Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye

Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.     

Temperature dependence of oxygen isotope acid fractionation for modern and fossil tooth enamels

The oxygen isotope ratio of CO(2) liberated from structural carbonate in tooth enamel apatite was measured at phosphoric acid reaction temperatures of 25 degrees C, 60 degrees C and 90 degrees C, and it was found that apparent acid fractionation factors for pristine enamel, fossilized enamel, and calcite follow different temperature relationships. Using sealed vessel reactions normalized to alpha(25) = 1.01025 (the fractionation factor for calcite at 25 degrees C), the apparent fractionation factor at 90 degrees C (alpha*(90)) for pristine enamel ranged between 1.00771 and 1.00820, and between 1.00695 and 1.00772 for fossilized enamel. Apparent fractionation factors for common acid bath reactions are similar to those for sealed vessel reactions. A significant correlation exists between alpha*(90) and F(-) content, suggesting that change in the acid fractionation factor may be related to the replacement of OH(-) with F(-) during fossilization of bioapatite. These results have important implications for making accurate comparisons between modern and fossil tooth enamel delta(18)O values, and for the uniformity of isotope data produced in different laboratories using different acid reaction temperatures.     

Electron hole flow patterns through the RNA-cleaving 8-17 deoxyribozyme yield unusual information about its structure and folding

DNA double helices have been shown to conduct electron holes over significant distances. Here, we report on the hole flow patterns within a more intricately folded DNA complex, the 8-17 deoxyribozyme bound to a DNA pseudosubstrate, incorporating three helical elements and two catalytically relevant loops. The observed hole flow patterns within the complex permitted a quantitative assessment of the stacking preferences of the three constituent helices and provided evidence for significant transitions within the complex's global geometry. The patterns further suggested varying levels of solvent exposure of the complex's constituent parts, and revealed that a catalytically relevant cytosine within the folded complex exists in an unusual structural/electronic environment. Our data suggest that the study of charge flow may provide novel perspectives on the structure and folding of intricately folded DNAs and RNAs.     

Vibrational overtone spectroscopy of three-membered rings

We have recorded vapor-phase photoacoustic spectra of cyclopropane, ethylene oxide, and ethylene sulfide in the third, fourth, and fifth CH-stretching overtone regions. We have used a harmonically coupled anharmonic oscillator local mode model to facilitate analysis of the spectra. Fermi resonance between the CH-stretching and HCH-bending vibrations is essential to explain the observed wide and multistructured CH-stretching overtone bands. A number of weak combination bands can account for the remaining experimental features observed to the blue of the CH-stretching regions. We have reassigned the fundamental spectra of these three-membered rings.     

Analyses of macrolide antibiotic residues in eggs, raw milk, and honey using both ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry and high-performance liquid chromatography/tandem mass spectrometry

Two liquid chromatography mass spectrometric techniques, i.e. ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC/Q-Tof MS) and high-performance liquid chromatography/tandem mass spectrometry (LC/MS/MS), were used for quantification, confirmation or identification of six macrolide antibiotic residues and/or their degradation products in eggs, raw milk, and/or honey. Macrolides were extracted from food samples by acetonitrile or phosphate buffer (0.1 M, pH 8.0), and sample extracts were further cleaned up using solid-phase extraction cartridges. UPLC/Q-Tof data were acquired in Tof MS full scan mode that allowed both quantification and confirmation of macrolides, and identification of their degradation products. LC/MS/MS data acquisition was achieved using multiple reaction monitoring (MRM), i.e. two transitions, to provide a high degree of sensitivity and repeatability. Matrix-matched standard calibration curves with the use of roxithromycin as an internal standard were utilized to achieve the best accuracy of the method. Both techniques demonstrated good quantitative performance in terms of accuracy and repeatability. LC/MS/MS had advantages over UPLC/Q-Tof MS in that its limits of detection were lower and repeatability was somewhat better. UPLC/Q-Tof provided ultimate and unequivocal confirmation of positive findings, and allowed degradation product identification based on accurate mass. The combination of the two techniques can be very beneficial or complementary in routine analysis of macrolide antibiotic residues and their degradation products in food matrices to ensure the safety of food supply.     

Interaction potentials and transport properties of coinage metal cations in rare gases

High-level ab initio calculations are performed on the coinage metal cations (Cu+, Ag+, and Au+) interacting with each of the rare gases [Rg (Rg=He to Rn)]. The RCCSD(T) procedure is employed, with basis sets being of approximately quintuple-zeta quality, but with the heavier species using relativistic effective core potentials. The interaction potentials are compared to experimental and theoretical data where they exist. In addition, transport coefficients for the mobility and diffusion of the cations in the rare gases are calculated. The latter have involved a rewriting of some of the programs used, and the required modifications are discussed. The mobility results indicate that, rather than being a rare occurrence, mobility minima may be common phenomena. Finally, a new estimate is put forward for the validity of zero-field mobilities in ion mobility spectrometry.     

