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.     

Highly efficient synthesis of 2′,3′-didehydro-2′,3′-dideoxy-β-nucleosides through a sulfur-mediated reductive 2′,3′-trans-elimination. From iodomethylcyclopropanes to thiirane analogs

Taking into account the thiophilic properties of iodine, a very simple methodology to achieve 2′,3′-didehydro-2′,3′-dideoxy-β-nucleosides in high yield was performed, using mild, and inexpensive conditions, by means of the treatment of 2′-deoxy-3′,5′-dibenzoyl-2′-iodo-β-nucleoside derivatives with NaHS. The process has shown to be highly dependent of the relative geometry between the iodine atom and the adjacent leaving group. In this way, different essays carried out with pyranose derivatives have concluded in no reaction when the vicinal groups to eliminate do not adopt a trans-diaxial disposition. In addition, the treatment of 2-iodomethyl-cyclopropane-1,1-dicarboxylic acid diethyl ester under the same conditions softly and readily leads to the obtention of a mixture of the expected 2-allyl-malonic acid diethyl ester (as the minor product) and the thiirane derivative 2-thiiranylmethyl-malonic acid diethyl ester (as the major product). In this case, the responsible of the reaction progress are the nucleophilic properties of the sulfur atom rather than the thiophilic character of the iodine atom.     

Effects of double substitution on the thermodynamic stabilities of nitrogen radicals

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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.     

Synthesis and characterisation of bis(pentafluorophenyl)antimony(V) cations, [(C6F5)2SbL3]

Pentacoordinate complex cations of the general formula [(C₆F₅)₂SbL₃]³⁺ stabilized as solid salts in combination with tetraphenylborate (BPh₄), tetrafluorobroate (BF₄) anions, where L=DMSO, Ph₃AsO, PyO, DMF, α-, β- and γ-picoline have been isolated. The newly formed complexes were characterized by elemental analysis, molar conductance measurements, solid-state IR and and NMR. From these results, a five-fold coordination around antimony was required.     

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.