A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm

Rational drug design involves finding solutions to large combinatorial problems for which an exhaustive search is impractical. Genetic algorithms provide a novel tool for the investigation of such problems. These are a class of algorithms that mimic some of the major characteristics of Darwinian evolution. LEA has been designed in order to conceive novel small organic molecules which satisfy quantitative structure-activity relationship based rules (fitness). The fitness consists of a sum of constraints that are range properties. The algorithm takes an initial set of fragments and iteratively improves them by means of crossover and mutation operators that are related to those involved in Darwinian evolution. The basis of the algorithm, its implementation and parameterization, are described together with an application in de novo molecular design of new retinoids. The results may be promising for chemical synthesis and show that this tool may find extensive applications in de novo drug design projects.     

Structural and electrochemical studies of novel bis(mu-methoxo)diiron complexes: observation of Fe(III)Fe(IV) and Fe(IV)Fe(IV) states resonating with phenoxyl radicals

Novel diiron complexes with an Fe2(mu-OMe)2 core were studied as models of the active site of nonheme iron-containing enzymes. X-ray crystal structures of the complexes showed the existence of two types of ligand folding-parallel and twisted-both of which have four virtually equivalent phenolato groups sticking out from the Fe2O2 rhombic plane. Cyclic voltammetry measurements revealed two or more distinct redox waves in a region of relatively high potential, in addition to known Fe(II)/Fe(III) redox waves in a region of lower potential. These new peaks were assigned to the high-valence state of iron atoms, that is, Fe(III)Fe(IV) and Fe(IV)Fe(IV), resonating with the phenoxyl radical(s). The split width of the redox waves ranged from 0.14 to 0.20 eV, which may be a measure of the electronic interaction of the phenolate groups through the Fe2(mu-OMe)2 core.     

Spectroscopic study of a magnetically rotating arc between opper electrodes in contaminated argon

The effects of N₂ and CO contaminants in atmospheric-pressure argon on an arc rotating between two concentric copper electrodes has been studied using optical spectroscopy of copper lines. The axial temperature of the magnetically driven arc in Ar + %N₂ was determined to be around 10,000 K for arc currents of SO to 200 A. The diffusion process of the copper vapor from the cathode was also studied. A copper density maximum 1 mm from the cathode along the arc column was found in Ar + %N₂. Removal of the contaminated cathode surface layers by the arc when contaminant injection in the plasma gas was stopped was found to be a slow process with a time scale depending on the type of the gas contaminant. The presence of gas contaminant in the electrode material controls the cathode erosion mechanism and the overall arc behavior in the transition between a contaminated to a pure argon arc.     

Effective interactions in the colloidal suspensions from hypernetted-chain theory

The hypernetted-chain (HNC) Ornstein-Zernike integral equations are used to determine the properties of simple models of colloidal solutions where the colloids and ions are immersed in a solvent considered as a dielectric continuum and have a size ratio equal to 80 and a charge ratio varying between 1 and 4000. At an infinite dilution of colloids, the effective interactions between colloids and ions are determined for ionic concentrations ranging from 0.001 to 0.1 mol/l and compared to those derived from the Poisson-Boltzmann theory. At finite concentrations, we discuss on the basis of the HNC results the possibility of an unambiguous definition of the effective interactions between the colloidal molecules.     

New fluorinated polysiloxanes containing an ester function in the spacer. I. Synthesis and characterization

Unsaturated perfluoroalkyl esters derived from undecylenic acid: CH₂?CH? (CH₂)₈? COO? CH₂? CH₂? R_F (with R_F?C₆F₁₃, 2a and R_F?C₈F₁₇, 2b ) and C₈F₁₇? (CH₂)₁₀? COO? CH₂? CH?CH₂, 2c were prepared with excellent yields. Their hydrosilylation by methylhydrodimethylsiloxane copolymers of various Si? H contents gives new fluorinated polysiloxanes which were examined by ¹H- and ¹³C-NMR, GPC, differential scanning calorimetry, and optical polarizing microscopy. Polymers derived from compounds 2a and 2b exhibit mesomorphic structures. © 1994 John Wiley & Sons, Inc.     

