Molecular dynamics simulations of a chemical reaction; conditions for local equilibrium in a temperature gradient

We have examined a simple chemical reaction in a temperature gradient; 2F <==> F2. A mechanical model was used, based on Stillinger and Weber's 2- and 3-body potentials. Equilibrium and non-equilibrium molecular dynamics simulations showed that the chemical reaction is in local thermodynamic as well as in local chemical equilibrium (delta(r)G = 0) in the supercritical fluid, for temperature gradients up to 10(12) K m(-1). The reaction is thus diffusion-controlled. The velocity distributions of both components were everywhere close to being Maxwellian. The peak distributions were shifted slightly up or down from the average velocity of all particles. The shift depended on the magnitude of the temperature gradient. The results support the assumption that the entropy production of the reacting mixture can be written as a product sum of fluxes and forces. The temperature gradient promotes interdiffusion of components in the stationary state, a small reaction rate and an accumulation of the molecule in the cold region and the atom in the hot region.     

Three Mach-uniform algorithms

We focus on the construction of Mach-uniform algorithms. The basic idea is to remove the severe time step restrictions for low speed flows, by treating the acoustic terms implicitly. The way to solve the obtained semi-implicit system can be chosen. Three different solution techniques are presented, varying between a fully coupled algorithm and a fully segregated pressure correction algorithm. We show that the number of time steps to reach steady state is comparable for the fully coupled as well as the fully segregated method. Therefore, the more segregation is introduced, the more efficient the calculation can be done.     

Eine neue Schnellmethode zur Bestimmung des Quecksilbers

Ohne Zusammenfassung     

Synthesis,characterization and in vitro cytotoxicity of palladium(II) complexes with mixed ligands. X‐ray diffraction study of C31H36ClNPPdS2

Pd(II) complexes with organophosphines and dithiocarbamates derivatives of α‐amino acids were synthesized by reacting N,N‐dicyclohexyldithiocarbamate (DCHDTC, compounds 1 – 3 ) and N‐methylcyclohexyldithiocarbamate (MCHDTC, compounds 4 – 6 ) with (R₃P)₂PdCl₂ (R = Ph, o‐tolyl, Ph₂Cl) in a 1:1 molar ratio. The complexes were characterized by elemental analyses, FT‐IR, multinuclear (¹H, ¹³C and ³¹P) NMR and single X‐ray crystallography, showing that the dithiocarbamate acts as a bidentate ligand and binds to Pd(II) via two sulfur atoms, resulting in a square planar geometry around Pd(II). The cytotoxicity of compounds 2, 3 and 4 was determined in vitro against six human tumour cell lines, MCF7, EVSA‐T, WIDR, IGROV, M19 MEL, A498 and H226. Compounds 3 and 4 showed a moderate to low cytotoxicity, whereas compound 2 exhibited a very low cytotoxicity. The results of antifungal assays showed that compounds 1 – 6 possess antifungal activity against Fusarium moniliformes, Fusarium saolani, Mucor sp., Aspergillus niger and Aspergillus fumigatus. The anti‐inflammatory screening results of 1–6 are quite similar to those observed for the standard drug Declofenac at 10 mg kg^?1, which inhibited the odema by 74% after 4 h. Copyright © 2007 John Wiley & Sons, Ltd.     

Beitr?ge zur Untersuehung von Alkaloiden

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Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes

Many genomics assays use profluorescent oligonucleotide probes that are covalently labeled at the 5' end with a fluorophore and at the 3' end with a quencher. It is generally accepted that quenching in such probes without a stem structure occurs through F?rster resonance energy transfer (FRET or FET) and that the fluorophore and quencher should be chosen to maximize their spectral overlap. We have studied two dual-labeled probes with two different fluorophores, the same sequence and quencher, and with no stem structure: 5'Cy3.5-beta-actin-3'BHQ1 and 5'FAM-beta-actin-3'BHQ1. Analysis of their absorption spectra, relative fluorescence quantum yields, and fluorescence lifetimes shows that static quenching occurs in both of these dual-labeled probes and that it is the dominant quenching mechanism in the Cy3.5-BHQ1 probe. Absorption spectra are consistent with the formation of an excitonic dimer, an intramolecular heterodimer between the Cy3.5 fluorophore and the BHQ1 quencher.     

Heteronuclear dipolar recoupling in solid-state nuclear magnetic resonance by amplitude-, phase-, and frequency-modulated Lee-Goldburg cross-polarization

This paper presents a theoretical, numerical, and experimental study of phase- and frequency-switched Lee-Goldburg cross-polarization (FSLG-CP) under magic-angle spinning conditions. It is shown that a well-defined amplitude modulation of one of the two radio-frequency (rf) fields in the FSLG-CP sequence results in highly efficient heteronuclear dipolar recoupling. The recoupled dipolar interaction is gamma-encoded and, under ideal conditions, the effective spin Hamiltonian is equivalent to that in continuous-wave Lee-Goldburg CP. In practice, however, FSLG-CP is less susceptible to rf field mismatch and inhomogeneity, and provides better suppression of (1)H spin diffusion. The performance of FSLG-CP is experimentally demonstrated on liquid-crystalline samples exhibiting motionally averaged dipolar couplings.     

Alkaloids from the Tunicate Polycarpa aurata from Chuuk Atoll

Two new alkaloids, polycarpine (1) and N,N-didesmethylgrossularine-1 (4), have been isolated from extracts of the ascidian Polycarpa aurata collected in Chuuk, Federated States of Micronesia. Three degradation products of 1 were also isolated. The structures of 1, 2, and 4 were determined by X-ray crystallography. The dimeric disulfide 1 inhibited the enzyme inosine monophosphate dehydrogenase, but the inhibition could be reversed by addition of excess dithiothreitol suggesting that 1 reacts with sulfhydryl groups on the enzyme.     

Structural basis for the enantioselectivity of an epoxide ring opening reaction catalyzed by halo alcohol dehalogenase HheC

Halo alcohol dehalogenase HheC catalyzes the highly enantioselective dehalogenation of vicinal halo alcohols to epoxides, as well as the reverse reaction, the enantioselective and beta-regioselective nucleophilic ring opening of epoxides by pseudo-halides such as azide and cyanide. To investigate this latter reaction, we determined X-ray structures of complexes of HheC with the favored and unfavored enantiomers of para-nitrostyrene oxide. The aromatic parts of the two enantiomers bind in a very similar way, but the epoxide ring of the unfavored (S)-enantiomer binds in a nonproductive inverted manner, with the epoxide oxygen and Cbeta atom positions interchanged with respect to those of the favored (R)-enantiomer. The calculated difference in relative Gibbs binding energy is in agreement with the observed loss of a single hydrogen bond in the S bound state with respect to the R bound state. Our results indicate that it is the nonproductive binding of the unfavored (S)-enantiomer, rather than the difference in affinity for the two enantiomers, that allows HheC to catalyze the azide-mediated ring opening of para-nitrostyrene oxide with high enantioselectivity. This work represents a rare opportunity to explain the enantioselectivity of an enzymatic reaction by comparison of crystallographic data on the binding of both the favored and unfavored enantiomers.