THz and above THz electron or hole oscillations in DNA dimers and trimers

A non conventional source or receiver of THz and above THz electromagnetic radiation is proposed. Specifically, electron or hole oscillations in DNA dimers (two interacting DNA base‐pairs or monomers) are predicted, with frequency in the range 0.25–100 THz (period 10–4000 fs) i.e. potentially absorbing or emitting electromagnetic radiation mainly in the mid‐ and far‐infrared with wavelengths ≈ 3–1200 μm. The efficiency of charge transfer between the two monomers which make up the dimer is described with the maximum transfer percentage p  and the pure maximum transfer rate . For dimers made of identical monomers , but for dimers made of different monomers . The investigation is extended to DNA trimers (three interacting DNA base‐pairs or monomers). For trimers made of identical monomers the carrier oscillates periodically with 0.5–33 THz ( 30–2000 fs); for 0 times crosswise purines , for 1 or 2 times crosswise purines . For trimers made of different monomers the carrier movement may be non periodic. Generally, increasing the number of monomers above three, the system becomes more complex and periodicity is lost; even for the simplest tetramer the carrier movement is not periodic.     

Modeling flexible pharmacophores with distance geometry, scoring, and bound stretching

The study of pharmacophores, i.e., of common features between different ligands, is important for the quantitative identification of "compatible" enzymes and binding species. A pharmacophore-based technique is developed that combines multiple conformations with a distance geometry method to create flexible pharmacophore representations. It uses a set of low-energy conformations combined with a new process we call bound stretching to create sets of distance bounds, which contain all or most of the low-energy conformations. The bounds can be obtained using the exact distances between pairs of atoms from the different low-energy conformations. To avoid missing conformations, we can take advantage of the triangle distance inequality between sets of three points to logically expand a set of upper and lower distance bounds (bound stretching). The flexible pharmacophore can be found using a 3-D maximal common subgraph method, which uses the overlap of distance bounds to determine the overlapping structure. A scoring routine is implemented to select the substructures with the largest overlap because there will typically be many overlaps with the maximum number of overlapping bounds. A case study is presented in which 3-D flexible pharmacophores are generated and used to eliminate potential binding species identified by a 2-D pharmacophore method. A second case study creates flexible pharmacophores from a set of thrombin ligands. These are used to compare the new method with existing pharmacophore identification software.     

Transport of Neutrally Buoyant and Dense Variably Sized Colloids in a Two-Dimensional Fracture with Anisotropic Aperture

The transport of monodisperse as well as polydisperse colloid suspensions in a two-dimensional, water saturated fracture with spatially variable and anisotropic aperture is investigated with a particle tracking model. Both neutrally buoyant and dense colloid suspensions are considered. Although flow and transport in fractured subsurface formations have been studied extensively by numerous investigators, the transport of dense, polydisperse colloid suspensions in a fracture with spatially variable and anisotropic aperture has not been previously explored. Simulated snapshots and breakthrough curves of ensemble averages of several realizations of a log-normally distributed aperture field show that polydisperse colloids exhibit greater spreading than monodisperse colloids, and dense colloids show greater retardation than neutrally buoyant colloids. Moreover, it is demonstrated that aperture anisotropy oriented along the flow direction substantially increases colloid spreading; whereas, aperture anisotropy oriented transverse to the flow direction retards colloid movement.     

Diastereocontrol in the intramolecular cycloadditions of 2-substituted-erythro-3,4-isopropylidenedioxyhex-5-enenitrile oxides

The influence of the 2-substituent on the diastereoselectivity of the intramolecular cycloadditions in a series of 2-substituted-erythro-3,4-isopropylidene-dioxyhex-5-enenitrile oxides, generated in situ from selected sugar derivatives, was examined.     

Assessing the role of chemical components in cellular responses to atmospheric particle matter (PM) through chemical fractionation of PM extracts

