Identification tree based on fragmentation rules for structure elucidation of organophosphorus esters by electrospray mass spectrometry

Organophosphorus compounds have played important roles as pesticides, chemical warfare agents and extractors of radioactive material. Structural elucidation of phosphonates poses a particular challenge because their initial forms can be hydrolyzed, thus, degradation products may predominate in samples acquired in the field. The analysis of non‐volatile organophosphorus compounds and their degradation products is possible using electrospray tandem mass spectrometry ESI‐MS/MS. Here, we present a generic strategy that allows the unambiguous identification of substituents for two families of organophosphorus compounds: the phosphonates and phosphates. General fragmentation rules were deduced based on the study of decomposition pathways of 55 organophosphorus esters, including examples found in the literature. Multistage MS (MSⁿ) experiments at high resolution in a hybrid mass spectrometer provide accurate mass measurements, whereas collision‐induced dissociation experiments in a triple quadrupole give access to small fragment ions. The creation of a specific nomenclature for each possible structure of organophosphorus compound, depending on the alkyl side chain linked to the oxygen, was achieved by applying these fragmentation rules. This led to the creation of an ‘identification tree’ based upon the unique consecutive decomposition pathways uncovered for each individual compound. Hence, seven structural motifs were created that orient an unequivocal identification using the ‘identification tree’. Despite the similar structures of the ensemble of phosphate and phosphonate esters, distinct identifications based upon characteristic neutral losses and diagnostic fragment ions were possible in all cases. Copyright © 2013 John Wiley & Sons, Ltd.     

Quantification of the effect of nonphotochemical quenching on the determination of in vivo chl a from phytoplankton along the water column of a freshwater reservoir

Nonphotochemical quenching (NPQ) is a well-known collection of different photoprotective mechanisms of plants and algae to avoid photodamage under an excess of light energy. In order to evaluate the overall effect of NPQ processes on the fluorometric determination of in vivo Chl a from a phytoplankton community dominated by diatoms, we compared the results obtained by two different fluorometric field devices with the total concentration of extracted Chl a measured by HPLC ( in vitro Chl a ). A different set of measurements were made to assess the performance of these fluorometers at high, moderate and low irradiance conditions. The Fbbe fluorometer, which is capable of distinguishing different algal groups according to their pigment content, allowed a better determination of in vivo Chl a under high irradiance conditions, with only a 10% mean difference from the in vitro Chl a concentration. In turn, the FMII fluorometer underestimated by as much as 50% the in vitro Chl a concentration under the same light conditions. As data from both fluorometers were in accordance with the in vitro Chl a values at moderate irradiance levels, the differences observed at high irradiances were attributed to the decrease in the yield of Chl a fluorescence caused by photoprotective NPQ processes. Accordingly, we estimated the effect of NPQ processes on the in vivo Chl a determination and the results allow us to provide an equation to correct this effect when in situ fluorometric measurements are carried out under high irradiance regimes. Our results demonstrate that under certain circumstances NPQ seriously compromises the results obtained by in situ fluorometric probes and highlight the need for a cautious interpretation of field data under such environmental conditions.     

Polypeptide folding on a conformational‐space network: Dependence of network topology on the structural discretization procedure

Mapping the conformational space of a polypeptide onto a network of conformational states involves a number of subjective choices, mostly in relation to the definition of conformation and its discrete nature in a network framework. Here, we evaluate the robustness of the topology of conformational‐space networks derived from Molecular Dynamics (MD) simulations with respect to the use of different discretization (clustering) methods, variation of their parameters, simulation length and analysis time‐step, and removing high‐frequency motions from the coordinate trajectories. In addition, we investigate the extent to which polypeptide dynamics can be reproduced on the resulting networks when assuming Markovian behavior. The analysis is based on eight 500 ns and eight 400 ns MD simulations in explicit water of two 10‐residue peptides. Three clustering algorithms were used, two of them based on the pair‐wise root‐mean‐square difference between structures and one on dihedral‐angle patterns. A short characteristic path length and a power‐law behavior of the probability distribution of the node degree are obtained irrespective of the clustering method or the value of any of the tested parameters. The average cliquishness is consistently one or two orders of magnitude larger than that of a random realization of a network of corresponding size and connectivity. The cliquishness as function of node degree and the kinetic properties of the networks are found to be most dependent on clustering method and/or parameters. Although Markovian simulations on the networks reproduce cluster populations accurately, their kinetic properties most often differ from those observed in the MD simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Model-independent constraints on spin observables

We discuss model-independent constraints on spin observables in exclusive and inclusive reactions, with special attention to the case of photoproduction.     

Current trends in the computational modelling of polyoxometalates

Computational chemistry applied to the study of polyoxometalates has achieved its maturity in the last years. During two decades, important advances have been made using theoretical tools in the comprehension and interpretation of many relevant issues. In the present mini-review, we want to stress that different techniques have been incorporated to the routine of computation: from the very first Hartree?CFock LCAO-SCF calculation on the decavanadate anion, followed by numerous density functional theory?Cbased studies on increasingly complex systems, also applying correlated ab initio techniques for magnetism and, more recently, using molecular dynamics to analyse properties in liquid media, the information provided by computational chemistry gets more and more relevant.     

DFT Mechanistic Study on Diene Metathesis Catalyzed by Ru‐Based Grubbs–Hoveyda‐Type Carbenes: The Key Role of π‐Electron Density Delocalization in the Hoveyda Ligand

The catalytic activity and catalyst recovery of two heterogenized ruthenium‐based precatalysts ( H and NO₂(4) ) in diene ring‐closing metathesis have been studied by means of density functional calculations at the B3LYP level of theory. For comparison and rationalization of the key factors that lead to higher activities and higher catalyst recoveries, four other Grubbs–Hoveyda complexes have also been investigated. The full catalytic cycle (catalyst formation, propagation, and precatalyst regeneration) has been considered. DFT calculations suggest that either for the homogeneous and heterogenized systems the activity of the catalysts mainly depends on the ability of the precursor to generate the propagating carbene. This ability does not correlate with the traditionally identified key factor, the Ru???O interaction strength. In contrast, precatalysts with lower alkoxy‐dissociation energy barriers and lower stabilities compared with the propagating carbene also present larger C1? C2 bond length (i.e., lower π character of the C? C bond that exists between the metal–carbene (Ru?C) and the phenyl ring of the Hoveyda ligand). Catalyst recovery, regardless of whether a release–return mechanism occurs or not, is also mainly determined by the π delocalization. Therefore, future Grubbs–Hoveyda‐type catalyst development should be based on fine‐tuning the π‐electron density of the phenyl moiety, with the subsequent effect on the metalloaromaticity of the ruthenafurane ring, rather than considering the modification of the Ru???O interaction.     

Analytical approach for CRLH-based antennas design

This paper presents an analytical model for CRLH (Composite Right-Left Handed) antennas preliminary design. The objective of this work is to develop a tool to estimate quickly the scattering and radiating characteristics of these CRLH-based structures. The analytical model provides thus a set of parameters which roughly fulfill desired requirements. Afterwards, the antenna designer can refine the CRLH-based antenna performances with full 3D electromagnetic simulation software.