OptiDock: virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space

Products from combinatorial libraries generally share a common core structure that can be exploited to improve the efficiency of virtual high-throughput screening (vHTS). In general, it is more efficient to find a method that scales with the total number of reagents (Sigma growth) rather with the number of products (Pi growth). The OptiDock methodology described herein entails selecting a diverse but representative subset of compounds that span the structural space encompassed by the full library. These compounds are docked individually using the FlexX program (Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol. 1995, 251, 470-489) to define distinct docking modes in terms of reference placements for combinatorial core atoms. Thereafter, substituents in R-cores (consisting of the core structure substituted at a single variation site) are docked, keeping the core atoms fixed at the coordinates dictated by each reference placement. Interaction energies are calculated for each docked R-core with respect to the target protein, and energies for whole compounds are calculated by finding the reference core placement for which the sum of corresponding R-core energies is most negative. The use of diverse whole compounds to define binding modes is a key advantage of the protocol over other combinatorial docking programs. As a result, OptiDock returns better-scoring conformers than does serially applied FlexX. OptiDock is also better able to find a viable docked pose for each library member than are other combinatorial approaches.     

Acceleration of convergence in Monte Carlo simulations of aqueous solutions using the metropolis algorithm. Hydrophobic hydration of methane

Convergence problems encountered in the computer simulations of aqueous solutions are discussed. Solute–solvent radial distribution functions are shown to converge very poorly when the standard Metropolis Monte Carlo procedure is applied. To overcome this difficulty, several modifications are made in the Metropolis method. Optimum maximum step sizes are determined for simulations of liquid water. A scheme is employed for preferential sampling of both the solvent and the solute molecules. To test these modifications, a simulation is carried out for pure liquid water, treating a single water molecule as a “solute.” The convergence of the radial distribution functions is found to be accelerated significantly. A further test is made by simulating an aqueous solution of methane, consisting of one methane molecule (using the EPEN /2 potential for methane–water interactions) and 124 water molecules (using the MCY potential for water–water interactions). Again, the convergence of solute–solvent radial distribution functions is found to be accelerated. The computation of partial molar thermodynamic quantities, however, still suffers from convergence difficulties. This problem is discussed in detail. The EPEN /2 potential is found to yield structural and thermodynamic features of hydrophobic hydration that are consistent with available experimental and theoretical results for aqueous solutions of methane.     

Effect of solution components on the termination mechanism in acrylamide microemulsion polymerizations

A study of the effect of the various solution components on the kinetics of the polymerization of acrylamide in water/oil (w/o) microemulsions has been performed. For the polymerizations with toluene as the continuous phase, both the rate of polymerization, R_p, and the molecular weight of the polyacrylamide were found to be first order in monomer concentration. Furthermore, for the low temperatures (10°C) involved in these experiments, nondegradative chain transfer to monomer appears to be insignificant. When the continuous-phase solvent was changed, an exponential dependence, X, of R_p on the incident light intensity in the order of toluene (X = 1.06) > heptane (X = 0.73) > benzene (X = 0.55) was found. Thus, the monoradical termination found in the toluene microemulsions is likely due to degradative transfer to toluene, forming a stable benzyl radical, while polymerization in benzene (no labile hydrogen atoms) leads to biradical termination     

PHOTOINHIBITION OF PHOTOSYNTHESIS IN NATURAL WATERS*

Abstract— A quantitative analysis of the wavelength-dependent influence of solar irradiance on natural phytoplankton photosynthesis has been made. The effect on productivity due to several different UV radiation regimes has been measured. In the course of this analysis, it has been shown that the biological weighting function for photoinhibition of chloroplasts (Jones and Kok, 1966) allows the calculation of a biologically effective dose which is consistent with the measured photoinhibition in natural phytoplankton populations. The ecological implications of a change in available UV radiation, possibly due to anthropogenic altering of the ozone layer, are explored and it is found that the present static bottle ^l4C technique of measuring in situ phytoplankton productivity does not lend itself to assessing accurately the potential ecological consequences of possible increased MUV (middle ultraviolet radiation in the 280–340 nm region) on phytoplankton populations. A small change in MUV has a relatively minor effect on photoinhibition dose rates whereas it has a large potential effect on DNA dose rates.     

Chiroptical properties of n-nitrosopyrrolidines and n-nitrosamino acids : Implications for the nitrosamine sector rule

CD data for a variety of N-nitrosamino acids and N-nitrosopyrrolidines are presented. The effects of nitrosamino group conformation, pyrrolidine ring geometry, different perturbing substituents, and especially intramolecular H-bonding upon the n → π^* CD band are discussed. Stereochemical conclusions can be made with confidence in many cases, although no sector diagram, as yet published, successfully correlates all the available chiroptical data in this series of compounds. However, a negative CD band due to the π → π* transition was observed tor all N-nitrosamines having the L-proline configuration at C-2, regardless of nitroso group conformation; it is suggested that this band be used whenever possible for stereochemical correlations.     

