Investigation of the prototype silylene reaction, SiH2+H2O(and D2O): time-resolved gas-phase kinetic studies, isotope effects, RRKM calculations, and quantum chemical calculations of the reaction energy surface

Time-resolved kinetic studies of the reaction of silylene, SiH2, with H2O and with D2O have been carried out in the gas phase at 296 and at 339 K, using laser flash photolysis to generate and monitor SiH2. The reaction was studied over the pressure range 10-200 Torr with SF6 as bath gas. The second-order rate constants obtained were pressure dependent, indicating that the reaction is a third-body assisted association process. Rate constants at 339 K were about half those at 296 K. Isotope effects, k(H)/k(D), were small averaging 1.076 0.080, suggesting no involvement of H- (or D-) atom transfer in the rate determining step. RRKM modeling was undertaken based on a transition state appropriate to formation of the expected zwitterionic donoracceptor complex, H2Si...OH2. Because the reaction is close to the low pressure (third order) region, it is difficult to be definitive about the activated complex structure. Various structures were tried, both with and without the incorporation of rotational modes, leading to values for the high-pressure limiting (i.e., true secondorder) rate constant in the range 9.5 x 10(-11) to 5 x 10(-10) cm(3) molecule' s(-1). The RRKM modeling and mechanistic interpretation is supported by ab initio quantum calculations carried out at the G2 and G3 levels. The results are compared and contrasted with the previous studies.

Time-resolved gas-phase kinetic study of the germylene addition reaction, GeH2 + C2D2

Time-resolved studies of germylene, GeH2, generated by laser. ash photolysis of 3,4-dimethyl-1-germacyclopent-3-ene, have been carried out to obtain rate coefficients for its bimolecular reaction with C2D2. The reaction was studied in the gas phase, mainly at a total pressure of 1.3 kPa (in SF6 bath gas) at five temperatures in the range 298-558 K. Pressure variation measurements over the range 0.13-13 kPa ( SF6) at 298, 397 and 558 K revealed a small pressure dependence but only at 558 K. After correction for this, the second-order rate coefficients gave the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) = (-10.96 +/- 0.05) + ( 6.16 +/- 0.37 kJ mol(-1))/RT ln 10 Comparison with the reaction of GeH2 + C2H2 (studied earlier) showed a similar behaviour with almost identical rate coefficients. The lack of a significant isotope effect is consistent with a rate-determining addition process and is explained by irreversible decomposition of the reaction intermediate to give Ge(P-3) + C2H4. This result contrasts with that for GeH2 + C2H4/C2D4 and those for the analogous silylene reactions. The underlying reasons for this are discussed.

Reaction of a phospholipid monolayer with gas-phase ozone at the air-water interface: measurement of surface excess and surface pressure in real time

The reaction between gas-phase ozone and monolayers of the unsaturated lipid 1-palmitoy1-2-oleoyl-sn-glycero-3-phosphocholine, POPC, on aqueous solutions has been studied in real time using neutron reflection and surface pressure measurements. The reaction between ozone and lung surfactant, which contains POPC, leads to decreased pulmonary function, but little is known shout the changes that occur to the interfacial material as a result of oxidation. The results reveal that the initial reaction of ozone with POPC leads to a rapid increase in surface pressure followed by a slow decrease to very low values. The neutron reflection measurements, performed on an isotopologue of POPC with a selectively deuterated palmitoyl strand, reveal that the reaction leads to loss of this strand from the air-water interface. suggesting either solubilization of the product lipid or degradation of the palmitoyl strand by a reactive species. Reactions of H-1-POPC on D2O reveal that the headgroup region of the lipids in aqueous solution is not dramatically perturbed by the reaction of POPC monolayers with ozone supporting degradation of the palmitoyl strand rather than solubilization. The results are consistent with the reaction of ozone with the oleoyl strand of POPC at the air water interface leading to the formation of OH radicals. the highly reactive OH radicals produced can then go on to react with the saturated palmitoyl strands leading to the formation or oxidized lipids with shorter alkyl tails.

