Shamrock surfactants with terminal carboxylate headgroups and a central phosphorodithioate or quaternary ammonium headgroup

Surfactants 3 (tripotassium O,O'-di-[11-(carboxylato)undecyl]phosphorodithioate) and 4 (sodium 12-[dimethyl-(11-carboxylatoundecyl)ammonio]dodecanoate), which are new shamrock surfactants, were prepared and characterized. Shamrock surfactants represent a novel class of surfactants that contain a central headgroup connected to two flanking headgroups by hydrocarbon chains; they do not contain long-chain alkyl groups. Surfactants 3 and 4 were characterized in water by measurement of their Krafft temperatures and critical aggregation concentrations, and their aggregates were studied by 1H and 31P NMR spectroscopy, dynamic laser light scattering, and phase-contrast optical microscopy. Aqueous 3 and 4 were also studied by cryoetch high-resolution scanning electron microscopy, which revealed fences with interposed lacelike patterns for the former and compartments formed by irregular fences for the latter. Coacervates were likely formed upon the undisturbed hydration of 3 and 4, as determined by phase-contrast optical microscopy.     

The nicholas approach to natural product hybrids

The intermolecular Nicholas reaction of terpene-based scaffolds is an excellent access to natural product hybrid compounds. These intermolecular reactions have a low selectivity and are scarcely efficient for non-conjugated cations, but they are highly efficient to produce new terpene structures through an intramolecular reaction pathway. The use of cations derived from natural product derived [Co(2)(CO)(6)]-enyne complexes is, in contrast, a highly efficient regio- and stereoselective procedure to prepare very complex structures, incorporating diverse densely functionalized or labile moieties. Thus, beta-pinene-diterpene-alkaloid or homohybrids can be accessed in totally stereo-, regio- and siteselective fashion. This approach efficiently discriminates between different propargylic positions by selecting the nature of the alcohol, being the enyne-derived cations the most reactive. The chimera 38 with a steroid-terpene-indole skeleton was prepared in this way.     

Determination of 2,4,6-trichloroanisole and guaiacol in cork stoppers by pressurised fluid extraction and gas chromatography-mass spectrometry

This paper describes the development of an analytical method consisting of pressurised fluid extraction (PFE) and gas chromatography-mass spectrometry (GC-MS) using experimental designs to determine two volatile compounds in naturally-tainted cork stoppers. The target analytes, 2,4,6-trichloroanisole (2,4,6-TCA) and guaiacol, are involved in the cork taint of wine. First, a Plackett-Burman experimental design was carried out in order to determine the significant experimental parameters affecting the PFE process, and then a central composite design was used to optimise these significant parameters. Once the method had been optimised, the influence of the number of extraction cycles was studied. The method was applied to determine the concentration of 2,4,6-TCA and guaiacol in three cork samples, and the results were compared with the ones obtained by multiple headspace-solid-phase microextraction (MHS-SPME) and by Soxhlet extraction.     

A new approach for separating low-molecular-weight RNA molecules by staircase electrophoresis in non-sequencing gels

Low-molecular-weight (LMW) RNA profiles, which include ribosomal and transfer RNA molecules with similar small sizes, are molecular signatures of microorganisms with a great potential in microbial identification. The greatest resolution of these profiles was achieved by staircase electrophoresis in sequencing gels. Nevertheless, this technique is difficult to use because it takes 7 h, the gels have large sizes and it is necessary to heat the system and to recycle the buffer to maintain the denaturing conditions and avoid smile effects. Most available sequencing slabs have no internal temperature control or homogenizing devices, which by contrast are present in some newly designed non-sequencing slabs. Nevertheless, these slabs present two important problems for separating LMW RNA molecules, the size of gels is only 20 cm (instead of 40 cm) and the maximum voltage that can be reached is only 840 V (instead 2400 V). Staircase electrophoresis follows a model in which the external polarization is incrementally modified with a constant time step value. In the present work, we experimentally confirmed that by reducing the time step and increasing the total number of steps a suitable resolution is achieved. Under these conditions, despite the smaller size of the gels and the lower values of the electric field, the intensity reaches higher values than in sequencing gels and the LMW RNA profiles are correctly separated in 5 h. The resolution of these profiles obtained in non-sequencing gels is similar to that obtained in sequencing ones facilitating the analysis of large populations of microorganisms in any laboratory.     

