Competition between the shake-off and knockout mechanisms in the double and triple photoionization of the halothane molecule (C2HBrClF3).

The ratios of single, double, and triple ionizations to the total photoionization of the halothane (C2HBrClF3) molecule have been investigated by a single-photon ionization in the energy range from 21.21 eV to 320 eV. In the valence region, the multiple ionization results can be described by a sum of contributions generated from the shake-off and the two-step one models. At low photon energies (from the threshold of triple ionization up to 100 eV), the triple photoionization dynamics of halothane can be reasonably well described by a model involving a classical electron impact double ionization of the singly ionized parent ion.

Photoabsorption and Photoionization Cross Sections of Pyridine in the Vacuum-Ultraviolet Energy Range.

We have performed an experimental investigation into the interaction of vacuum-ultraviolet synchrotron radiation with pyridine molecules in the gas phase. Specifically, a double-ion chamber spectrometer was used to measure the absolute photoabsorption cross sections and the photoionization quantum yields from the ionization threshold to 21.5 eV. Moreover, photoionization and neutral-decay cross sections in absolute scale were derived from these data. In addition, the fragmentation pattern was investigated as a function of the photon energy by using a time-of-flight mass spectrometer and the photoelectron-photoion coincidence technique. Thus, the absolute partial ionization cross sections for each ionic fragment were obtained. Comparisons are made with experimental data available in the literature.

Fragmentation of Valence and Carbon Core Excited and Ionized CH2FCF3 Molecule.

The photofragmentation dynamics of 1,1,1,2-tetrafluoroethane (R134a) with photon energies from 12 eV up to 320 eV, surrounding the C 1s edge is discussed. The ionic moieties were measured in coincidence with the ejected electrons (PEPICO mode), and detected as a function of the photon energy. Around the C K core edge, the fragmentation profiles are examined regarding the site specific excitation of the CH2FCF3 molecule. In the present case, site-selectivity is favored by the distinct chemical environments surrounding both C atoms. NEXAFS spectrum at the C 1s edge simulation has been obtained at the TDDFT level and excited state geometry optimization calculations have been performed at the inner-shell multiconfigurational self-consistent field level. Our observations indicate that the C(H2F) 1s excitation to a highly repulsive potential expels a fluorine atom leaving the heavier radical fragment C2F3H2* which relaxes to the fundamental state of the ion C2F3H2+. On the other hand, the excitation from the C(F3) 1s carbon to a repulsive state in the C-C bond, leads to a C-C bond cleavage, explaining the observed site specific fragmentation.

Atomic versus molecular Auger decay in CH2Cl2 and CD2Cl2 molecules.

Autoionization spectra of CH2Cl2 and CD2Cl2 molecules after Cl 2p excitation are studied. The two molecular and atomic Auger transitions are examined and assigned. The contribution of atomic Auger transitions is lower in the deuterated molecule. In addition, to support the presence of the ultrafast dissociation mechanism in the dichloromethane molecule, a series of high-level ab initio quantum mechanical calculations were performed at multiconfigurational self-consistent field (MCSCF) and multireference configuration interaction (MRCI) levels of theory. Minimum energy pathways for the dissociation of the dichloromethane molecule have been calculated by taking into account the spin-orbit splitting between the singlet and triplet transitions in the Cl 2p edge.

Deep-core photoabsorption and photofragmentation of tetrachloromethane near the Cl K-edge.

The fragmentation of the tetrachloromethane molecule following core-shell photoexcitation and photoionization in the neighborhood of the chlorine K-edge has been studied by using time-of-flight mass spectroscopy and monochromatic synchrotron radiation. Branching ratios for ionic dissociation were derived for all the detected ions, which are informative of the decay dynamics and photofragmentation patterns of the core-excited species. In addition, the absorption yield has been measured with a new assignment of the spectral features. The structure that appears above the Cl 1s ionization potential in the photoionization spectrum has been ascribed to the existing connection with electron-CCl4 scattering through experimental data and calculations for low-energy electron-molecule cross sections. In addition, the production of the doubly ionized Cl fragment, Cl2+, as a function of the photon energy has been analysed in the terms of a simple and an appealing physical picture, the half-collision model.

Fragmentation of Valence and Core-Shell (Cl 2p) Excited C2Cl4 Molecule.

