Empirical entropic contributions in computational docking: evaluation in APS reductase complexes

The results from reiterated docking experiments may be used to evaluate an empirical vibrational entropy of binding in ligand-protein complexes. We have tested several methods for evaluating the vibrational contribution to binding of 22 nucleotide analogues to the enzyme APS reductase. These include two cluster size methods that measure the probability of finding a particular conformation, a method that estimates the extent of the local energetic well by looking at the scatter of conformations within clustered results, and an RMSD-based method that uses the overall scatter and clustering of all conformations. We have also directly characterized the local energy landscape by randomly sampling around docked conformations. The simple cluster size method shows the best performance, improving the identification of correct conformations in multiple docking experiments.     

Surface charging of layered double hydroxides during dynamic interactions of anions at the interfaces

In this research, we investigated the effect of dynamic anion adsorption/exchange on the surface charging property of Mg(2)AlClLDH and Mg(2)AlCO(3)LDH particles that show the average zeta potential of 41 and 34 mV in the as-prepared suspension, respectively. The addition of NaCl up to 3x10(-3) M in the suspension does not obviously affect the zeta potential of both LDHs, which can be attributed to the less affinity of Cl(-) to LDH. The introduction of Na(2)CO(3) severely reduces the zeta potential at the CO(3)(2-) concentration higher than 1x10(-4) M, and to the negative value in both LDH systems at ca. 2x10(-3) M, which is presumably resulted from the exchange and the re-orientation of CO(3)(2-) in a tilt/vertical style on the surface. All four organic anions (dodecyl sulfate, folate, citrate and polyacrylate) also significantly affect the zeta potential of the LDH particles. At the lower concentrations of organic anionic groups (<1x10(-4) M), the zeta potential was slightly affected, i.e. limited exchange/adsorption. However, the concentration increasing to some point suddenly decreases and reverses the zeta potential of the LDH particles, which is presumably caused by the hydrophobic interactions that bind the hydrophobic hydrocarbon chains (especially in dodecyl sulfate) into the micelle-like bilayer bunches on the LDH surface. In addition, the effect of pH in 5.5-11.0 on the LDH particle surface charging is mainly reflected through the conversion of CO(3)(2-) to HCO(3)(-)/H(2)CO(3) when pH decreases from ca. 11 to 6, with limited contribution from protonation/deprotonation and exchange/adsorption.     

Experimental and theoretical study of the carbon-13 and deuterium kinetic isotope effects in the Cl and OH reactions of CH3F

A laser flash photolysis-resonance fluorescence technique has been employed to determine absolute rate coefficients for the CH3F + Cl reaction in N2 bath gas in the temperature range of 200-700 K and pressure range of 33-133 hPa. The data were fitted to a modified Arrhenius expression k(T) = 1.14 x 10(-12) x (T/298)2.26 exp{-313/T}. The OH and Cl reaction rates of (13)CH3F and CD3F have been measured by long-path FTIR spectroscopy relative to CH3F at 298 +/- 2 K and 1013 +/- 10 hPa in purified air. The FTIR spectra were fitted using a nonlinear least-squares spectral fitting method including line data from the HITRAN database and measured infrared spectra as references. The relative reaction rates defined by alpha = k(light)/k(heavy) were determined to be k(OH+CH3F)/k(OH+CD3F) = 4.067 +/- 0.018, k(OH+CH3F)/k(OH+(13)CH3F) = 1.067 +/- 0.006, k(Cl+CH3F)/k(Cl+CD3F) = 5.11 +/- 0.07, and k(Cl+CH3F)/k(Cl+(13)CH3F) = 1.016 +/- 0.006. The carbon-13 and deuterium kinetic isotope effects in the OH and Cl reactions of CH3F have been further investigated by quantum chemistry methods and variational transition state theory.     

The scanned nanopipette: a new tool for high resolution bioimaging and controlled deposition of biomolecules

The boundary between the physical and biological sciences has been eroded in recent years with new physical methods applied to biology and biological molecules being used for new physical purposes. We have pioneered the application of a form of scanning probe microscopy based on a scanned nanopipette, originally developed by Hansma and co-workers, for reliable non-contact imaging over the surface of a live cell. We have found that the nanopipette can also be used for controlled local voltage-driven application of reagents or biomolecules and this can be used for controlled deposition and the local delivery of probes for mapping of specific species. In this article we review this progress, focussing on the physical principles and new phenomena that we have observed, and then outline the future applications that are now possible.     

Recycling of homogeneous Pd catalysts using superparamagnetic nanoparticles as novel soluble supports for Suzuki, Heck, and Sonogashira cross-coupling reactions

Recycling of homogeneous catalysts could be achieved by using magnetic nanoparticles and solid-phase beads, but nanoparticle-supported catalysis proceeded much faster than its counterpart on resins.     

A diode laser system for long-path,automatic monitoring of SO2

A diode laser system for automatic monitoring of SO₂ along a 60 m atmospheric path is reported. The laser is wavelength modulated and is used to obtain i.r. absorption spectra from the measurement path. These spectra are automatically correlated with reference spectra obtained simultaneously from a calibration cell. The minimum detectable SO₂ concentration is at present around 100 ppb.     

Antisymmetric problems in shock diffraction theory

Various aspects of the diffraction of plane shock waves by moving antisymmetric thin bodies are examined. A method is presented for removing the inhomogeneity in the shock condition. This is done without knowledge of the explicit form of the solution, and is applicable to both symmetric and antisymmetric problems. With this reduction, explicit solutions have been previously obtained for symmetric bodies. For the antisymmetric case, the problem has been previously reduced to a complicated set of integrodifferential equations. In the cases where the flow field exhibits conical properties or when the body is slender, solutions may be obtained without recourse to solving the governing integral equations. In this paper it is shown that two-dimensional conical solutions are obtainable for moving antisymmetric wings only in the restricted case of the wing Mach numbers relative to the stream ahead of and behind the shock being the same. An analytical solution is presented for the above problem. In the case of slender bodies, it is shown that the classical steady slender body theory may be extended to shock diffraction problems and again analytical solutions are presented. It is shown that for general slender bodies, the lift and moment coefficients, and therefore the center of lift is influenced by the shock wave only through the Mach number change across the shock. Results are presented for the pressure distribution on the body, the lift and moment coefficients, and the center of lift for various slender body configurations at angle of attack.

