Measurement of PCDDs, PCDFs, and non-ortho-PCBs by comprehensive two-dimensional gas chromatography-isotope dilution time-of-flight mass spectrometry (GC x GC-IDTOFMS)

Comprehensive two-dimensional gas chromatography with isotope-dilution time-of-flight mass spectrometry (GC × GC-IDTOFMS) was used to measure polychlorinated dibenzo-p-dioxin (PCDD), polychlorinated dibenzofuran (PCDF), and coplanar polychlorinated biphenyl (cPCB) concentrations in ash, sediment, vegetation, and fish samples. The GC × GC capability was achieved by using a quad jet, dual stage, thermal modulator. Zone compression of the GC peaks from modulation resulted in a significant increase of the signal intensity over classical GC-IDTOFMS. The GC × GC column set used an Rtx-Dioxin 2 phase as the first dimension (¹D) and an Rtx-500 as the second dimension (²D). The chromatographic separation of the 17 PCDD/Fs and the 4 cPCBs was attained in ¹D except for 2,3,7,8-TCDD and CB126 for which deconvoluted ion currents (DIC) were required to be reported separately. The Rtx-500 phase separated the bulk matrix interfering compounds from the target analytes in ²D. The instrumental limit of detection (iLODs) was 0.5 pg for 2,3,7,8-TCDD. The calibration curves showed good correlation coefficients for all the compounds investigated in the concentration range of 0.5–200 pg. GC × GC-IDTOFMS results compared favorably to those from conventional isotope-dilution one-dimensional gas chromatography-high resolution mass spectrometry (GC-IDHRMS). The comprehensive mass analysis of the TOFMS further permitted the identification of other contaminants of concern in the samples.     

Rigid NON- and NSN-ligand complexes of tetravalent and trivalent uranium: comparison of U-OAr2 and U-SAr2 bonding

A rigid NSN-donor proligand, 4,5-bis(2,6-diisopropylanilino)-2,7-di-tert-butyl-9,9-dimethylthioxanthene (H(2)[TXA(2)], 1) was prepared by palladium-catalyzed coupling of 2,6-diisopropylaniline with 4,5-dibromo-2,7-di-tert-butyl-9,9-dimethylthioxanthene. Deprotonation of 1 using (n)BuLi provided Li(2)(DME)(2)[TXA(2)] (2), and subsequent reaction with UCl(4) afforded [Li(DME)(3)][(TXA(2))UCl(3)] (4). The analogous NON-donor ligated complex [(XA(2))UCl(3)K(DME)(3)] [3; XA(2) = 4,5-bis(2,6-diisopropylanilino)-2,7-di-tert-butyl-9,9-dimethylxanthene] was prepared by the reaction of K(2)(DME)(x)[XA(2)] with UCl(4). A cyclic voltammogram (CV) of 3 in THF/[NBu(4)][B(C(6)F(5))(4)] at 200 mV s(-1) showed an irreversible reduction to uranium(III) at E(pc) = -2.46 V versus FeCp(2)(0/+1), followed by a product wave at E(1/2) = -1.83 V. Complex 4 also underwent irreversible reduction to uranium(iii) [E(pc) = -2.56 V], resulting in an irreversible product peak at E(pa) = -1.83 V. One-electron reduction of complexes 3 and 4 using K(naphthalenide) under an argon atmosphere in DME yielded 6-coordinate [(XA(2))UCl(DME)] (5) and the thermally unstable 7-coordinate [(TXA(2))U(DME)Cl(2)Li(DME)(2)] (6), respectively. The U-S distances in 4 and 6 are uncommonly short, the C-S-U angles are unusually acute, and the thioxanthene backbone of the TXA(2) ligand is significantly bent. By contrast, the xanthene backbone in XA(2) complexes 3 and 5 is planar. However, κ(3)-coordination and an approximately meridional arrangement of the ancillary ligand donor atoms is maintained in all complexes. DFT and Atoms in Molecules (AIM) calculations were carried out on 3, 4, 5, 6, [(XA(2))UCl(3)](-) (3B), [(TXA(2))UCl(2)(DME)](-) (6B) and [(TXA(2))UCl(DME)] (6C) to probe the extent of covalency in U-SAr(2) bonding relative to U-OAr(2) bonding.     

The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years

The future of the advancement as well as the reputation of computer-aided drug design will be guided by a more thorough understanding of the domain of applicability of our methods and the errors and confidence intervals of their results. The implications of error in current force fields applied to drug design are given are given as an example. Even as our science advances and our hardware become increasingly more capable, our software will be perhaps the most important aspect in this realization. Some recommendations for the future are provided. Education of users is essential for proper use and interpretation of computational results in the future.     

PVM-AMBER: A parallel implementation of the AMBER molecular mechanics package for workstation clusters

A parallel version of the popular molecular mechanics package AMBER suitable for execution on workstation clusters has been developed. Computer-intensive portions of molecular dynamics or free-energy perturbation computations, such as nonbonded pair list generation or calculation of nonbonded energies and forces, are distributed across a collection of Unix workstations linked by Ethernet or FDDI connections. This parallel implementation utilizes the message-passing software PVM (Parallel Virtual Machine) from Oak Ridge National Laboratory to coordinate data exchange and processor synchronization. Test simulations performed for solvated peptide, protein, and lipid bilayer systems indicate that reasonable parallel efficiency (70–90%) and computational speedup (2–5 × serial computer runtimes) can be achieved with small workstation clusters (typically six to eight machines) for typical biomolecular simulation problems. PVM-AMBER is also easily and rapidly portable to different hardware platforms due to the availability of PVM for numerous computers. The current version of PVM-AMBER has been tested successfully on Silicon Graphics, IBM RS6000, DEC ALPHA, and HP 735 workstation clusters and heterogeneous clusters of these machines, as well as on CRAY T3D and Kendall Square KSR2 parallel supercomputers. Thus, PVM-AMBER provides a simple and cost-effective mechanism for parallel molecular dynamics simulations on readily available hardware platforms. Factors that affect the efficiency of this approach are discussed. © 1995 by John Wiley & Sons, Inc.     