Rotational spectroscopy and molecular structure of 1,1,2-trifluoroethylene and the 1,1,2-trifluoroethylene-hydrogen fluoride complex

Fourier transform microwave rotational spectra in the 6-22 GHz region are obtained for the complex formed between 1,1,2-trifluoroethylene and hydrogen fluoride, including the normal isotopomer, the two singly substituted 13C species, and the complex obtained with DF. A unique planar structure for the complex is determined from a combined analysis of the rotational constants derived from the spectra and atomic positions obtained using Kraitchman [Am. J. Phys. 21, 17 (1953)] substitution coordinates. Consistent with this structure, no hyperfine splitting of rotational lines due to the nuclear quadrupole coupling interaction is observed for the D-containing species. Although the primary interaction in the complex is a hydrogen-fluorine hydrogen bond, as is the case for all previously studied Lewis acid-fluoroethylene complexes, the CF2CHF-HF complex adopts a distinctly different geometry in which both the primary and secondary interactions occur between the HF molecule and a F atom and a H atom, respectively, bonded to the same carbon of CF2CHF. The 2.020(41) A hydrogen bond has hydrogen fluoride as the donor and 1,1,2-trifluoroethylene as the acceptor and forms a 109.0(13) degrees C-F...H angle. The secondary interaction between the hydrogen fluoride F atom and the H atom geminal to the acceptor F atom causes the hydrogen bond to deviate 41.6(51) degrees from linearity. Structural comparisons with analogous complexes formed with mono- and difluorinated ethylenes suggest that the primary hydrogen bond strength and the fluoroethylene fluorine atom basicity both decrease with increasing fluorine substitution. In the course of this work, it was necessary to obtain additional rotational spectra for the 1,1,2-trifluroethylene monomer and to improve the precision of the values of the structural parameters for this molecule.     

Time-resolved spectroscopy of silver nanocubes: observation and assignment of coherently excited vibrational modes

The response of single crystal, cubic silver particles to ultrafast laser-induced heating has been examined experimentally and theoretically. The transient absorption traces display clear modulations due to coherently excited vibrational modes. Nanocube samples with edge lengths smaller than 50 nm show a single modulation, whereas samples larger than 50 nm show two vibrational modes. The results are compared to finite element calculations, where the cubes are modeled as having cubic crystal symmetry with the principal axes parallel to the sides of the particle. The action of the laser pulse is treated in two ways, first, as creating a uniform initial strain. In this case the predominant mode excited is the breathing mode. The period of this mode is in reasonable agreement with the vibrational periods measured for the smaller cubes and with the higher frequency modulation observed for the larger cubes. A nonuniform initial strain is also considered, which could arise from nonuniform heating for particles larger than the optical skin depth of the metal. In this case the predominant mode excited is a nontotally symmetric mode. The calculated periods from this analysis are in reasonable agreement with the lower frequency modulations observed for the larger samples. The results from this study show that, to within the accuracy of these measurements, the elastic constants of cubic silver nanoparticles are the same as bulk silver.     

Quasiclassical trajectory calculations of the OH+NO2 association reaction on a global potential energy surface

We report a full-dimensional potential energy surface (PES) for the OH+NO(2) reaction based on fitting more than 55,000 energies obtained with density functional theory-B3LYP6-311G(d,p) calculations. The PES is invariant with respect to permutation of like nuclei and describes all isomers of HOONO, HONO(2), and the fragments OH+NO(2) and HO(2)+NO. Detailed comparison of the structures, energies, and harmonic frequencies of various stationary points on the PES are made with previous and present high-level ab initio calculations. Two hydrogen-bond complexes are found on the PES and confirmed by new ab initio CASPT2 calculations. Quasiclassical trajectory calculations of the cross sections for ground rovibrational OH+NO(2) association reactions to form HOONO and HONO(2) are done using this PES. The cross section to form HOONO is larger than the one to form HONO(2) at low collision energies but the reverse is found at higher energies. The enhancement of the HOONO complex at low collision energies is shown to be due, in large part, to the transient formation of a H-bond complex, which decays preferentially to HOONO. The association cross sections are used to obtain rate constants for formation of HOONO and HONO(2) for the ground rovibrational states in the high-pressure limit.