The dynamics of the photofragmentation pathways of tetrachloroethylene with photon energies from 15 up to 250 eV encompassing the Cl 2p edge is presented. In order to distinguish the fragmentation channels, the ionic fragments were separated according to their mass-to-charge ratio, measured in coincidence with the photoelectrons, and collected as a function of the incident photon energy. Distinct minima or maxima are found in the partial ion yield in the region between 40 and 50 eV. These features are believed to be associated with the Cooper minimum which results from a molecular orbital with a strong atomic 3p subshell character. In the shallow core region, some fragmentation patterns are considered in terms of fast fragmentation of the C2Cl4 molecule, despite the heavy mass of its fragments. In the present case, the fast fragmentation is favored by the very strong antibonding character of the LUMO, understandable in the frame of the core equivalent model for halogen-containing molecules. In addition, ab initio calculations were performed to obtain states at the Cl 2p edge. Singlet and triplet states at the Cl 2p edge of the C2Cl4 molecule, corresponding to the Cl(2p → 9b1u*) and Cl(2p → 8b2u*) transitions, were calculated in order to form a basis set of molecular states from which the spin-orbit splitting can be inferred. Multiconfigurational self-consistent field (MCSCF) calculation followed by multireference configuration interaction (MRCI) was the method chosen to establish a set of singlet and triplet states at the 2p excitation edge in addition to the ground state.

Kinetic Energy Release of the Singly and Doubly Charged Methylene Chloride Molecule: The Role of Fast Dissociation.

The center of mass kinetic energy release distribution (KERD) spectra of selected ionic fragments, formed through dissociative single and double photoionization of CH2Cl2 at photon energies around the Cl 2p edge, were extracted from the shape and width of the experimentally obtained time-of-flight (TOF) distributions. The KERD spectra exhibit either smooth profiles or structures, depending on the moiety and photon energy. In general, the heavier the ionic fragments, the lower their average KERDs are. In contrast, the light H(+) fragments are observed with kinetic energies centered around 4.5-5.5 eV, depending on the photon energy. It was observed that the change in the photon energy involves a change in the KERDs, indicating different processes or transitions taking place in the breakup process. In the particular case of double ionization with the ejection of two charged fragments, the KERDs present have characteristics compatible with the Coulombic fragmentation model. Intending to interpret the experimental data, singlet and triplet states at Cl 2p edge of the CH2Cl2 molecule, corresponding to the Cl (2p → 10a1*) and Cl (2p → 4b1*) transitions, were calculated at multiconfigurational self-consistent field (MCSCF) level and multireference configuration interaction (MRCI). These states were selected to form the spin-orbit coupling matrix elements, which after diagonalization result in a spin-orbit manifold. Minimum energy pathways for dissociation of the molecule were additionally calculated aiming to give support to the presence of the ultrafast dissociation mechanism in the molecular breakup.

High yield of functional metagenomic library from mangroves constructed in fosmid vector.

In the present study, metagenomic technique and fosmid vectors were used to construct a library of clones for exploring the biotechnological potential of mangrove soils by isolation of functional genes encoding hydrolytic enzymes. The library was built with genomic DNA from the soil samples of mangrove sediments and the functional screening of 1824 clones (~64 Mbp) was performed to detect the hydrolytic activity specific for cellulases, amylases (at acidic, neutral and basic pH), lipases/esterases, proteases, and nitrilases. Significant numbers of clones, positive for the tested enzyme activities were obtained. Our results indicate the importance and biotechnological potential of mangrove soils especially when compared to those obtained using other soil metagenomic libraries.

Strong Electronic Selectivity in the Shallow Core Excitation of the CH2Cl2 Molecule.

The photoexcitation and multiphotoionization of the dichloromethane molecule have been studied for photons with energies from 100 eV to the Cl 2p edge, using the time-of-flight multicoincidence technique and synchrotron radiation. The electronic de-excitation gives rise to one to three electrons and an ionic molecule that decays onto smaller moieties through several fragmentation channels. To discern the channels, sets of fragments have been dispersed in time, measured in coincidence, and recorded as a function of incident photon energy. The chlorine ion, Cl(+), has the highest intensity around and above the Cl 2p edge, while the CHnCl(+) ion, corresponding to the loss of one neutral chlorine atom, dominates the mass spectra in the valence region. In addition, strong electronic selectivity has been observed for the core-excited molecule.

Application of a multivariate normal distribution methodology to the dissociation of doubly ionized molecules: The DMDS (CH3 -SS-CH3 ) case.

