Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin

The study presented here consists of three parts. In the first, the ability of a set of differently substituted diazobenzene-based linkers to act as photoswitchable beta-turn building blocks was assessed. A 12-residue peptide known to form beta-hairpins was taken as the basis for the modeling process. The central (beta-turn) residue pair was successively replaced by six symmetrically ((o,o), (m,m), or (p,p)) substituted (aminomethyl/carboxymethyl or aminoethyl/carboxyethyl) diazobenzene derivatives leading to a set of peptides with a photoswitchable backbone conformation. The folding behavior of each peptide was then investigated by performing molecular dynamics simulations in water (4 ns) and in methanol (10 ns) at room temperature. The simulations suggest that (o,o)- and (m,m)-substituted linkers with a single methylene spacer are significantly better suited to act as photoswitchable beta-turn building blocks than the other linkers examined in this study. The peptide containing the (m,m)-substituted linker was synthesized and characterized by NMR in its cis configuration. In the second part of this study, the structure of this peptide was refined using explicit-solvent simulations and NOE distance restraints, employing a variety of refinement protocols (instantaneous and time-averaged restraining as well as unrestrained simulations). We show that for this type of systems, even short simulations provide a significant improvement in our understanding of their structure if physically meaningful force fields are employed. In the third part, unrestrained explicit-solvent simulations starting from either the NMR model structure (75 ns) or a fully extended structure (25 ns) are shown to converge to a stable beta-hairpin. The resulting ensemble is in good agreement with experimental data, indicating successful structure prediction of the investigated hairpin by classical explicit-solvent molecular dynamics simulations.     

Reaction between palladium(II) and gallium(III) halogenides in arenes: influence of halogen nature on the formation of binuclear palladium(I) clusters

Palladium(II) bromide reacts with gallium(III) bromide in the presence of arenes yielding binuclear palladium(I) complexes [Pd₂(GaBr₄)₂(arene)₂], where arene=benzene (1), toluene (2) and p-xylene (3). Reaction of palladium(II) chloride with gallium(III) chloride in p-xylene leads to the analogous palladium(I) compound [Pd₂(GaCl₄)₂(p-xylene)₂] (4); the X-ray structures of 1-4 were determined.     

Biosynthesis of δ-Jasmin Lactone ( = (Z)-Dec-7-eno-5-lactone) and (Z,Z)-Dodeca-6,9-dieno-4-lactone in the Yeast Sporobolomyces odorus

(all-Z)-(9,10,12,13,15,16-²H₆)Octadeca-9,12,15-trienoic acid ( = α-linolenic acid; D₆- 4 ) was synthesized to investigate the biochemical formation of linolenic-acid-derived aroma compounds in cultures of the yeast Sporobolomyces odorus, using an established gas chromatographic/mass spectrometric (GC/MS) method. Three compounds were identified as labeled: (Z)-dec-7-eno-5-lactone (δ-jasmin lactone), (Z,Z)-dodeca-6,9-dieno-4-lactone, and (2E,4Z)-hepta-2,4-dienoic acid. Both lactones were biosynthesized mostly under conservation of the initial configuration from their corresponding oxygenated linolenic-acid intermediates. The application of (13S,9Z,11E,15Z)-13-hydroxy(9,10,12,13,15, 16-²H₆)octadeca-9,11,15-trienoic acid (D₆- 7 ) as a OH-functionalized precursor of δ-jasmin lactone allowed to gain insight into the stereochemical course of the biosynthesis to both enantiomers of this lactone. In this experiment, 88.3% of the metabolized labeled precursor was transformed under retention of the original configuration of the (R)-enantiomer. This investigation is also a contribution to a better understanding of the C?C bond isomerization steps which took place during the β-oxidative degradation of the substrate.     

