A further exploration of a nucleophilicity index based on the gas-phase ionization potentials

An empirical nucleophilicity index based on the gas-phase ionization potentials has been recently shown to be useful categorizing and settling the nucleophilicity power of a series of captodative ethylenes reacting in cycloaddition reactions (L.R. Domingo, E. Chamorro, P. Perez, Journal of Organic Chemistry 73 (2008) 4615-4624). In the present work, the applicability of such model is tested within a broader series of substituted alkenes, substituted aromatic compounds and simple nucleophilic molecules. This index obtained within a Koopman`s theorem framework has been evaluated here in both gas and solution phases for several well-known nucleophiles. These results are found to be linearly correlated. Finally, the feasibility of the predictive character of this index has been discussed in comparison to the available experimental nucleophilicities of some amines in water. These results further support and validate the usefulness of such approximation in the modeling of the global nucleophilicity. (C) 2008 Elsevier B.V. All rights reserved.

The gas-phase alcoholysis of protonated homoleptic alkoxysilanes

Tetra-alkoxysilanes are common and useful reagents in sol-gel processes and understanding their reactivity is important in the design of new materials. The mechanism of gas-phase reactions that mimic alcoholyis of Si(OMe)(4) (usually known as TMOS) under acidic conditions have been studied by Fourier transform ion cyclotron resonance techniques and density functional calculations at the B3LYP/6-311+G(d,p) level. The proton affinity of TMOS has been estimated at 836.4 kJ mol(-1) and protonation of TMOS gives rise to an ionic species that is best represented as trimethoxysilyl cations associated with a methanol molecule. Protonated TMOS undergoes rapid and sequential substitution of the methoxy groups in the gas-phase upon reaction with alcohols. The calculated energy profile of the reaction indicates that the substitution reaction through an S(N)2 type mechanism may be more favorable than frontal attack at silicon. Furthermore, the sequential substitution reactions are promoted by a mechanism that involves proton shuttle from the most favorable protonation site to the oxygen of the departing group mediated by the neutral reagent molecule.

Penetration of 38% hydrogen peroxide into the pulp chamber in bovine and human teeth submitted to office bleach technique

This study evaluated the pulp chamber penetration of peroxide bleaching agent in human and bovine teeth after office bleach technique. All the teeth were sectioned 3 mm apical of the cement-enamel junction and were divided into 2 groups, A (70 third human molars) and B (70 bovine lateral incisors), that were subdivided into A1 and B1 restored by using composite resin, A2 and B2 by using glass ionomer cement, and A3 and B3 by using resin-modified glass ionomer cement; A4, A5, B4, and B5 were not restored. Acetate buffer was placed in the pulp chamber, and the bleaching agent was applied for 40 minutes as follows: A1-A4 and B1-B4, 38% hydrogen peroxide exposure and A5 and B5, immersion into distilled water. The buffer solution was transferred to a glass tube in which leuco crystal violet and horseradish peroxidase were added, producing a blue solution. The optical density of the blue solution was determined by spectrophotometer and converted into microgram equivalents of hydrogen peroxide. Data were submitted to analysis of variance and Dunnett, Kruskal-Wallis, and Tukey tests (5%). A higher level of hydrogen peroxide penetrated into the pulp chamber in resin-modified glass ionomer cements in bovine (0.79 +/- 0.61 mu g) and human (2.27 +/- 0.41 mu g) groups. The bleaching agent penetration into the pulp chamber was higher in human teeth for any experimental situation. The penetration of the hydrogen peroxide depends on restorative materials, and under the conditions of this study human teeth are more susceptible to penetration of bleaching agent into the pulp chamber than bovine teeth.

Selectivity and Mechanisms Driven by Reaction Dynamics: The Case of the Gas-Phase OH-+CH3ONO2 Reaction

Well-established statistical approaches such as transition-state theory based on high-level calculated potential energy profiles are unable to account for the selectivity observed in the gas-phase OH- + CH3ONO2 reaction. This reaction can undergo bimolecular nucleophilic displacement at either the carbon center (S(N)2@C) or the nitrogen center (S(N)2@N) as well as a proton abstraction followed by dissociation (E(CO)2) pathway. Direct dynamics simulations yield an S(N)2:E(CO)2 product ratio in close agreement with experiment and show that the lack of reactivity at the nitrogen atom is due to the highly negative electrostatic potential generated by the oxygen atoms in the ONO2 group that scatters the incoming OH-. In addition to these dynamical effects, the nonstatistical behavior of these reactions is attributed to the absence of equilibrated reactant complexes and to the large number of recrossings, which might be present in several ion-molecule gas-phase reactions.

Investigation of the reactivity of metal oxide catalysts for the gas-phase phenol methylation

The gas-phase phenol methylation with methanol was investigated both from catalitic and spectroscopic point of view. In particular, the work focus on the behavior of metal oxide catalysts, like iron(III) vanadate and aluminum vanadate. Spectroscopic studies include: X-ray diffraction and Raman analysis for catalyst charactrerization; Diffuse reflectance infrared fourier transform spectroscopy and in-situ Infrared spectroscopy in vacuum for investigation of interactions between reactants and surface of catalysts.

