Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

Effects of double substitution on the thermodynamic stabilities of nitrogen radicals

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Aldol condensations over reconstructed Mg-Al hydrotalcites: structure-activity relationships related to the rehydration method

Two different rehydration procedures in the liquid or gas phase have been applied to reconstruct mixed oxides derived from calcined hydrotalcite-like materials to be used as catalysts for aldol condensation reactions. The as-synthesized hydrotalcite, its decomposition product, as well as the reconstructed solids upon rehydration were characterized by XRD, N(2) adsorption, He pycnometry, FTIR, SEM, TEM, (27)Al MAS-NMR and CO(2)-TPD (TPD=temperature-programmed desorption). Compared to the Mg-Al mixed oxide rehydrated in the gas phase (HT-rg), that rehydrated in the liquid phase (HT-rl) exhibits a superior catalytic performance with respect to the aldol condensation of citral with ketones to yield pseudoionones and in the self-aldolization of acetone. The textural properties of HT-rl and HT-rg differ strongly and determine the catalytic behavior. A memory effect led to a higher degree of reconstruction of the lamellar structure when the mixed oxide was rehydrated in the gas phase rather than in the liquid phase, although liquid-phase rehydration under fast stirring produced a surface area that was 26 times greater. This contrasts to typical statements in the literature claiming a higher degree of reconstruction in the presence of large amounts of water in the medium. CO(2)-TPD shows that the number of OH(-) groups and their nature are very similar in HT-rg and HT-rl, and cannot explain the markedly different catalytic behavior. Accordingly, only a small fraction of the available basic sites in the rehydrated samples is active in liquid-phase aldol condensations. Our results support the model in which only basic sites near the edges of the hydrotalcite platelets are partaking in aldol reactions. Based on this, reconstructed materials with small crystallites (produced by exfoliation during mechanical stirring), that is, possessing a high external surface area, are beneficial in the reactions compared to larger crystals with a high degree of intraplatelet porosity.     

Preparation and characterization of trans-RhCl(CO)(TPPTS)2-intercalated layered double hydroxides

trans-RhCl(CO)(TPPTS)₂ (TPPTS=tris(m-sulfonatophenyl)phosphine) has been intercalated into Zn-Al layered double hydroxides (LDHs) by the method of ion exchange. The structure, composition and thermal stability of the composite material have been characterized by powder X-ray diffraction, Fourier transform infrared and ³¹P solid-state magic-angle spinning nuclear magnetic resonance spectroscopy, elemental analysis, thermogravimetry, and differential thermal analysis. The geometry of trans-RhCl(CO)(TPPTS)₂ was fully optimized using the PM3 semiempirical molecular orbital method, and a schematic model for the intercalated species has been proposed. The thermal stability of trans-RhCl(CO)(TPPTS)₂ is significantly enhanced by intercalation, which suggests that such materials may have prospective application as the basis of a supported catalyst system for the hydroformylation of higher olefins.     

Sugar-anionic clay composite materials: intercalation of pentoses in layered double hydroxide

The intercalation of non-ionized guest pentoses (ribose and 2-deoxyribose) into the Mg-Al and Zn-Al layered double hydroxides (LDHs) was carried out at 298 K by the calcination-rehydration reaction using the Mg-Al and Zn-Al oxide precursors calcined at 773 K. The resulting solid products reconstructed the LDH structure with incorporating pentoses, and the maximum amount of ribose intercalated by the Mg-Al oxide precursor was approximately 20 times that by the Zn-Al oxide precursor. The ribose/Mg-Al LDH was observed to have the expanded LDH structure with a broad (003) spacing of 0.85 nm. As the thickness of the LDH hydroxide basal layer is 0.48 nm, the interlayer distance of the ribose/Mg-Al LDH is 0.37 nm. This value corresponds to molecular size of ribose in thickness (0.36 nm), supporting that ribose is horizontally oriented in the interlayer space of LDH. The maximum amount of ribose intercalated by the Mg-Al oxide precursor was approximately 5 times that of 2-deoxyribose. Ribose is substituted only by the hydroxyl group at C-2 position for 2-deoxyribose. Therefore, the number of hydroxyl group of sugar is essentially important for the intercalation of sugar molecule into the LDH, suggesting that the intercalation behavior of sugar for the LDH was greatly influenced by hydrogen bond between hydroxyl group of the intercalated pentose and the LDH hydroxide basal layers.     

