Restricted diffusion in silica particles measured by pulsed field gradient NMR

The restricted diffusion coefficient of water through porous silica is measured by pulsed field gradient (PFG) NMR as a function of loading in order to develop a model for self-diffusion at full pore filling in sol-gel-made porous silica particles. This model describes the pore or intraparticle diffusion coefficient as a function of particle porosity, tortuosity, and the steric hindrance applied on the molecules by the pore space. The particle morphology is characterized by nitrogen adsorption and an appropriate tortuosity model is chosen in comparison with literature data. To characterize the material, NMR relaxation and diffusion studies at different degrees of pore filling were carried out in relation to the silica/water adsorption isotherm.     

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin

The binding of a set of 10 triphenoxypyridine derivatives to two serine proteases, factor Xa and trypsin, has been used to analyze factors related to sampling and convergence in free energy calculations based on molecular dynamics simulation techniques. The inhibitors investigated were initially proposed as part of the Critical Assessment of Techniques for Free Energy Evaluation (CATFEE) project for which no experimental results nor any assessment of the predictions submitted by various groups have ever been published. The inhibitors studied represent a severe challenge for explicit free energy calculations. The mutations from one compound to another involve up to 19 atoms, the creation and annihilation of net charge and several alternate binding modes. Nevertheless, we demonstrate that it is possible to obtain highly converged results (+/- 5-10 kJ/mol) even for such complex multi-atom mutations by simulating on a nanosecond time scale. This is achieved by using soft-core potentials to facilitate the creation and deletion of atoms and by a careful choice of mutation pathway. The results show that given modest computational resources, explicit free energy calculations can be successfully applied to realistic problems in drug design.     

A facile and general route to 4-substituted-2 butenolides

Grignard reagents react with 7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboxylic anhydride and produce in high yields the corresponding substituted bicyclo-γ-butanolides. These lactones produce the title compounds by retro Diels-Alder reaction during distillation.     

Effect of Co-Existing Cations and Anions on the Adsorption of Antibiotics on Iron-Containing Minerals

The adsorption of antibiotics on minerals is an important process in their environment behavior. The adsorption behavior of antibiotics on iron-containing minerals and the effect of co-existing cations and anions were studied in this work. Magnetite, hematite, goethite and kaolin were selected as the representative minerals and characterized by SEM, XRD and BET. A total of eight antibiotics, including three quinolones, three sulfonamides and two mycins were chosen as the research targets. Results showed a higher adsorption amount of quinolones than that of sulfonamides and mycins on the surface of iron-containing minerals in most mineral systems. The adsorption isotherms of quinolones can be well fitted using the Freundlich models. The effects of five cations and five anions on the adsorption of quinolones were investigated, among which Mg²⁺, Ca²⁺, HCO₃⁻ and H₂PO₄⁻ mainly showed significant inhibition on the adsorption, while the effects of K⁺, Na⁺, NH₄⁺, Cl⁻, NO₃⁻ and SO₄²⁻ showed less. Natural surface water samples were also collected and used as media to investigate the adsorption behavior of quinolones on iron-containing minerals. The buffering capacity of the natural water kept the reaction solution at circumneutral conditions, and the adsorption amount was mostly promoted in the goethite system (from 0.56~0.78 μmol/g to 0.52~1.43 μmol/g), but was inhibited in the other systems (magnetite: from 1.13~1.33 μmol/g to 0.45~0.76 μmol/g; hematite: from 0.52~0.65 μmol/g to 0.02~0.18 μmol/g; kaolin: from 1.98~1.99 μmol/g to 0.90~1.40 μmol/g). The results in this work help to further understand the transportation and fate of antibiotics in an aqueous environment.     

