Performing solvation free energy calculations in LAMMPS using the decoupling approach

Journal of Computer-Aided Molecular Design - The decoupling approach to solvation free energy calculations requires scaling the interactions between the solute and the solution with all...     

Observation of the decay B+/--->pi+/-pi0, study of B+/--->K+/-pi0, and search for B0-->pi0pi0

We present results for the branching fractions and charge asymmetries in B+/--->h(+/-)pi(0) (where h(+/-)=pi(+/-),K+/-) and a search for the decay B0-->pi(0)pi(0) using a sample of approximately 88 x 10(6) BBmacr; pairs collected by the BABAR detector at the PEP-II asymmetric-energy B Factory at SLAC. We measure B(B+/--->pi(+/-)pi(0))=(5.5(+1.0)(-0.9)+/-0.6)x10(-6), where the first error is statistical and the second is systematic. The B+/--->pi(+/-)pi(0) signal has a significance of 7.7sigma including systematic uncertainties. We simultaneously measure the K+/-pi(0) branching fraction to be B(B+/--->K+/-pi(0))=(12.8(+1.2)(-1.1)+/-1.0)x10(-6). The charge asymmetries are Api(+/-)(pi(0))=-0.03(+0.18)(-0.17)+/-0.02 and AK+/-(pi(0))=-0.09+/-0.09+/-0.01. We place a 90% confidence-level upper limit on the branching fraction B(B0-->pi(0)pi(0)) of 3.6 x 10(-6).     

Dynamic Lone Pair Expression as Chemical Bonding Origin of Giant Phonon Anharmonicity in Thermoelectric InTe

Loosely bonded (“rattling”) atoms with s² lone pair electrons are usually associated with strong anharmonicity and unexpectedly low thermal conductivity, yet their detailed correlation remains largely unknown. Here we resolve this correlation in thermoelectric InTe by combining chemical bonding analysis, inelastic X-ray and neutron scattering, and first principles phonon calculations. We successfully probe soft low-lying transverse phonons dominated by large In¹⁺ z-axis motions, and their giant anharmonicity. We show that the highly anharmonic phonons arise from the dynamic lone pair expression with unstable occupied antibonding states induced by the covalency between delocalized In¹⁺ 5s² lone pair electrons and Te 5p states. This work pinpoints the microscopic origin of strong anharmonicity driven by rattling atoms with stereochemical lone pair activity, important for designing efficient materials for thermoelectric energy conversion.     

Une nouvelle voie d’acces aux indoles par condensation ylure-amide

Abstract-o-Acylaminobenzylidenephosphoranes lead to indoles in good yield by an intramolecular Wittig reaction with the amide carbonyl group. Mechanistic aspects are discussed. A general method is described for the synthesis of indoles from o-nitrobenzyl bromides and o-aminobenzyl alcohols.     

“Surface-enhanced Raman spectroscopy studies of the passive layer formation in gold leaching from thiosulfate solutions in the presence of cupric ion”

Complementary electrochemical and spectroscopic techniques were used to characterize the behavior and composition of the passive layer formed at the gold surface in a thiosulfate electrolyte in the presence of cupric ions. Raman studies of three different cationic (calcium, ammonium, and sodium) thiosulfate leaching solutions revealed that the concentrations of thiosulfate, trithionate, sulfate, and tetrathionate remained constant in the bulk solution over a 3-h time period. The initial leaching current densities of these three systems were identical; however, significant differences in the open circuit potentials of these systems were observed. To provide additional information about the nature of the passive layer, gold nanorod array electrodes were fabricated and employed as substrates for studying the species present at the gold–thiosulfate interface using surface-enhanced Raman spectroscopy (SERS). The composition and behavior of the passive layer at the gold–thiosulfate interface greatly differed from those of the bulk solutions. The passive layer consisted primarily of elemental sulfur and sulfide-like species, with thiosulfate and its oxidation products, such as tri- and tetrathionates, as minority components. The nature of the cation (calcium, sodium, or ammonium) of the thiosulfate salt showed no significant effect on the composition of the passive layer at leaching times longer than 100 min. In addition, the presence of cupric ions also had no significant effect on the formation of the passive layer. However, copper is a much better oxidant than oxygen in gold–thiosulfate leaching reactions.     

