Effects of thioamide substitutions on the conformation and stability of alpha- and 3(10)-helices

Thiopeptides, formed by replacing the amide oxygen atom with a sp(2) sulfur atom, are useful in protein engineering and drug design because they confer resistance to enzymatic degradation and are predicted to be more rigid. This report describes our free molecular dynamics simulations with explicit water and free energy calculations on the effects of thio substitutions on the conformation of alpha-helices, 3(10)-helices, and their relative stability. The most prominent structural effect of thio substitution is the increase in the hydrogen bond distance from 2.1 A for normal peptides to 2.7 A for thiopeptides. To accommodate for the longer C[double bond]S...H-N hydrogen bond, the (phi, psi) dihedral angles of the alpha-helix changed from (-66 degrees, -42 degrees) to (-68 degrees, -38 degrees), and the rise per turn increased from 5.5 to 6.3 A. For 3(10)-helices, the (phi, psi) dihedral angles (-60 degrees, -20 degrees) and rise per turn (6.0 A) changed to (-66 degrees, -12 degrees) and 6.8 A, respectively. In terms of relative stability, the most prominent change upon thio substitution is the decrease in the free energy difference, Delta A(alpha --> 3(10)), from 14 to 3.5 kcal/mol. Therefore, normal peptides are less likely to form 3(10)-helix than are thiopeptides. Component analysis of the Delta A(alpha --> 3(10)) reviews that the entropy advantage of the 3(10)-helix for both Ac-Ala(10)-NHMe and Act-Alat(10)-NHMe is attributed to the 3(10)-helix being more flexible than the alpha-helix. Interestingly, upon thio substitution, this differential flexibility is even more apparent because the alpha-helix conformation of Act-Alat(10)-NHMe becomes more rigid due to the bulkier sulfur atom.     

Electronic effects steer the mechanism of asymmetric hydrogenations of unfunctionalized aryl-substituted alkenes

Density functional theory (PBE and B3LYP) was used to study asymmetric hydrogenations of alkenes catalyzed by an iridium imidazolylidine oxazoline complex. The calculation predicts that the alkene preferentially coordinates to the site trans to the carbene. The coordinated alkene then reacts first with the H2 ligand, then with the hydride to form alkane. Finally, the alkane is released by equilibrating with extrinsic H2 and alkene. Enantioface selectivities for hydrogenations of trisubstituted alkenes seem to be driven primarily by steric interactions with the adamantyl part of the ligand; only the smallest substituents can adopt a site close to it. Application of this theoretical model leads to correct predictions regarding the experimentally observed sense and magnitude of the enantioselectivities.     

A rigid linker-scaffold for solid-phase synthesis of dimeric pharmacophores

Bifunctional linker-scaffolds (compounds 1-3) were designed to meet several criteria for solid-phase syntheses of bivalent ligands. They have two amine-functionalized arms that can be differentially protected. Elaboration of these arms could give ligand-pharmacophore dimers wherein the two active components are held reasonably rigidly at around 10 A separation. Their bifunctional design also enables reactions of libraries with libraries to amplify diversity in a truly combinatorial fashion. Molecules 1-3 are also designed so that cleavage of the linker liberates the scaffold entity into solution under conditions that create only byproducts that should not interfere with biological assays. Thus they contain 2-nitrobenzene sulfonamide components that cleave in the presence of good nucleophiles. In the event, the linker-scaffolds 1-3 were prepared (Schemes 1 and 2). The N-benzyl system 2 was shown to have good stability to the types of conditions that might be used to functionalize the scaffold arms and to be sufficiently labile to the cleavage nucleophile (vide infra). The nucleophiles generally used to cleave nitrobenzene sulfonamides either generate undesirable byproducts (thiophenol or alkane thiols) or proved to be insufficiently reactive for the required solid-phase transformations (n-propylamine). However, sodium sulfide was investigated as a new alternative and shown to be a highly reactive cleavage agent that gives only volatile byproducts and sodium hydroxide. It is suggested that sodium sulfide is a highly desirable nucleophile for cleavage of 2-nitrobenzene sulfonamides, in general. The linker-scaffolds 1-3 were used to prepare a small library of bivalent ligands targeted to a protein receptor having charged cavities separated by approximately 10 A. These systems were made from guanidine, pyridinium, carboxylic acid, and sulfonic acid constituents (Tables 1 and 2).     

