Proposed terminology of ‘lato sensu metrology’ for scientific methodology

Currently, there are two international scientific vocabularies devoted to properties: one dealing on quantities and the other one dealing on nominal properties. In this article, I am proposing the two mentioned vocabularies be merged in order to make available most of the basic concepts, terms, and definitions needed in observational and experimental scientific methodology in a single vocabulary. In addition, I propose the provisional use of the term “lato sensu metrology” to describe the new vocabulary.     

Three new monoterpene indole alkaloids from Psychotria umbellata Thonn.

Three new psychollatine-derived monoterpene indole alkaloids were obtained from Psychotria umbellata Thonn.: 3,4-Dehydro-18,19-β-epoxy-psychollatine (2), N⁴-[1-((R)-2-hydroxypropyl)]-psychollatine (3), and N⁴-[1-((S)-2-hydroxypropyl)]-psychollatine (4). Their structures were determined by ¹H and ¹³C NMR spectra, 2D correlations (COSY, HMQC, and HMBC), and mass and UV spectra. Compounds 3 and 4 were synthesized for structural confirmation and for the determination of the stereochemistry of the hydroxyl group.     

Screening of Wood/Forest and Vine By-Products as Sources of New Drugs for Sustainable Strategies to Control Fusarium graminearum and the Production of Mycotoxins

Fusarium graminearum is a fungal pathogen that can colonize small-grain cereals and maize and secrete type B trichothecene (TCTB) mycotoxins. The development of environmental-friendly strategies guaranteeing the safety of food and feed is a key challenge facing agriculture today. One of these strategies lies on the promising capacity of products issued from natural sources to counteract crop pests. In this work, the in vitro efficiency of sixteen extracts obtained from eight natural sources using subcritical water extraction at two temperatures was assessed against fungal growth and TCTB production by F. graminearum. Maritime pine sawdust extract was shown to be extremely efficient, leading to a significant inhibition of up to 89% of the fungal growth and up to 65% reduction of the mycotoxin production by F. graminearum. Liquid chromatography/mass spectrometry analysis of this active extract revealed the presence of three families of phenolics with a predominance of methylated compounds and suggested that the abundance of methylated structures, and therefore of hydrophobic compounds, could be a primary factor underpinning the activity of the maritime pine sawdust extract. Altogether, our data support that wood/forest by-products could be promising sources of bioactive compounds for controlling F. graminearum and its production of mycotoxins.     

Variational wave functions and their overlap with the ground state

An intrinsic measure of the quality of a variational wave function is given by its overlap with the ground state of the system. We derive a general formula to compute this overlap when quantum dynamics in imaginary time is accessible. The overlap is simply related to the area under the E(tau) curve, i.e., the energy as a function of imaginary time. This has important applications to, for example, quantum Monte Carlo simulations where the overlap becomes as a simple by-product of routine simulations. As a result, we find that the practical definition of a good variational wave function for quantum Monte Carlo simulations, i.e., fast convergence to the ground state, is equivalent to a good overlap with the actual ground state of the system.     

Angle-resolved three-dimensional analysis of surface films by coherence scanning interferometry

The Fourier components of interference signals generated by scanning a high-numerical-aperture objective orthogonal to an object surface correspond to different angles of incidence on the surface. The phase and amplitude of these Fourier components relate to the structure of the object, including in particular the 3D topography and thickness profiles of thin-film layers.     