Time-resolved gas-phase kinetic study of the germylene addition reaction, CH3C CCH3

Time-resolved kinetic studies of the reaction of germylene, GeH2, generated by laser. ash photolysis of 3,4-dimethyl-1-germacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with 2-butyne, CH3C CCH3. The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at five temperatures in the range 300-556 K. The second order rate constants obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) = (-10.46 +/- 10.06) + (5.16 +/- 10.47) kJ mol(-1)/ RT ln 10 Calculations of the energy surface of the GeC4H8 reaction system were carried out employing the additivity principle, by combining previous quantum chemical calculations of related reaction systems. These support formation of 1,2-dimethylvinylgermylene (rather than 2,3-dimethylgermirene) as the end product. RRKM calculations of the pressure dependence of the reaction are in reasonable agreement with this finding. The reactions of GeH2 with C2H2 and with CH3CRCCH3 are compared and contrasted.

Direct time-resolved study of the kinetics of the reaction of silylene with phenylsilane in the gas phase. Does SiH2 react with the aromatic ring?

Laser flash photolysis studies of silylene, SiH2, generated by the 193 nm laser flash photolysis phenylsilane, PhSiH3, have been carried out to obtain rate constants for its bimolecular reaction with PhSiH3 itself, in the gas phase. The reaction was studied in SF6 (mostly at 10 Torr total pressure) over the temperature range 298-595 K. The rate constants (also found to be pressure independent) gave the following Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-9.92 +/- 0.04) + (3.31 +/- 0.27) kJ mol(-1)/RT ln 10 Similar investigations of the reaction of silylene with benzene, C6H6, (295-410 K) gave data suggestive of the fact that SiH2 might be reacting with photochemical products of C6H6 as well as with C6H6 itself. However, in the latter system, apparent rate constants were sufficiently low to indicate that in the reaction of SiH2 with PhSiH3 addition to the aromatic ring was unlikely to be in excess of 3% of the total. Quantum chemical calculations of the energy surface for SiH2 + C6H6 indicate that 7-silanorcaradiene and 7-silacycloheptatriene are possible products but that PhSiH3 formation is unlikely. RRKM calculations suggest that 7-silanorcaradiene should be the initial product but that it cannot be collisionally stabilized under experimental conditions

A real-time polymerase chain reaction assay for the identification and quantification of American Leishmania species on the basis of glucose-6-phosphate dehydrogenase

A real-time polymerase chain reaction (PCR) test was developed on the basis of the Leishmania glucose-6-phosphate dehydrogenase locus that enables identification and quantification of parasites. Using two independent pairs of primers in SYBR-Green assays, the test identified etiologic agents of cutaneous leishmaniasis belonging to both subgenera, Leishmania (Viannia) and Leishmania (Leishmania) in the Americas. Furthermore, use of TaqMan probes enables distinction between L. (V.) braziliensis or L. (V.) peruviania from the other L. (Viannia) species. All assays were negative with DNA of related trypanosomatids, humans, and mice. The parasite burden was estimated by normalizing the number of organisms per total amount of DNA in the sample or per host glyceraldehyde-3-phosphate dehydrogenase copies. The real-time PCR assay for L. (Leishmania) subgenus showed a good linear correlation with quantification on the basis of a limiting dilution assay in experimentally infected mice. The test successfully identifies and quantifies Leishmania in human biopsy specimens and represents a new tool to study leishmaniasis.

Mass transport effects in the borohydride oxidation reaction-Influence of the residence time on the reaction onset and faradaic efficiency

The borohydride oxidation reaction (BOR) was studied on Pt and Au electrodes by cyclic voltammetry in dilute alkaline borohydride solutions (0.1 M NaOH + 10(-3) mol L(-1) NaBH(4)). More specifically, the electrodes were considered as either Vulcan XC72-supported Pt or Au (noted as Pt/C and Au/C, respectively) active layers or smooth Pt or Au surfaces, the latter possibly being covered by a layer of (non-metalized) Vulcan XC72 carbon powder. The BOR onset potential and the number of electrons (n(e-)) exchanged per BH(4)(-) anion (faradaic efficiency) were investigated for these electrodes, to determine whether the residence time of reaction intermediates (at the electrode surface or inside the porous layer) does influence the overall reaction pathway/completion. For the carbon-supported platinum, n(e-) strongly depends on the thickness of the active layer. While thin (ca. 0.5 mu m-thick) Pt/C active layers yield n(e-) < 4, thick layers (approximately 3 mu m) yield n(e-)approximate to 8, which can be ascribed to the sufficient residence time of the molecules formed within the active layer (H(2), by heterogeneous hydrolysis, or BOR intermediates) enabling further (near-complete) oxidation. This puts into evidence that not only the nature of the electrocatalyst is important to reach high BOR efficiency, but also the structure/thickness of the active layer. The same trend applies for Au/C active layers and for smooth Pt or Au surfaces covered with a layer of (inactive) Vulcan XC72. In addition, the BOR onset usually shifts negative when the reaction intermediates are trapped, which suggests that some of the intermediates are more easily oxidized than BH(4)(-) itself; based on literature data, BH(3)OH(-) species is a likely candidate. (C) 2011 Elsevier B.V. All rights reserved.