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Résumé Les différents aspects de la diffraction des ondes de choc par les corps antisymétriques en mouvement sont examinés. Une méthode pour éliminer l'inhomogénéité dans la condition de choc, sans avoir recours à la forme explicite de la solution est présentée. Cette méthode peut être utilisée pour l'étude des problèmes symétriques aussi bien qu'antisymétriques. A l'aide de cette réduction, des solutions explicites ont été obtenues précédemment pour les corps symétriques. Dans les cas antisymétriques, il est connu que le problème peut être réduit à la résolution d'un système d'équations intégro-différentielles assez compliquées. Dans le cas où le champ d'écoulement possède certaines propriétés coniques, ou quand le corps est mince, on obtient des solutions sans reoudre les équations intégrales associées. Dans cet article il est démontré que des solutions coniques bi-dimensionnelles peuvent être obtenues pour des mouvements des ailes antisymétriques seulement dans le cas restrictif ou le nombre de Mach de l'aile relatif au courant en amont ainsi qu'en aval du choc est le même. Dans le cas des corps minces il est montré que la théorie classique pour les corps minces en équilibre peut être étendue aux problèmes de diffraction des chocs et on obtient des expressions analytiques pour la représentation des solutions. En outre, il est montré que pour des corps minces en général le coefficient de la portance et le coefficient du moment et, par conséquent, le centre de portance sont influencés uniquement par le changement du nombre de Mach causé par le choc. On obtient ainsi des résultats relatifs à la distribution de la pression sur le corps, le coefficient de la portance, le coefficient du moment et le centre de portance pour différentes configurations des corps minces avec un angle d'attaque.

     

On the Macrolactonization of β-Hydroxy Acids. Crystal structures of the pentolide and the hexolide from (R)-3-hydroxybutanoic acid. Molecular modeling studies of the tetrolide

The temperature and concentration dependence of the previously reported formation of oligolides from (R)- or (S)-3-hydroxybutanoic acid under Yamaguchi's macrolactonization conditions (2,4,6-trichlorobenzoyl chloride/base) was studied. While the content of hexolide 2 in the product mixture is almost invariably ca. 35%, the amounts of pentolide 1 and of the larger rings strongly depend upon the temperature employed (Fig.1). Cyclic oligomers ( 5,6 ) are also obtained from 3-hydroxypentanoic acid. Enantiomerically pure β-butyrolactone can be used for the preparation of pento-, hexo-, and heptolide under Shanzer's macrolactonization conditions (tetra-oxadistannacyclodecane ‘template’). The X-ray crystal structures of the pentolide 1 and of two modifications (space groups C 2 and P 2₁) of the hexolide 2 were determined (Figs. 2–6 and Tables 1 and 5). No close contacts between substituent atoms and atoms in the rings or between ring atoms are observed in these structures. The hexolide C 2 modification is ‘just a large ring’, while the crystals of the P 2₁ modification contain folded rings the backbones of which resemble the seam of a tennis ball. A comparison of the torsion angles in the folded hexolide ring of the P 2₁ modification with those in the helical poly-(R)-3-hydroxybutanoate ( PHB ) suggests (Table 2) that the same interactions might be responsible for folding in the first and helix formation in the second case. Molecular modeling with force-field energy minimization of the tetrolide from four homochiral β-hydroxybutanoic acid units was undertaken, in order to find possible reasons for the fact that we failed to detect the tetrolide in the reaction mixtures. The calculated conformational energies (per monomer) for some of the tetrolide models (Figs. 7–9 and Tables 3 and 4) are not significantly higher than for the pentolide and hexolide crystal structures. We conclude that thermodynamic instability is an unlikely reason for the lack of tetrolide isolation. This result and failure to observe equilibration of pentolide 1 to a mixture of oligomers under the reaction conditions suggest that product distribution is governed by kinetic control.     

Analytische Anwendung von Polymethylenammoniumsalzen

Zusammenfassung Unter den Hexamethonium [HM]-Übergangsmetall-Halogeniden, bzw. Halogenoiden, von welchen eine Reihe der komplexen Rhodanide beschrieben werden, sind die Verbindungen [HM][PtCl₆], [HM][PdCl₄] und [HM][IrCl₆] zum Nachweis der betreffenden Platinmetalle mit Empfindlichkeiten zwischen 0,2 und 3g Metall geeignet. Das Hexamethonium-Ion kann als [HM][Cr(NCS)₄(NH₃)₂]₂ in Mengen ab 1,5 mg gravimetrisch bestimmt werden.

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Summary The hexamethonium [HM] compounds of transition metal halogenides and halogenoides have been examined and some complex rhodanides have been described. The compounds [HM][PtCl₆], [HM][PdCl₄], and [HM][IrCl₆] have proved to be suitable for the detection of the metals concerned with sensitivities between 0,2 and 3g of the metal. The gravimetric determination of the hexamethonium ion in quantities above 1.5mg has been achieved by help of the compound [HM][Cr(NCS)₄(NH₃)₂]₂.

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II. Teil:Ziegler, M., u. G.Pape ¹.

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HerrWolfgang Renner hat in dankenswerter Weise Darstellung und Analysen der Rhodanokomplexe ausgeführt.