Investigation of the enzymatic and nonenzymatic cope rearrangement of carbaprephenate to carbachorismate

The dimethyl esters of carbaprephenate and 4-epi-carbaprephenate were prepared by modification of published procedures. In methanol these compounds are converted quantitatively to isomeric 6-hydroxytricyclo[3.3.1.0(2,7)]non-3-en-1,3-dimethyl esters via a two-step sequence involving an initial Cope rearrangement, followed by intramolecular Diels-Alder reaction of the dimethyl carbachorismate or 4-epi-carbachorismate intermediates. Carbaprephenate and its epimer were obtained by alkaline hydrolysis of the corresponding dimethyl esters. These compounds, in contrast to their ester precursors, undergo spontaneous acid-catalyzed decarboxylation in aqueous solution. Only at high pH does the Cope rearrangement compete with decarboxylation. At pH 12 and 90 degrees C, carbaprephenate slowly rearranges to carbachorismate, which rapidly loses water to give 3-(2-carboxyallyl)benzoic acid as the major product. A small amount of the intramolecular Diels-Alder adduct derived from carbachorismate is also observed by NMR as a minor product. Carbaprephenate is not a substrate for the enzyme chorismate mutase from Bacillus subtilis (BsCM), nor does carbaprephenate inhibit the normal chorismate mutase activity of this enzyme, even when present in 200-fold excess over chorismate. Its low affinity for the enzyme-active site is presumably a consequence of placing a methylene group rather than an oxygen atom proximal to the essential cationic residue Arg90. Nevertheless, BsCM variants that lack this cation (R90G and R90A) do not accelerate the Cope rearrangement of carbaprephenate either, and a catalytic antibody 1F7, which exhibits modest chorismate mutase activity, is similarly inactive. Poor substrate binding and the relatively high barrier for the Cope compared to the Claisen rearrangement presumably account for the lack of detectable catalysis. Acceleration of this sigmatropic rearrangement apparently requires more than an active site that is complementary in shape to the reactive substrate conformer.     

Correlations of13C chemical shifts and geometry modifications

The effect of geometry modifications of¹³C chemical shifts has been investigated in a small subset of molecules using both LO-INDO and Gaussian 70 (4–31) calculations. The Gaussian calculations, while known to give poor absolute shifts, compare well to the reparameterized semi-empirical INDO determinations in calculated shift changes. In virtually all cases the signs of the shift changes were found to be opposite to that of the changes in the calculated electronic energy.     

Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method

The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom-diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mechanical calculations were performed, and the probabilities for nonadiabatic reaction and nonreactive deexcitation (quenching) were found to be on the order of 10(-8). For such low-probability events the anteater sampling scheme requires a large number of trajectories ( approximately 10(10)) to obtain good statistics and converged semiclassical results. In contrast by using the new army ants algorithm converged results were obtained by running 10(5) trajectories. Furthermore, the results were found to be in excellent agreement with the quantum mechanical results. Sampling errors were estimated using the bootstrap method, which is validated for use with the army ants algorithm.     

An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies

The recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intramolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three-centered hydrogen bonding geometries for the intermolecular interactions.     

Comparison of diatomics-in-molecules and simple valence-bond potential surfaces for FH2

The method of diatomics-in-molecules (DIM) is applied to the FH₂ system. With spin—orbit interaction neglected, all elements of the 24 × 24 hamiltonian matrix are tabulated as analytic functions of the six diatomic fragment potential curves. It is found that neglect of off-diagonal 8 × 8 blocks in the DIM hamiltonian matrix leads to an energy expression for the ground 1 ²A′ level which is identical to the valence-bond formula used by Blais and Truhlar in dynamical studies of the F + D₂ reaction. The ²A″ excited level from DIM theory is identical to the result derived by Blais and Truhlar, without neglect of the 8 × 8 off-diagonal blocks. The DIM and simple valence-bond energies are compared numerically for noncollinear geometries.     