The Effect of a Supragingival Plaque-Control Regimen on the Subgingival Microbiota in Smokers and Never-Smokers: Evaluation by Real-Time Polymerase Chain Reaction

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Polymerase chain reaction and real-time PCR for diagnosing of Leishmania infantum chagasi in dogs

A importância do cão como reservatório de L. infantum chagasi no meio urbano tem estimulado a realização de inúmeros trabalhos de avaliação de técnicas de diagnóstico, uma vez que este procedimento, quando realizado corretamente, torna-se um importante passo na prevenção da doença em humanos. Dentre os métodos de diagnóstico, as técnicas moleculares têm adquirido destaque. Objetivou-se neste trabalho verificar o desempenho da Reação em Cadeia da Polimerase (PCR) e da PCR em tempo real (qPCR) para diagnóstico da Leishmaniose Visceral Canina (LVC) utilizando diferentes amostras biológicas. Para tanto foram utilizados 35 cães provenientes de uma área endêmica para LVC, onde foram utilizados para o diagnóstico molecular, aspirado de medula óssea, fragmentos de linfonodo e baço. Neste estudo a qPCR foi capaz de detectar um maior número de animais positivos quando comparada com a PCR. Já entre as diferentes amostras biológicas utilizadas não foi observada diferença significativa na detecção de DNA de L. infantumchagasi por meio da PCR e qPCR. Mesmo assim, considerando a facilidade de obtenção, o linfonodo pode ser considerada como a melhor amostra para diagnóstico molecular da infecção por L. infantum chagasi.

Periodontal status in smokers and never-smokers: Clinical findings and real-time polymerase chain reaction quantification of putative periodontal pathogens

Background: Smoking is a well-known risk factor for destructive periodontal disease, but its relationship with periodontal status and subgingival microbiota remains unclear. Inherent limitations of microbiological methods previously used may partly explain these mixed results, and real-time polymerase chain reaction (PCR) has been presented as a valid alternative. The aim of the present study was to investigate the clinical condition and microbiological profile of patients with chronic periodontitis as related to the habit of smoking.Methods: Fifty patients (33 to 59 years old), 25 smokers and 25 never-smokers, constituted the sample. The visible plaque index (VPI), gingival bleeding index (GBI), bleeding on probing (BOP), periodontal probing depth (PD), clinical attachment loss (CAL), and gingival crevicular fluid (GCF) volume were recorded. Real-time PCR quantified Porphyromonas gingivalis, Micromonas micros, Dialister pneumosintes, Actinobacillus actinomycetemcomitans and total bacteria in subgingival samples.Results: Smokers and never-smokers showed similar values for VPI, GBI, and BOP. Smokers had deeper PD in buccal/lingual sites and higher CAL independently of the tooth surface. The GCF volume was smaller in smokers, independent of the PD. Similar amounts of total bacteria and P. gingivalis were observed for both groups. Significantly higher numbers of D. pneumosintes and M. micros were present in smokers and associated with moderate and deep pockets. When heavy smokers were considered, higher counts of total bacteria, M. micros, and D. pneumosintes were observed.Conclusions: Smoking seems to have a detrimental impact on the periodontal status and microbiological profile of patients with periodontitis. Compared to never-smokers, smokers had deeper pockets, greater periodontal destruction, and higher counts of some putative periodontal pathogens.