Influence of the solvent quality on the AhR mediated Procept assay measurement of dioxin and dioxin-like compounds

Polychlorodibenzo-p-dioxins, polychorodibenzofurans and “dioxin-like” polychlorinated biphenyls are widespread persistent organic pollutants sharing a similar toxicological pathway mediated by the aryl-hydrocarbon receptor (AhR). Since the confirmatory method for their measurement at trace levels in complex matrices (using isotopic dilution and gas chromatography-high resolution mass spectrometry) remains time and cost-consuming, growing efforts of the scientific community have been focused on the development of screening approaches, including AhR mediated assays. Unfortunately, AhR ligands are highly diverse and agonistic/antagonistic effects can be observed on procedural blanks and/or sample extracts. In this study, the influence of solvent grade quality on the response of a DNA-binding AhR mediated assay used for screening dioxins has been investigated. Our results demonstrated a very critical impact of this parameter with both strong agonistic and antagonistic effects observed for any tested solvent lot. A small silver nitrate silica column removed partly these interfering compounds and then can be recommended as final purification step. Some preferable grades can be identified and selected in order to guarantee the best possible performances. However, it appears necessary to test every new lot, even if a grade appeared previously compliant.     

Effect of Extraction Solvent and Temperature on Polyphenol Profiles,Antioxidant and Anti-Inflammatory Effects of Red Grape Skin By-Product

A fully-detailed LC-MS qualitative profiling of red grape skin, extracted with a mixture of ethanol and water (70:30 v:v) has permitted the identification of 65 compounds which can be classified into the following chemical classes: organic and phenolic acids (14 compounds), stilbenoids (1 compound), flavanols (21 compounds), flavonols (15 compounds) and anthocyanins (14 compounds). The extraction yield obtained with water at different temperatures (100 °C, 70 °C, room temperature) was then evaluated and the overall polyphenol content indicates that EtOH:H₂O solvent is the most efficient and selective for polyphenol extraction. However, by analyzing the recovery yield of each single polyphenol, we found that water extraction under heating conditions is effective (extraction yield similar or even better in respect to the binary solvent) for some polyphenolic classes, such as hydrophilic procyanidins, phenolic acids, flavonol glucosides and stilbenoids. However, according to their lipophilic character, a poor yield was found for the most lipophilic components, such as flavonol aglycones, and in general for anthocyanins. The radical scavenging activity was in accordance with the polyphenol content, and hence, much higher for the extract obtained with the binary solvent in respect to water extraction. All the tested extracts were found to have an anti-inflammatory activity in the R3/1 cell line with NF-kb reporter challenged with 0.01 µg/mL of IL-1α, in a 1 to 250 µg/mL concentration range. An intriguing result was that the EtOH:H₂O extract was found to be superimposable with that obtained using water at 100 °C despite the lower polyphenol content. Taken together, the results show the bioactive potentialities of grape skin extracts and the possibility to exploit this rich industrial waste. Water extraction carried out by heating is an easy, low-cost and environmentally friendly extraction method for some polyphenol classes and may have great potential for extracts with anti-inflammatory activities.     

Synthesis,Structural Characterization,and In Vitro and In Silico Antifungal Evaluation of Azo-Azomethine Pyrazoles (PhN2(PhOH)CHN(C3N2(CH3)3)PhR,R = H or NO2)

The azo-azomethine imines, R¹-N=N-R²-CH=N-R³, are a class of active pharmacological ligands that have been prominent antifungal, antibacterial, and antitumor agents. In this study, four new azo-azomethines, R¹ = Ph, R² = phenol, and R³ = pyrazol-Ph-R’ (R = H or NO₂), have been synthesized, structurally characterized using X-ray, IR, NMR and UV–Vis techniques, and their antifungal activity evaluated against certified strains of Candida albicans and Cryptococcus neoformans. The antifungal tests revealed a high to moderate inhibitory activity towards both strains, which is regulated as a function of both the presence and the location of the nitro group in the aromatic ring of the series. These biological assays were further complemented with molecular docking studies against three different molecular targets from each fungus strain. Molecular dynamics simulations and binding free energy calculations were performed on the two best molecular docking results for each fungus strain. Better affinity for active sites for nitro compounds at the “meta” and “para” positions was found, making them promising building blocks for the development of new Schiff bases with high antifungal activity.     

Molecular design based on 3D-pharmacophore. Application to 5-HT subtypes receptors

A first definition of a pharmacophore for the serotonin reuptake inhibitors was carried out by considering a three-dimensional model which correlates the chemical structures of series of reuptake inhibitors with their biological affinities. A molecular design was described by analyzing two different 3D serotonin pharmacophores. This successful approach enabled us to consider the design of new serotonin ligands by the same method.