Comparison between computational fluid dynamics,fluid–structure interaction and computational structural dynamics predictions of flow-induced wall mechanics in an anatomically realistic cerebral aneurysm model

Haemodynamically induced stress plays an important role in the progression and rupture of cerebral aneurysms. The current work describes computational fluid dynamics (CFD), fluid–structure interaction (FSI) and computational structural dynamics (CSD) simulations in an anatomically realistic model of a carotid artery with two saccular cerebral aneurysms in the ophthalmic region. The model was obtained from three-dimensional (3D) rotational angiographic imaging data. CFD and FSI were studied under a physiologically representative waveform of inflow. The arterial wall was assumed elastic or hyperelastic, as a 3D solid or as a shell depending on the type of modelling used. The flow was assumed to be laminar, non-Newtonian and incompressible. The CFD, FSI and CSD models were solved with the finite elements package ADINA. Predictions of velocity field and wall shear stress (WSS) on the aneurysms made using CFD and FSI were compared. The CSD model of the aneurysms using complete geometry was compared with isolated aneurysm models. Additionally, the effects of hypertensive pressure on CSD aneurysm models are also reported. The vortex structure, WSS, effective stress, strain and displacement of the aneurysm walls showed differences, depending on the type of modelling used.     

Optical Absorption in Periodic Graphene Superlattices: Perpendicular Applied Magnetic Field and Temperature Effects

A detailed study of the magneto‐optical absorption is presented for graphene superlattices (SLs) subjected to a perpendicular magnetic field. For a given temperature, this quantity exhibits a resonant peak structure whose characteristics depend on the magnetic field regime, circular polarization of light and SL barrier height. For the intermediate field regime, we demonstrated that the resonant peak structure of is directly correlated to the partial joint density of states. Specifically, the latter exhibits van Hove‐like singularities and peaks at energies where takes its maximum values. We also investigated the magnetoabsorption in the weak field regime for SLs exhibiting one and extra Dirac points in the absence of the field. It was found that for SLs with only one Dirac point, the absorption spectra consist of resonant peaks satisfying the same circular polarization dependent selection rule as that for pristine graphene, except for one of them. For SLs with extra Dirac points, the resonant peaks arise from transitions between singlet subbands or between doublet subbands and satisfy a circular polarization and peak intensity dependent selection rule. It was also found that the resonant structure of can be observed experimentally at room temperature in clean SLs.     

Refinements of the Weyl Pure Geometrical Thick Branes From Information‐Entropic Measure

This work aims to analyse the so‐called configurational entropy in the Weyl pure geometrical thick brane model. The Weyl structure plays a prominent role in the brane thickness of this model. We find a set of parameters associated to the brane width where the configurational entropy exhibits critical points. The information‐theoretical measure sets bounds into parameter of Weyl pure geometrical brane model. In addition, we also argue that a similar approach can be useful to analyze the corrections to Newtonian and Coulombian potentials in Weyl scenarios.     

CRDOCK: An Ultrafast Multipurpose Protein-Ligand Docking Tool

An ultrafast docking and virtual screening program, CRDOCK, is presented that contains (1) a search engine that can use a variety of sampling methods and an initial energy evaluation function, (2) several energy minimization algorithms for fine tuning the binding poses, and (3) different scoring functions. This modularity ensures the easy configuration of custom-made protocols that can be optimized depending on the problem in hand. CRDOCK employs a precomputed library of ligand conformations that are initially generated from one-dimensional SMILES strings. Testing CRDOCK on two widely used benchmarks, the ASTEX diverse set and the Directory of Useful Decoys, yielded a success rate of ～75% in pose prediction and an average AUC of 0.66. A typical ligand can be docked, on average, in just ～13 s. Extension to a representative group of pharmacologically relevant G protein-coupled receptors that have been recently cocrystallized with some selective ligands allowed us to demonstrate the utility of this tool and also highlight some current limitations. CRDOCK is now included within VSDMIP, our integrated platform for drug discovery.     

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)](2+) gas phase unimolecular reactivity via chemical dynamics simulations

In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.