RATIONALE: The ion-ion-coincidence mass spectroscopy technique brings useful information about the fragmentation dynamics of doubly and multiply charged ionic species. We advocate the use of a matrix-parameter methodology in order to represent and interpret the entire ion-ion spectra associated with the ionic dissociation of doubly charged molecules. This method makes it possible, among other things, to infer fragmentation processes and to extract information about overlapped ion-ion coincidences. This important piece of information is difficult to obtain from other previously described methodologies. METHODS: A Wiley-McLaren time-of-flight mass spectrometer was used to discriminate the positively charged fragment ions resulting from the sample ionization by a pulsed 800 eV electron beam. We exemplify the application of this methodology by analyzing the fragmentation and ionic dissociation of the dimethyl disulfide (DMDS) molecule as induced by fast electrons. The doubly charged dissociation was analyzed using the Multivariate Normal Distribution. RESULTS: The ion-ion spectrum of the DMDS molecule was obtained at an incident electron energy of 800 eV and was matrix represented using the Multivariate Distribution theory. The proposed methodology allows us to distinguish information among [CHn SHn ]+ /[CH3 ]+ (n = 1-3) fragment ions in the ion-ion coincidence spectra using ion-ion coincidence data. Using the momenta balance methodology for the inferred parameters, a secondary decay mechanism is proposed for the [CHS]+ ion formation. As an additional check on the methodology, previously published data on the SiF4 molecule was re-analyzed with the present methodology and the results were shown to be statistically equivalent. CONCLUSIONS: The use of a Multivariate Normal Distribution allows for the representation of the whole ion-ion mass spectrum of doubly or multiply ionized molecules as a combination of parameters and the extraction of information among overlapped data. We have successfully applied this methodology to the analysis of the fragmentation of the DMDS molecule. Copyright © 2015 John Wiley & Sons, Ltd.

Single and double ionization of the camphor molecule excited around the C 1s edge.

RATIONALE: An interesting class of volatile compounds, the monoterpenes, is present in some plants although their functions are not yet fully understood. We have studied the interaction of the camphor molecule with monochromatic high-energy photons (synchrotron radiation) using time-of-flight mass spectrometry and coincidence techniques. METHODS: A commercial sample of S-camphor was admitted into the vacuum chamber, without purification, through an inlet system. Monochromatic light with energy around the C 1s edge was generated by the TGM beamline at the Brazilian Synchrotron Facility. A Wiley-McLaren mass spectrometer was used to characterize and detect the ions formed by the camphor photoionization. The data analysis was supported by energy calculations. RESULTS: Although the fragmentation patterns were basically the same at 270 eV and 330 eV, it was observed that above the C 1s edge the contribution to the spectrum from lower mass/charge fragment ions increased, pointing to a higher degree of dissociation of the molecule. Projections of the PEPIPICO spectra demonstrated the existence of unstable doubly charged species. The Gibbs free energy was calculated using the Møller-Plesset perturbation theory (MP2) for the neutral, singly and doubly excited camphor molecule. CONCLUSIONS: Our PEPIPICO spectrum clearly demonstrated the formation of doubly ionic dissociative species. From a slope analysis, we propose a secondary decay after a deferred charge separation mechanism in which, after a few steps, the camphor dication dissociates into C2 H3 (+) and C3 H5 (+) . This is the main relaxation route observed at 270 eV and 330 eV. The large energy difference between the mono and the dication (of the order of 258.2 kcal/mol) may explain the experimentally observed absence of stable dications in the spectra, because their formation is disadvantaged energetically.

Evaluation of the biodegradability of petroleum in microcosm systems by using mangrove sediments from Camamu Bay, Bahia, Brazil.

We investigated the biodegradability of oil in mangrove sediment from Camamu Bay and measured its effect on the bacterial community. Microcosms of mangrove sediment were contaminated with 0.1, 0.5, 1, 2, and 5% (w/v) oil, and the microbial activity was compared to that in uncontaminated sediment. The evolution of CO2 and gas chromatography showed the mineralization of oil compounds, which could reach 100%. Bacterial diversity was determined by polymerase chain reaction using a set of primers for the V3 and V6-V8 regions of 16S rDNA. The band profile obtained by denaturing gradient gel electrophoresis of the amplicons that were obtained for the V3 region showed a negative correlation between band number and oil concentration, whereas that of the V6-V8 region showed a positive correlation between band numbers and oil concentration. The latter also gave similar results for microcosms that were contaminated with 2 and 5% oil. These results demonstrate the mangrove sediment's capacity to recover from oil contamination (in vitro) and suggest that native mangrove microorganisms contain enzymes necessary for the catabolism of oil.

