FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.     

Syntheses,Structures, Luminescent Properties and Photocatalytic Activities of Two Lead（II） Compounds

Two lead（ll） compounds, [Pb（qlc）（phen）2（NO3）]e-H20 （1） and [Pb（qlc）z（phen）]-3H20 （2） （Hqlc = quinoline-3-carboxylic acid, phen = 1,10-phenanthroline）, were synthesized and charac- terized by elemental analysis, single-crystal X-ray diffraction, IR and thermogravimetric analysis. Crystal 1 is of monoclinic, space group C2/c with a = 25.246（5）, b = 12.543（3）, c = 18.917（4） A, β = 105.77（3）°, V= 5765（2） A3, Z = 4, C68H46N12OllPb2, Mr = 1621.53, Dc = 1.886 g.cm-3,/.t（MoKa） = 5.912 mm-1, F（000） = 3152, GOOF = 1.080, the final R = 0.022 and wR = 0.0571 for 4822 observed reflections （1 〉 2a（/））. Crystal 2 is oftriclinic, space group Pi with a = 8.7883（10）, b = 11.7031 （13）, c = 15.9320（17） A, a = 69.9400（10）, fl = 78.9780（10）, 7 = 79.1650（10）°, V = 1497.4（3） A3, Z = 2, C32H26NaO7Pb, Mr. = 785.71, Dc = 1.729 g.cm-s, p（MoKa） = 5.688 mm-1, F（000） = 756, GOOF = 1.106, the final R = 0.0313 and wR = 0.088 for 59i5 observed reflections （1 〉 2σ（I））. Single-crystal X-ray diffraction analysis reveals that 1 exhibits a two-dimensional （2D） layer based on π-π stacking interactions between phen. Simultaneously, the adjacent 2D layers are assembled via π-π stacking interactions between phen and quinoline tings into a 3D supramolecular structure. The zero- dimensional structure of 2 is also further extended by π-π interactions to form a 2D supramolecular layer. Furthermore, these two compounds exhibit photoluminescence at room temperature in the solid state and their photocatalytic activities have been studied by degradation methylene blue.     

Application of the Combustion Method in a Closed Flask to the Lead Determination in Atmospheric Aerosols

Abstract

The destruction of the filter for metal determination in atmospheric aerosols is an important step in the analysis. Nowadays the decomposition of this kind of sample has not been completely solved, so it is interesting to study new methods for filter sample attack. In the present work the application of the combustion method in a closed flask for mixed cellulose esters filter decomposition for lead determination is proposed. For this purpose optimum operating conditions as stopper flask design, sample size, flask volume, shaking time and volume and concentration of absorbing solution are established, and accuracy and precision of the proposed method using AAS for the measurements is given. The results obtained by the closed flask combustion are compared with those found by wet attack with HNO₃. The method proposed is rapid, has low reagent contamination and no loss of lead by volatilization or by amalgamation occurs. This method shows an accuracy and a precision in good agreement with the standard method.     

The Photodecomposition of 1,l-Dichloro-2,2-bis(5′-chloro-2′-methoxyphenyl)ethylene (MPE), an Analogue of DDE

The solution-phase photodecomposition of l, l-dichloro-2,2-bis(5′-chloro-2′-methoxy-phenyl)ethylene (MPE) has been studied at an excitation wavelength of 313 nm in the presence of O₂ as well as in vacuum-degassed solutions. Only two non-volatile compounds are produced: 2,5-dichloro-3-(5′-chloro-2′-methoxyphenyl)benzofuran (BFD) and a minor product which was not identified. The BFD represents approximately 90% of the total non-volatiles. The volatile products were identified as CH₃Cl, CH₄ and HC1, with CH₃C1 being approximately 99.9 % of the total volatiles. Photolyses were carried out in C₆H₁₂ and CCI₄ solvents, the same products being observed in both solvents. Variation of MPE concentration has little or no effect on the relative quantum yield of decomposition. The photodecomposition of MPE does not follow the same pathway as the photodecomposition of DDE.     

