Linear quadrupoles with added octopole fields

Two methods of adding relatively small octopole fields to the main quadrupole field of quadrupoles and linear ion traps with cylindrical rods are investigated. The first, 'stretching' the quadrupole by moving two rods out from the axis, produces a combination of higher order fields with similar magnitudes in which the octopole field is not necessarily the greatest. The quadrupole field strength is changed significantly and a large potential appears on the axis. The second method uses rod pairs of different diameters. It adds octopole components of up to several percent while all other higher order fields remain small. An axis potential is also added, but it is only a few percent of the radio-frequency (RF) voltage and approximately equal to the strength of the octopole field. The axis potential can be removed by moving the larger rod pair out from the axis or applying unbalanced RF to the electrodes.     

Nickel(II) complexes of a thiosemicarbazone prepared from 2-Acetylpyridine

Summary The ligand 3-azabicyclo[3.2.2]nonane-3-thiocarboxylic acid 2-[1-(2-pyridinyl)ethylidene]hydrazide (HL), which is observed in an unusual tautomeric form in the solid state, and its selenium analogue (HLSe) have been used to prepare a series of nickel(II) complexes. Compounds of the general formula [NiLX] (X=Cl, Br, NCS, N₃, NO₂ or NCSe) as well as [Ni(LSe)Cl] have been found to be diamagnetic, planar complexes. A single crystal study of [NiL(NCS)] shows the deprotonated ligand bound in a tridentate mannervia its pyridyl nitrogen, imine nitrogen and the thione sulphur atom with the nitrogen atom of the thiocyanato-ligand occupying the fourth coordination position. The solids prepared from the nickel(II) salts having tetrafluoroborate, nitrate and iodide ions approximate to octahedral symmetry and have neutral HL ligands coordinated in a bidentate fashionvia the pyridine and imine nitrogens with the remaining coordination sites being occupied by the anions or water molecules. The [NiL₂] solid is also octahedral with the two deprotonated ligands bonding as tridentate groupsvia the same atoms as in the [NiLX] complexes.     

Controlling the outcome of an N-alkylation reaction by using N-oxide functional groups

Covalent modifiers of proteins are of importance in chemical proteomics, an emerging chemical technology used to assign protein function. In this study, high-field (1)H NMR techniques were used to analyze the reaction of the bioactive compound, 2,3-bis(bromomethyl)quinoxaline 1,4-dioxide, with amines (a model system for proteins containing nitrogen-based nucleophiles). Unexpectedly, the results show that a double nucleophilic substitution reaction involving 2 equiv of the amine is preferred to an intramolecular cyclization pathway. A direct comparison with the reaction carried out on a substrate lacking the N-oxide functional groups is also provided. X-ray crystal structures and computational studies are used to rationalize the observed differences in reactivity between the two systems.     

Sensitivity-enhanced quantitative 13C NMR spectroscopy via cancellation of 1J(CH) dependence in DEPT polarization transfers

A scheme has been developed to eliminate virtually all signal intensity dependence on 1JCH in polarization transfers between 1H and 13C nuclei, reducing differences in signal intensity to only 1.5% over the entire natural 1JCH range. The scheme relies on the summation of time-domain data acquired with four suitably selected Delta delays so that the J dependence is essentially canceled in the final, signal-averaged free-induction decay. These Delta delays have been incorporated into the DEPT pulse sequence to create sensitivity-enhanced experiments for collecting quantitative 13C{1H} spectra. Four experiments, each with unique read pulse angles, give quantitative spectra with 200-300% more sensitivity than conventional 13C spectra acquired with inverse-gated 1H decoupling. The experiments are ideal for recording spectra with improved quantitative information or for substantially reducing the long acquisition times indicative of quantitative 13C experiments. The ability of the experiments to provide quantitative spectra was demonstrated with a simple ethylbenzene solution, however, they can easily be adapted to various applications for analysis of complex mixtures.     

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.     

