Ligand-protein docking with water molecules

The presence of water molecules plays an important role in the accuracy of ligand-protein docking predictions. Comprehensive docking simulations have been performed on a large set of ligand-protein complexes whose crystal structures contain water molecules in their binding sites. Only those water molecules found in the immediate vicinity of both the ligand and the protein were considered. We have investigated whether prior optimization of the orientation of water molecules in either the presence or absence of the bound ligand has any effect on the accuracy of docking predictions. We have observed a statistically significant overall increase in accuracy when water molecules are included during docking simulations and have found this to be independent of the method of optimization of the orientation of water molecules. These results confirm the importance of including water molecules whenever possible in a ligand-protein docking simulation. Our findings also reveal that prior optimization of the orientation of water molecules, in the absence of any bound ligand, does not have a detrimental effect on the improved accuracy of ligand-protein docking. This is important, given the use of docking simulations to predict the binding modes of new ligands or drug molecules.     

Determination of arsenic in diesel, gasoline and naphtha by graphite furnace atomic absorption spectrometry using microemulsion medium for sample stabilization

A procedure for the determination of As in diesel, gasoline and naphtha at μg L⁻¹ levels by GFAAS is proposed. Sample stabilization was achieved by the formation of three component solutions prepared by mixing appropriate volumes of the samples propan-1-ol and nitric acid aqueous solution. This mixture resulted in a one-phase medium, which was indefinitely stable. No changes in the analyte signals were observed over several days in spiked samples, proving long-term stabilization ability. The use of conventional (Pd) and permanent (Ir) modification was investigated and the former was preferred. Central composite design multivariate optimization defined the optimum microemulsion composition as well as the temperature program. In this way, calibration using aqueous analytical solutions was possible, since the same sensitivity was observed in the investigated microemulsion media and in 0.2% v/v HNO₃. Coefficients of correlation larger than 0.999 and an As characteristic mass of 22 pg were observed. Recoveries (n=4) obtained from spiked samples were 98±4, 99±3 and 103±5%, and the limits of detection in the original samples were 1.8, 1.2 and 1.5 μg L⁻¹ for diesel, gasoline and naphtha, respectively. Validation was performed by the analysis of a set of commercial samples by independent comparative procedures. No significant difference (Student’s t-test, p<0.05) was observed between comparative and proposed procedure results. The total determination cycle lasted 4 min for diesel and 3 min for gasoline and naphtha, equivalent to a sample throughput of 7 h⁻¹ for diesel and 10 h⁻¹ for gasoline and naphtha.     

Speciation of very low amounts of arsenic and antimony in waters using dispersive liquid–liquid microextraction and electrothermal atomic absorption spectrometry

A new procedure for the determination of inorganic arsenic (III,V) and antimony (III,V) in water samples by dispersive liquid–liquid micro extraction separation and electrothermal atomic absorption spectrometry (ETAAS) is presented. At pH 1, As(III) and Sb(III) are complexed with ammonium pyrrolidine dithiocarbamate and extracted into the fine droplets formed when mixing carbon tetrachloride (extraction solvent), methanol (disperser solvent) and the sample solution. After extraction, the phases are separated by centrifugation, and As(III) and Sb(III) are determined in the organic phase. As(V) and Sb(V) remain in the aqueous layer. Total inorganic As and Sb are determined after the reduction of the pentavalent forms with sodium thiosulphate. As(V) and Sb(V) are calculated by difference. The detection limits are 0.01 and 0.05 µg L^− 1 for As(III) and Sb(III), respectively, with an enrichment factor of 115. The relative standard deviation is in the 2.9–4.5% range. The procedure has been applied to the speciation of inorganic As and Sb in bottled, tap and sea water samples with satisfactory results.     