A general approach toward the synthesis of C-nucleoside pyrazolo[1,5-a]-1,3,5-triazines and their 3',5'-bisphosphate C-nucleotide analogues as the first reported in vivo stable P2Y(1)-receptor antagonists

In our effort to identify potent purinergic P2Y(1) receptor antagonists as potent platelet aggregation inhibitors with enhanced metabolic stability, we developed an efficient route for the large-scale preparation of 2'-deoxy-C-nucleosides of pyrazolo[1,5-a]-1,3,5-triazine. The key strategic elements of this novel synthetic approach involved the following: (i) the use of a novel activating group, the N-methyl-N-phenylamino group, which was easily generated in high yield by treatment of the pyrazolo[1,5-a]-1,3,5-triazin-4-one (5) with phosphorus oxychloride and dimethylaniline under high pressure, (ii) a regio- and stereospecific palladium-mediated coupling reaction of the readily available unprotected glycal 1,4-anhydro-2-deoxy-D-erythro-pent-1-enitol (4b) and the 8-iodo derivative (16), and (iii) the stereoselective reduction of the ketone group of the furanosyl ring followed by the subsequent displacement of the N-methyl-N-phenylamino group upon treatment with methylamine. The beta configuration at the anomeric C-1' position of the glycal moieties was perfectly retained throughout this conversion. This procedure afforded 8-(2'-deoxy-beta-D-ribofuranosyl)-2-methyl-4-(N-methylamino)pyrazolo[1,5-a]-1,3,5-triazine (21) and 8-(2'-deoxy-beta-D-xylofuranosyl)-2-methyl-4-(N-methylamino)pyrazolo[1,5-a]-1,3,5-triazine (24) with an overall yield of 50% and 39%, respectively. Finally, the conversion of nucleosides 21 and 24 to the pyrazolotriazine C-nucleotides 3',5'-bisphosphate 2 and 3',5'-cyclophosphate 26 is also described herein and represents the first reported nucleotide derivatives within the pyrazolo[1,5-a]-1,3,5-triazine series. Preliminary biological testing has shown that compound 2 strongly inhibits ADP-induced human platelet aggregation and shape change and possesses significant efficacies 30 min after injection in rat, highlighting a strong P2Y(1)-receptor antagonist activity in vitro combined with a prolonged duration of action in vivo.     

Epoxy‐functionalized,low‐glass‐transition‐temperature latex. II. Interdiffusion versus crosslinking in the presence of a diamine

This article describes the results of experiments examining the competition between the polymer diffusion rate and the crosslinking rate in low‐glass‐transition‐temperature, epoxy‐containing latex films in the presence of a diamine. We examined films formed from donor‐ and acceptor‐labeled poly(butyl acrylate‐co‐methyl methacrylate‐co‐glycidyl methacrylate) copolymer latex and studied the influence of several parameters on the growth rate of gel content and the rate of polymer diffusion. These factors include the molecular weight of the latex polymer, the presence or absence of a diamine crosslinking agent, and the cure protocol. The results were compared to the predictions of a recent theory of the competition between crosslinking and polymer diffusion across interfaces. In the initially formed films, polymer diffusion occurs more rapidly than the chemical reaction rate. Therefore, these films fall into the fast‐diffusion category of this model. In our system (unlike in the model), the latex polymer has a broad distribution of molecular weights and a distribution of diffusivities. The shortest chains contribute to the early time diffusion that we measure. At later stages of our experiment, slower diffusing species contribute to the signal that we measure. The diffusion time decreases substantially, and we observe a crossover to a regime in which the chemical reaction dominates. The increases in chain branching and gel formation bring polymer diffusion to a halt. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4098–4116, 2002     