Cloud point extraction for the determination of cadmium and lead employing sequential multi-element flame atomic absorption spectrometry

A cloud point extraction procedure for pre-concentration and determination of cadmium and lead in drinking water using sequential multi-element flame atomic absorption spectrometry is described. 4-(2-thiazolylazo)-orcinol (TAO) has been used as complexing agent and the micellar phase was obtained using the non-ionic surfactant octylphenoxypolyethoxyethanol (Triton X-114) and centrifugation. The conditions for reaction and extraction (surfactant concentration, reagent concentration, effect of incubation time, etc) were studied and the analytical characteristics of the method were determined. The method allows the determination of cadmium and lead with quantification limits of 0.30?µg?L^?1 and 2.6?µg?L^?1, respectively. A precision expressed as relative standard deviation (RSD, n?=?10) of 2.3% and 2.6% has been obtained for cadmium concentrations of 10?µg?L^?1 and 30?µg?L^?1, respectively, and RSD of 1.3% and 1.7% for lead concentrations of 10?µg?L^?1 and 30?µg?L^?1, respectively. The accuracy was confirmed by analysis of a natural water certified reference material. The method has been applied for the determination of cadmium and lead in drinking water samples collected in the cities of Ilhéus and Itabuna, Brazil. Recovery tests have also been performed for some samples, and results varied from 96 to 105% for cadmium and 97 to 106% for lead. The cadmium and lead concentrations found in these samples were always lower than the permissible maximum levels stipulated by World Health Organization and the Brazilian Government.     

Synthesis and characterisation of a silicon oxide film solid-phase extraction system for lead traces determination: an all the way green analytical method

In this work, an all the way green analytical procedure based on a silicon oxide film-solid phase extraction system is proposed for lead traces determination. From the synthesis of a solid phase extraction (SPE) system and throughout the metal preconcentration and determination only aqueous media were employed. Characterisation of the film was carried out by Scanning Electron Microscopy and Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy. Preconcentration conditions, prior to Pb(II) Electrothermal Atomic Absorption Spectrometry (ETAAS) determination, such as adsorption and desorption time, pH and temperature, were optimised. Langmuir, Freundlich and Dubinin-Radushkevich isotherm models were analysed along with the evaluation of adsorption energy and standard free energy (ΔG ⁰). The greatest adsorption was obtained with incubation at pH 7 and 37°C. By using a small volume of 0.5?mol?L^?1 HNO₃ (0.5?mL) lead was desorbed from the silicon oxide film after 2?h incubation, generating low amount of waste. The films showed better adjustment for the Langmuir model (R^{2 ?}=?0.989). The detection limit (3.29σ) for Pb(II) was 0.228?µg?L^?1. The developed procedure is 10-fold more sensitive in comparison to direct ETAAS determination. Recovery values from soft tap-water and soft well-water were above 95%. When hard water was analysed, Pb(II) adsorption was found to be interfered by Mg²⁺ and Ca²⁺. After five preconcentration cycles relative recovery was found not to decay below 90%, indicating that the silicon oxide film could be used for multiple lead determinations.     

Determination of lead (II) ion by highly selective and sensitive lead (II) membrane electrode based on 2-(((E)-2-((E)-1-(2-hydroxyphenyl) methyliden)hydrazono)metyl)phenol

A PVC (poly vinyl chloride) membrane electrode for lead ion based on 2-(((E)-2-((E)-1-(2-hydroxyphenyl)methyliden)hydrazono)metyl)phenol (HMHMP) as a membrane carrier was prepared. This electrode exhibited linear response with Nernstian slope of 29.2?±?0.2?mV per decade within the concentration range of 2.0?×?10^?7–1.0?×?10^?1?M lead ion. The limit of detection, as determined from the intersection of the extrapolated linear segments of the calibration plot, was 8.0?×?10^?8 M. The electrode exhibited high selectivity for Pb (II). The response time of the electrode was about 5–10?s for different concentrations. The electrode is suitable for use in aqueous solutions in a pH range of 5.0–7.5. It was used as an indicator electrode in a titration of Pb (II) with chromate at constant pH. This electrode was used for the determination of lead in ore samples, and the results were in agreement with those obtained with an atomic absorption spectroscopy (AAS) method. Also lead selective electrode was used for monitoring of lead in spiked samples of the Zayanderud River and waste water by the potentiometry technique.     

Solid‐State Structural Transformations and Photoreactivity of 1D‐Ladder Coordination Polymers of PbII

