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.     

Isolierung und Struktur von Pteridinen (Lumazinen) aus Russula sp. (Täublinge; Basidiomycetes)

Isolation and Structure Elucidation of Pteridines (Lumazines) from Russula sp. (Basidiomycetes) Extensive chromatogaphic separations and spectroscopic investigations have led to the isolation and identification of several water-soluble pteridines from Russula sp., the so-called russupteridines, namely: 1-(5-amino-2-6-dioxo-1,2,3,6-tetrahydeopyrimidin-4-yl)amino-1-deoxy-D -ribitol ( 1 ; a pro-lumazine; first identification in a basidiomycete(; l-deoxy-l-(6-methyl-2-4,7-trioxo-1,2,3,4,7,8-hexahydro-pteridin-8-yl)-D -ribitol ( 3 ) and l-deoxy-1-(2,4,7-trioxo-1,2,3,4,7,8-hexahydeopteridin-8-yl)-D -ribitol ( 4 ); both compounds found for the first time in higher fungi; they belong to the components with the strongest violet-blue fluorescence in Russula sp.; riboflavine ( 6 ; now recognized as an important yellow colorant in a great many of Russula sp.); russupteridine-yellow I (= l-(6-amino-7-(N-fromylimino)-2,4-dioxo-1,2,3,4,7,8-hexahydropteridin-8-yl)-1-deoxy-D -ribitol; 5 ; a component with very strong fluorescence; the first derivative of the novel 6,7-diamino-lamazine); russupteridine-yellow IV (= l-deoxy-1-)(2,6,8-trioxo-2,4,5,6,7,8-hexahydro-1H-imidazolo[4,5-g]pteridin-4-yl)-D -ribitol (7)). Two further yellow russupteridines (yellow II and Yellow V) with very strong fluorescence have been isolated and characterized.     

Investigation of drift gas selectivity in high resolution ion mobility spectrometry with mass spectrometry detection

Recent studies in electrospray ionization (ESI)/ion mobility spectrometry (IMS) have focussed on employing different drift gases to alter separation efficiency for some molecules. This study investigates four structurally similar classes of molecules (cocaine and metabolites, amphetamines, benzodiazepines, and small peptides) to determine the effect of structure on relative mobility changes in four drift gases (helium, nitrogen, argon, carbon dioxide). Collision cross sections were plotted against drift gas polarizability and a linear relationship was found for the nineteen compounds evaluated in the study. Based on the reduced mobility database, all nineteen compounds could be separated in one of the four drift gases, however, the drift gas that provided optimal separation was specific for the two compounds.     

Syntheses, structures, and surface aromaticity of the new carbaalane [(AlH)(6)(AlNMe(3))(2)(CCH(2)R)(6)] (R = Ph, CH(2)SiMe(3)) and a stepwise functionalization of the inner and outer sphere of the cluster

The reaction of the acetylene RC triple bond CH (R = Ph, CH(2)SiMe(3)) with an excess of AlH(3).NMe(3) in boiling toluene leads to the carbaalane [(AlH)(6)(AlNMe(3))(2)(CCH(2)R)(6)] (R = Ph 1, CH(2)SiMe(3) 2) in good yield. Treatment of 2 with BCl(3) under varying conditions gives the chlorinated products [(AlCl)(6)(AlNMe(3))(2)(CCH(2)CH(2)SiMe(3))(6)] 3 and [(AlCl)(6)(AlNMe(3))(2)(CCH(2)CH(2)SiMe(2)Cl)(6)] 4, respectively. The latter clearly demonstrates that the cluster can be stepwise functionalized within the inner and outer sphere. The X-ray single-crystal structures of 1, 2, and 4 have been determined. All compounds have in common that the central core consists of a cluster having eight aluminum and six carbon atoms. The bonding properties in this cluster are described as a new manifestation of three-dimensional surface aromaticity. Each Al(4)C fragment of the cube is formed by four bonds with three electron pairs, thus leading to a strong delocalization of the electrons. A phenomenological modeling using a three-dimensional Hückel scheme with fitted parameters to reproduce the energies from ab initio calculations revealed that the orbital scheme localized at one Al(4)C fragment possesses an orbital sextet with a large HOMO-LUMO gap. This is in line with the criteria of aromaticity. The idea of aromaticity was sustained also by qualitative valence bond reasons enumerating the different resonance structures by means of graph theoretical methods.     

Synthesis of γ-lactones from alkenes employing p-methoxybenzyl chloride as CH2---CO2 equivalent

The ZnCl₂ catalyzed reaction of p-methoxybenzyl chloride with alkenes yields the 1:1 addition products 3, which are converted into the γ-lactones 4 via Ru(VIII) catalyzed oxidative degradation of the aromatic ring.