Mass spectrometric approaches for elucidation of antigenantibody recognition structures in molecular immunology

Mass spectrometric approaches have recently gained increasing access to molecular immunology and several methods have been developed that enable detailed chemical structure identification of antigen-antibody interactions. Selective proteolytic digestion and MS-peptide mapping (epitope excision) has been successfully employed for epitope identification of protein antigens. In addition, "affinity proteomics" using partial epitope excision has been developed as an approach with unprecedented selectivity for direct protein identification from biological material. The potential of these methods is illustrated by the elucidation of a beta-amyloid plaque-specific epitope recognized by therapeutic antibodies from transgenic mouse models of Alzheimer's disease. Using an immobilized antigen and antibody-proteolytic digestion and analysis by high resolution Fourier transform ion cyclotron resonance mass spectrometry has lead to a new approach for the identification of antibody paratope structures (paratope-excision; "parex-prot"). In this method, high resolution MS-peptide data at the low ppm level are required for direct identification of paratopes using protein databases. Mass spectrometric epitope mapping and determination of "molecular antibody-recognition signatures" offer high potential, especially for the development of new molecular diagnostics and the evaluation of new vaccine lead structures.     

Infrared action spectroscopy and dissociation dynamics of the HOOO radical

The HOOO radical has long been postulated to be an important intermediate in atmospherically relevant reactions and was recently deemed a significant sink for OH radicals in the tropopause region. In the present experiments, HOOO radicals are generated in a pulsed supersonic expansion by the association of O(2) and photolytically generated OH radicals, and the spectral signature and vibrational predissociation dynamics are investigated via IR action spectroscopy, an IR-UV double resonance technique. Rotationally resolved IR action spectra are obtained for trans-HOOO in the fundamental (nu(OH)) and overtone (2nu(OH)) OH stretching regions at 3569.30 and 6974.18 cm(-1), respectively. The IR spectra exhibit homogeneous line broadening, characteristic of a approximately 26-ps lifetime, which is attributed to intramolecular vibrational redistribution and/or predissociation to OH and O2 products. In addition, an unstructured feature is observed in both the OH fundamental and overtone regions of HOOO, which is likely due to cis-HOOO. The nascent OH X(2)Pi, v = 0 or v = 1, products following vibrational predissociation of HOOO, nu(OH) or 2nu(OH), respectively, have been investigated using saturated laser-induced fluorescence measurements. A distinct preference for population of Pi(A') Lambda-doublets in OH was observed and is indicative of a planar dissociation of trans-HOOO in which the symmetry of the bonding orbital is maintained.     

Design of a novel G-quenched molecular beacon: a simple and efficient strategy for DNA sequence analysis

G-quenched MBs are devised from readily available starting materials and used for sequence specific DNA detection with high efficiency.     

4H-Chromenone Glycosides from Eranthis hyemalis (L.) SALISBURY

Investigation of the tubers of Eranthis hyemalis (Ranunculaceae) afforded six chromenone glycosides. Their structures have been elucidated mainly by spectroscopic (FAB-MS, 2D-NMR techniques) and chemical methods (acidic and enzymatic hydrolysis) as 9-{[(β-D -glucopyranosyl)oxy]methyl}-8,11-dihydro-5-hydroxy-2-methyl-4H-pyrano[2,3-g][1]benzoxepin-4-one ( 1 ), 9-{[(β-D -gentiobiosyl)oxy]methyl}-8,11-dihydro-5-hydroxy-2-methyl-4H-pyrano[2,3-g][1]benzoxepin-4-one( 2 ), 9-{[(β-D -glucopyranosvl)oxy]melhyl}-8,11-dihydro-5-hydroxy-2-(hydroxy-methyl)-4H-pyrano[2,3-g][1]benzoxepin-4-one( 3 ), 8-{(2E)-4-[(β-D -glucopyranosyl)oxy]-3-methylbut-2-enyl}-5,7-dihydroxy-2-methyl-4H-1-benzopyran-4-one ( 4 ), 8-{(2E)-4-[(β-D -glucopyranosyi)oxy]-3-methylbut-2-enyl}-5,7-dihydroxy-2-(hydroxymethyl)-4H-1-benzopyran-4-one ( 5 ), and 7-{[(β-D -glucopyranosy1)oxy]methyl}-2,3-dihydro-2-(l-hydroxy-1-methylethyl)-4-methoxy-5H-furo[3,2-g][1]benzopyran-5-one ( 6 ). Compound 2 exhibited negative inotropic activity.     

