Topology and phase transitions: paradigmatic evidence

We report upon the numerical computation of the Euler characteristic chi (a topologic invariant) of the equipotential hypersurfaces Sigma(v) of the configuration space of the two-dimensional lattice varphi(4) model. The pattern chi(Sigma(v)) versus v (potential energy) reveals that a major topology change in the family Sigma(v)(vinR) is at the origin of the phase transition in the model considered. The direct evidence given here-of the relevance of topology for phase transitions-is obtained through a general method that can be applied to any other model.     

Finite planar spaces with a spread of short lines

In this paper a class of finite planar spaces with a spread of short lines is characterized.     

Chromium removal from water using LTA zeolites: effect of pH

The effect of pH changes on the ability of the synthetic zeolite NaA to remove Cr(3+) from water by ion exchange was investigated. The exchange rate was improved by working near neutrality. Despite of the occurrence of simultaneous adsorption, precipitation or cation exchange phenomena, spectroscopic analyses of samples taken at different contact times suggested the presence of an unique chromium environment in the solid phase. The increase in pH observed during the ion exchange favored polymerization-precipitation of chromium species present in solution, which, in turn, improved the metal removal capacity of zeolite NaA above the values expected for a pure cationic exchange reaction.     

Synthesis and anti‐staphylococcal activity of new halogenated pyrroles related to Pyrrolomycins F

The chemical synthesis of new halogenated pyrroles related to pyrrolomycins F is described and the anti‐staphylococcal activity compared. The replacement of 4′‐bromo atom of parent compounds with two chloro atoms at 3′ and 5′ position increase the antibacterial activity against a reference strain of S. aureus.     

Determination of the absolute configuration of a chiral oxadiazol-3-one calcium channel blocker, resolved using chiral chromatography, via concerted density functional theory calculations of its vibrational circular dichroism, electronic circular dichroism, and optical rotation

The chiral oxadiazol-3-one 2 has recently been shown to exhibit myocardial calcium entry channel blocking activity, substantially higher than that of diltiazem. To determine the enantioselectivity of this activity, the enantiomers of 2 have been resolved using chiral chromatography. The absolute configuration (AC) of 2 has been determined by comparison of density functional theory (DFT) calculations of its vibrational circular dichroism (VCD) spectrum, electronic circular dichroism (ECD) spectrum, and optical rotation (OR) to experimental VCD, ECD, and OR data. All three chiroptical properties yield identical ACs; the AC of 2 is unambiguously determined to be S(+)/R(-).     

Oxidative nucleophilic substitution of hydrogen versus ring-opening in the reaction of 4-R-2-nitrothiophenes with amines. The crucial effect of 4-alkyl groups

4-Alkyl-2-nitrothiophenes [10: R = CH3, CH(OH)CH3, CH(OCH3)CH3] react with secondary aliphatic amines, in the presence of AgNO3, to give 3-alkyl-2-amino-5-nitrothiophenes (12) through an oxidative nucleophilic substitution of hydrogen (ONSH) of synthetic interest. This behavior is in striking contrast with that of the parent 2-nitrothiophene (6), which was found to undergo ring-opening in analogous reaction conditions. A possible rationale for the crucial effect of alkyl groups is suggested, grounded also on a study of the corresponding Meisenheimer-like adducts.     