An attempt has been made to design double‐stranded ladder‐like coordination polymers (CPs) of hemidirected Pb^II. Four CPs, [Pb(μ‐bpe)(O₂C‐C₆H₅)₂] ? 2H₂O ( 1 ), [Pb₂(μ‐bpe)₂(μ‐O₂C‐C₆H₅)₂(O₂C‐C₆H₅)₂] ( 2 ), [Pb₂(μ‐bpe)₂(μ‐O₂C‐p‐Tol)₂(O₂C‐p‐Tol)₂] ? 1.5 H₂O ( 3 ) and [Pb₂(μ‐bpe)₂(μ‐O₂C‐m‐Tol)₂(O₂C‐m‐Tol)₂] ( 4 ) (bpe=1,2‐bis(4′‐pyridyl)ethylene), have been synthesised and investigated for their solid‐state photoreactivity. CPs 2 – 4 , having a parallel orientation of bpe molecules in their ladder structures and being bridged by carboxylates, were found to be photoreactive, whereas CP 1 is a linear one‐dimensional (1D) CP with guest water molecules aggregating to form a hydrogen‐bonded 1D structure. The linear strands of 1 were found to pair up upon eliminating lattice water molecules by heating, which led to the solid‐state structural transformation of photostable linear 1D CP 1 into photoreactive ladder CP 2 . In the construction of the double‐stranded ladder‐like structures, the parallel alignment of C?C bonds in 2 – 4 is dictated by the chelating and μ₂‐η²:η¹ bridging modes of the benzoate and toluate ligands. The role of solvents in the formation of such double‐stranded ladder‐like structures has also been investigated. A single‐crystal‐to‐single‐crystal transformation occurred when 4 was irradiated under UV light to form [Pb₂(rctt‐tpcb)(μ‐O₂C‐m‐Tol)₂(O₂C‐m‐Tol)₂] ( 5 ).     

Synthesis,Structure, and Reactivity of Lewis Base Stabilized Plumbacyclopentadienylidenes

Plumbacyclopentadienylidenes, in which the lead atoms have divalent states and are coordinated by THF, pyridine and N‐heterocyclic carbene, were synthesized and characterized. The THF‐ and pyridine‐stabilized compounds can be regarded as rare examples of hypervalent 10‐X‐4 species. The equilibrium between the THF adduct and the free plumbacyclopentadienylidene was evidenced by spectroscopic analysis and theoretical calculations. The THF adduct in benzene converted into a plumbylene dimer, where one of the lead centers is coordinated by THF and the other lead atom is coordinated by a divalent lead atom, the dimer gradually decomposing into spiroplumbole. The THF adduct unexpectedly reacted with trifluoroborane and trichlorogallane to afford fluoroborole and chlorogallole, which are the first examples of non‐annulated fluoroborole and gallole, respectively.     

Acid–Base‐Controlled Stereoselective Metalation of Overhanging Carboxylic Acid Porphyrins: Consequences for the Formation of Heterobimetallic Complexes

Overhanging carboxylic acid porphyrins have revealed promising ditopic ligands offering a new entry in the field of supramolecular coordination chemistry of porphyrinoids. Notably, the adjunction of a so‐called hanging‐atop (HAT) Pb^II cation to regular Pb^II porphyrin complexes allowed a stereoselective incorporation of the N‐core bound cation, and an allosterically controlled Newton’s cradle‐like motion of the two Pb^II ions also emerged from such bimetallic complexes. In this contribution, we have extended this work to other ligands and metal ions, aiming at understanding the parameters that control the HAT Pb^II coordination. The nature of the N‐core bound metal ion (Zn^II, Cd^II), the influence of the deprotonation state of the overhanging COOH group and the presence of a neutral ligand on the opposite side (exogenous or intramolecular), have been examined through ¹H NMR spectroscopic experiments with the help of radiocrystallographic structures and DFT calculations. Single and bis‐strap ligands have been considered. They all incorporate a COOH group hung over the N‐core on one side. For the bis‐strap ligands, either an ester or an amide group has been introduced on the other side. In the presence of a base, the mononuclear Zn^II or Cd^II complexes incorporate the carbonyl of the overhanging carboxylate as apical ligand, decreasing its availability for the binding of a HAT Pb^II. An allosteric effector (e.g., 4‐dimethylaminopyridine (DMAP), in the case of a single‐strap ligand) or an intramolecular ligand (e.g., an amide group), strong enough to compete with the carbonyl of the hung COO^?, is required to switch the N‐core bound cation to the opposite side with concomitant release of the COO^?, thereby allowing HAT Pb^II complexation. In the absence of a base, Zn^II or Cd^II binds preferentially the carbonyl of the intramolecular ester or amide groups in apical position rather than that of the COOH. This better preorganization, with the overhanging COOH fully available, is responsible for a stronger binding of the HAT Pb^II. Thus, either allosteric or acid–base control is achieved through stereoselective metalation of Zn^II or Cd^II. In the latter case, according to the deprotonation state of the COOH group, the best electron‐donating ligand is located on one or the other side of the porphyrin (COO^?>CONHR>COOR>COOH): the lower affinity of COOH for Zn^II and Cd^II, the higher for a HAT Pb^II. These insights provide new opportunities for the elaboration of innovative bimetallic molecular switches.