Compehensive two-dimensional gas chromatography (GC×GC) and its applicability to the characterization of complex (petrochemical) mixtures

In general, petrochemical products contain only a limited number of chemical classes of compounds (sample dimensionality). The enormous number of individual components within these classes, however, soon puts limitations upon a single chromatographic technique when it comes to adequate characterization of these products. Comprehensive two-dimensional gas chromatography (GC×GC) clearly opens the possibility of estimating the composition of hydrocarbon mixtures in a far more detailed fashion than hitherto possible. Although the emphasis of papers of GCxGC thus far almost exclusively applies to the unsurpassed peak-capacity, in the oil industry there is a need for characterization, rather than for analyzing all the individual compounds. In principle a GCxGC system can provide an almost perfect match between its intrinsic properties and the dimensionality of oil samples. To establish the applicability of GCxGC towards petrochemical analytical challenges, a commercially aavailable prototype instrument was subjected to an exhaustive characterization of a typical hydrocarbon precess stream and a fast characterization of a light gas oil. Although there are no fundamental limitations towards the quantitative aspects of a GCxGC system, this paper confines itself to qualitative results only. Quantitative aspects of GCxGC will be published in a forthcoming paper.     

Structure and Thermodynamics of NaF-AlF(3) Melts with Addition of CaF(2) and MgF(2)

The NaF-AlF(3) system with additions of CaF(2) and MgF(2) has been studied with Raman and vapor pressure measurements for 3 >/= CR (NaF/AlF(3) molar ratio) >/= 1 and up to 50 mol % additive. The results show that the binary melt can be described using the two equilibria AlF(6)(3)(-) = AlF(6)(2)(-) + F(-) and AlF(5)(2)(-) = AlF(4)(-) + F(-) with equilibrium constants 0.25 and 0.05, respectively, at 1293 K. Both reactions have positive reaction enthalpies. The first equilibrium is strongly shifted to the right resulting in a melt mixture with very low AlF(6)(3)(-) concentrations even at the Na(3)AlF(6) composition. Evidence for nonideal mixing of anions was found. For the ternaries, models based on Raman data are presented and compared with vapor pressure measurements. Good agreement is observed when association between the additives, CaF(2) or MgF(2), with the AlF(5)(2)(-) ions in the melt was considered. This association could be experimentally observed through a band broadening and a slight shift in the AlF(5)(2)(-) band frequency. Our vapor pressures and Raman data both indicate that MgF(2) clearly acts as an acid when added to NaF-AlF(3) melts of any composition. When CaF(2) is added, a slight decrease of vapor pressure occurs. Raman data indicate a decrease of AlF(4)(-) concentration, corresponding to a dissociation of CaF(2) with liberation of F(-) ions. All these results are, however, very much dependent on the initial melt composition. These data are explained in terms of acid-base, dilution, and association reactions of the solute with the solvent.     

Spectrophotometric study of molybdophosphoric acid methods for phosphorus using propylene carbonate as extractant

Summary A spectrophotometric study has been made of the solvent extraction of molybdophosphoric acid and its blue reduction product with propylene carbonate from acidic solutions. Molybdophosphoric acid forms an adduct with propylene carbonate which is readily extracted with chloroform. The molar absorptivity of the molybdophosphoric acid in the propylene carbonate-chloroform phase is 22300 1 mole^–1 cm^–1 at 308 nm. Although experimental conditions for the extraction of the heteroply blue must be more carefully controlled, this extract exhibits a molar absorptivity of 28500 1 mole^–1 cm^–1 at 790 nm.

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Zusammenfassung Eine spektrophotometrische Untersuchung der Extrahierbarkeit der Molybdänphosphorsäure und ihres blauen Reduktionsproduktes mit Propylencarbonat aus saurer Lösung wurde durchgeführt. Molybdänphosphorsäure bildet mit Propylencarbonat ein Addukt, das mit Chloroform gut extrahierbar ist. Ihre molare Absorption in der Propylencarbonat-Chloroform-Phase beträgt 223001·mol^–1 · cm^–1 bei 308 nm. Die experimentellen Bedingung für die Extraktion der blauen Heteropolysäuren müssen zwar noch genauer geprüft werden, die molare Extinktion kann jedoch mit 285001·mol^–1·cm^–1 bei 790 nm angegeben werden.

     

Alkaline hydrolysis of 2-(trifluoromethyl)imidazo[4,5-f] and -[4,5-h]quinolines

2-(Trifluoromethyl)imidazo[4,5-$\text{f}$] and -[4,5-$\text{h}$]quinoline have been prepared from 5(6),acetamido-2-(trifluoromethyl)benzimidazole and 7,8-diaminoquinoline respectively. These (trifluoromethyl)- quinolines like 2-(trifluoromethyl)imidazoles but unlike 2-(trifluoromethyl) benzimidazoles, undergo hydrolysis in dilute sodium hydroxide to give ultimately the corresponding imidazo[4,5-$\text{f}$] and -[4,5-$\text{h}$]- quinoline, respectively.     

Synthesis and Conformational Analysis of the Multidrug Resistance-Reversing Agent Hapalosin and Its Non-N-methyl Analog

Hapalosin was initially synthesized by macrolactonization, and a second synthesis was achieved by cycloamidation. In both syntheses, three of the five stereocenters in hapalosin were established by two Brown allylboration reactions. The synthesis of the non-N-Me analog of hapalosin involved chelation-controlled reduction of a gamma-amino-beta-keto ester and cycloamidation. In CDCl(3) at 25 degrees C, synthetic hapalosin exists as a 2.3:1 mixture of conformers, while its non-N-Me analog exists only as a single conformer. (1)H,(1)H-NOESY and computation reveal that the configuration of the amide bond is responsible for the conformations of the two compounds. The major conformer of hapalosin is found to be an s-cis amide, the minor conformer an s-trans amide, and the non-N-Me analog an s-trans amide. Applying distance constraints to protons that exhibit NOESY correlations, computation shows that the major conformer of hapalosin and the non-N-Me analog have very different conformations. By contrast, the minor conformer of hapalosin and the non-N-Me analog have very similar conformations.