New approach to molecular docking and its application to virtual screening of chemical databases

This paper describes the validation of a molecular docking method and its application to virtual database screening. The code flexibly docks ligand molecules into rigid receptor structures using a tabu search methodology driven by an empirically derived function for estimating the binding affinity of a protein-ligand complex. The docking method has been tested on 70 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. The lowest energy geometry produced by the docking protocol is within 2.0 A root mean square of the experimental binding mode for 79% of the complexes. The method has been applied to the problem of virtual database screening to identify known ligands for thrombin, factor Xa, and the estrogen receptor. A database of 10,000 randomly chosen "druglike" molecules has been docked into the three receptor structures. In each case known receptor ligands were included in the study. The results showed good separation between the predicted binding affinities of the known ligand set and the database subset.     

Ion atmosphere relaxation and percolative electron transfer in Co bipyridine DNA molten salts

Polypyridyl complexes of Co decorated with 350-Da polyether chains (Co(350)(2+)) form molten phases of nucleic acids when paired with DNA counterions (Co(350)DNA) or 25-mer oligonucleotides. Analysis of voltammetry and chronoamperometry of mixtures of these phases with complexes having ClO(4)(-) counterions (Co(350)(ClO(4))(2)) and no other diluent provides charge transport rates from the oxidation and reduction currents for the complexes. As the mole fraction of the Co(350)(ClO(4))(2) complex in the mixture is varied from ca. 0.25 to 1, the physical diffusion constants derived from the Co(III/II) wave increase from 1 x 10(-11) cm(2)/s to 5 x 10(-10) cm(2)/s, and apparent diffusion constants dominated by the Co(II/I) electron self-exchange increase from 1 x 10(-10) cm(2)/s to 2 x 10(-8) cm(2)/s. Pure Co(350)DNA melts, containing no Co(350)(ClO(4))(2) complex, do not exhibit recognizable voltammetric waves; DNA suppresses the Co(II/I) electron transfer reactions of Co complexes for which it is the counterion. There are therefore two microscopically distinct kinds of Co(350) complexes, those with DNA and those with ClO(4)(-) counterions, with respect to their Co(II/I) electron-transfer dynamics, leading to percolative behavior in their mixtures. The electron-transfer rates of the Co(II/I) couple are controlled by the diffusive relaxation of the ionic atmosphere around the reaction pair, and the inactivity of the bound Co complexes can be attributed to the very low mobility of the anionic phosphate groups in the DNA counterion. Substitution of sulfonated polystyrene for DNA produced similar results, suggesting that this phenomenon is general to other polymer counterions of low mobility. We conclude that the measured Co(II/I) charge transport and electron-transfer rate constants reflect more the diffusive mobility of the perchlorate counterion than the intrinsic Co(II/I) electron hopping rate.     

Imaging the quantum-state specific differential cross sections of HCl formed from reactions of chlorine atoms with methanol and dimethyl ether

Center-of-mass frame scattering angle distributions obtained directly from crossed molecular beam velocity map images are reported for HCl formed in different rotational levels of its vibrational ground state by reaction of Cl atoms with CH3OH and CH3OCH3. Products are observed to scatter over all angles, with peaks in the distribution in the forward and backward directions (theta = 0 and 180 degrees with respect to the relative velocity vectors of the Cl atoms). Products of both reactions exhibit differential cross sections that vary with the rotational quantum number of the HCl, with a greater propensity for forward scatter for J = 2, shifting to more pronounced backward scatter for J = 5. This trend is, however, more evident for reaction of dimethyl ether than for methanol. The mean fractions of the available energy channeled into product kinetic energy vary with scattering angle, but the angle-averaged fractions are, respectively, 0.37 and 0.42 for the methanol and dimethyl ether reactions. On average, 46% or more of the available energy of the reactions becomes internal energy of the radical co-product. Results are interpreted with the aid of computed energies of transition states and molecular complexes along the reaction pathways, and comparisons are drawn with recent measurements of the scattering distributions and energy release for reactions of Cl atoms with small alkanes.     