Syntheses and Crystal Structure of Erbium(Ⅲ) Coordination Polymers with Two Flexible Double Betaine Ligands

1INTR0DUCTI0NLanthanidecarboxylatecomplexeshavebeenwidelystudiedt1iandm0starefoundtoexhibitavarietyofdimericorinfinitechainstructures.Recentstudiesinourlaboratoryhavedem0nstratedthattheprototypetertiaryaminebetaine(Me,N CHzC0z-)anditsderivativesareusefulinthegenerationoflanthanidecarb0xylate-likecomplexeswithnewstructuralfeaturesduetotheiroverallchargeneutralityandpossibleinclusionofvariouskindsofcounteranionsinthestructuret2~4i.Thelan-thanidecomplexesisolatedsofarhavebeenfoundtobemononu…     

Effect of Inorganic Ions on Oleate Adsorption at a Nigerian Hematite–Water Interface

Using “pure” natural hematite selected from a high silica Nigerian hematitic ore, oleate adsorption densities at the hematite–water interface were determined in the presence of various inorganic ions (anions and cations) of different charges and at varying concentrations. Adsorption density was determined using electrical conductivity measurements. The specific surface area of the hematite particles was determined using the method of adsorption of paranitrophenol in aqueous solution. Inorganic ions in solution depressed oleate adsorption at the aqueous hematite surface. The charge of the ion proved to be the dominant factor determining the depression of oleate adsorption. Ionic strength also was an influence, up to a limiting value at which monolayer oleate coverage of the hematite surface occurred. The inorganic ions in solution are considered to function through nonspecific adsorption in the diffuse region of the electric double layer.     

Double Electric Layer on Liquid Sn-Ga Alloy in Acetonitrile Solutions of Electrolytes

The structure of the double electric layer (DEL) on a liquid dropping Sn-Ga electrode containing 8 at. % of Sn is studied in acetonitrile (AN) solutions of electrolytes. It is shown that the transition from aqueous to AN solutions of electrolytes makes it possible to expand the region of investigation of parameters of DEL on an Sn-Ga electrode from negative charges to a zero charge and to small positive charges. As follows from the obtained data, throughout the entire interval of charges studied, an excess, as compared with an Hg electrode, chemisorption interaction (Sn-Ga)-AN is absent. It is established that the distance of the closest approach of AN dipoles to an ionic core increases upon going from Hg to Sn-Ga to Ga. The Ga, Bi-Ga, and Sn-Ga electrodes, which possess close values of the “electrochemical work function,” are used as an example to show that the metal-solvent chemisorption interaction increases with decreasing distance of the closest approach of its dipoles to the ionic core of the metal. The effect of this factor becomes stronger as the donor number of the solvent increases.     

Stabilization of p-block organoelement terminal hydroxides, thiols, and selenols requires newer synthetic strategies

Metal hydroxides represent a very interesting and highly useful class of compounds that have been known to chemists for a very long time. While alkali and alkaline earth metal hydroxides (s‐block) are commonplace chemicals in terms of their abundance and their use in a chemical laboratory as bases, the interest in Brønsted acidic molecular terminal hydroxides of p‐block elements, such as aluminum and silicon, has been of recent origin, with respect to the variety of applications these compounds can offer both in materials science and catalysis. Moreover, these systems are environmentally friendly, relative to the metal halides, owing to their ‐OH functionality (resembling that of water). Design and conceptualization of the corresponding terminal thiols, selenols, and tellurols (M? SH, M? SeH, and M? TeH) offer even more challenging problems to synthetic inorganic chemists. This concept summarizes some of the recent strategies developed to stabilize these otherwise very unstable species. The successful preparation of a number of silicon trihydroxides a few years back resulted in the generation of several model compounds for metal–silicates. The recent synthesis of unusual aluminum compounds such as RAl(OH)₂, RAl(SH)₂, and RAl(SeH)₂ with terminal EH (E=O, Se, or Se) groups is likely to change the ways in which some of the well‐known catalytic conversions are being carried out. The need for very flexible and innovative synthetic strategies to achieve these unusual compounds is emphasized in this concept.     

Fabrication of PbTiO3 Ceramic Fibers by Sol-Gel Processing

The sol-gel processing was applied to the fabrication of PbTiO₃ fibers. Pb(CH₃COO)₂·3H₂O and Ti(OC₃H ₇ ⁱ )₄ were refluxed with stirring in 2-methoxyethanol to form Pb-methoxyethoxide and Ti-methoxyethoxide, respectively, followed by mixing with stirring in 2-methoxyethanol to form Pb−Ti double alkoxide. The hydrolysis and polycondensation reaction of this double alkoxide gave polymerized products, and as a result the viscosity of the solution increased, suggesting that linear polymers were produced through the hydrolysis and polycondensation reaction. Homogeneous PbTiO₃ gel fibers were drawn from the spinnable viscous solutions, which were wellcrystallized into perovskite type PbTiO₃ at 650°C. The heat-treated fibers were a few centimeters long and from 10 to 100 μm in diameter. The fiber was made up of extremely uniform grains. Electron diffraction revealed a preferred growth of (101) planes along the fiber axis, which might be due to the linear molecular characteristics of the alkoxide.