The synthesis of diene and of vinyl copolymers containing predetermined quantities of polynuclear hydrocarbon or heterocyclic adducts—VI. Copolymers of butadiene,acenaphthylene or phenanthrene,and a linking agent

Reactions of tetrahydrofuran solutions of butadiene and acenaphthylene with alkali metal produce dianionic species which give quantitative yields of copolymers when subsequently titrated with alkyl dibromides. These polymers, however, crosslink on standing; this has been correlated with the presence of a proportion of 1,5-dihydroacenaphthylene adduct in the product.Similar reactions involving phenanthrene are not quantitative and yield materials containing only a small proportion of the phenanthrene added. The low efficiency has been attributed to the low electron affinity of phenanthrene and to the ability of its dianion to react with alkyl halides by electron transfer rather than metathetically.     

The synthesis of diene and of vinyl copolymers containing predetermined quantities of polynuclear hydrocarbon or heterocyclic adducts—II. The reaction of alkali metal salts of anthracene with alkyl halides

The reactions of alkali metal salts of anthracene with alkyl halides result in the formation of 9,10-dialkyl 9,10-dihydroanthracenes as the principal product, although appreciable quantities of other adducts, notably the 1,2- and 1,4-dialkyl compounds, are also formed.When the disodium salt is used, these adducts account for the total anthracene consumed, but with the dilithium salt appreciable quantities of 9,(4-hydroxybutyl) anthracene compounds are produced; they resulted from additive reaction of the salt with the tetrahydrofuran solvent. In the present experiments, these adducts account for about 20 per cent of the anthracene, but this proportion may be increased by prolonging the standing of the dilithium anthracene solution before reacting with alkyl halide.     

Solvatochromism and piezochromism of dicyano-, tricyano-, and tetracyano-diimine-iron(II) complexes

The solvatochromism of several dicyano-bis-diimine-iron(II) complexes in various binary aqueous solvent mixtures has been established, at 25 °C. A solvent sensitivity scale has been developed for these complexes. The solvatochromic properties of two tricyano-terdentate ligand iron(II) complexes in several solvents have also been determined, as have those of a series of tetracyano-diimine complexes in DMSO–water media. These results have been analysed and systematic but varied trends of solvation were demonstrated. Piezochromic parameters for two complexes have been obtained and are discussed in the context of a solvatochromism/piezochromism correlation.     

Adsorption of<Emphasis Type="Italic"> N</Emphasis>-dodecyl-<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-dimethyl-3-ammonio-1-propanesulfonate (DDAPS), a model zwitterionic surfactant,on the Au(111) electrode surface

Electrochemical measurements including cyclic voltammetry, differential capacity, and chronocoulometry have been used to characterize the adsorption behaviors of the zwitterionic surfactant N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (DDAPS) on the Au(111) electrode surface. The thermodynamics of the ideally polarized electrode have been employed to determine the Gibbs excess and the Gibbs energy of adsorption. The results show that the adsorption of DDAPS has a multistate character. The first two states are observed at potentials close to zero charge. At low bulk DDAPS concentrations, it corresponds to the formation of a film of nearly flat adsorbed molecules. At higher concentrations it is converted into a hemimicellar state. The second state is formed at negative potentials and charge densities close to 0 C cm^–2. It corresponds to a film of tilted molecules oriented with the hydrocarbon tail towards the metal and the polar head toward the solution.Dedicated to Professor Zbigniew Galus on the occasion of his 70^th birthday and in recognition of his many contributions to electrochemistry.     

Use of basic dyes in the determination of anions, particularly as a means of determining antimony, thallium, and gallium

The use of xanthene, triphenylmethane and other basic dye cations as reagents for the determination of anions is reviewed. Elements and anions determined include Sb, Tl, Ga, Au, Te, In, Zn, Ta, Hg, Re, Sn, U, Os, B, Cr, Ag, ClO(4)(-), PO(4)(-), SO(4)(2-) and NO(3)(-). Difficulties encountered in developing satisfactory procedures involving basic dyes are discussed. Procedures for the purification and analysis of basic dye samples are outlined.