Insights into Antimalarial Activity of N-Phenyl-Substituted Cinnamanilides

Due to the urgent need of innovation in the antimalarial therapeutic arsenal, a series of thirty-seven ring-substituted N-arylcinnamanilides prepared by microwave-assisted synthesis were subjected to primary screening against the chloroquine-sensitive strain of P. falciparum 3D7/MRA-102. The lipophilicity of all compounds was experimentally determined as the logarithm of the capacity factor k, and these data were subsequently used in the discussion of structure-activity relationships. Among the screened compounds, fourteen derivatives exhibited IC₅₀ from 0.58 to 31 µM, whereas (2E)-N-(4-bromo-2-chlorophenyl)-3-phenylprop-2-enamide (24) was the most effective agent (IC₅₀ = 0.58 µM). In addition, (2E)-N-[2,6-dibromo-4-(trifluoromethyl)- phenyl]-3-phenylprop-2-enamide (36), (2E)-N-[4-nitro-3-(trifluoromethyl)phenyl]-3-phenylprop- 2-enamide (18), (2E)-N-(2-bromo-5-fluorophenyl)-3-phenylprop-2-enamide (23), and (2E)-3-phenyl-N-(3,4,5-trichlorophenyl)prop-2-enamide (33) demonstrated efficacy in the IC₅₀ range from 2.0 to 4.3 µM, comparable to the clinically used standard chloroquine. The results of a cell viability screening performed using THP1-Blue™ NF-κB cells showed that none of these highly active compounds displayed any significant cytotoxic effect up to 20 μM, which makes them promising Plasmodium selective substances for further investigations.     

Three's a crowd – stabilisation,structure, and applications of DNA triplexes

DNA is a strikingly flexible molecule and can form a variety of secondary structures, including the triple helix, which is the subject of this review. The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex forming oligonucleotide (TFO) to a DNA duplex. As the TFO will bind to the duplex with sequence specificity, there is significant interest in developing TFOs with potential therapeutic applications, including using TFOs as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies, which may increase triplex stability or in vivo degradation, is essential – these areas will be discussed in this review. Ruthenium polypyridyl complexes, which are able to photooxidise DNA and act as luminescent DNA probes, may serve as a suitable photophysical payload for a TFO system and the developments in this area in the context of DNA triplexes will also be reviewed.

Triplex-forming oligonucleotides can target specific DNA sequences by binding in the duplex major groove. Chemical modifications and ligand binding have been explored, for use in a variety of biological applications.     

Hexafluoroisobutylation of enolates through a tandem elimination/allylic shift/hydrofluorination reaction

The isobutyl side chain is a highly prevalent hydrophobic group in drugs, and it notably constitutes the side chain of leucine. Its replacement by a hexafluorinated version containing two CF₃ groups may endow the target compound with new and advantageous properties, yet this modification remains overlooked due to the absence of a general and practical synthetic methodology. Herein, we report the first general method to introduce the hexafluoroisobutyl group into ketoesters, malonates, 1,3-diketones, Schiff base esters and malononitrile. We demonstrated that the reaction occurs through an elimination/allylic shift/hydrofluorination cascade process which efficiently overcomes the usual fluoride β-elimination observed with α-CF₃-vinyl groups. We showed that with alkali metal bases, a pentafluorinated alkene is obtained predominantly, whereas the use of tetrabutylammonium fluoride (TBAF) allows hydrofluorination to occur. This tandem process represents a conceptually new pathway to synthesize bis-trifluoromethylated compounds. This methodology was applied to the multigram-scale synthesis of enantiopure (S)-5,5,5,5′,5′,5′-hexafluoroleucine.

Hexafluoroisobutylation of ketoesters, malonates, diketones, Schiff base esters and malononitrile is reported. The reaction involves an elimination/allylic shift/hydrofluorination cascade process that efficiently overcomes the usual S_N2′ mechanism.     

Anodic TiO2 Nanotube Layers for Wastewater and Air Treatments: Assessment of Performance Using Sulfamethoxazole Degradation and N2O Reduction

The preparation of anodic TiO₂ nanotube layers has been performed using electrochemical anodization of Ti foil for 4 h at different voltages (from 0 V to 80 V). In addition, a TiO₂ thin layer has been also prepared using the sol–gel method. All the photocatalysts have been characterized by XRD, SEM, and DRS to investigate the crystalline phase composition, the surface morphology, and the optical properties, respectively. The performance of the photocatalyst has been assessed in versatile photocatalytic reactions including the reduction of N₂O gas and the oxidation of aqueous sulfamethoxazole. Due to their high specific surface area and excellent charge carriers transport, anodic TiO₂ nanotube layers have exhibited the highest N₂O conversion rate (up to 10% after 22 h) and the highest degradation extent of sulfamethoxazole (about 65% after 4 h) under UVA light. The degradation mechanism of sulfamethoxazole has been investigated by analyzing its transformation products by LC-MS and the predominant role of hydroxyl radicals has been confirmed. Finally, the efficiency of the anodic TiO₂ nanotube layer has been tested in real wastewater reaching up to 45% of sulfamethoxazole degradation after 4 h.