Ionization and fragmentation of methane induced by 40 eV to 480 eV synchrotron radiation: from valence to beyond core electron ionization.

Photoionization and fragmentation of gaseous methane induced by tunable synchrotron radiation were investigated in a wide energy range, from 40 eV up to 480 eV. We report electron-ion coincidence experiments by measuring the relative partial-ion yields and precursor-specific relative yields for individual fragment ions and for ion fragment pairs as a function of photon energy. The fragmentation patterns are discussed with emphasis on the transition behavior of the bond breaking reactions and of the hydrogen rearrangements from valence to core electron ionization. Below the C 1s threshold, a comparison between photon induced dissociation and electron impact data showed that the ionic fragments formation depends for both projectiles on the same final electronic state reached upon ionization.

African ancestry protects against Alzheimer's disease-related neuropathology.

Previous studies in dementia epidemiology have reported higher Alzheimer's disease rates in African-Americans when compared with White Americans. To determine whether genetically determined African ancestry is associated with neuropathological changes commonly associated with dementia, we analyzed a population-based brain bank in the highly admixed city of São Paulo, Brazil. African ancestry was estimated through the use of previously described ancestry-informative markers. Risk of presence of neuritic plaques, neurofibrillary tangles, small vessel disease, brain infarcts and Lewy bodies in subjects with significant African ancestry versus those without was determined. Results were adjusted for multiple environmental risk factors, demographic variables and apolipoprotein E genotype. African ancestry was inversely correlated with neuritic plaques (P=0.03). Subjects with significant African ancestry (n=112, 55.4%) showed lower prevalence of neuritic plaques in the univariate analysis (odds ratio (OR) 0.72, 95% confidence interval (CI) 0.55-0.95, P=0.01) and when adjusted for age, sex, APOE genotype and environmental risk factors (OR 0.43, 95% CI 0.21-0.89, P=0.02). There were no significant differences for the presence of other neuropathological alterations. We show for the first time, using genetically determined ancestry, that African ancestry may be highly protective of Alzheimer's disease neuropathology, functioning through either genetic variants or unknown environmental factors. Epidemiological studies correlating African-American race/ethnicity with increased Alzheimer's disease rates should not be interpreted as surrogates of genetic ancestry or considered to represent African-derived populations from the developing nations such as Brazil.

Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments.

Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

Lactic acid bacteria dynamics during spontaneous fermentation of cocoa beans verified by culture-independent denaturing gradient gel electrophoresis.

Cocoa is naturally fermented in the field before the cocoa seeds are removed for processing. We assessed the dynamics of lactic acid bacteria during cocoa fermentation in Bahia, Brazil. During five days of fermentation, temperature and pH were measured and beans were collected for genomic DNA extraction every 12 h. The DNA was used as a template for amplification with Lac1-Lac2 and Lac3-Lac2 for denaturing gradient gel electrophoresis analyses. pH values ranged from 3.34 to 4.98, while the temperature varied from 23° to 50°C. Lac1-Lac2 primers permitted detection of 11 operational taxonomic units. Twenty-eight operational taxonomic units were obtained with the primer pair Lac3-Lac2. It was observed that there were variations between the numbers of operational taxonomic units throughout the process, probably because of changes in pH and temperature. The greatest similarity in amplified samples was obtained with the primers Lac3-Lac2.

The influence of urea feeding on the bacterial and archaeal community in the forestomach of collared peccary (Artiodactyla, Tayassuidae).

