A genetic algorithm for structure-based de novo design

Genetic algorithms have properties which make them attractive in de novo drug design. Like other de novo design programs, genetic algorithms require a method to reduce the enormous search space of possible compounds. Most often this is done using information from known ligands. We have developed the ADAPT program, a genetic algorithm which uses molecular interactions evaluated with docking calculations as a fitness function to reduce the search space. ADAPT does not require information about known ligands. The program takes an initial set of compounds and iteratively builds new compounds based on the fitness scores of the previous set of compounds. We describe the particulars of the ADAPT algorithm and its application to three well-studied target systems. We also show that the strategies of enhanced local sampling and re-introducing diversity to the compound population during the design cycle provide better results than conventional genetic algorithm protocols.     

Novel heterocycle-based two-photon absorbing dyes

[structure: see text]. The synthesis and nonlinear optical characterization of two novel heteroaromatic-based chromophores is described. The new dyes present an A-pi-D-pi-A general framework, where A is a pi-deficient heteroaromatic ring (pyridine, quinoline, benzothiazole) and D a pi-excessive pyrrolyl moiety. Both systems exhibit large two-photon absorption (TPA) values in the femtoseconds regime (TPA cross section as high as 150 x 10(-50) cm(4) s photon(-1) molecule(-1) with 150 fs laser pulses). Their TPA-based optical limiting activity is also shown.     

Thermal behaviour and slow molecular mobility in two isomers of biphenylmethanol

This research was aimed to investigate the role of clay on the combustion and kinetic behavior of crude oils in limestone matrix. For this purpose, simultaneous TG (thermogravimetry) and DTA (differential thermal analysis) experiments were performed at three different heating rates as 10–15 and 20°C min^–1, respectively. A uniform trend of decreasing activation energies was observed with the addition of clay. It was concluded that clays surface area affects the values of Arrhenius constant, while it is the catalytic properties of clay, which lower the activation energies of all the reactions, involved in the combustion process.     

Synthesis of Coumarins and Derivatives. Part 1. Biomimetic synthesis of esculetin and halogenated derivatives

Esculetin ( 1 ) and the novel compounds 5-chloroesculetin ( 5 ) and 5-bromoesculetin ( 6 ) were obtained from a light-induced cyclization of trans-caffeic acid ( 3 ) catalyzed by [FeNa(edta)] and/or H₂SO₄, HCI, or HBr (Scheme 1). The experimental conditions for trans-cis-isomerization of the cinnamic-acid derivative 3 and subsequent non-enzymatic cyclization were described. The photoperiod and the presence of air and iron-chelate catalyst are shown to be important parameters that markedly affect yields. The reactions probably occur by a free-radical mechanism involving a photo-initiated one-electron redox process (Scheme 2).     

Determination of dinoseb by adsorptive stripping voltammetry using a mercury film electrode

An adsorptive stripping voltammetric method for the determination of the pesticide dinoseb (2-sec.-butyl-4,6-dinitrophenol) at the mercury film electrode is described. The deposition of the mercury film on a glassy carbon disk electrode was optimized. The temperature, at which the mercury film was deposited, was demonstrated to have a strong influence on the stripping peaks, the first one being much more intense than the second. A systematic study of the variables affecting the stripping response was carried out by differential pulse voltammetry. The results obtained have been compared with those at the HMDE; a significant improvement in the sensitivity of the method developed with the MFE was observed. Using a 300 s accumulation time, the limits of determination and detection were 3.6 × 10^–10 and 1.1 × 10^–10 mol L^–1, respectively. The effect of the presence of several herbicides on the dinoseb response was also tested. The method has been applied to the determination of the pesticide in spiked apple juice at two concentration levels: 12.0 and 1.2 g L^–1 of juice.     

Excess thermodynamic properties of the 2-propanol + dichloromethane system at 25°C

Densities, viscosities, enthalpies, vapor-liquid equilibria, and surface tensions were determined at 25°C for the 2-propanol+dichloromethane system. From the experimental results excess volumes, viscosities, enthalpies, Gibbs energies, and excess surface tensions were calculated. An attempt has been made to explain the observed deviations from ideal behavior on the basis of intermolecular interactions.     

