Individual genomic DNA isolation of Entomogenous nematodes: the Deladenus study case.

Estudos populacionais envolvem a extração de DNA de um único indivíduo para permitir a genotipagem. No caso de alguns nematoides parasíticos, suas dimensões reduzidas e o grande número de indivíduos por infestação tornam a genotipagem difícil. Com o objetivo de desenvolver um protocolo, foram feitos ajustes em métodos já disponíveis, visando melhor ganho em pureza e concentração de DNA genômico. Espécimes foram digeridos em tampão de digestão de verme e submetidos à amplificação por PCR, como prova de conceito. Foi possível a obtenção de boa quantidade e concentração de DNA de indivíduos. A qualidade foi suficiente para garantir o sequenciamento da região ITS1.Nota científica

Infrared spectroscopy of ionized corannulene in the gas phase

The gas-phase infrared spectra of radical cationic and protonated corannulene were recorded by infrared multiple-photon dissociation (IRMPD) spectroscopy using the IR free electron laser for infrared experiments. Electrospray ionization was used to generate protonated corannulene and an IRMPD spectrum was recorded in a Fourier-transform ion cyclotron resonance mass spectrometer monitoring H-loss as a function of IR frequency. The radical cation was produced by 193-nm UV photoionization of the vapor of corannulene in a 3D quadrupole trap and IR irradiation produces H, H2, and C2Hx losses. Summing the spectral response of the three fragmentation channels yields the IRMPD spectrum of the radical cation. The spectra were analyzed with the aid of quantum-chemical calculations carried out at various levels of theory. The good agreement of theoretical and experimental spectra for protonated corannulene indicates that protonation occurs on one of the peripheral C-atoms, forming an sp3 hybridized carbon. The spectrum of the radical cation was examined taking into account distortions of the C5v geometry induced by the Jahn-Teller effect as a consequence of the degenerate 2E1 ground electronic state. As indicated by the calculations, the five equivalent Cs minima are separated by marginal barriers, giving rise to a dynamically distorted system. Although in general the character of the various computed vibrational bands appears to be in order, only a qualitative match to the experimental spectrum is found. Along with a general redshift of the calculated frequencies, the IR intensities of modes in the 1000-1250 cm−1 region show the largest discrepancy with the harmonic predictions. In addition to CH "in-plane" bending vibrations, these modes also exhibit substantial deformation of the pentagonal inner ring, which may relate directly to the vibronic interaction in the radical cation

Direct evidence for the ring opening of monosaccharide anions in the gas phase: photodissociation of aldohexoses and aldohexoses derived from disaccharides using variable-wavelength infrared irradiation in the carbonyl stretch region

a b s t r a c t All eight D-aldohexoses and aldohexoses derived from the non-reducing end of disaccharides were investigated by variable-wavelength infrared multiple-photon dissociation (IRMPD) as anions in the negative-ion mode. Spectroscopic evidence supports the existence of a relatively abundant open-chain configuration of the anions in the gas phase, based on the observation of a significant carbonyl absorption band near 1710 cm À1 . The abundance of the open-chain configuration of the aldohexose anions was approximately 1000-fold or greater than that of the neutral sugars in aqueous solution. This provides an explanation as to why it has not been possible to discriminate the anomeric configuration of aldohexose anions in the gas phase when derived from the non-reducing sugar of a disaccharide. Evidence from photodissociation spectra also indicates that the different aldohexoses yield product ions with maximal abundances at different wavelengths, and that the carbonyl stretch region is useful for differentiation of sugar stereochemistries. Quantum-chemical calculations indicate relatively low energy barriers to intramolecular proton transfer between hydroxyl groups and adjacent alkoxy sites located on open-chain sugar anions, suggesting that an ensemble of alkoxy charge locations contributes to their observed photodissociation spectra. Ring opening of monosaccharide anions and interconversion among configurations is an inherent property of the ions themselves and occurs in vacuo independent of solvent participation

Action spectroscopy of gas-phase carboxylate anions by multiple photon IR electron detachment/attachment

We report on a form of gas-phase anion action spectroscopy based on infrared multiple photon electron detachment and subsequent capture of the free electrons by a neutral electron scavenger in a Fourier Transform Ion Cyclotron Resonance (FTICR) mass spectrometer. This method allows one to obtain background-free spectra of strongly bound anions, for which no dissociation channels are observed. The first gas-phase spectra of acetate and propionate are presented using SF6 as electron scavenger and a free electron laser as source of intense and tunable infrared radiation. To validate the method, we compare infrared spectra obtained through multiple photon electron detachment/attachment and multiple photon dissociation for the benzoate anion. In addition, different electron acceptors are used, comparing both associative and dissociative electron capture. The relative energies of dissociation (by CO2 loss) and electron detachment are investigated for all three anions by DFT and CCSD(T) methods. DFT calculations are also employed to predict vibrational frequencies, which provide a good fit to the infrared spectra observed. The frequencies of the symmetric and antisymmetric carboxylate stretching modes for the aliphatic carboxylates are compared to those previously observed in condensed-phase IR spectra and to those reported for gas-phase benzoate, showing a strong influence of the solution environment and a slight substituent effect on the antisymmetric stretch.Comment: Revised version, Submitted to J Phys Chem

Spectroscopic Evidence for an Oxazolone Structure in Anionic b-Type Peptide Fragments

Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b2 fragments of deprotonated AlaAlaAla and AlaTyrAla have been recorded over the 800–1800 cm–1 spectral range by multiple-photon dissociation (MPD) spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Structural characterization of the b-type fragments is accomplished by comparison with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. Although diketopiperazine structures represent the energetically lowest isomers, the IR spectra suggest an oxazolone structure for the b2 fragments of both peptides. Deprotonation is shown to occur on the oxazolone α-carbon, which leads to a conjugated structure in which the negative charge is practically delocalized over the entire oxazolone ring, providing enhanced gas-phase stability

Probing the competition among different coordination motifs in metal-ciprofloxacin complexes through IRMPD spectroscopy and DFT calculations

The vibrational spectra of ciprofloxacin complexes with monovalent (Li+, Na+, K+, Ag+) and polyvalent (Mg2+, Al3+) metal ions are recorded in the range 1000-1900 cm(-1) by means of infrared multiple-photon dissociation (IRMPD) spectroscopy. The IRMPD spectra are analyzed and interpreted in the light of density functional theory (DFT)-based quantum chemical calculations in order to identify the possible structures present under our experimental conditions. For each metal-ciprofloxacin complex, four isomers are predicted, considering different chelation patterns. A good agreement is found between the measured IRMPD spectrum and the calculated absorption spectrum of the most stable isomer for each complex. Metal ion size and charge are found to drive the competition among the different coordination motifs: small size and high charge density metal ions prefer to coordinate the quinolone between the two carbonyl oxygen atoms, whereas large-size metal ions prefer the carboxylate group as a coordination site. In the latter case, an intramolecular hydrogen bond compensates the weaker interaction established by these cations. The role of the metal cation on the stabilization of ionic and nonionic structures of ciprofloxacin is also investigated. It is found that large-size metal ions preferentially stabilize charge separated motifs and that the increase of metal ion charge has a stabilizing effect on the zwitterionic form of ciprofloxacin

Protomers of Benzocaine: Solvent and Permittivity Dependence

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid, which finds an application as a local anesthetic (LA), is found to adopt in its protonated form at least two populations of distinct structures in the gas phase and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization (ESI) process. Here we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry (IM-MS) to yield gas-phase IR spectra of simultaneously m/z and drift-time resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species - the N- and O-protonated form. Density functional theory (DFT) calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation has been suggested