AIMS: This study was carried out to test whether bacterial and archaeal populations, and products of fermentation in each compartment of collared peccary stomach, vary significantly with urea feeding. Bacteria and archaeal population variation among the four stomach compartments were also compared. METHODS AND RESULTS: Archaeal and bacterial communities in the forestomach of four individuals per treatment - peccaries fed diets with and without urea - were analysed at molecular level using PCR followed by denaturing gradient gel electrophoresis. Volatile fatty acids profiles in the three different compartments of the forestomach were also compared. The bacterial community composition varied considerably among each compartment and with urea provision, but no variation was observed between archaeal populations. Differences in bacterial communities between treatments - with and without urea - were greater than amongst stomach compartments. The acetate: propionate proportion decreased with urea provision in diet. Some differences in bacterial but not archaeal community composition were observed in each compartment of the collared peccary forestomach. CONCLUSIONS: There are some differences in bacterial but not archaeal populations in each compartment of collared peccary stomach. Use of urea in the diet of peccary can substantially modify the profile of volatile fatty acids released in its forestomach, but does not influence the archaeal community composition. Urea has an important effect on bacterial population DGGE profile present in the peccary's forestomach. SIGNIFICANCE AND IMPACT OF THE STUDY: These results demonstrate the ability of the collared peccary to use urea as source of nonprotein nitrogen, and confirm a hypothesis that the collared peccary has a digestive physiology more similar to ruminant than nonruminant animals.

Simple DNA extraction protocol for a 16S rDNA study of bacterial diversity in tropical landfarm soil used for bioremediation of oil waste.

Landfarm soil is used to bioremediate oil wastes from petrochemical industries. We developed a simplified protocol for microbial DNA extraction of tropical landfarm soil using only direct lysis of macerated material. Two samples of tropical landfarm soil from a Brazilian refinery were analyzed by this protocol (one consisted of crude oil-contaminated soil; the other was continuously enriched for nine months with petroleum). The soil samples were lysed by maceration with liquid nitrogen, eliminating the need for detergents, organic solvents and enzymatic cell lysis. Then, the DNA from the lysed soil sample was extracted using phenol-chloroform-isoamyl alcohol or guanidium isothiocyanate, giving high DNA yields (more than 1 micro g DNA/g soil) from both soil types. This protocol compared favorably with an established method of DNA template preparation that included mechanical, chemical and enzymatic treatment for cell lysis. The efficiency of this extraction protocol was confirmed by polymerase chain reaction amplification of the 16S rRNA gene, denaturing gradient gel electrophoresis and cloning assays. Fifty-one different clones were obtained; their sequences were classified into at least seven different phyla of the Eubacteria group (Proteobacteria - alpha, gamma and delta, Chloroflexi, Actinobacteria, Acidobac teria, Planctomycetes, Bacteroidetes, and Firmicutes). Forty percent of the sequences could not be classified into these phyla, demonstrating the genetic diversity of this microbial community. Only eight isolates had sequences similar to known sequences of 16S rRNA of cultivable organisms or of known environmental isolates and therefore could be identified to the genus level. This method of DNA extraction is a useful tool for analysis of the bacteria responsible for petroleum degradation in contaminated environments.

Mass spectrometry study of the fragmentation of valence and core-shell (Cl 2p) excited CHCl3 and CDCl3 molecules.

The dissociative photoionization of the chloroform and chloroform-d molecules has been studied in the valence region and around the chlorine 2p edge. Time-of-flight mass spectrometry in the coincidence mode-namely, photoelectron-photoion coincidence (PEPICO)-was employed. He I lamp and tunable synchrotron radiation were used as light sources. Total and partial ion yields have been recorded as a function of the photon energy. Singly, doubly, and triply ionized species have been observed below (195 eV), on (201 eV), and above (230 eV) the Cl 2p resonances. A definite degree of site-selective fragmentation was observed at the Cl 2p resonance as the relative contributions of several ionic species were seen to go through a maximum at 201 eV. At the same time all stable doubly charged ions were also observed at 198 eV (below the 2p resonances), resulting from direct ionization processes. Isotopic substitution is shown to provide a very efficient means of improving the mass resolution and assignment of unresolved peaks in spectra of CHCl(3), particularly for those fragments differing by a hydrogen atom. It is suggested that ultrafast fragmentation of the system following 2p excitation to a strongly antibonding state contributes to the large amount of Cl(+) observed in the PEPICO spectrum measured at 201 eV. Kinetic energy distributions were determined for the H(+), D(+), and Cl(+) fragments.

Effective strength of the electron-electron interaction in simultaneous projectile and target ionization.

The determination of the right balance between the strong-field interaction of the screened target nucleus and the two-center electron-electron interaction has been controversial since the early attempts to describe the stripping of light, swift ions, by heavy targets. In this work, we find a region of influence for the electron-electron contribution which clearly indicates that this interaction is an essential contribution to the stripping process for both light and heavy targets.