Solid-phase synthesis of the cyclic lipononadepsipeptide [N-Mst(Ser1), d-Ser4, L-Thr6, L-Asp8, L-Thr9]syringotoxin

An optimized solid-phase strategy for the preparation of the cyclic lipononadepsipeptide [N-Mst(L-Ser1), D-Ser4, L-Thr6, L-Asp8, L-Thr9]syringotoxin is reported. The strategy is based on the use of a mild orthogonal protection scheme and the incorporation of the nonproteinogenic amino acid (Z)-Dhb into the peptide chain as the dipeptide Fmoc-Thr(tBu)-(Z)-Dhb-OH. The didehydrodipeptide was synthesized by a water-soluble carbodiimide-induced beta-elimination of a protected dipeptide containing a residue of Thr with its free hydroxy side chain unprotected.     

Uranium analysis in urine by inductively coupled plasma dynamic reaction cell mass spectrometry

Urine uranium concentrations are the best biological indicator for identifying exposure to depleted uranium (DU). Internal exposure to DU causes an increased amount of urine uranium and a decreased ratio of ²³⁵U/²³⁸U in urine samples, resulting in measurements that vary between 0.00725 and 0.002 (i.e., natural and depleted uraniums ²³⁵U/²³⁸U ratios, respectively). A method based on inductively coupled plasma dynamic reaction cell mass spectrometry (ICP-DRC-MS) was utilized to identify DU in urine by measuring the quantity of total U and the ²³⁵U/²³⁸U ratio. The quantitative analysis was achieved using ²³³U as an internal standard. The analysis was performed both with and without the reaction gas oxygen. The reaction gas converted ionized ²³⁵U⁺ and ²³⁸U⁺ into ²³⁵UO₂⁺ (m/z=267) and ²³⁸UO₂⁺ (m/z=270). This conversion was determined to be over 90% efficient. A polyatomic interference at m/z 234.8 was successfully removed from the ²³⁵U signal under either DRC operating conditions (with or without oxygen as a reaction gas). The method was validated with 15 urine samples of known uranium compositions. The method detection limit for quantification was determined to be 0.1 pg U mL^–1 urine and an average coefficient of variation (CV) of 1–2% within the sample measurements. The method detection limit for determining ²³⁵U/²³⁸U ratio was 3.0 pg U mL^–1 urine. An additional 21 patient samples were analyzed with no information about medical history. The measured ²³⁵U/²³⁸U ratio within the urine samples correctly identified the presence or absence of internal DU exposure in all 21 patients.The opinions and assertions expressed herein are those of the authors and are not to be construed as official or as representing the views of the Armed Forces Institute of Pathology, the Department of the Army, or the Department of Defense     

ITQ-15: the first ultralarge pore zeolite with a bi-directional pore system formed by intersecting 14- and 12-ring channels, and its catalytic implications

The pore topology of ITQ-15 zeolite consists of an ultra-large 14-ring channel that is intersected perpendicularly by a 12-ring pore; acid sites have been introduced in its framework and this unique structure shows advantages over unidirectional ultralarge pore zeolites for diffusing and reacting large molecules.     

Pozzolanic properties of a residual FCC catalyst during the early stages of cement hydration

The catalyst used in fluidized catalytic cracking (FCC) units of refineries after several recovery cycles in regeneration units, reduces its activity and it is partially substituted by new catalyst in the process. As it has a high silicon and aluminum oxides content, the pozzolanic properties of a Brazilian FCC spent residual catalyst, used in different substitution degrees to cement, were evaluated by three thermal analysis techniques during the early stages of hydration of a type II Portland cement. NCDTA curves show in real time that the residual catalyst, accelerates the stages of cement hydration. TG and DSC curves of respective pastes after 24 h of hydration evidence the pozzolanic activity of the waste, respectively, by the lower water mass loss during the dehydroxylation of the residual calcium hydroxide and by the lower dehydroxylation endothermal effect. Within the analyzed period, the higher is the cement substitution degree, the higher is the pozzolanic activity of the residual catalyst.