A computational model of the nicotinic acetylcholine binding site

We have derived a model of the nicotinic acetylcholine binding site. This was accomplished by using three known agonists (acetylcholine, nicotine and epibatidine) as templates around which polypeptide side chains, found to be part of the receptor cavity from published molecular biology studies, are allowed to flow freely in molecular dynamics simulations and mold themselves around these templates. The resulting supramolecular complex should thus be a complement, both in terms of steric effects as well as electronic effects, to the agonists and it should be a good estimation of the true receptor cavity structure. The shapes of those minireceptor cavities equilibrated rapidly on the simulation time scale and their structural congruence is very high, implying that a satisfactory model of the nicotinic acetylcholine binding site has been achieved. The computational methodology was internally tested against two rigid and specific antagonists (dihydro--erytroidine and erysoidine), that are expected to give rise to a somewhat differently shaped binding site compared to that derived from the agonists. Using these antagonists as templates there were structural reorganizations of the initial receptor cavities leading to distinctly different cavities compared to agonists. This indicates that adequate times and temperatures were used in our computational protocols to achieve equilibrium structures for the agonists. Overall, both minireceptor geometries for agonists and antagonists are similar with the exception of one amino acid (ARG209).     

Peptoids as source of compounds eliciting antibacterial activity

N-Alkylglycine oligomers (peptoids) constitute a family of non-natural peptidomimetics attractive for the early drug discovery process because of their physicochemical features, easy of adaptation to combinatorial chemistry approaches and their proteolytic stability. Consequently, peptoid libraries have found application for discovering hits against a wide diversity of pharmaceutical targets, among which different examples of antibacterials are found. In the present work, research efforts addressed towards the identification of peptoids as antibacterial agents are discussed.     

Electrochemical Synthesis of MII Complexes with a Schiff Base containing an Amido Group. Crystal Structure of a Cobalt(II) Complex with a Reorganised Ligand

M(HL)(H₂O)_n complexes have been obtained by the electrochemical reaction of Fe, Co, Ni, Cu, Zn and Cd anodes with the potentially pentadentate and trianionic asymmetrical Schiff base 3‐aza‐N‐{2‐[1‐aza‐2‐(5‐nitro‐2‐hydroxylphenyl)‐vinyl]phenyl}‐4‐(5‐nitro‐2‐hydroxyphenyl)but‐3‐enamide (H₃L), containing a hard amido donor atom. The complexes have been characterized by elemental analysis, mass spectrometry, IR and ¹H NMR spectroscopies, magnetic measurements and molar conductivities. Co(HL)(H₂O) ( 2 ) has been found to rearrange in DMF solution into a crystallographically solved octahedral complex, CoL¹(H₂O)₂ ( 7 ) [where H₂L¹ is the symmetrical Schiff base ligand N,N′‐(1,2‐phenylene)‐bis(5‐nitro‐3‐hydroxysalicylidenimine)]. A hydrolysis mechanism is discussed to explain this rearrangement.     

Flexible ureasil hybrids with tailored optical properties through doping with metal nanoparticles

Hybrid organic-inorganic nanocomposites containing uniform distributions of metal nanoparticles have been prepared by mixing a preformed nanoparticle colloid with the precursors of a ureasil, prior to the sol-gel transition. These nanocomposites possess not only high optical quality and optical features dictated by the size and shape of the nanoparticle dopants but also a high degree of flexibility, which can largely enhance the range of applications in practical devices. The deposition of a uniform silica shell on the nanoparticle surface prior to the sol-gel transition was found to be required to maintain the colloidal stability during the process and, thus, to retain the optical properties in the final nanocomposite material. This method can be readily extended to other materials, such as semiconductor and magnetic nanoparticles.     

Charge and Potential of the Diffuse Part of the Double Layer for Sodium Dodecyl Sulfate Micelles in NaCl Solutions

A method is proposed for calculating the ψ_d potential of the diffuse part of the electrical double layer in micelles on the basis of data concerning the binding of counterions by these micelles, the composition of the intermicellar medium, and the association of surface-active ions. The charges of sodium dodecyl sulfate micelles in aqueous solutions at various concentrations of the surfactant and background electrolyte are determined by the potentiometric method. The calculated ψ_d values turned out to be much lower than the values of the electrokinetic potentials, thus allowing the conclusion that the slipping plane corresponding to the electrophoretic motion of micelles with respect to the intermicellar medium is localized in the dense part of the double layer.__________Translated from Kolloidnyi Zhurnal, Vol. 67, No. 3, 2005, pp. 410–415.Original Russian Text Copyright © 2005 by Us’yarov.     