A.C. Cyclic voltammetry: A digital simulation study of the slow scan limit condition for a reversible electrode process

Rate laws presented to date for analysis of a.c. cyclic voltammetric data have invoked the so-called “slow scan limit approximation” which requires that ΔEω ? v, where Δ E and ω are the applied a.c. potential amplitude and angular frequency, respectively, and v is the d.c. potential scan rate. To provide a more useful guideline for the experimentalist than this qualitative condition, a pure digital simulation approach has been used to compute the a.c. cyclic time domain waveform for a reversible process under small amplitude conditions. The a.c. content of this waveform is extracted by the digital FFT alogirthm. Results of this study are presented here. Among the conclusions reached are more quantitative limitations for the slow scan limit rate laws describing the fundamental and second harmonic responses (approximately 128 a.c. cycles/d.c. cyclic sweep and 512 a.c. cycles/d.c. cyclic sweep, respectively) and an interesting prediction that the latter limitations can be relaxed further by a current waveform subtraction strategy, to as low as about 16 a.c. cycles/d.c. cyclic sweep for the fundamental and second harmonics. The cycles/sweep values assume one triangular wave potential scan of ±200 mV is encompassed.     

Atomic force microscopy study for supermolecular microstructures in side-chain liquid crystalline polymer films

Atomic force microscopy (AFM) is employed to study the supermolecular microstructures of disclinations and inversion walls in thin films of a smectic side-chain liquid crystalline polymer. Two-dimensional nanostripes are formed in thin films when the material enters the smectic phase. A possible mechanism for their formation is also suggested. The stripes run parallel to the local director and thus decorate the overall patterns of nematic director around the disclinations and inversion walls. Three patterns involving radial, spiral, and circular supermolecular microstructures of a positive disclination with s = +1 and one hyperbolic pattern of a negative disclination with s = -1 are observed. The cores of all these microstructures exhibit circular dark centers in AFM height images. It is found that the specific configurations of a pair of (+1, -1) disclinations form during the late stage of annihilation and inversion walls always separate a pair of (+1, +1) disclinations. The analysis on the director fields around disclinations and inversion walls shows that the bend and splay elastic constants are of the same order of magnitude in the side-chain liquid crystalline polymer.     

Styrene emulsion polymerization: Particle-size distributions

Data are presented on the time evolution of particle-size distributions (PSDs) in seeded and ab initio styrene emulsion polymerization systems. Initiation was by chemical reagent (potassium persulfate) or γ-radiation. The unswollen PSDs at various times during interval II of the polymerization were obtained by direct measurement of calibrated electron micrographs. Experimental results were fitted with the equations that describe the time evolution of an initial PSD. Analytic solutions to these equations that allow for entry, exit, and propagation of free radicals were obtained. The values of the rate coefficients for these processes used to fit the experimental data were in excellent agreement with those obtained from dilatometric kinetics experiments.     

Determination of lincomycin and tylosin residues in honey by liquid chromatography/tandem mass spectrometry

A simple and rapid analytical method was developed for the determination of lincomycin and tylosin residues in honey as part of field studies examining the efficacy and target animal safety of these antibiotics to control American foulbrood disease in honey bees. Residues of the antibiotics were determined using liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS). Honey samples were diluted and injected directly into the LC/MS/MS system without additional cleanup by solid-phase extraction or liquid-liquid partitioning. A six-port valve system was utilized to selectively route eluant from the LC column into the mass spectrometer only during a relatively short portion of the chromatographic run corresponding to the elution of the analytes of interest. Minimal contamination of the MS source chamber was observed despite the analysis of large numbers of samples. Using internal standard quantitation, excellent accuracy and precision were obtained with no apparent matrix-to-matrix variation. Based on the analysis of fortified replicates, the mean percent deviation from the theoretical concentration and the percent relative standard deviation were both less than 10% for tylosin over an analytical range of 10-1000 microg/kg. Slightly higher mean percent deviations and relative standard deviations were observed for the analysis of lincomycin in fortified replicate samples. The method detection limits were determined to be 5 and 2 microg/kg for lincomycin and tylosin, respectively.