The magnetic moment of103Ru

The nuclear magnetic moment of¹⁰³Ru has been determined using the technique of low-temperature nuclear orientation on¹⁰³Ru as a dilute impurity in Fe. The Fe lattice was cooled to 1.7 mK using a PrNi₅ enhanced nuclear demagnetisation stage precooled with a³He–⁴He dilution refrigerator. The¹⁰³RuFe system was observed to have a long nuclear spin-lattice relaxation time, but analysis of the relaxation indicates that the¹⁰³Ru nuclei are close to thermal equilibrium with the Fe lattice at times>200 min after demagnetising. From the near thermal equilibrium anisotropy of the 497 keV -ray in¹⁰³Rh we have deduced the nuclear magnetic moment as |(¹⁰³Ru)|=0.18(2)_N. This value is almost independent of the choice of spinI=3/2 or 5/2 for the nucleus, but is only consistent with systematics ifI(¹⁰³Ru)=3/2 and <0. UsingI=3/2 we obtain the E2/M1 mixing ratio of the 497 keV -ray as =–0.42(4). The sign of the anisotropy of the 610 keV -ray from the 650 keV level in¹⁰³Rh is only consistent with an allowed -decay to the state ifI(650 keV,¹⁰³Rh)=5/2. The E2/M1 mixing ratio of the 610 keV -ray is then =+0.15(3) or +60( _–40 ⁺ ), <–80. From the initial rise in -ray anisotropy following demagnetisation we determine the Korringa constant for¹⁰³RuFe to beC=5.7(5) K·s.     

Reciprocity principles associated with the general linear gravity wave problem

Summary Reziprocity principles are presented which hold for the general problem of small amplitude wave motion on the surface of an incompressible liquid. The effects of viscosity, surface tension, irrotationality, free surface sources and solid boundary geometry at liquid-solid intersections are discussed.

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Zusammenfassung Reziprozitätsprinzipien, die für das allgemeine Problem der Wellenbewegung mit kleinen Amplituden auf der Oberfläche einer inkompressiblem Flüssigkeit gelten, werden angegeben. Die Einflüsse von Viskosität, Oberflächenspannung, Wirbelfreiheit, Quellen an der freien Oberfläche un die Geometrie fester Ränder bei flüssig-festen Übergängen werden diskutiert.

     

Isobutane chemical ionization mass spectra of unsaturated alcohols

Analysis of the isobutane chemical ionization mass spectra of hexenols, cyclohexenols and various syn/anti pairs of bicyclic and tricyclic homoallylic alcohols shows that: (i) the spectra of the allylic alcohols are dominated by [M + H – H₂O]⁺ and [M + C₄H₉–H₂O]⁺ ions and contain traces of [M + H]⁺ ions; (ii) [M + H]⁺ ions are prominent in the spectra of acyclic and certain cyclic homoallylic alcohols; and (iii) [M + H]⁺ ions dominate the spectra of other acyclic unsaturated alcohols. The [M + H]⁺ ions may result from either: (a) protonation of the hydroxyl group, followed by a very rapid intramolecular proton transfer from the protonated hydroxyl group to the carbon–carbon double bond or internal solvation of the protonated hydroxyl group by the carbon–carbon double bond; and/or (b) direct protonation of the carbon–carbon double bond with significant internal solvation of the resulting carbocation by the hydroxyl group, which may lead to carbon–oxygen bond formation to give a protonated cyclic ether. The consequences of placing various geometric constraints on the possible intramolecular interactions between the hydroxyl group and the carbon–carbon double bond in unsaturated alcohols are explored.     