Thiocarbonyl rhodium complexes with tricyclohexylphosphine and other nitrogen and phosphorus donor ligands

Summary The preparation of the covalent Rh(OCIO₃)(CS)(PCy₃)₂ and Rh(OClO₃)(CS)(PPh₃)(PCy₃) perchlorato complexes is described, These complexes react with mono- or bidentate nitrogen donor ligands to give new cationic complexes of the [Rh(CS)(PCY₃)₂L]ClO4 and [Rh(CS)(PPh,)(PCy₃)L]ClO₄ types,     

Synthesis and hydrolysis of substituted tetrahydropyrimidinium salts. Behaviour of the degradation products on varying pH

Reaction of 1,2-diaryl-3-methyl-1,4,5,6-tetrahydropyrimidinium iodides 1a-i with alkaline solutions afforded N-aroyl-N-aryl-N'-methyltrimethylenediamines 2a-i . Compounds 2 are stable under acid conditions but in neutral or alkaline media spontaneously rearrange giving N-aroyl-N'-aryl-N-methyltrimethylenediamines 3a-i . Treating compounds 3 with concentrated acids reverse reaction takes place. Kinetic studies were performed on this intramolecular N → N' aroyl transfer over the H_o-pH range -0.9 to 2.30. Compounds 3 undergo acyl transfer to give 2 by a mechanism which involves a change in the rate determining step from formation to acid-catalysed decomposition of a six-membered heterocyclic intermediate on going from H_o to pH values. The existence of maxima in the pH rate profile allow to determine apparent pKa values of the hexahydropyrimidine intermediates which gave good correlation with the Swain F substituent constants. Stability of these heterocycles was also predicted by determination of thermodinamic parameters. Comparisons are made with the behaviour of five-membered heterocyclic intermediates (imidazolidine derivatives) which were studied in an earlier paper.     

Optimization of the Conditions for the Cr (III) Adsorption on Activated Carbon

In order to understand the patterns of the adsorption equilibrium of Cr (III) on activated carbon, the adsorption process was studied by two different ways: classical batch experiments on commercial Norit and Merck activated carbons and their oxidized forms in a wide range of pHs; and extended time-based tests at the same pH values on the same adsorbents. This approach allowed us to understand the role of texture, chemical carbon surface functionality and experimental conditions (initial pH of the solution, contact time and adsorbate/adsorbent ratio) on the effectiveness of Cr (III) removal. The adsorption process of Cr (III) at (24 ± 1^∘C) on Merck and Norit activated carbons and their oxidized forms were studied at pH values between 1.5 and 5 (either adjusted or buffered). Chromium concentration was fixed at 200 ppm. The carbon loading ranged from 1.2 to 20 g/l. The carbon/Cr (III) solution contact time was varied from 0.5–1 month to 5 months, to ensure that the saturation of the carbon level was reached. According to the data obtained, the presence of carboxylic groups on carbon surface seems to enhance Cr (III) uptake at initial pH of the solution in the range between 2 and 4. Depending on the nature of the adsorbent surface chemistry, the contact time to reach equilibrium may range from 3 to 5 months. There is an optimum carbon loading which limits the Cr (III) uptake/removal at given pH value. In order to understand the adsorption process, an ion exchange, surface complex and surface precipitation were considered. This paper was presented in the 5th Brazilian Meeting on Adsorption, held at Natal, Brazil, 18-21 July, 2004.     

Optimization of culture medium and conditions for penicillin acylase production by Streptomyces lavendulae ATCC 13664

The culture medium for Streptomyces lavendulae ATCC 13664 was optimized on a shake-flask scale by using a statistical factorial design for enhanced production of penicillin acylase. This extracellular enzyme recently has been reported to be a penicillin K acylase, presenting also high hydrolytic activity against penicillin V and other natural aliphatic penicillins such as penicillin K, penicillin F, and penicillin dihydroF. The factorial design indicated that the main factors that positively affect penicillin acylase production by S. lavendulae were the concentration of yeast extract and the presence of oligoelements in the fermentation medium, whereas the presence of olive oil in the medium had no effect on enzyme production. An initial concentration of 2.5% (w/v) yeast extract and 3 microg/mL of CuSO4 x 5H2O was found to be best for acylase production. In such optimized culture medium, fermentation of the microorganism yielded 289 IU/L of enzyme in 72 h when employing a volume medium/volume flask ratio of 0.4 and a 300-rpm shaking speed. The presence of copper, alone and in combination with other metals, stimulated biomass as well as penicillin acylase production. The time course of penicillin acylase production was also studied in the optimized medium and conditions. Enzyme production showed catabolite repression by different carbon sources such as glucose, lactose, citrate, glycerol, and glycine.     

Synthesis of beta-lactams by Ag+-induced ring expansion of 1-hydroxycyclopropylamines: a theoretical analysis

A theoretical analysis of the silver-induced ring expansion of N-chloro-N-methyl-1-hydroxycyclopropylamine to form N-methyl-2-azetidinone, and of the Cl(-) elimination from this substrate without Ag(+) assistance, was performed using the B3LYP method and the 6-31+G(d) basis set for C, N, O, H, and Cl atoms and the relativistic effective core pseudopotential LANL2DZ complemented with one set of f polarization functions (zeta(f) = 0.473) for the Ag atom. The partial Ag(+)-assisted extrusion of Cl(-) at the rate-determining transition state provokes an important change in the nodal properties of the frontier molecular orbitals of the H(3)CClNCOHAg(+) fragment, thus making very stabilizing HOMO-LUMO interactions between this fragment and the C(2)H(4) moiety possible. This interaction leads to the ring opening and release of most of the strain energy, giving rise to a low energy barrier for the process. Also, by assisting the Cl(-) extrusion, Ag(+) avoids the elimination of the hydroxyl hydrogen atom, which would provoke the fragmentation of the system instead of the formation of the beta-lactam.