A novel synthesis of 7-acetyl-4,5,5a,6,6a,7,8,9-octahydroindeno[7,1-fg]quinolin-9-one

Treatment of the acetylenic acid 3 with magnesium carbonate in water at 60° yielded the tetracyclic ketone 5.     

Rotational cooling of rigid rotors desorbed from flat surfaces

A simple model is presented for predicting the final rotational state distribution of an initially physisorbed rigid rotor. Based on the assumptions that the adsorbed rotor is freely rotating and that desorption occurs by a weak coupling between the rotational and desorbing degrees of freedom, a significant rotational “cooling” is predicted.     

A statistical-based approach to assessing the fidelity of combinatorial libraries encoded with electrophoric molecular tags. Development and application of tag decode-assisted single bead LC/MS analysis

A statistical sampling protocol is described to assess the fidelity of libraries encoded with molecular tags. The methodology, termed library QA, is based on the combined application of tag decode analysis and single bead LC/MS. The physical existence of library compounds eluted from beads is established by comparing the molecular weight predicted by tag decode with empirical measurement. The goal of sampling is to provide information on overall library fidelity and an indication of the performance of individual library synthons. The minimal sampling size n for library QA is l0 x the largest synthon set. Data are reported as proportion (p) +/- lower and upper boundary (lb-ub) computed at the 95% confidence level (alpha = 0.05). As a practical demonstration, library QA was performed on a 25,200-member library of statine amides (size = 40 x 63 x 10). Sampling was conducted three times at n approximately 630 beads per run for a total of 1902 beads. The overall proportions found for the three runs were consistent with one another: p = 84.4%, lb-ub = 81.5-87.2%; p = 83.1%, lb-ub = 80.2-85.95; and p = 84.5%, lb-ub = 81.8-87.3%, suggesting the true value of p is close to 84% compound confirmation. The performance pi of individual synthons was also computed. Corroboration of QA data with biological screening results obtained from assaying the library against cathepsin D and plasmepsin II is discussed.     

High-temperature rate constant determination for the reaction of OH with iso-butanol

This work presents the first direct experimental study of the rate constant for the reaction of OH with iso-butanol (2-methyl-1-propanol) at temperatures from 907 to 1147 K at near-atmospheric pressures. OH time-histories were measured behind reflected shock waves using a narrow-linewidth laser absorption method during reactions of dilute mixtures of tert-butylhydroperoxide (as a fast source of OH) with iso-butanol in excess. The title reaction's overall rate constant (OH + iso-butanol →(k(overall)) all products) minus the rate constant for the β-radical-producing channel (OH + iso-butanol →(k(β)) 1-hydroxy-2-methyl-prop-2-yl radical + H(2)O) was determined from the pseudo-first-order rate of OH decay. A two-parameter Arrhenius fit of the experimentally determined rate constant in the current temperature range yields the expression (k(overall) - k(β)) = 1.84 × 10(-10) exp(-2350/T[K]) cm(3) molecule(-1) s(-1). A recommendation for the overall rate constant, including k(β), is made, and comparisons of the results to rate constant recommendations from the literature are discussed.     

Rotational rainbows in inelastic atom—molecule differential cross sections

The existence of rotational raibows in atom-rigid rotor inelastic differential cross sections is shown by considering the classical limit of the centrifugal sudden-rotational sudden expression for the scattering amplitude.     

Isotopic oxygen exchange rates between [V18O42]12− and water

Summary From kinetic studies of¹⁸O-exchange between aqueous solutions of K₁₂V₁₈O₄₂ · 16H₂O and water it is concluded that [V₁₈O₄₂]^12– exists as a discrete ion in this medium. The rate of exchange is relatively slow (t_1/2 ca. 6×10⁴s at 0°C) and obeys the McKay equation within the precision obtainable. The sensitivity of the ion to its environment in the solid state, leading to induced exchange, prevented a decision as to whether all oxygens are kinetically equivalent. It is clear, however, that the ions remains intact for long periods in solution in the absence of air.     