Computer-assisted protein domain boundary prediction using the DomPred server

Domain prediction from sequence is a particularly challenging task, and currently, a large variety of different methodologies are employed to tackle the task. Here we try to classify these diverse approaches into a number of broad categories. Completely automatic domain prediction from sequence alone is currently fraught with problems, but this should not be so surprising since human experts currently have significant disagreement on domain assignment even when given the structures. It can be argued that we should only test the domain prediction methods on benchmark data that human experts agree upon and this is the approach we take in this paper. Even for the data sets on which human experts agree, automatic structure-based domain assignment still cannot always agree, and so again it is still unlikely that domain prediction methods will reliably obtain correct results completely automatically. We make the argument that computer-assisted domain prediction is a more achievable goal. With this aim in mind, we present the DomPred server. This server provides the user with the results from two completely different categories of method (DPS and DomSSEA). In this paper, each method is individually benchmarked against one of the latest domain prediction benchmarks to provide information about their respective reliabilities. A variety of different benchmark scores are employed since the accuracy of a domain prediction method depends critically on what types of results one wishes to obtain (single/multi-domain classification, domain number, residue linker positions, etc.). Also both of these methods, implemented within the DomPred server, can suggest alternative domain predictions, allowing the user to make the final decision based on these results and applying their own background knowledge to the problem. The DomPred server is available from the URL:http://bioinf.cs.ucl.ac.uk/software.html.     

A deep insight into the mechanism of the acid‐catalyzed rearrangement of the Z‐phenylhydrazone of 5‐amino‐3‐benzoyl‐1,2,4‐oxadiazole in a non‐polar solvent

The conversion of the Z‐phenylhydrazone of 5‐amino‐3‐benzoyl‐1,2,4‐oxadiazole ( 1a ) into the relevant 1,2,3‐triazole ( 2a) has been quantitatively studied in toluene in the presence of several halogenoacetic acids ( HAA s, 3a – h ). Again, the occurrence of two reaction pathways has been pointed out: they require one or two moles of acid, respectively, thus repeating the situation previously observed in the presence of trichloroacetic acid. The observed rate constant ratios (k_III/k_II) are only slightly affected by the nature of the acid used. To gain a deeper insight into the action of the acids used we have measured the association constants of the HAA s ( 3a – h) with 4‐nitroaniline ( 4 ) in toluene. Also in this case, the formation of two complexes requiring one (K₂) or two (K₃) moles of acid has been evidenced, but now the K₃/K₂ ratios are significantly affected by the strength of the acid examined. The variation of the K₃/K₂ ratios larger than those concerning the k_III/k_II ratios appears useful to enlighten the very nature of the acid‐catalyzed pathways in toluene, which has been elucidated also carrying out the rearrangement in the presence of mixtures of tribromo‐ and trichloro‐acetic acids at different concentrations. Copyright © 2010 John Wiley & Sons, Ltd.     

Identification of the Schistosoma mansoni molecular target for the antimalarial drug artemether

Plasmodium falciparum and Schistosoma mansonii are the parasites responsible for most of the malaria and schistosomiasis cases in the world. Notwithstanding their many differences, the two agents have striking similarities in that they both are blood feeders and are targets of an overlapping set of drugs, including the well-known artemether molecule. Here we explore the possibility of using the known information about the mode of action of artemether in Plasmodium to identify the molecular target of the drug in Schistosoma and provide evidence that artemether binds to SmSERCA, a putative Ca2?-ATPase of Schistosoma . We also predict the putative binding mode of the molecule for both its Plasmodium and Schistosoma targets. Our analysis of the mode of binding of artemether to Ca2?-ATPases also provides an explanation for the apparent paradox that, although the molecule has no side effect in humans, it has been shown to possess antitumoral activity.     

Application of the thin-shell formulation to the numerical modeling of Stern layer in biomolecular electrostatics

In this article, the thin-shell formulation is applied to efficiently modeling the Stern layer within computational algorithms oriented toward the boundary element solution of the linearized Poisson-Boltzmann equation. The attention is focused on the calculation of the electrostatic potential in proximity to a biomolecule immersed in an electrolyte medium. Following the proposed approach, the Stern layer is made to collapse to a zero-thickness region (two-dimensional surface) with interface conditions linking the electrostatic potential over the molecular and the bulk ion accessible surfaces. Advantages lie in the limitation of divergent integral problems and in the halving of the unknown number, with a significant impact on computational time and memory requirements when modeling large biomolecules.