 5′-bromo-5′-deoxythymidine

5′-Bromo-5′-deoxythymidine (1) crystallizes with four molecules in a monoclinic unit cell of space group C2. The ribose ring adopts an envelope conformation, transient between T and E₀ (O4′-exo), with the C1′ atom being in the flap position. In the crystal lattice, the molecules are connected by intermolecular one-dimensional chains of hydrogen bondings from the hydroxyl hydrogen H3′(O3′) to the carbonyl oxygen O4. The differences in conformation and a hydrogen-bonding system of 1 with comparison to the structure of thymidine are observed. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9: 591–596, 1998     

Identification of Bacteria Associated with Post-Operative Wounds of Patients with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Approach

The bacterial infection of post-operative wounds is a common health problem. Therefore, it is important to investigate fast and accurate methods of identifying bacteria in clinical samples. The aim of the study was to analyse the use of the MALDI-TOF MS technique to identify microorganism wounds that are difficult to heal. The most common bacteria are Escherichia coli, Staphylococcus spp., and Enterococcus spp. We also demonstrate the effect of culture conditions, such as the used growth medium (solid: Brain Heart Infusion Agar, Mueller Hilton Agar, Glucose Bromocresol Purple Agar, and Vancomycin Resistance Enterococci Agar Base and liquid: Tryptic Soy Broth and BACTEC Lytic/10 Anaerobic/F), the incubation time (4, 6, and 24h), and the method of the preparation of bacterial protein extracts (the standard method based on the Bruker guideline, the Sepsityper method) to identify factors and the quality of the obtained mass spectra. By comparing the protein profiles of bacteria from patients not treated with antibiotics to those treated with antibiotics based on the presence/absence of specific signals and using the UniProt platform, it was possible to predict the probable mechanism of the action of the antibiotic used and the mechanism of drug resistance.     

Stereoselective Cyclopropanation of 2‐[(S)‐(4‐Methylphenyl)sulfinyl]cyclopent‐2‐en‐1‐one with Sulfur Ylides and α‐Halo Carbanions. Preliminary Communication

The cyclopropanation of the title compound (S)‐ 2 with various sulfur ylides has been examined. The reaction with methylenesulfonium ylides gave the corresponding cyclopropanes 4 with low diastereoselectivity. The formation of the second product 5 arising from the subsequent methylenation of the CO group was also observed. A clean cyclopropanation of (S)‐ 2 took place with ethyl (dimethylsulfanylidene)acetate affording the cyclopropanes 6 , with high π‐facial selectivity, but low endo/exo ratio. A high endo/exo selectivity, but low π‐facial selectivity was observed in the reaction of (S)‐ 2 with (2‐ethoxy‐2‐oxoethyl)(diphenyl)sulfonium tetrafluoroborate. The use of α‐bromoacetate carbanion as the cyclopropanation reagent resulted in the formation of 6 with very high facial and endo/exo‐selectivity. In a proposed explanation of the stereochemical outcome of the cyclopropanations investigated, the ground‐state conformation of the sulfoxide 2 and the transition‐state structure of the initial addition step were taken into account.     

High‐energy‐resolution diced spherical quartz analyzers for resonant inelastic X‐ray scattering

A novel diced spherical quartz analyzer for use in resonant inelastic X‐ray scattering (RIXS) is introduced, achieving an unprecedented energy resolution of 10.53 meV at the Ir L₃ absorption edge (11.215 keV). In this work the fabrication process and the characterization of the analyzer are presented, and an example of a RIXS spectrum of magnetic excitations in a Sr₃Ir₂O₇ sample is shown.     

Dissipative plasmon‐solitons in multilayer graphene

Nonlinear properties of a multi‐layer stack of graphene sheets are studied. It is predicted that such a structure may support dissipative plasmon‐solitons generated and supported by an external laser radiation. Novel nonlinear equations describing spatial dynamics of the nonlinear plasmons driven by a plane wave in the Otto configuration are derived and the existence of single and multi‐hump dissipative solitons in the graphene structure is predicted.     

Catalytic C-H amination with aromatic amines

Aniline joins the club: A β-diketiminato copper(I) catalyst enables C-H amination of anilines employing low catalyst loadings to preclude oxidation to the diazene ArN=NAr. Electron-poor anilines are particularly resistant towards diazene formation and participate in the amination of strong and unactivated C-H bonds. N-alkyl anilines also take part in C-H amination.