An adiabatic capture theory and quasiclassical trajectory study of C + NO and O + CN on the 2A', 2A", and 4A" potential energy surfaces

The adiabatic capture centrifugal sudden approximation (ACCSA) has been applied to the C + NO and O + CN reactions, along with quasiclassical trajectory simulations. Existing global analytic fits to the potential energy surfaces of the CNO system in the (2)A', (2)A", and (4)A" electronic states have been used. Thermal rate constants for reaction in each of the electronic states have been calculated. In all cases a strong temperature dependence is evident in the calculated rate constants. The agreement between the calculated adiabatic capture and quasiclassical trajectory rate constants is excellent in some cases, but these rate constants differ considerably in other cases. This behavior is analyzed in terms of the anisotropy of the potential energy surfaces. On the basis of this analysis, we propose a new diagnostic for the reliability of ACCSA capture calculations.     

Photokinetic,Biochemical and Structural Features of Chimeric Photoactive Yellow Protein Constructs

Of the 10 photoactive yellow protein (PYPs) that have been characterized, the two from Rhodobacter species are the only ones that have an additional intermediate spectral form in the resting state (λ_max = 375 nm), compared to the prototypical Halorhodospira halophila PYP. We have constructed three chimeric PYP proteins by replacing the first 21 residues from the N‐terminus (Hyb1PYP), 10 from the β4–β5 loop (Hyb2PYP) and both (Hyb3PYP) in Hhal PYP with those from Rb. capsulatus PYP. The N‐terminal chimera behaves both spectrally and kinetically like Hhal PYP, indicating that the Rcaps N‐terminus folds against the core of Hhal PYP. A small fraction shows dimerization and slower recovery, possibly due to interaction at the N‐termini. The loop chimera has a small amount of the intermediate spectral form and a photocycle that is 20 000 times slower than Hhal PYP. The third chimera, with both regions exchanged, resembles Rcaps PYP with a significant amount of intermediate spectral form (λ_max = 380 nm), but has even slower kinetics. The effects are not strictly additive in the double chimera, suggesting that what perturbs one site, affects the other as well. These chimeras suggest that the intermediate spectral form has its origins in overall protein stability and solvent exposure.     

Separation of Natural Food Pigments in Saponified and Un-Saponified Paprika Oleoresin by Ultra High Performance Supercritical Fluid Chromatography (UHPSFC)

The natural pigments in paprika were rapidly and efficiently separated by ultra high performance supercritical fluid chromatography. The separation of both un-saponified and saponified mixtures of paprika oleoresin were optimized, with run times of 10.6 min. Three different C18 columns, a cyano, silica and diol column, all 3 × 100 mm, with 1.8 μm particles were compared. The best separation for the un-saponified sample was found with an SB-C18 column, while the saponified samples were best separated on a bare silica, RX-Sil column. A SB-CN column allowed near optimum separation of both the unsaponified, and saponified samples, with similar run times. The best mobile phase was carbon dioxide (CO₂) modified with isopropyl alcohol (IPA), with a composition gradient. Fingerprints of several commercial pepper products indicated that one appeared to be colored with artificial dyes, while the color of a chili powder may have been enhanced with a paprika extract. Spectra, using CO₂ with IPA as modifier, produced a single maximum at 453 nm, which appears to represent up to a 30 nm solvatochromic shift from the maxima in most organic solvents. Acetonitrile (ACN) as modifier produced spectra with two maxima and a similar solvatochromic shift. These results appear to be the first on saponified paprika oleoresin samples using SFC. It is also the first detailed report on the separation of un-saponified samples. The results are up to six times faster than comparable results by HPLC. It appears that SFC is a viable, superior alternative to HPLC for the analysis of this important commercial product, without using ACN, or chlorinated solvents.

     

Solid-State 13C-NMR spectral evidence for charge transfer complex formation in aromatic diimides and dianhydrides

Solution and solid-state proton decoupled ¹³C-NMR spectra were determined on two diimides derived from 4, 4′-oxydiphthalic anhydride. Comparison of the individual diimide spectra to that of a mixture of the two diimides indicates that ordering of these materials occurs in the solid state via charge transfer complex formation. A similar study was conducted using two isomeric dianhydrides, 4, 4′-isophthaloyldiphthalic anhydride (IDPA) and 4, 4′-terephthaloyldiphthalic anhydride (TDPA). The solution spectra of these compounds are similar and are those which would be expected for these compounds. However, their solid state spectra differ from each other. The solid-state spectrum of TDPA resembles its solution spectrum, whereas, that of IDPA differs greatly from its solution spectrum and indicates charge transfer complex formation occurs with this molecule. This difference is explained in terms of the stereochemistry of the two isomeric dianhydrides.     

Self-assembling porphyrin-modified peptides

[structure: see text] We report the synthesis and characterization of a novel supramolecular assembly that features long-range electronic coupling between porphyrins covalently attached to a designed peptide scaffold. The resulting construct self-assembles to form extended organized aggregates in which the porphyrins engage in exciton coupling.