Temperature dependent equilibrium native to unfolded protein dynamics and properties observed with IR absorption and 2D IR vibrational echo experiments

Dynamic and structural properties of carbonmonoxy (CO)-coordinated cytochrome c(552) from Hydrogenobacter thermophilus (Ht-M61A) at different temperatures under thermal equilibrium conditions were studied with infrared absorption spectroscopy and ultrafast two-dimensional infrared (2D IR) vibrational echo experiments using the heme-bound CO as the vibrational probe. Depending on the temperature, the stretching mode of CO shows two distinct bands corresponding to the native and unfolded proteins. As the temperature is increased from low temperature, a new absorption band for the unfolded protein grows in and the native band decreases in amplitude. Both the temperature-dependent circular dichroism and the IR absorption area ratio R(A)(T), defined as the ratio of the area under the unfolded band to the sum of the areas of the native and unfolded bands, suggest a two-state transition from the native to the unfolded protein. However, it is found that the absorption spectrum of the unfolded protein increases its inhomogeneous line width and the center frequency shifts as the temperature is increased. The changes in line width and center frequency demonstrate that the unfolding does not follow simple two-state behavior. The temperature-dependent 2D IR vibrational echo experiments show that the fast dynamics of the native protein are virtually temperature independent. In contrast, the fast dynamics of the unfolded protein are slower than those of the native protein, and the unfolded protein fast dynamics and at least a portion of the slower dynamics of the unfolded protein change significantly, becoming faster as the temperature is raised. The temperature dependence of the absorption spectrum and the changes in dynamics measured with the 2D IR experiments confirm that the unfolded ensemble of conformers continuously changes its nature as unfolding proceeds, in contrast to the native state, which displays a temperature-independent distribution of structures.     

Formaldehyde photodissociation: dependence on total angular momentum and rotational alignment of the CO product

Quasiclassical trajectory calculations are reported to investigate the effects of rotational excitation of formaldehyde on the branching ratios of the fragmentation products, H2+CO and H+HCO. The results of tens of thousands of trajectories show that increased rotational excitation causes suppression of the radical channel and enhancement of the molecular channel. Decomposing the molecular channel into "direct" and "roaming" channels shows that increased rotation switches from suppressing to enhancing the roaming products across our chosen energy range. However, decomposition into these pathways is difficult because the difference between them does not appear to have a distinct boundary. A vector correlation investigation of the CO rotation shows different characteristics in the roaming versus direct channels and this difference is a potentially useful signature of the roaming mechanism, as first speculated by Kable and Houston in their experimental study of photodissociation of acetaldehyde [P. L. Houston and S. H. Kable, Proc. Nat. Acad. Sci. 103, 16079 (2006)].     

Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment

Protein folding is a fundamental process in biology, key to understanding many human diseases. Experimentally, proteins often appear to fold via simple two- or three-state mechanisms involving mainly native-state interactions, yet recent network models built from atomistic simulations of small proteins suggest the existence of many possible metastable states and folding pathways. We reconcile these two pictures in a combined experimental and simulation study of acyl-coenzyme A binding protein (ACBP), a two-state folder (folding time ～10 ms) exhibiting residual unfolded-state structure, and a putative early folding intermediate. Using single-molecule FRET in conjunction with side-chain mutagenesis, we first demonstrate that the denatured state of ACBP at near-zero denaturant is unusually compact and enriched in long-range structure that can be perturbed by discrete hydrophobic core mutations. We then employ ultrafast laminar-flow mixing experiments to study the folding kinetics of ACBP on the microsecond time scale. These studies, along with Trp-Cys quenching measurements of unfolded-state dynamics, suggest that unfolded-state structure forms on a surprisingly slow (～100 μs) time scale, and that sequence mutations strikingly perturb both time-resolved and equilibrium smFRET measurements in a similar way. A Markov state model (MSM) of the ACBP folding reaction, constructed from over 30 ms of molecular dynamics trajectory data, predicts a complex network of metastable stables, residual unfolded-state structure, and kinetics consistent with experiment but no well-defined intermediate preceding the main folding barrier. Taken together, these experimental and simulation results suggest that the previously characterized fast kinetic phase is not due to formation of a barrier-limited intermediate but rather to a more heterogeneous and slow acquisition of unfolded-state structure.     

Multimode calculations of rovibrational energies and dipole transition intensities for polyatomic molecules with torsional motion: application to H2O2

We report rigorous calculations of rovibrational energies and dipole transition intensities for hydrogen peroxide using a new version of MULTIMODE as applied to molecules with torsional (reaction path) motion. The key features which permit such calculations for moderately sized polyatomic molecules of this general type are briefly described. A previous, accurate potential energy surface and a new high-level ab initio dipole moment surface are employed in these calculations. Detailed comparisons are made with high-resolution experimental spectral intensities from the HITRAN database.