Crystallographic evidence for different modes of interaction of BF3/BF4 species with water molecules and 18-crown-6

We report the crystal and molecular structures of the complex of 18-C-6 with H₃O⁺BF₄⁻ (I) and the complex of 18-C-6 with BF₃OH₂·H₂O (II). The different modes of appearance of the “BF₃” species as BF₃, BF₃OH₂, BF₃OH₂·H₂O and BF₄⁻, as well as their structurally significant intermolecular and intramolecular interactions, are discussed. In complex I the oxonium ion is bound at the centre of the 18-C-6 macrocycle. The oxonium oxygen is located practically equidistant (2.68–2.73 Å) from the six macrocyclic ethereal oxygens. The BF₄⁻ counter-ion is positioned 7.3 Å away from the oxonium ion in the same general plane of the crown ether. This anion is not involved in any direct intermolecular contacts, a fact that may explain why it is spherically disordered. In complex II there is no guest molecule (or ion) present in the “cavity” of the macrocycle, but there are two hydrogen-bonded systems of BF₃OH₂·H₂O that are interacting with the crown ether on either side of the general macrocyclic plane. Complex II features three types of hydrogen bonds—the O(water)-HO(crown) bonds (2.83 and 2.85 Å), the O(water)H-O(BF₃) bond (2.49 Å) and the O(BF₃)-HO(crown) bond (2.65 Å). The strong intermolecular O(crown)O(water)O(BF₃) and O(crown)O(BF₃) interactions stabilize the normally unstable BF₃OH₂·H₂O species.     

Extended Hückel MO calculations of the conformation of several amino acids

The conformation of the amino acid residues, glycine, alanine, proline, and phenylalanine have been predicted from molecular orbital calculations of appropriate model compounds. Using the current main chain rotation convention (, ) the principle conformations were found to be glycine (0, 0), alanine (240, 240), proline (120, 330) and phenylalanine (30, 330). Several secondary conformations were also found for glycine. A comparison of the predicted conformations is in good agreement with experimental data on comparable residues or model compounds.Supported by National Institutes of Health Grants No. FR 5409-07 and GM 16312-01.Recipient of a Public Health Service Research Career Development Award AM 1159-01.     

Rapid synthesis of α-ketoamides using microwave irradiation-simultaneous cooling method

Microwave-assisted acyl chloride-isonitrile condensation and CaCO₃-mediated hydrolysis constitute a one-pot, 2-minute process to prepare α-ketoamides.     

Synthesis, binding affinity, and relaxivity of target-specific MRI contrast agents

Although magnetic resonance imaging (MRI) is one of the most important imaging modalities of the central nervous system (CNS), one of the main drawbacks of MRI is its limited specificity. This can potentially be partially alleviated by target-specific contrast agents. In the present paper we describe a simple high yield synthesis of two such gadolinium-based spiperone targeted MRI contrast agents, 1a and 1b. The R₁ relaxivities of 1a and 1b were evaluated and found to be 5.94 and 8.31 mM⁻¹ s⁻¹, respectively at 9.4T, while their R₂ relaxivities at the same magnetic field were found to be 18.05 and 22.60 mM⁻¹ s⁻¹, respectively. In addition and very importantly compound 1a, which is a gadolinium-based, spiperone-targeted MRI contrast agent, was found to preserve some of the spiperone affinity toward the dopamine D2 receptor. Compounds 1a and 1b thus represent potential agents for in vitro dopamine receptor imaging using MRI in experimental models. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structure of microemulsions with gemini surfactant studied by solvatochromic probe and diffusion NMR

The structure of microemulsions prepared by the anionic gemini surfactant didodecyl diphenyl ether disulfonate (C12-DADS) was investigated by a solvatochromic probe and nuclear magnetic resonance (NMR) diffusion measurements. The NMR measurements indicate the presence of bicontinuous and oil-in-water microemulsions depending on microemulsion composition. The absorbance spectra of the solvatochromic probe, Nile red, indicate the solubilization of the probe in different sites, in agreement with the NMR findings. It was also found that the microemulsions were capable of dissolving the hydrophobic probe, Nile red, up to four times better than expected if it were simply dissolved in the toluene phase.     

A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins

Peptides bind to class II major histocompatibility complex (MHC) proteins in an extended conformation. Pockets in the peptide binding site spaced to accommodate peptide side chains at the P1, P4, P6, and P9 positions have been previously characterized and help to explain the obtained peptide binding specificity. However, two peptides differing only at P10 have significantly different binding affinities for HLA-DR1. The structure of HLA-DR1 in complex with the tighter binding peptide shows that the peptide binds in the usual polyproline type II conformation, but with the P10 residue accommodated in a shallow pocket at the end of the binding groove. HLA-DR1 variants with polymorphic residues at these positions were produced and found to exhibit different side chain specificity at the P10 position. These results define a new specificity position in HLA-DR proteins.     

Electrokinetic effects of adsorbed neutral polymers

On the basis of a previously developed hydrodynamic model for adsorbed polymers the charge flow along a charged interface with adsorbed (uncharged) polymer is calculated. An effective electrokinetic layer thickness is defined and its dependence on the characteristics of the adsorbed polymer and the ionic strength is studied. It is found that tails are very important for the hydrodynamic effects considered because they effectively screen the solvent flow from inner parts of the absorbed layer. The electrokinetic layer thickness increases with decreasing ionic strength, and tends to a limit equal to the hydrodynamic thickness at very low ionic strength.     

Biomimetic cycloaddition approach to tropolone natural products via a tropolone ortho-quinone methide

[reaction: see text] A study toward a possible biomimetic hetero Diels-Alder reaction is reported between humulene and a novel tropolone ortho-quinone methide. A suitable tropolone ortho-quinone methide precursor has been prepared from 3-methyl-2-furoate. Heating the ortho-quinone methide precursor gave a tropolone ortho-quinone methide, which in the presence of humulene underwent a hetero Diels-Alder reaction to give a deoxy analogue of epolone B.     

Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Ion spray-tandem mass spectrometry of supramolecular coordination complexes

Double-helical [M₂L₂] ⁿ⁺, triple-helical [M₂L₃] ⁿ⁺, and toroidal [M₃L₃] ⁿ⁺ (M = Cu, Co, Fe, Ni, La, Eu, Gd, Tb, or Lu) supramolecular complexes have been fully characterized by ion spray mass spectrometry (IS-MS). The IS-MS spectra from pure acetonitrile solutions reflect the nature of the cations present in solution with conservation of the charge state and allow an efficient qualitative speciation of the compounds. The mass spectrometry results can be correlated with other powerful techniques (nuclear magnetic resonance and electronic spectroscopy) for the characterization of supramolecular complexes in solution, Structural information is obtained by collision-induced dissociation, which strongly depends on the metal ions used in the supramolecular complexes and on the various connectivities and topologies of the ligands. When the ligand contains 3,5dimethoxybenzyl groups bound to the benzimidazole rings, the partial fragmentation of the complexes is associated with a decrease of the total charge of the complexes and the appearance of the characteristic fragment at m/z 151 that corresponds to the 3,5-dimethoxybenzyl cation. A detailed analysis of the fragmentation pathways of these supramolecular complexes suggests that the metal-nitrogen coordination bonds are very strong in the gas phase.