Molecular dynamics simulations of a nucleoside analogue of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid synthesized as a potential antiviral agent: Conformational studies in vacuum and in water

Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K.     

Construction of 4D-QSAR Models for Use in the Design of Novel p38-MAPK Inhibitors

The p38-mitogen-activated protein kinase (p38-MAPK) plays a key role in lipopolysaccharide-induced tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) release during the inflammatory process, emerging as an attractive target for new anti-inflammatory agents. Four-dimensional quantitative structure-activity relationship (4D-QSAR) analysis [Hopfinger et al., J. Am. Chem. Soc., 119 (1997) 10509] was applied to a series of 33 (a training set of 28 and a test set of 5) pyridinyl-imidazole and pyrimidinyl-imidazole inhibitors of p38-MAPK, with IC50 ranging from 0.11 to 2100 nM [Liverton et al., J. Med. Chem., 42 (1999) 2180]. Five thousand conformations of each analogue were sampled from a molecular dynamics simulation (MDS) during 50 ps at a constant temperature of 303 K. Each conformation was placed in a 2 angstroms grid cell lattice for each of three trial alignments. 4D-QSAR models were constructed by genetic algorithm (GA) optimization and partial least squares (PLS) fitting, and evaluated by leave-one-out cross-validation technique. In the best models, with three to six terms, the adjusted cross-validated squared correlation coefficients, Q2adj, ranged from 0.67 to 0.85. Model D (Q2adj = 0.84) was identified as the most robust model from alignment 1, and it is representative of the other best models. This model encompasses new molecular regions as containing pharmacophore sites, such as the amino-benzyl moiety of pyrimidine analogs and the N1-substituent in the imidazole ring. These regions of the ligands should be further explored to identify better anti-inflammatory inhibitors of p38-MAPK.     

Study of benznidazole–cyclodextrin inclusion complexes, cytotoxicity and trypanocidal activity

The current chemotherapy for Chagas disease is still based on benznidazole, which has low solubility, but complexation with cyclodextrins provides a way of increasing the solubility. The objective of this work was to characterize the inclusion complexes formed between benznidazole (BNZ) and randomly 2-methyled-β-cyclodextrin (RM-β-CD) in aqueous solution and study cytotoxicity and trypanocidal. BNZ:RM-β-CD solution complex systems were prepared and characterized using the phase solubility diagram, nuclear magnetic resonance and a photostability assays, also to investigate the in vitro trypanocidal activity with epimastigote forms of Trypanossoma cruzi and the study of cytotoxicity against mammal cells. The phase-solubility diagram displayed an A _L-type feature, providing evidence of the formation of soluble inclusion complexes. The continuous variation method showed the existence of a complex with 1:1 stoichiometry. Toxicity assays demonstrated that inclusion complexes were able to reduce the toxic effects caused by benznidazole alone and that this did not interfere with the trypanocidal activity of the benznidazole. The use of inclusion complexes benznidazole:cyclodextrin is thus a promising alternative for the development of a safe and stable liquid formulation and a new option for the treatment of Chagas disease.     

Growth of carbon nanotubes with alkaline earth carbonate as support

Multiwalled carbon nanotubes (MWCNTs) were grown by chemical vapor deposition by applying C(2)H(2) fluxed over Fe(1)(-x)Co(x) catalyst supported by alkaline earth carbonate. Detailed investigations of the chemical process occurring prior and during the growth allowed us a significant improvement of the nanotube production rate and quality. We observed a strong influence of the catalyst stoichiometry on the carbon deposition rate and the nanotube characteristics. We also found evidence for the active role of the support in the growth process, which is explained by the decomposition of the carbonate at the growth temperature. Using the optimized parameters obtained from our study performed in a fixed bed furnace, we could improve the production rate to about 500 g/day of purified MWCNTs in our large-scale rotary tube furnace.     

The clemmensen reduction of α,β-unsaturated ketones

The deoxygenation of the α,β-unsaturated ketones (1) and (5) under the Clemmensen condition yielded the olefins (2) and (6) along with their respective dimers (3+4) and (8+9). The α , β-unsaturated ketone (13) under similar treatment yielded the olefin (14) in satisfactory yield but the dimer could not be characterized. The deoxygenation of the α,β-unsaturated ketones (10) and (16) under similar con- ditions afforded the olefins (12) and (15) respectively in satisfactory yield along with the rearranged olefins (11) and (17) respectively. Epox-idation of the olefin (17) followed by heating with p-toluenesulfonic acid yielded the ketone (18).     

Alkylammonium-based protic ionic liquids. II. Ionic transport and heat-transfer properties: fragility and ionicity rule

The physicochemical characterization of six alkylammonium-based protic ionic liquids (PILs) is presented. These compounds were prepared through a simple and atom-economic neutralization reaction between a tertiary amine and a Br?nsted acid, HX, where X- is HCOO-, CH3COO-, HF2-. The temperature dependency and the effect of added water on properties such as density, viscosity, ionic conductivity, and the thermal comportment of these PILs were measured and investigated. The results allowed us to classify them according to a classical Walden diagram and to appreciate their great "fragility". PILs have applicable perspectives in replacements of conventional inorganic acids for fuel cell devices and thermal transfer fluids.     

A Fast‐Initiating Ionically Tagged Ruthenium Complex: A Robust Supported Pre‐catalyst for Batch‐Process and Continuous‐Flow Olefin Metathesis

In this study, a new pyridinium‐tagged Ru complex was designed and anchored onto sulfonated silica, thereby forming a robust and highly active supported olefin‐metathesis pre‐catalyst for applications under batch and continuous‐flow conditions. The involvement of an oxazine–benzylidene ligand allowed the reactivity of the formed Ru pre‐catalyst to be efficiently controlled through both steric and electronic activation. The oxazine scaffold facilitated the introduction of the pyridinium tag, thereby affording the corresponding cationic pre‐catalyst in good yield. Excellent activities in ring‐closing (RCM), cross (CM), and enyne metathesis were observed with only 0.5 mol % loading of the pre‐catalyst. When this powerful pre‐catalyst was immobilized onto a silica‐based cationic‐exchange resin, a versatile catalytically active material for batch reactions was generated that also served as fixed‐bed material for flow reactors. This system could be reused at 1 mol % loading to afford metathesis products in high purity with very low ruthenium contamination under batch conditions (below 5 ppm). Scavenging procedures for both batch and flow processes were conducted, which led to a lowering of the ruthenium content to as little as one tenth of the original values.     

Photoaddition of benzophenone to azaindole,synthesis of the oxetane of 7-azaindole

7-Azaindole did not react with benzophenone on irradiation. However, irradiation of benzophenone in the presence of 1-acetyl-7-azaindole produced an oxetane by cycloaddition of the ketone to the 7-azaindole 2,3-double bond. The nmr and the mass spectra of the oxetane have also been studied in some detail.     

Growth of single-crystalline KNbO3 nanostructures

This communication reports on the growth of highly uniform KNbO3 nanowires exhibiting a narrow diameter distribution around 60 nm and a length-to-width ratio up to 100. The nanowires were prepared by a hydrothermal route, which enables simple, gram-scale production. A systematic study of the synthesized nanowires in terms of the morphological and chemical characteristics was carried out by varying the temperature-pressure conditions and the composition of the starting mixture. The results indicate that highly uniform single-crystalline nanowires form within a narrow window of the ternary phase diagram of KOH-Nb2O5-H2O.