Exploration of the Potential Energy Surfaces, Prediction of Atmospheric Concentrations, and Prediction of Vibrational Spectra for the HO2···(H2O)n (n = 1−2) Hydrogen Bonded Complexes

The hydroperoxy radical (HO2) plays a critical role in Earth's atmospheric chemistry as a component of many important reactions. The self-reaction of hydroperoxy radicals in the gas phase is strongly affected by the presence of water vapor. In this work, we explore the potential energy surfaces of hydroperoxy radicals hydrogen bonded to one or two water molecules, and predict atmospheric concentrations and vibrational spectra of these complexes. We predict that when the HO2 concentration is on the order of 108molecules·cm-3 at 298 K, that the number of HO2···H2O complexes is on the order of 107molecules·cm-3 and the number of HO2···(H2O)2 complexes is on the order of 106molecules·cm-3. Using the computed abundance of HO2···H2O, we predict that, at 298 K, the bimolecular rate constant for HO2···H2O + HO2 is about 10 times that for HO2 + HO2.

Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone

While keto-amino cytosine is the dominant species in aqueous solution, spectroscopic studies in molecular beams and in noble gas matrices show that other cytosine tautomers prevail in apolar environments. Each of these offers two or three H-bonding sites (Watson–Crick, wobble, sugar-edge). The mass- and isomer-specific S1 ← S0 vibronic spectra of cytosine·2-pyridone (Cyt·2PY) and 1-methylcytosine·2PY are measured using UV laser resonant two-photon ionization (R2PI), UV/UV depletion, and IR depletion spectroscopy. The UV spectra of the Watson–Crick and sugar-edge isomers of Cyt·2PY are separated using UV/UV spectral hole-burning. Five different isomers of Cyt·2PY are observed in a supersonic beam. We show that the Watson–Crick and sugar-edge dimers of keto-amino cytosine with 2PY are the most abundant in the beam, although keto-amino-cytosine is only the third most abundant tautomer in the gas phase. We identify the different isomers by combining three different diagnostic tools: (1) methylation of the cytosine N1–H group prevents formation of both the sugar-edge and wobble isomers and gives the Watson–Crick isomer exclusively. (2) The calculated ground state binding and dissociation energies, relative gas-phase abundances, excitation and the ionization energies are in agreement with the assignment of the dominant Cyt·2PY isomers to the Watson–Crick and sugar-edge complexes of keto-amino cytosine. (3) The comparison of calculated ground state vibrational frequencies to the experimental IR spectra in the carbonyl stretch and NH/OH/CH stretch ranges strengthen this identification.

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

In situ measurements of hydrogen sulfide, oxygen, and temperature in diffuse fluids of the ultramafic-hosted Logatchev hydrothermal vent field (Mid-Atlantic Ridge)

The Logatchev hydrothermal vent field (14°45'N, Mid-Atlantic Ridge) is located in a ridge segment characterized by mantle-derived ultramafic outcrops. Compared to basalt-hosted vents, Logatchev high temperature fluids are relatively low in sulfide indicating that the diffuse, low temperature fluids of this vent field may not contain sufficient sulfide concentrations to support a chemosymbiotic invertebrate community. However, the high abundances of bathymodiolin mussels with bacterial symbionts related to free-living sulfur oxidizing bacteria suggested that bioavailable sulfide is present at Logatchev. To clarify if diffuse fluids above mussel beds of Bathymodiolus puteoserpentis provide the reductants and oxidants needed by their symbionts for aerobic sulfide oxidation, in situ microsensor measurements of dissolved hydrogen sulfide and oxygen were combined with simultaneous temperature measurements. High temporal fluctuations of all three parameters were measured above the mussel beds. H2S and O2 co-existed with mean concentrations between 9-31 µM (H2S) and 216-228 µM (O2). Temperature maxima (<= 7.4°C) were generally concurrent with H2S maxima (<= 156 µM) and O2 minima (>= 142 µM). Long-term measurements for 250 days using temperature as a proxy for oxygen and sulfide concentrations indicated that the mussels were neither oxygen- nor sulfide-limited. Our in situ measurements at Logatchev indicate that sulfide may also be bioavailable in diffuse fluids from other ultramafic-hosted vents along slow- and ultraslow-spreading ridges.

Structure, energetics and reactions of metal cation complexes of dipeptides in the gas phase

Structure, energetics and reactions of ions in the gas phase can be revealed by mass spectrometry techniques coupled to ions activation methods. Ions can gain enough energy for dissociation by absorbing IR light photons introduced by an IR laser to the mass spectrometer. Also collisions with a neutral molecule can increase the internal energy of ions and provide the dissociation threshold energy. Infrared multiple photon dissociation (IRMPD) or sustained off-resonance irradiation collision-induced dissociation (SORI-CID) methods are combined with Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometers where ions can be held at low pressures for a long time. The outcome of ion activation techniques especially when it is compared to the computational methods results is of great importance since it provides useful information about the structure, thermochemistry and reactivity of ions of interest. In this work structure, energetics and reactivity of metal cation complexes with dipeptides are investigated. Effect of metal cation size and charge as well as microsolvation on the structure of these complexes has been studied. Structures of bare and hydrated Na and Ca complexes with isomeric dipeptides AlaGly and GlyAla are characterized by means of IRMPD spectroscopy and computational methods. At the second step unimolecular dissociation reactions of singly charged and doubly charged multimetallic complexes of alkaline earth metal cations with GlyGly are examined by CID method. Also structural features of these complexes are revealed by comparing their IRMPD spectra with calculated IR spectra of possible structures. At last the unimolecular dissociation reactions of Mn complexes are studied. IRMPD spectroscopy along with computational methods is also employed for structural elucidation of Mn complexes. In addition the ion-molecule reactions of Mn complexes with CO and water are explored in the low pressures obtained in the ICR cell.

Effect of support redox character on catalytic performance in the gas phase hydrogenation of benzaldehyde and nitrobenzene over supported gold

Peer reviewed