Determination and characterization of a transition structure for water–formaldehyde addition

Quantum mechanical calculations of the geometric, energetic, electronic, and vibrational features of a transition structure for gas-phase water–formaldehyde addition (FW1?) are described, and a new transition-structure search algorithm is presented. Basis-set-dependent effects are assessed by comparisons of computed properties obtained from self-consistent field (SCF) molecular orbital (MO) calculations with STO-3G, 4-31G, and 6-31G^** basis sets in the absence of electron correlation. The results obtained suggest that STO-3G-level calculations may be sufficiently reliable for the prediction of the transition structure of FW1? and for the transition structures of related carbonyl addition reactions. Moreover, the calculated activation energy for formation of FW1? from water and formaldehyde (?44 kcal mol^?1) is very similar in all three basis sets. However, the energy of formaldehyde hydration predicted by STO-3G (? ?45 kcal mol^?1) is about three times larger than that predicted by the other two basis sets, with the activation energy for dihydroxymethane dehydration also being too large in STO-3G. Calculated force constants in all three basis sets are generally too large, leading to vibrational frequencies that are also too large. However, uniformly scaled force constants (in internal coordinates) give much better agreement with experimental frequencies, scaled 4-31G force constants being slightly superior to scaled STO-3G force constants.     

Synthesis and characterization of the new 22-π aromatic furan-containing macrocycle, “ozaphyrin”

The new 22-π, aromatic “pentaplanar” macrocycle, ozaphyrin ( 6 ), has been synthesized by a McMurry coupling of 5,5′-diformyl-4,4′-dipropyl-2,2′-bipyrrole ( 1 ) with 2,5-bis(5-formyl-4-propyl-2-pyrrolyl)furan ( 5 ). This synthetic pathway to ozaphyrin and its characterization by ¹H nmr spectroscopy, uv-visible spectroscopy, cyclic voltammetry, and X-ray crystallography are described. The structure consists of layers of planar, staggered macrocycles stacked perpendicular to the α-axis. Ozaphyrin crystallizes with four formula units in the monoclinic space group C⁵_2h-P2₁/n in a cell of dimensions a = 10.481(7) Å, b = 17.353(17) Å, c = 18.726(12) Å, and β = 102.84(5)° (108 K). The structure has been refined on F² (5171 unique reflections, 411 variables) to R_w(F_o²) = 0.165. The conventional agreement index R(F) is 0.074 for the 3289 reflections have F_o²>2o(F_o²).     

Determination of retinyl palmitate (vitamin A) in fortified fluid milk by liquid chromatography: collaborative study

A liquid chromatographic (LC) method was developed for fast and simple measurement of retinyl palmitate (vitamin A) in fortified milk. Retinyl acetate internal standard was added to a test portion of milk followed by extraction into hexane. The hexane extract was analyzed by LC using a normal-phase silica gel column equilibrated with mobile phase (conditioned hexane-isopropanol, 99.85 + 0.15, v/v) about 1 h before injections. The retinyl palmitate concentration was calculated by using a relative response factor determined with calibration standards. In the collaborative study, 11 laboratories analyzed 13 pairs of fluid milk materials in blind duplicate. Twelve of the materials were composed of skim milk (< 0.5% fat), 1% fat milk, 2% fat milk, and 1% fat chocolate milk. Each material was fortified at 3 concentrations of retinyl palmitate of approximately 581 microg/L (1000 IU/qt), 1163 microg/L (2000 IU/qt), and 2236 microg/L (4000 IU/qt). The 13th material, unfortified skim milk, served as a matrix blank. Repeatability standard deviations (RSDr) without outliers ranged from 1.5 to 5.7% and reproducibility standard deviations (RSDR) without outliers ranged from 5.0 to 22.7%. cis-Isomers co-eluted with the predominant trans-retinyl palmitate isomer and were included in the results reported by all the collaborative laboratories. Endogenous long-chain esters from milk fat were also measured with the retinyl palmitate additive. The Study Director recommends that this method for determination of retinyl palmitate in fluid milk by LC be adopted First Action.