In order to further our understanding of the influence of chemical components and ultimately specific sources of atmospheric particulate matter (PM) on pro-inflammatory and other adverse cellular responses, we promulgate and apply a suite of chemical fractionation tools to aqueous aerosol extracts of PM samples for analysis in toxicity assays. We illustrate the approach with a study that used water extracts of quasi-ultrafine PM (PM_0.25) collected in the Los Angeles Basin. Filtered PM extracts were fractionated using Chelex, a weak anion exchanger diethylaminoethyl (DEAE), a strong anion exchanger (SAX), and a hydrophobic C18 resin, as well as by desferrioxamine (DFO) complexation that binds iron. The fractionated extracts were then analyzed using high-resolution sector field inductively coupled plasma mass spectrometry (SF-ICPMS) to determine elemental composition. Cellular responses to the fractionated extracts were probed in an in vitro rat alveolar macrophages model with measurement of reactive oxygen species (ROS) production and the cytokine tumor necrosis factor-α (TNF-α). The DFO treatment that chelates iron was very effective at reducing the cellular ROS activity but had only a small impact on the TNF-α production. In contrast, the hydrophobic C18 resin treatment had a small impact on the cellular ROS activity but significantly reduced the TNF-α production. The use of statistical methods to integrate the results across all treatments led to the conclusion that sufficient iron must be present to participate in the chemistry needed for ROS activity, but the amount of ROS activity is not proportional to the iron solution concentration. ROS activity was found to be most related to cationic mono- and divalent metals (i.e., Mn and Ni) and oxyanions (i.e., Mo and V). Although the TNF-α production was not significantly affected by the chelexation of iron, it was greatly impacted by the removal of organics with the C18 resin and all other metal removal methods, suggesting that iron is not a critical pathway leading to TNF-α production, but a wide range of soluble metals and organic compounds in particulate matter play a role. Although the results are specific to the Los Angeles Basin, where the samples used in the study were collected, the method employed in the study can be widely employed to study the role of components of particulate matter in in vitro or in vivo assays.     

Development and validation of a rapid HPLC method for the determination of five banned fat-soluble colorants in spices using a narrow-bore monolithic column

This work reports a fast and simple liquid chromatographic method for the simultaneous determination of five banned fat-soluble synthetic colorants, namely Sudan I-IV and Para-Red, in spice samples. The analytes were successfully separated isocratically in less than 5 min on the new narrow bore monolithic column, FastGradient^® Chromolith (50 mm × 2.0 mm i.d.) using a mobile phase of 0.1% (v/v) HCOOH/acetonitrile (35/65%, v/v) at a flow rate of 1.5 mL min⁻¹. All colorants were detected at 506 nm. The main parameters (mobile phase composition, flow rate, injection volume) affecting the separation were studied. The proposed method was thoroughly validated in terms of linearity, LODs, precision and accuracy. The method was applied to the determination of the studied azo-dyes in various spices (paprika, chilli and mixed spice powders) after ultrasound-assisted extraction. Satisfactory recoveries, ranging from 92% to 109% were obtained.     

One-pot synthesis of functionalized spirobenzofuranones via MCR involving 3-cyanochromones

Another aspect concerning chromone chemistry leading to the one-pot synthesis of functionalized novel spirobenzofuranones has been described. The synthesis involves reaction of the zwitterionic intermediates formed by the 1:1 interaction between isocyanides and acetylenecarboxylates with 3-cyanochromones, whereupon through an unexpected and unprecedented reaction of the chromone moiety the isolated benzofuranones are formed. The regioselectivity of the reaction was investigated by DFT calculations. The geometries of the intermediates, transition structures, and intermediate products, leading to the final products, were optimized using the B3LYP functional with the 6-31G(d) basis set. The structures of the products were elucidated by 1D and 2D NMR experiments. Full assignment of all (1)H and (13)C NMR chemical shifts has been achieved. A plausible mechanistic rationale is proposed.     

Development and validation of a gas chromatography-mass spectrometric method for the determination of sildenafil and desmethyl-sildenafil in whole blood

Sildenafil (SDL) is a phosphodiesterase type 5 inhibitor and it is approved for the treatment of erectile dysfunction and pulmonary hypertension. SDL is extensively metabolized to its pharmacologically active metabolite, desmethyl‐sildenafil (DSDL). A sensitive and specific GC/MS method for the determination of SDL and DSDL in whole blood was developed and validated to support therapeutic drug monitoring of SDL patients. The combination of solid‐phase extraction with derivatization using BSTFA with 1% TMCS in acetonitrile efficiently reduced matrix effect and improved sensitivity of the method. In this assay, protriptyline was used as internal standard for both analytes. The LODs were 1.50 and 5.00 ng/mL for SDL and DSDL, respectively, whereas the respective LOQs were 5.00 and 15.0 ng/mL. The calibration curves were linear up to 500.0 ng/mL (SDL: R² 0.992, DSDL: R² 0.990). Absolute recovery values for both analytes ranged from 83.1 to 93.2%. Within‐ and between‐batch accuracy was less than 11.8 and 10.2%, respectively, whereas within‐ and between‐batch precision was less than 8.1 and 10.8%, correspondingly. The developed method is suitable for the determination of SDL and DSDL concentrations in blood samples obtained from patients under Viagra^® treatment, for pharmacokinetic studies or for the investigation of related forensic cases.