An improved process of separation of R- and S-timolol

Diastereomeric timolol tartrates 4 are obtained in a one-pot synthesis from the racemic base 2 and optically active O,O-diacetyl- or O,O-dibenzoyltartaric anhydrides 3 , as only one of the diastereomers precipitates from acetone solution. Acidic hydrolysis as the corresponding 4 leads to timolol in high yield and optical purity.     

Green chemical syntheses and applications within organophosphorus chemistry

Application of the microwave (MW) technique offers many advantages in organophosphorus syntheses. Reluctant reactions may take place on MW irradiation. In most cases, MWs make the reactions more efficient in respect of rate, selectivity and yield. The benefits are shown via representative examples. MW irradiation may replace a catalyst, or simplify catalytic systems. The synthesis of catalysts incorporating heterocyclic P-ligands is also discussed. Where it was relevant, structural chemical details were also provided.     

Evaluating the accuracy of theoretical one‐bond 13C─13C scalar couplings and their ability to predict structure in a natural product

This study explores the feasibility of using a combination of experimental and theoretical 1‐bond ¹³C─¹³C scalar couplings (¹J_CC) to establish structure in organic compounds, including unknowns. Historically, ⁿJ_CC and ⁿJ_CH studies have emphasized 2 and 3‐bond couplings, yet ¹J_CC couplings exhibit significantly larger variations. Moreover, recent improvements in experimental measurement and data processing methods have made ¹J_CC data more available. Herein, an approach is evaluated in which a collection of theoretical structures is created from a partial nuclear magnetic resonance structural characterization. Computed ¹J_CC values are compared to experimental data to identify candidates giving the best agreement. This process requires knowledge of the error in theoretical methods, thus the B3LYP, B3PW91, and PBE0 functionals are evaluated by comparing to 27 experimental values from INADEQUATE. Respective errors of ±1.2, ±3.8, and ±2.3 Hz are observed. An initial test of this methodology involves the natural product 5‐methylmellein. In this case, only a single candidate matches experimental data with high statistical confidence. This analysis establishes the intramolecular hydrogen‐bonding arrangement, ring heteroatom identity, and conformation at one position. This approach is then extended to hydroheptelidic acid, a natural product not fully characterized in prior studies. The experimental/theoretical approach proposed herein identifies a single best‐fit structure from among 26 candidates and establishes, for the first time, 1 configuration and 3 conformations to complete the characterization. These results suggest that accurate and complete structural characterizations of many moderately sized organic structures (<800 Da) may be possible using only ¹J_CC data.     

Weak approximation of the stochastic wave equation

We investigate the accuracy of approximation of E[φ(u(t))], where {u(t):t∈[0,∞)} is the solution of the stochastic wave equation driven by the space-time white noise and φ is an R-valued function defined on the Hilbert space L²(R). The approximation is done by the leap-frog scheme. We show that, under certain conditions on φ, the approximation by the leap-frog scheme is of order two.     

Coherent storage of photoexcited triplet states using 29Si nuclear spins in silicon

Pulsed electron paramagnetic resonance spectroscopy of the photoexcited, metastable triplet state of the oxygen-vacancy center in silicon reveals that the lifetime of the m(s)=±1 sublevels differs significantly from that of the m(s)=0 state. We exploit this significant difference in decay rates to the ground singlet state to achieve nearly ~100% electron-spin polarization within the triplet. We further demonstrate the transfer of a coherent state of the triplet electron spin to, and from, a hyperfine-coupled, nearest-neighbor (29)Si nuclear spin. We measure the coherence time of the (29)Si nuclear spin employed in this operation and find it to be unaffected by the presence of the triplet electron spin and equal to the bulk value measured by nuclear magnetic resonance.