Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

Summary The use of a recently proposed hydrophobic similarity index for the alignment of molecules and the prediction of their differences in biological activity is described. The hydrophobic similarity index exploits atomic contributions to the octanol/water transfer free energy, which are evaluated by means of the fractional partitioning scheme developed within the framework of the Miertus-Scrocco-Tomasi continuum model. Those contributions are used to define global and local measures of hydrophobic similarity. The suitability of this computational strategy is examined for two series of compounds (ACAT inhibitors and 5-HT₃ receptor agonists), which are aligned to maximize the global hydrophobic similarity using a Monte Carlo-simulated protocol. Indeed, the concept of local hydrophobic similarity is used to explore structure–activity relationships in a series of COX-2 inhibitors. Inspection of the 3D distribution of hydrophobic/hydrophilic contributions in the aligned molecules is valuable to identify regions of very similar hydrophobicity, which can define pharmacophoric recognition patterns. Moreover, low similar regions permit to identify structural elements that modulate the differences in activity between molecules. Finally, the quantitative relationships found between the pharmacological activity and the hydrophobic similarity index points out that not only the global hydrophobicity, but its 3D distribution, is important to gain insight into the activity of molecules. J.M.M. and S.P. have contributed equally to this study.     

Synthesis of di- and monobromo(ferrocenylvinyl)cyclopropanes

The Wittig olefination of ferrocene-containing chalcones leads to 1,3-dienes and their cyclodimers. The reaction of 1,3-dienes with dibromocarbene yields gem-dibromo(ferrocenylvinyl)cyclopropanes. Upon reductive dehalogenation with ethylmagnesium bromide they afford the corresponding monobromo derivatives. All the obtained compounds were characterized by ¹H and ¹³C NMR, elemental analysis, and mass spectrometry. The structures of compounds 5a,b, 6g, 6h, and 7i were confirmed by X-ray diffraction analysis.     

Adsorption of Bovine Serum Albumin onto Polystyrene Latex Particles Bearing Saccharidic Moieties

The adsorption of bovine serum albumin (BSA) onto polystyrene latexes bearing various amounts of sugar moieties has been investigated as a function of pH and ionic strength and the results were compared to those for bare polystyrene latexes having negative surface charges. The functionalized latexes were produced by seeded copolymerization of (0.3 μm) liposaccharidic monomer onto polystyrene particles obtained by soap-free emulsion polymerization of styrene using potassium persulfate as initiator. At first, the electrophoretic mobility behavior of the various latexes was examined as a function of pH: a significant decrease was observed in the case of saccharide-containing latex particles compared to the bare particles. The adsorption of BSA onto these latexes exhibited a reduced amount of adsorbed BSA for those latex particles bearing saccharide groups. This adsorbed amount depends on the yield of saccharidic monomer incorporated onto the surfaces of the latex particles.     

Synthesis and Characterization of Pyrrolthiosemicarbazone Complexes of Palladium(II). Crystal Structures of [{Pd[C4H4NC(H)=NNC(S)NHMe](Cl)}2{μ‐Ph2P(CH2)3PPh2}] and [Pd{C4H4NC(H)=NNC(S)NHMe}{Ph2P(CH2)2PPh2‐P,P}](Cl)

Reaction of the thiosemicarbazone ligands C₄H₄NC(H)=NN(H)C(S)NHR (R = Me, a ; Et, b ) with Li₂[PdCl₄] gave the dinuclear complexes [Pd{C₄H₄NC(H)=NNC(S)NHR}(μ‐Cl)]₂ (R = Me, 1a ; Et, 1b ) with a central Pd₂Cl₂ core and with deprotonation of the thiosemicarbazones at the hydrazinic nitrogen atom. Treatment of 1a and 1b with triphenylphosphine gave the mononuclear compounds [Pd{C₄H₄C(H)=NNC(S)NHR}(Cl)(PPh₃)] (R = Me, 2a ; Et, 2b ), whereas reaction of 1a and 1b with tertiary diphosphines gave mono‐ and dinuclear compounds, as appropriate, with the corresponding diphosphine acting as a monodentate ( 6b ), chelating ( 3a ) and bridging ligand ( 4a, 5a , 4b, 5b ). Treatment of 1a and 1b with (Ph₂PCH₂CH₂PPh₂)W(CO)₅ gave the new heterobimetallic complexes 7a and 7b . The crystal structures of complexes 3a and 4a are described.     

Nitrosation of Phenolic Compounds: Effects of Alkyl Substituents and Solvent

Summary.  Nitrosation reactions of phenol, o-cresol, 2,6-dimethylphenol, o-tert-butylphenol, 2-hydroxyacetophenone, and 2-allylphenol in water and water/acetonitrile were studied. Kinetic monitoring of the reactions was accomplished by spectrophotometric analysis of the nitrosated products at 345 nm. The dominant reaction was C-nitrosation via a mechanism consisting of an attack on the nitrosatable substrate by NO⁺/NO₂H₂ ⁺ followed by a slow proton transfer. The values of the rate constants of phenolic C-nitrosation were increased by electron donating substituents, and a good Hammett correlation was observed with ρ = −6.1. The results also revealed the strong effect of pH and the permitivity of the reaction medium on the rate constant, whose maximum values were observed for pH ≈ 3, decreasing strongly for higher pH values. The study in water/acetonitrile with up to 25% acetonitrile showed that it is possible to inhibit the reaction strongly by increasing the percentage of the organic component. The conclusions drawn show that (i) it is possible to predict the rate of nitrosation of phenolics as a function of the meta-substituents on the phenol ring and (ii) the nitrosation of phenolics can be strongly inhibited by increasing the pH of the reaction medium as well as by lowering its dielectric constant. Received July 13, 2001. Accepted (revised) September 18, 2001     

Comparative study of separation and determination of triazines by micellar electrokinetic capillary chromatography and nonaqueous capillary electrophoresis: application to residue analysis in natural waters

The separation and determination of a mixture of chloro- and methylthiotriazines in water samples by both micellar electrokinetic capillary chromatography (MEKC) and nonaqueous capillary zone electrophoresis (NA-CZE) were compared. The characteristics of both methods proved to be very similar in terms of separation efficiency and analysis times, but application of these methods for the analysis of triazines in natural waters, with a prior preconcentration step, revealed significant differences. A preconcentration step by solid-phase extraction (SPE) with Oasis HLB cartridges was accomplished for the determination of triazines at sub-ppb levels in drinking and river waters; when NA-CZE was used after this SPE step, electropherograms with fewer interferences and more stable baselines were obtained than when separation was carried out using MEKC. Another aspect related to the application to real samples was the lack of precision encountered upon evaluating the electrophoretic signals generated when using SPE coupled with NA-CZE. Here, we demonstrate the importance of choosing an appropriate internal standard for analyte quantification. It is recommended that a triazine belonging to the same family as that of the triazine to be determined should be used as internal standard.     

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.     

Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions

Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.     

Salt Stress Proteins Identified by a Functional Approach in Yeast

We have performed functional genomics of salt stress by overexpression of gene libraries in yeast and selection for salt tolerance. Thirty halotolerance genes were isolated from yeast, Arabidopsis, and sugar beet. The results indicate that Na⁺ transport (uptake, efflux, and compartmentation), sulfate activation, RNA processing, and protein synthesis are crucial for salt tolerance.