Ultraviolet photodissociation dynamics of the phenyl radical

Ultraviolet (UV) photodissociation dynamics of jet-cooled phenyl radicals (C(6)H(5) and C(6)D(5)) are studied in the photolysis wavelength region of 215-268 nm using high-n Rydberg atom time-of-flight and resonance enhanced multiphoton ionization techniques. The phenyl radicals are produced from 193-nm photolysis of chlorobenzene and bromobenzene precursors. The H-atom photofragment yield spectra have a broad peak centered around 235 nm and are in good agreement with the UV absorption spectra of phenyl. The H + C(6)H(4) product translational energy distributions, P(E(T))'s, peak near ~7 kcal/mol, and the fraction of average translational energy in the total excess energy, , is in the range of 0.20-0.35 from 215 to 268 nm. The H-atom product angular distribution is isotropic. The dissociation rates are in the range of 10(7)-10(8) s(-1) with internal energy from 30 to 46 kcal/mol above the threshold of the lowest energy channel H + o-C(6)H(4) (ortho-benzyne), comparable with the rates from the Rice-Ramsperger-Kassel-Marcus theory. The results from the fully deuterated phenyl radical are identical. The dissociation mechanism is consistent with production of H + o-C(6)H(4), as the main channel from unimolecular decomposition of the ground electronic state phenyl radical following internal conversion of the electronically excited state.     

Unzipping Nucleoside Channels by Means of Alcohol Disassembly

Gold nanoparticles capped with simple adenosine derivatives can form colloidal aggregates in nonpolar solvents. Theoretical calculations indicate the formation of organic channels by the supramolecular assembly of the nanoparticles by means of hydrogen bonds between the adenine moieties. The aggregates were only negligibly sensitive to nPrOH, iPrOH, and tBuOH, whereas some showed a similar response to MeOH and EtOH, and others showed high selectivity toward MeOH. DNA nucleoside derivatives (1‐(2‐deoxy‐β‐D ‐ribofuranosyl)‐5‐methyluracil and 2′,3′‐O‐isopropylideneadenosine) as well as thymine and other aromatic compounds such as pyrene derivatives (pyrene, 1‐chloropyrene, 1‐hydroxypyrene, (1‐pyrenyl)methanol, and 2‐hydroxynapthalene) did not induce disassembly of the nanoparticle aggregates. Data suggest that the nucleoside channels allow access to alcohols according to their size, and an efficient interaction between the alcohol and the adenine units destabilizes the hydrogen bonds, which eventually leads to nanoparticle disassembly.     

DFT in a nutshell

The purpose of this short essay is to introduce students and other newcomers to the basic ideas and uses of modern electronic density functional theory, including what kinds of approximations are in current use, and how well they work (or not). The complete newcomer should find it orients them well, while even longtime users and aficionados might find something new outside their area. Important questions varying in difficulty and effort are posed in the text, and are answered in the Supporting Information. © 2012 Wiley Periodicals, Inc.     

Sun Exposure over a Lifetime in Australian Adults from Latitudinally Diverse Regions

Spatio‐temporal patterns in sun exposure underlie variations in skin cancer incidence and vitamin D deficiency, indicate effectiveness of sun protection programs and provide insights into future health risks. From 558 adults across four regions of Australia (Brisbane (27°S), Newcastle (33°S), Geelong and the Western Districts of Victoria (37°S) and Tasmania (43°S)), we collected: self‐report data on time‐in‐the‐sun from age 6 years; natural skin color and ethnicity; silicone skin casts (for cumulative skin damage); and serum for vitamin D status. Ambient ultraviolet radiation (UVR) at the location of residence, with time‐in‐the‐sun, was used to calculate a “UVR dose” for each year of life. Individuals maintained their ranking compared to their peers for time‐in‐the‐sun in summer compared to winter and across ages (Spearman rho 0.24–0.84, all P < 0.001). Time‐in‐the‐sun decreased with age in all birth cohorts, and over calendar time. Summer time‐in‐the‐sun increased with increasing latitude (P < 0.001). Seasonal variation in vitamin D status had greater amplitude and vitamin D deficiency increased with increasing latitude. Temporal patterns are consistent with effectiveness of sun protection programs. Higher relative time‐in‐the‐sun persists from childhood through adulthood. Lower summer time‐in‐the‐sun in the warmest location may have implications for predictions of UVR‐related health risks of climate change.     

