Methyl guanine isomer distinction by hydrogen / deuterium exchange using a fourier transform mass spectrometer

Analytical Chemistry Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Differentiation of the seven isomers of methyl guanine has been accomplished by monitoring gas-phase hydrogen/deuterium (H/D) exchange reactions of the protonated molecular ions with deuterium oxide (D₂O) in a Fourier transform mass spectrometer. In each case a distinctive reaction rate for the first H/D exchange was observed, and exchanges of up to three deuterium atoms occurred with characteristic ion abundances that could be used to differentiate the isomers. O⁶-Methyl guanine, for example, showed only one slow H/D exchange with D₂O, whereas l-methyl guanine exchanged two hydrogen atoms at a significantly faster rate. On comparison of the possible resonance structures of each protonated isomer with the experimental information about the number and rate of H/D exchanges observed, a reaction mechanism involving a concerted proton abstraction-deuterium cation donation was proposed.     

Dependence of collision‐induced dissociation energy on molecular degrees of freedom as a means to assess relative binding affinity in multivalent complexes

In collision‐induced dissociation mass spectrometry experiments, the collision energy required for dissociation linearly depends on the degrees of freedom in the precursor ion. The magnitude of the slope of this relationship previously has been shown to qualitatively correlate to the relative binding strength of a noncovalently bound, monovalent complex. The goal of the work presented here is to determine if a similar methodology can be applied for assessing relative binding strengths in multivalent species. We have tested the method on complexes formed from 18‐crown‐6 and a variety of protonated, primary alkylamines, [C_nH_2n+1NH₃]⁺ (n = 9, 12, 14, 16 and 18) and alkyldiamines, [H₃NC_nH_2nNH₃]²⁺ (n = 3, 5, 6, 9 and 12), and compared our results with dissociation energies calculated using density functional theory at the B3LYP/6‐31G* level. We found that the method correctly assessed the stronger crown ether/headgroup interaction in the two divalent species (1:1 and 2:1 complexes formed from the diaminoalkanes) compared with the weaker interaction in the monovalent species (1:1 complexes formed from mono‐aminoalkanes). However, the experimental method could not distinguish between the binding strengths of the two divalent complexes, perhaps because their calculated dissociation energies were quite similar. Our preliminary results suggest that this method could potentially be used for a quick and simple analysis of binding strengths in multivalent species if the binding strengths of the species are significantly different from one another. Copyright © 2011 John Wiley & Sons, Ltd.     

Micro-rheology of dense particulate flows: Application to immersed avalanches

We rely here on a non-smooth contact dynamics (NSCD) approach to treat particle collisions in a direct numerical simulation of a dense particulate flow. Interactions between particles are considered by a non-smooth formulation of particle dynamics at the microscopic scale, which enables one to straightforwardly implement complex contact laws. The hydrodynamic coupling is achieved by a distributed Lagrange multiplier/fictitious domain (DLM/FD) method. As a preliminary step, the relevance of our NSCD-DLM/FD method is assessed by comparing results of 2D sedimentation simulations with those obtained with a usual molecular dynamics collision model. Then, we use it to investigate how a fully immersed granular packing collapses depending on its initial particle volume fraction, providing clues on the micro-rheology of dense particulate flows.     

The photoelectron spectrum and molecular geometry of bicyclo[2.1.1]hexane

The He(I) photoelectron spectrum of bicyclo[2.1.1]hexane shows excellent correlation with a theoretical spectrum based on the eigenvalues obtained in an ab initio calculation at the theoretical molecular geometry. By contrast, a calculation performed at the experimental geometry exhibits an effect of enhanced ring strain in showing a first ionization energy which is considerably lower than the experimental value. This observation offers experimental support for the recent claim that the published structure for bicyclo [2.1.1]hexane based on electron-diffraction measurements is incorrect. It also accounts for inconsistencies observed in the calculated values of some spin—spin coupling constants for substituted bicyclo[2.1.1]hexanes.     

Aluminium triflate: a remarkable Lewis acid catalyst for the ring opening of epoxides by alcohols

Al(OTf)3 was found to be an extremely effective catalyst (at ppm levels) for ring opening reactions of epoxides using a range of alcohols.     

The effects of substrate orientation on the mechanism of a phosphotriesterase

While the underlying chemistry of enzyme-catalyzed reactions may be almost identical, the actual turnover rates of different substrates can vary significantly. This is seen in the turnover rates for the catalyzed hydrolysis of organophosphates by the bacterial phosphotriesterase OpdA. We investigate the variation in turnover rates by examining the hydrolysis of three classes of substrates: phosphotriesters, phosphothionates, and phosphorothiolates. Theoretical calculations were used to analyze the reactivity of these substrates and the energy barriers to their hydrolysis. This information was then compared to information derived from enzyme kinetics and crystallographic studies, providing new insights into the mechanism of this enzyme. We demonstrate that the enzyme catalyzes the hydrolysis of organophosphates through steric constraint of the reactants, and that the equilibrium between productively and unproductively bound substrates makes a significant contribution to the turnover rate of highly reactive substrates. These results highlight the importance of correct orientation of reactants within the active sites of enzymes to enable efficient catalysis.     

Effect of sulfur coverage on Fe(110) adhesion: a DFT study

The effect of adsorbed S at different coverages on the adhesion of Fe(110) surfaces in match and mismatch is examined using density functional theory (DFT). S is adsorbed in atop, bridge, and 4-fold hollow sites on one side of the interface in c(2 x 2) and p(1 x 1) arrangements, corresponding to coverages of 1/2 and 1 monolayer, respectively. The calculated adhesion energy values at different interfacial separations are fitted to the universal binding energy relation, and the effect of the S coverages on the adhesive strength is analyzed. The effect of relaxation of the interfaces at equilibrium is also investigated, and the resulting interfacial structures and related magnetic and charge density properties are compared.     

The preference for anti over Gauche migration in the Baeyer-Villiger reaction

Explanations for stereoselectivity in the Baeyer-Villiger reaction have relied on the assumption that the antiperiplanar (app) group migrates. However, the magnitude of the preference for app-migration over gauche migration is unknown. To investigate this, the energy differences between the two were estimated from ab initio calculations. App-migration was found to be the preferred pathway since no transition structure could be located for gauche migration. Barriers for gauche migration were estimated by performing constrained optimizations. App-migration was found to be strongly favored with a barrier that is at least 3.8 kcal/mol and as much as 58.0 kcal/mol lower in energy than the gauche migration barrier.     

Detection of hypophosphite, phosphite, and orthophosphate in natural geothermal water by ion chromatography

Current doctrine states that phosphorus is incorporated into cells in the pentavalent(V) oxidation state as orthophosphate. However, recent studies show that microorganisms contain enzymes used to metabolize reduced forms of phosphorous, including phosphite(III) and hypophosphite(I), which suggests that there is a natural source for these chemical species. This paper will discuss suppressed conductivity ion chromatography methods developed to detect hypophosphite, phosphite, and orthophosphate in a geothermal water matrix containing fluoride, chloride, bromide, nitrate, hydrogen carbonate and sulfate. All peaks were clearly resolved, and calibrations were linear with estimated 3sigma detection limits of 0.83, 0.39, and 0.35 microM for hypophosphite, phosphite, and orthophosphate, respectively.