Presence of infectious agents and co-infections in diarrheic dogs determined with a real-time polymerase chain reaction-based panel

Background: Infectious diarrhea can be caused by bacteria, viruses, or protozoan organisms, or a combination of these. The identification of co-infections in dogs is important to determine the prognosis and to plan strategies for their treatment and prophylaxis. Although many pathogens have been individually detected with real-time polymerase chain reaction (PCR), a comprehensive panel of agents that cause diarrhea in privately owned dogs has not yet been established. The objective of this study was to use a real-time PCR diarrhea panel to survey the frequencies of pathogens and co-infections in owned dogs attended in a veterinary hospital with and without diarrhea, as well the frequency in different countries. Feces samples were tested for canine distemper virus, canine coronavirus, canine parvovirus type 2 (CPV-2), Clostridium perfringens alpha toxin (CPA), Cryptosporidium spp., Giardia spp., and Salmonella spp. using molecular techniques.Results: In total, 104 diarrheic and 43 control dogs that were presented consecutively at a major private veterinary hospital were included in the study. Overall, 71/104 (68.3%) dogs with diarrhea were positive for at least one pathogen: a single infection in 39/71 dogs (54.9%) and co-infections in 32/71 dogs (45.1%), including 21/32 dogs (65.6%) with dual, 5/32 (15.6%) with triple, and 6/32 (18.8%) with quadruple infections. In the control group, 13/43 (30.2%) dogs were positive, all with single infections only. The most prevalent pathogens in the diarrheic dogs were CPA (40/104 dogs, 38.5%), CPV-2 (36/104 dogs, 34.6%), and Giardia spp. (14/104 dogs, 13.5%). CPV-2 was the most prevalent pathogen in the dual co-infections, associated with CPA, Cryptosporidium spp., or Giardia spp. No statistical difference (P = 0.8374) was observed in the duration of diarrhea or the number of deaths (P = 0.5722) in the presence or absence of single or co-infections.Conclusions: Diarrheic dogs showed a higher prevalence of pathogen infections than the controls. Whereas the healthy dogs had only single infections, about half the diarrheic dogs had co-infections. Therefore, multiple pathogens should be investigated in dogs presenting with diarrhea. The effects of multiple pathogens on the disease outcomes remain unclear because the rate of death and the duration of diarrhea did not seem to be affected by these factors.

Assessment of a quantitative 5' nuclease real-time polymerase chain reaction using the nicotinamide adenine dinucleotide dehydrogenase gamma subunit (nuoG) for Bartonella species in domiciled and stray cats in Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Clinical and Microbiologic Evaluation, by Real-Time Polymerase Chain Reaction, of Non-Surgical Treatment of Aggressive Periodontitis Associated With Amoxicillin and Metronidazole

Background: The aim of the present study is to evaluate the clinical and microbiologic changes resulting from non-surgical periodontal treatment associated with amoxicillin and metronidazole in individuals with aggressive periodontitis. Methods: Fifteen individuals with aggressive periodontitis received non-surgical periodontal treatment and 45 days after completion of treatment were treated with antibiotics. Clinical data and samples of subgingival plaque were collected at baseline, 45 days after the non-surgical periodontal treatment, and 1 month after the use of antimicrobial agents. After 3 and 6 months, only clinical data were collected. The presence and quantification of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis (Pg), Tannerella forsythia (Tf), Treponema denticola (Td), and Dialister pneumosintes were determined by real-time polymerase chain reaction. Results: All clinical parameters, with the exception of clinical attachment level (CAL), had significantly (P<0.05) improved at the end of the third month after non-surgical therapy associated with antibiotics. There was significant (P<0.05) reduction in the quantities of Td and Tf. After 1 month, there were significant (P<0.05) reductions in the frequencies of Pg and Tf. Conclusion: Non-surgical mechanical treatment associated with the use of amoxicillin and metronidazole led to an improvement in all clinical parameters studied, except for CAL, and significantly reduced the amount of subgingival Tf and Td. J Periodontal 2012;83:744-752.

In Situ Quantification of Cu(II) during an Electrodeposition Reaction Using Time-Domain NMR Relaxometry

The use of a low-cost benchtop time-domain NMR (TD-NMR) spectrometer to monitor copper electrodeposition in situ is presented. The measurements are based on the strong linear correlation between the concentration of paramagnetic ions and the transverse relaxation rates (R-2) of the solvent protons Two electrochemical NMR (EC-NMR) cells were constructed and applied to monitor the Cu2+ concentration during the electrodeposition reaction. The results show that TD-NMR relaxometry using the Carr-Purcell-Meiboom-Gill pulse sequence can be a very fast, simple, and efficient technique to monitor, in real time, the variation in the Cu2+ concentration during an electrodeposition reaction. This methodology can also be applied to monitor the electrodeposition of other paramagnetic ions, such as Ni2+ and Cr3+, which are commonly used in electroplating.