Study by XPS of the chlorination of proteins aggregated onto tin dioxide during electrochemical production of hypochlorous acid

In solution, hypochlorous acid (HOCl) reacts with organic matter and notably with protein side-chains. In this study, HOCl was produced by an electrochemical way, by oxidation of chloride ions at a transparent tin dioxide electrode in the presence of a protein, the bovine serum albumin (BSA). A thick irregular layer is formed at the electrode when HOCl is produced at the SnO₂ surface. Indeed, SEM analyses show that an important deposit is formed during the anodic polarization of SnO₂ in the presence of chloride ions and proteins. Actually, two phenomena take place on the one hand the chlorination of the proteins due to the reaction of HOCl with some protein side-chains and on the other hand the aggregation of proteins onto the SnO₂ surface. The present X-ray photoelectron spectroscopy study points out the cross-linking of BSA molecules via formation of inter molecular sulfonamide groups. It also shows that the BSA chlorination is due on the one hand to the formation of sulfonyl chloride groups (-SO₂Cl) and on the other hand to formation of chloramine groups (N-Cl). The Cl2p and S2p photo-peak intensities allowed us to quantify the chloramines. It is found that, one BSA entity immobilized onto the SnO₂ surface contains about 50 chloramine groups.     

Comparison of the activation time effects and the internal energy distributions for the CID,PQD and HCD excitation modes

Reproducibility among different types of excitation modes is a major bottleneck in the field of tandem mass spectrometry library development in metabolomics. In this study, we specifically evaluated the influence of collision voltage and activation time parameters on tandem mass spectrometry spectra for various excitation modes [collision‐induced dissociation (CID), pulsed Q dissociation (PQD) and higher‐energy collision dissociation (HCD)] of Orbitrap‐based instruments. For this purpose, internal energy deposition was probed using an approach based on Rice–Rampserger–Kassel–Marcus modeling with three thermometer compounds of different degree of freedom (69, 228 and 420) and a thermal model. This model treats consecutively the activation and decomposition steps, and the survival precursor ion populations are characterized by truncated Maxwell–Boltzmann internal energy distributions. This study demonstrates that the activation time has a significant impact on MS/MS spectra using the CID and PQD modes. The proposed model seems suitable to describe the multiple collision regime in the PQD and HCD modes. Linear relationships between mean internal energy and collision voltage are shown for the latter modes and the three thermometer molecules. These results suggest that a calibration based on the collision voltage should provide reproducible for PQD, HCD to be compared with CID in tandem in space instruments. However, an important signal loss is observed in PQD excitation mode whatever the mass of the studied compounds, which may affect not only parent ions but also fragment ions depending on the fragmentation parameters. A calibration approach for the CID mode based on the variation of activation time parameter is more appropriate than one based on collision voltage. In fact, the activation time parameter in CID induces a modification of the collisional regime and thus helps control the orientation of the fragmentation pathways (competitive or consecutive dissociations). Copyright © 2014 John Wiley & Sons, Ltd.     

Chemical Synthesis, 3D Structure,and ASIC Binding Site of the Toxin Mambalgin‐2

Mambalgins are a novel class of snake venom components that exert potent analgesic effects mediated through the inhibition of acid‐sensing ion channels (ASICs). The 57‐residue polypeptide mambalgin‐2 (Ma‐2) was synthesized by using a combination of solid‐phase peptide synthesis and native chemical ligation. The structure of the synthetic toxin, determined using homonuclear NMR, revealed an unusual three‐finger toxin fold reminiscent of functionally unrelated snake toxins. Electrophysiological analysis of Ma‐2 on wild‐type and mutant ASIC1a receptors allowed us to identify α‐helix 5, which borders on the functionally critical acidic pocket of the channel, as a major part of the Ma‐2 binding site. This region is also crucial for the interaction of ASIC1a with the spider toxin PcTx1, thus suggesting that the binding sites for these toxins substantially overlap. This work lays the foundation for structure–activity relationship (SAR) studies and further development of this promising analgesic peptide.     

Recent Progress in Direct Introduction of Fluorinated Groups on Alkenes and Alkynes by means of CH Bond Functionalization

The direct introduction of fluorine and fluorinated building blocks has recently attracted a lot of attention and particularly the direct functionalization of alkenes and alkynes. This review will highlight the major progress recently made in that field, with a focus on photocatalyzed transformations, base‐promoted processes, and transition metal‐catalyzed functionalization of alkenes and alkynes. Special attention will be paid to explanations of the reaction mechanisms.