Routes to unique palladium A-frame complexes with a bridging fluoro-ligand

Treatment of a toluene solution of [PdMe(2)(Cy(2)PCH(2)PCy(2))](1) with pentafluoropyridine in the presence of traces of water affords the generation of the A-frame complexes [(PdMe)(2){mu-kappa(2)(P,P)Cy(2)PCH(2)PCy(2)}(2)(mu-F)][SiMeF(4)]() and [(PdMe)(2){mu-kappa(2)(P,P)Cy(2)PCH(2)PCy(2)}(2)(mu-F)][OC(5)NF(4)](2b). If the reaction is performed in an NMR tube equipped with a PFA inliner, complex 2b is produced, only. Treatment of 1 with pentafluoropyridine in the presence of an excess water yields the pyridyloxy complex [PdMe(OC(5)NF(4))(Cy(2)PCH(2)PCy(2))](3). Compound [(PdMe)(2){mu-kappa(2)(P,P)Cy(2)PCH(2)PCy(2)}(2)(mu-F)][FHF](2c) bearing a bifluoride anion instead of SiMeF(4)(-) or OC(5)NF(4)(-) can be generated by reaction of 1 with substoichiometric amounts of Et(3)N.3HF. The analogous complex [(PdMe)(2){mu-kappa(2)(P,P)Ph(2)PCH(2)PPh(2)}(2)(mu-F)][FHF] (5c) has been synthesized by addition of Ph(2)PCH(2)PPh(2) to a solution of [PdMe(2)(Me(2)NCH(2)CH(2)NMe(2))](4) in THF and subsequent treatment of the reaction mixture with Et(3)N.3HF. The structure of the A-frame complex 5c has been determined by X-ray crystallography.     

Ring-chain-transformations : Synthesis of ω-functionalized alkylthio-1,2,4-triazoles by reaction of cyclic S-analogous N-cyano or N-aroylcarbonimidoesters with hydrazines

Cyclic N-cyanocarbonimidodithioesters 4 or N-aroylcarbonimidothioic acid esters 10 react regioselectively with arylhydrazines and methylhydrazine by a ring chain transformation reaction forming ω-functionalized 3-alkylthio-1,2,4-triazoles 8 and 11 or 5-alkylthio-1,2,4-triazoles 9 .     

Unsaturated dodecahedranes—Synthesis of the highly pyramidalized,highly reactive C20H18 and C20H16 olefins

Methodological alternatives for the preparation of highly strained, highly pyramidalized dodecahedrene 2 (E_str=87.3 kcal mol^?1; ?=43.5°, MM2) and 1,16-dodecahedradiene 3 (E_str=105.3 kcal mol^?1; ?=42.9°, MM2) have been explored, protection/deprotection strategies have been tested—with the eye on their utilization for the generation of higher unsaturated dodecahedranes (e.g. 1,4, 16-triene 4, 1,4,10 (14),16-tetraene 5). For the acquisition of preparative quantities of monoene 2 the “P₂F” catalyzed cis-β-elimination in bromododecahedrane, of diene 3 the FVP fragmentation of a “twofold protected” precursor (bis-furan adduct) have become the protocols of choice, which both profit from the recent synthetic advances along the pagodane → dodecahedrane scheme. Because of unusually effective steric protection the highly tilted C=C double bonds of 2 (λ_max (CH₃CN) = 254 nm, ν _C=C = 1658 cm^?1, δ_C=C = 164.4) and 3 (δ_C=C = 170.5) enter into thermal stabilization pathways (dimerization, oligomerization) only at higher temperatures (for 2 ca. 50% consumption after 5 h at 100°C in a 3·10^?3 molar toluene solution); extreme sensitivity to oxygen is primarily attributed to kinetically and thermodynamically promoted allylic hydrogen abstraction.     

Übergangsmetall-silyl-komplexe: IV. Bildung eines ring-substituierten wolframocen dihydrid derivats durch reaktion von Cp2WCl2 MIT Li[Si(SiMe3)3]

In the reaction of Cp₂WGl₂ with Li[Si(SiMe₃)₃] the dihydrid tungstenocene derivative [(Me₃Si)₃SiC₅H₄]WH₂ (3) is formed with a 56% yield. 3 crystallizes in space group P$\text{1}$, with a 918.0(4), b 1580.9(4), c 1621.2(7) pm, α 117.63(2), β 89.95(3), γ 94.39(3)° at ?40° C. The dihedral angle between the Cp planes is 140.9°.     

Scanning force microscopy based rapid force curve acquisition on supported lipid bilayers: experiments and simulations using pulsed force mode.

In situ pulsed force mode scanning force microscopy (PFM-SFM) images of phase separated solid-supported lipid bilayers are discussed with the help of computer simulations. Simultaneous imaging of material properties and topography in a liquid environment by means of PFM-SFM is severely hampered by hydrodynamic damping of the cantilever. Stiffness and adhesion images of solid-supported membranes consisting of cholesterol, sphingomyelin, and 1,2-dioleyl-phosphatidylcholine obtained in aqueous solution exhibit contrast inversion of adhesion and stiff. ness images depending on parameters such as driving frequency, amplitude, and trigger setting. Simulations using a simple harmonic oscillator model explain experimental findings and give a deeper insight into the way PFM-SFM experiments have to be performed in order to obtain interpretable results and hence pave the way for reliable material contrast imaging at high speed.