A SIFT ion-molecule study of some reactions in Titan's atmosphere. reactions of N(+), N(2)(+), and HCN(+) with CH(4), C(2)H(2), and C(2)H(4)

The results of a study of the ion-molecule reactions of N(+), N(2)(+), and HCN(+) with methane, acetylene, and ethylene are reported. These studies were performed using the FA-SIFT at the University of Canterbury. The reactions studied here are important to understanding the ion chemistry in Titan's atmosphere. N(+) and N(2)(+) are the primary ions formed by photo-ionization and electron impact in Titan's ionosphere and drive Titan's ion chemistry. It is therefore very important to know how these ions react with the principal trace neutral species in Titan's atmosphere: Methane, acetylene, and ethylene. While these reactions have been studied before the product channels have been difficult to define as several potential isobaric products make a definitive answer difficult. Mass overlap causes difficulties in making unambiguous species assignments in these systems. Two discriminators have been used in this study to resolve the mass overlap problem. They are deuterium labeling and also the differences in reactivities of each isobar with various neutral reactants. Several differences have been found from the products in previous work. The HCN(+) ion is important in both Titan's atmosphere and in the laboratory.     

Factors controlling the formation and stability of air bubbles stabilized by partially hydrophobic silica nanoparticles

Air bubbles have been formed using partially hydrophobic silica nanoparticles as the stabilizer. The particles were of primary particle size 20 nm, chemically treated to different degrees with dichlorodimethylsilane to render them partially hydrophobic. Above a certain bubble size range (typically 80-microm diameter), the bubbles seemed to be almost indefinitely stable, while for any size above 20 microm their stability against disproportionation is far better than bubbles stabilized by any protein film investigated in previous studies. A possible theoretical justification for this observation is presented. Bubbles could be formed by shaking water with the particles, but a much higher volume fraction of bubbles was obtained by pressurizing the aqueous phase to 5 atm overnight followed by suddenly releasing the pressure to nucleate bubbles within the silica dispersion. Sonicating the silica dispersion before nucleation also gave more bubbles, which were also found to be more stable. There appeared to be an optimum degree of surface hydrophobicity that gave maximum foamability and foam stability, where around 20-33% of the silanol groups on the silica surface had been converted to dimethylsilane groups. However, a sharp increase in stability occurred when between 1.8 and 2 mol dm(-3) NaCl was also included in the aqueous phase. The change in stability due to inclusion of salt can be rationalized in terms of changes occurring in the value of the particle contact angle. The effects of increasing sonication and an optimum surface chemical treatment can be explained by the need to make the particles sufficiently hydrophobic so that they adsorb strongly enough, while at the same time minimizing their tendency to aggregate in the bulk aqueous phase, which hinders their adsorption. Furthermore, confocal laser scanning microscopy of the bubble dispersions suggests that a large volume fraction of stable bubbles is only formed when the particles adsorbed to the bubbles are also part of a spanning silica particle network in the bulk aqueous solution, forming a weak gel with a finite yield stress.     

Products of the addition of water molecules to Al3O3- clusters: structure, bonding, and electron binding energies in Al3O4H2-, Al3O5H4-, Al3O4H2, and Al3O5H4

Two stable products of reactions of water molecules with the Al3O3- cluster, Al3O4H2- and Al3O5H4-, are studied with electronic structure calculations. There are several minima with similar energies for both anions and the corresponding molecules. Dissociative absorption of a water molecule to produce an anionic cluster with hydroxide ions is thermodynamically favored over the formation of Al3O3-(H2O)n complexes. Vertical electron detachment energies of Al3O4H2- and Al3O5H4- calculated with ab initio electron propagator methods provide a quantitative interpretation of recent anion photoelectron spectra. Contrasts and similarities in these spectra may be explained in terms of the Dyson orbitals associated with each transition energy.     

Enantioselective synthesis of alpha-methyl-D-cysteine and lanthionine building blocks via alpha-methyl-D-serine-beta-lactone

[reaction: see text] We report here the enantioselective synthesis of Boc-alpha-methyl-d-cysteine(PMB)-OH and lanthionine building blocks through the regioselective ring opening of key intermediate Boc-alpha-methyl-d-serine-beta-lactone.