Synthesis, structure, and complexation of a large 28-mer macrocycle containing two binding sites for either anions or metal ions

The "one-pot" synthesis and characterization of a large 28-mer macrocycle (H(4)L(2)) with oxamido units capable of complexing guest ions through oxygen or nitrogen donor atoms is reported. Single-crystal structure determination of H(8)L(2)(NO(3))(4) and (Cu(2)[H(2)L(2)](H(2)O)(2))(NO(3))(2) demonstrated that the macrocycle contains two sites capable of complexing two nitrate anions or two copper(II) ions, involving a large structural reorganization in the conformation of the macrocyclic framework on coordination of the copper(II) ions when compared to the nitrate. Electrochemical and magnetic susceptibility measurements on the dinuclear Cu(II) complex and the related mononuclear and trinuclear Cu(II) complexes derived from the related 14-mer macrocycle were carried out and illustrate the role of the oxamido groups in mediating metal-metal interaction and delocalization.     

Monte Carlo versus molecular dynamics simulations in heterogeneous systems: an application to the n-pentane liquid-vapor interface

The Monte Carlo (MC) and molecular dynamics (MD) methodologies are now well established for computing equilibrium properties in homogeneous fluids. This is not yet the case for the direct simulation of two-phase systems, which exhibit nonuniformity of the density distribution across the interface. We have performed direct MC and MD simulations of the liquid-gas interface of n-pentane using a standard force-field model. We obtained density and pressure components profiles along the direction normal to the interface that can be very different, depending on the truncation and long range correction strategies. We discuss the influence on predicted properties of different potential truncation schemes implemented in both MC and MD simulations. We show that the MD and MC profiles can be made in agreement by using a Lennard-Jones potential truncated via a polynomial function that makes the first and second derivatives of the potential continuous at the cutoff distance. In this case however, the predicted thermodynamic properties (phase envelope, surface tension) deviate from experiments, because of the changes made in the potential. A further readjustment of the potential parameters is needed if one wants to use this method. We conclude that a straightforward use of bulk phase force fields in MD simulations may lead to some physical inconsistencies when computing interfacial properties.     

Open-tubular capillary electrochromatography/electrospray ionization-mass spectrometry using polymeric surfactant as a stationary phase coating

We describe the use of the polymeric surfactant poly(sodium undecylenic sulfate) (poly-SUS) as a stationary phase coating in open-tubular capillary electrochromatography (OT-CEC) coupled with electrospray ionization-mass spectrometry (ESI-MS) for the analysis of beta-blocker and benzodiazepine analytes. The production of a polymeric surfactant coating on the capillary inner wall involves (i) adsorption of the cationic polymer poly(diallyldimethylammonium chloride) (PDADMAC) to the inner surface of capillary, and (ii) adsorption of the negatively charged poly-SUS onto the cationic polymer layer via strong physical interaction of the two polymer layers. As compared with micellar electrokinetic chromatography (MEKC) coupled with ESI-MS, the main advantage of this proposed method is minimization of introduction of the monomeric or polymeric surfactant into the mass spectrometer, thus avoiding the interference of the nonvolatile micelle in ESI-MS. The effects of buffer pH and applied voltage on the separation of the analytes are also discussed. Under optimum conditions, four of the five beta-blockers and four benzodiazepines are separated.     

Covalent attachment of a nickel nitrilotriacetic acid group to a germanium attenuated total reflectance element

The surface of a germanium internal reflectance element (IRE) was modified to bind 6X-histidine (his)-tagged biomolecules. The step-by-step surface modification was monitored via single-pass attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR). Initially an adlayer of 7-octenyltrimethoxysilane (7-OTMS) was formed on the Ge crystal through the surface hydroxyl groups, which were produced via ozonolysis of the Ge surface. The vinyl moiety of 7-OTMS was oxidized to a carboxylic acid, which was activated by 1,1'-carbonydiimidazole (CDI) to produce a labile imidazole. The labile imidazole that resulted from the CDI coupling was then displaced by the primary amine of nitrilotriacetic acid (NTA). Nickel sulfate was added to the system, and it coordinated with the three carbonyl groups and the nitrogen on NTA, thus leaving the ability of Ni to coordinate with two adjacent histidine residues. Binding of his-tagged biotin to nickel nitrilotriacetic acid (Ni-NTA) was observed by ATR-FT-IR spectroscopy. The surface modification method presented in this paper had minimal nonspecific binding, the Ni-NTA surface was reusable if stored properly, and complete removal of the organic surface was achievable.     