Thermal and electrochemical C-X activation (X = Cl,Br, I) by the strong Lewis acid Pd3(dppm)3(CO)2+ cluster and its catalytic applications

The stoichiometric and catalytic activations of alkyl halides and acid chlorides by the unsatured Pd(3)(dppm)(3)(CO)(2+) cluster (Pd(3)(2+)) are investigated in detail. A series of alkyl halides (R-X; R = t-Bu, Et, Pr, Bu, allyl; X = Cl, Br, I) react slowly with Pd(3)(2+) to form the corresponding Pd(3)(X)(+) adduct and "R(+)". This activation can proceed much faster if it is electrochemically induced via the formation of the paramagnetic species Pd(3)(+). The latter is the first confidently identified paramagnetic Pd cluster. The kinetic constants extracted from the evolution of the UV-vis spectra for the thermal activation, as well as the amount of electricity to bring the activation to completion for the electrochemically induced reactions, correlate the relative C-X bond strength and the steric factors. The highly reactive "R(+)" species has been trapped using phenol to afford the corresponding ether. On the other hand, the acid chlorides react rapidly with Pd(3)(2+) where no induction is necessary. The analysis of the cyclic voltammograms (CV) establishes that a dissociative mechanism operates (RCOCl --> RCO(+) + Cl(-); R = t-Bu, Ph) prior to Cl(-) scavenging by the Pd(3)(2+) species. For the other acid chlorides (R = n-C(6)H(13), Me(2)CH, Et, Me, Pr), a second associative process (Pd(3)(2+) + RCOCl --> Pd(3)(2+.....)Cl(CO)(R)) is seen. Addition of Cu(NCMe)(4)(+) or Ag(+) leads to the abstraction of Cl(-) from Pd(3)(Cl)(+) to form Pd(3)(2+) and the insoluble MCl materials (M = Cu, Ag) allowing to regenerate the starting unsaturated cluster, where the precipitation of MX drives the reaction. By using a copper anode, the quasi-quantitative catalytic generation of the acylium ion ("RCO(+)") operates cleanly and rapidly. The trapping of "RCO(+)" with PF(6)(-) or BF(4)(-) leads to the corresponding acid fluorides and, with an alcohol (R'OH), to the corresponding ester catalytically, under mild conditions. Attempts were made to trap the key intermediates "Pd(3)(Cl)(+)...M(+)" (M(+) = Cu(+), Ag(+)), which was successfully performed for Pd(3)(ClAg)(2+), as characterized by (31)P NMR, IR, and FAB mass spectrometry. During the course of this investigation, the rare case of PF(6)(-) hydrolysis has been observed, where the product PF(2)O(2)(-) anion is observed in the complex Pd(3)(PF(2)O(2))(+), where the substrate is well-located inside the cavity formed by the dppm-Ph groups above the unsatured face of the Pd(3)(2+) center. This work shows that Pd(3)(2+) is a stronger Lewis acid in CH(2)Cl(2) and THF than AlCl(3), Ag(+), Cu(+), and Tl(+).     

Dynamic light scattering and cryogenic transmission electron microscopy investigations on metallo-supramolecular aqueous micelles: evidence of secondary aggregation

Metallo-supramolecular diblock copolymers consisting of a polystyrene (PS) block connected to a poly(ethylene oxide) (PEO) block by a bis(terpyridine)ruthenium complex (PS₂₀-[Ru]-PEO _y ) were used to prepare aqueous micelles. The length of the PS block was kept constant, while two PEOs of different molecular weight were used. The resulting hydrated micelles and aggregates were characterized by a combination of cryogenic transmission electron microscopy (cryo-TEM) and dynamic light scattering measurements. The results were compared to those obtained for a covalent counterpart (PS₂₂-b-PEO₇₀). Cryogenic transmission electron microscopy allowed visualization of the PS core of the micelles. Moreover, the aggregates result from clustering of individual micelles.