Density functional study on electronic structures and reactivity in methyl‐substituted chelates used in organic light‐emitting diodes

The electronic structure and reactivity trends of a set of tris‐(n‐methyl‐8‐quinolinolato) metal (III) (n = 0, 3, 4, 5; metal = Al⁺³, Ga⁺³) used as electron‐transport layer in organic light‐emitting diodes were studied and compared. All geometries were optimized at B3LYP/6‐31G(d,p) level of theory. The geometries of the ground state (S₀) of unsubstituted molecules AlQ3 and GaQ3 were found to be slightly affected by the methyl group, which is in agreement with previous works. Methyl‐derivatives conserve largely the electronic structures of AlQ3 and GaQ3. The energies of the frontier orbitals highest occupied and lowest unoccupied molecular orbital are raised by the electron‐releasing effect of methyl group. Molecular orbital contribution analysis reveals that the orbital population is essentially the same for both MQ3 and their derivatives. Analyses of the ionization potential and electron affinity showed that MQ3 tend to be better hole‐blockers than methylated analogues and 5Me‐MQ3 have higher hole‐injection capability than the other methyl‐substituted derivatives. The global reactivity analysis showed that the electrophilicity index can be an indicator of electron‐injection capability in these complexes. Local reactivity analysis showed that atomic sites that are prone to nucleophilic/electrophilic attack are atoms C‐4 in L3/C‐5 in L1. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Enantio- and diastereoselective synthesis of (E)-1,5-syn-diols: application to the synthesis of the C(23)-C(40) fragment of tetrafibricin

A highly stereoselective synthesis of (E)-1,5-syn-diols 6 is described. The kinetically controlled hydroboration of allenyltrifluoroborate 8 with Soderquist borane 2 provides the (Z)-allylic trifluoroborate 9, which undergoes sequential allylboration with two different aldehydes to provide (E)-1,5-syn-diols 6 in 72-98% yields with >95% ee and >20:1 dr. Application of this method to the synthesis of the tetrafibricin C(23)-C(40) fragment 19 is described.     

Solid-state ion exchange of ammonium heptamolybdate tetrahydrate into ZSM-5 zeolite

Journal of Thermal Analysis and Calorimetry - Thermal decomposition (2&nbsp;K&nbsp;min?1) of ammonium heptamolybdate tetrahydrate, performed between room temperature and...     

Assessment of amination reactions via nucleophilic aromatic substitution using conventional and eco-friendly energies

The efficiency of conventional heating energy source compared with Infrared (IR), Ultrasound (US), Microwave and the simultaneous combination US–IR eco-friendly approaches for preparation of new N-(5-R¹ _-amino-2-nitrophenyl)acetamides and 5-R¹-amino-2-nitroaniline by Nucleophilic Aromatic Substitution (S_NAr) via addition–elimination reactions on the halogens F, Cl, Br, I, employing amines as nucleophiles were explored. Moreover, phenyldiazenyl derivatives in good yields by an oxidative one-pot S_NAr-based amination reaction from an unusual oxidation of 2-phenylhydrazinyl derivatives in DMSO was prepared.     

Flow injection determination of cobalt after its sorption onto polyurethane foam loaded with 2-(2-thiazolylazo)-p-cresol (TAC)

An electrochemically stable monolayer of tris(2,2'-bipyridyl)ruthenium(II) was obtained for the first time. It was based on the electrostatic attachment of Ru(bpy)(3)(2+) to the benzene sulfonic acid monolayer film, which was covalently bound onto glassy carbon electrode by the electrochemical reduction of diazobenzene sulfonic acid. The surface-confined Ru(bpy)(3)(2+) underwent reversible surface process, and reacted with the coreactant, tripropylamine, to produce electrochemiluminescence. In view of the stability of the electrode, the results strongly suggested that light was emitted from the surface-confined Ru(bpy)(3)(2+), not from the detached Ru(bpy)(3)(2+). The Ru(bpy)(3)(2+) modified electrode was used to the determination of tripropylamine. It showed good linearity in the concentration range from 5 muM to 1 mM with a detection limit of 1 muM (S/N=4). The good stability of the Ru(bpy)(3)(2+) modified electrode also showed that the benzene sulfonic acid monolayer film prepared can be served as an excellent support to construct multilayers.     

Synthesis of methyl‐2,4‐bis(cyclohexane)dispiro‐1,2,3,4,4a,5,6,7‐octahydro‐(lH,3H)quinazoline‐8‐carbodithioate derived from cyclohexanone in one step

The new compound Methyl‐2,4‐bis(cyclohexane)dispiro‐1,2,3,4,4a,5,6,7‐octahydro‐(1H,3H)‐quinazo‐line‐8‐carbodithioate has been synthesized from cyclohexanone and carbon disulfide. It has been characterized by uv‐visible, FTTR , mass spectra and a complete structure proposed based on ¹H and ¹³C NMR spectroscopy.