Quantitative analysis of the low molecular weight serum proteome using 18O stable isotope labeling in a lung tumor xenograft mouse model

With advancements in the analytical technologies and methodologies in proteomics, there is great interest in biomarker discovery in biofluids such as serum and plasma. Current hypotheses suggest that the low molecular weight (LMW) serum proteome possesses an archive of clipped and cleaved protein fragments that may provide insight into disease development. Though these biofluids represent attractive samples from which new and more accurate disease biomarkers may be found, the intrinsic person-to-person variability in these samples complicates their discovery. Mice are one of the most extensively used animal models for studying human disease because they represent a highly controllable experimental model system. In this study, the LMW serum proteome was compared between xenografted tumor-bearing mice and control mice by differential labeling utilizing trypsin-mediated incorporation of the stable isotope of oxygen, 18O. The digestates were combined, fractionated by strong cation exchange chromatography, and analyzed by nanoflow reversed-phase liquid chromatography coupled online with tandem mass spectrometry, resulting in the identification of 6003 proteins identified by at least a single, fully tryptic peptide. Almost 1650 proteins were identified and quantitated by two or more fully tryptic peptides. The methodology adopted in this work provides the means for future quantitative measurements in comparative animal models of disease and in human disease cohorts.     

Ab initio benchmark study for the oxidative addition of CH4 to Pd: importance of basis-set flexibility and polarization

To obtain a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the methane C-H bond to the palladium atom, we have explored this PES using a hierarchical series of ab initio methods (Hartree-Fock, second-order M?ller-Plesset perturbation theory, fourth-order M?ller-Plesset perturbation theory with single, double and quadruple excitations, coupled cluster theory with single and double excitations (CCSD), and with triple excitations treated perturbatively [CCSD(T)]) and hybrid density functional theory using the B3LYP functional, in combination with a hierarchical series of ten Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Counterpoise corrected relative energies of stationary points are converged to within 0.1-0.2 kcal/mol as a function of the basis-set size. Our best estimate of kinetic and thermodynamic parameters is -8.1 (-8.3) kcal/mol for the formation of the reactant complex, 5.8 (3.1) kcal/mol for the activation energy relative to the separate reactants, and 0.8 (-1.2) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). This agrees well with available experimental data. Our work highlights the importance of sufficient higher angular momentum polarization functions, f and g, for correctly describing metal-d-electron correlation and, thus, for obtaining reliable relative energies. We show that standard basis sets, such as LANL2DZ+1f for palladium, are not sufficiently polarized for this purpose and lead to erroneous CCSD(T) results. B3LYP is associated with smaller basis set superposition errors and shows faster convergence with basis-set size but yields relative energies (in particular, a reaction barrier) that are ca. 3.5 kcal/mol higher than the corresponding CCSD(T) values.     

Study of ab initio molecular data for inelastic and reactive collisions involving the H3+ quasimolecule

The lowest two ab initio potential energy surfaces (PES), and the corresponding nonadiabatic couplings between them, have been obtained for the H3+ system; the molecular data are compared to those calculated with the diatomic in molecules (DIM) method. The form of the couplings is discussed in terms of the topology of the molecular structure of the triatomic. The method of Baer is employed to generate "diabatic" states and the residual nonadiabatic couplings are calculated. The ab initio results for these are markedly different from the corresponding DIM data, and show the need to consider the third PES.     

Regioselectivity of the Claisen rearrangement in meta-allyloxy aryl ketones: an experimental and computational study, and application in the synthesis of (R)-(-)-pestalotheol D

A study of the regioselectivity of the Claisen rearrangement of meta-allyloxy aryl ketones showed that the electron-withdrawing carbonyl group has a major influence and strongly directs rearrangement to the more hindered ortho position. However, when the ketone is part of a ring structure, its electronic effect can be negated by conversion into its triisopropylsilyl enol ether, which dramatically reverses the regiochemistry of the Claisen rearrangement. DFT calculations suggest that the effect is electronic although there is also a steric effect of the bulky silyl group. This strategy for influencing the regiochemical outcome of the Claisen rearrangement was then employed in a short synthesis of the furo[2,3-g]chromene, (-)-pestalotheol D, that confirms the absolute stereochemistry of the natural product.     

Optical detection of triggered atherosclerotic plaque disruption by fluorescence emission analysis

Fluorescence emission analysis (FEA) has proven to be very sensitive for the detection of elastin, collagen and lipids, which are recognized as the major sources of autofluorescence in vascular tissues. FEA has also been reported to detect venous thromboemboli. In this paper we have tested the hypothesis that FEA can reproducibly detect in vivo and in vitro triggered plaque disruption and thrombosis in a rabbit model. Fluorescence emission (FE) spectra, recorded in vivo, detected Russell's viper venom (RVV)-induced transformation of atherosclerotic plaque. FE intensity at 410-490 nm 4 weeks after angioplasty was significantly lower (P < 0.0033 by analysis of variance) in RVV-treated rabbits when compared to control animals with stable plaque. FE spectral profile analyses also demonstrated a significant change in curve shape as demonstrated by polynomial regression analysis (R2 from 0.980 to 0.997). We have also demonstrated an excellent correlation between changes in FE intensity and the structural characteristics detected at different stages of "unstable atherosclerotic plaque" development using multiple regression analysis (R2 = 0.989). Thus, FEA applied in vivo is a sensitive and highly informative diagnostic technique for detection of triggered atherosclerotic plaque disruption and related structural changes, associated with plaque transformation, in a rabbit model.