The use of comet assay data with a simple reaction mechanism to evaluate the relative effectiveness of free radical scavenging by quercetin, epigallocatechin gallate and N-acetylcysteine in UV-irradiated MRC5 lung fibroblasts

Comet assay data (tail DNA %) have been gathered for the concentration dependent role of three antioxidants (AOs); quercetin (Q), epigallocatechin gallate (EGCG) and N-acetylcysteine (NAC) in reducing UV-induced damage to DNA in normal fetal lung fibroblasts (MRC5). All three compounds demonstrate a concentration dependent reduction maximum with a pro-oxidant effect at higher (though not cytotoxic) concentrations. Manipulation of a simple 4-step reaction mechanism for free radical (FR) scavenging by AOs produced rate constant ratios which allowed the relative effectiveness (Q > EGCG > NAC) of the AOs to be evaluated.     

Hydrothermal synthesis and magnetic properties of novel Mn(II) and Zn(II) materials with thiolato-carboxylate donor ligand frameworks

The hydrothermal reaction of thiosalicylic acid, (C(6)H(4)(CO(2)H)(SH)-1,2) with manganese(III) acetate leads to formation of the coordination solid [Mn(5)((C(6)H(4)(CO(2))(S)-1,2)(2))(4)(mu3-OH)2] (1) via a redox reaction, where resulting manganese(II) centres are coordinated by oxygen donor atoms and S-S disulfide bridge formation is simultaneously observed. Reaction of the same ligand under similar conditions with zinc(II) chloride yields the layered coordination solid [Zn(C(6)H(4)(CO(2))(S)-1,2)] (2). Hydrothermal treatment of manganese(III) acetate with 2-mercaptonicotinic acid, (NC(5)H(3)(SH)(CO(2)H)-2,3) was found to produce the 1-dimensional chain structure [Mn(2)((NC(5)H(3)(S)(CO(2))-2,3)(2))(2)(OH(2))(4)].4H(2)O (3) which also exhibits disulfide bridge formation and oxygen-only metal interactions. Compound 3 has been studied by thermogravimetric analysis and indicates sequential loss of lattice and coordinated water, prior to more comprehensive ligand fragmentation at elevated temperatures. The magnetic behaviour of 1 and 3 has been investigated and both exhibit antiferromagnetic interactions. The magnetic behaviour of 1 has been modelled as two corner-sharing isosceles triangles whilst 3 has been modelled as a 1-dimensional chain.     

Photoinduced Ru-Yb energy transfer and sensitised near-IR luminescence in a coordination polymer containing co-crystallised [Ru(bipy)(CN)4]2- and Yb(III) units

Co-crystallisation of the anionic cyanometallate chromophore [Ru(bipy)(CN)4]2- with Yb(III) provides coordination polymers or oligomers containing Ru-CN-Yb bridges; in [K(H2O)4][Yb(H2O)6][Ru(bipy)(CN)4]2.5H2O Ru-->Yb energy-transfer (k > 5 x 10(6) s(-1)) results in partial quenching of the Ru-based luminescence and sensitised near-IR luminescence from the Yb(III) unit.     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

4-(9-fluorenylmethyloxycarbonyl)phenylhydrazine (FmPH): a new chromophoric reagent for quantitative monitoring of solid-phase aldehydes(1-3)

A direct method for quantifying solid-phase aldehydes has been developed, using a new reagent, 4-(9-fluorenylmethyloxycarbonyl)phenylhydrazine (FmPH). The FmPH reagent was synthesized in three steps (24% overall yield) from commercially available p-hydrazinobenzoic acid. Resin-bound aldehydes reacted quantitatively with FmPH, in the presence of trimethylorthoformate (TMOF) as a dehydrating agent, to form a highly conjugated, immobilized FmPH-hydrazone. Next, mild treatment of the hydrazone with an excess of piperidine-N,N-dimethylformamide (1:1) released the piperidine-dibenzofulvene adduct chromophore (epsilon(301nm) = 7800 M(-1) cm(-1)) from the support. FmPH quantitation of aldehydes proved to be a straightforward, sensitive, and reproducible technique for monitoring resin-bound aldehydes [albeit insufficiently reactive to allow reliable quantification of ketones]. The FmPH aldehyde assay is applicable to a range of solid supports, as demonstrated specifically for poly(ethylene glycol)-polystyrene (PEG-PS), aminomethylpolystyrene (AMP), and cross-linked ethoxylate acrylate resin (CLEAR).     

Adducts of Rh2[MTPA]4 with some phosphine chalcogenides: nature of binding and ligand exchange

Adducts of four phosphine chalcogenides with the chiral dirhodium complex ([Rh-Rh]) were investigated by variable-temperature 1H and 31P NMR spectroscopy in order to compare their properties as axial ligands. Whereas the selenide (1) and the sulfide (2) are strong ligands with electrostatic attraction and, in addition, a significant orbital (HOMO-LUMO) interaction, the phosphine oxide compounds (P=O) bind primarily via electrostatic attraction and are relatively weak donors. Moreover, the overall bond strength in these adducts depends on steric congestion around the P=O group.