An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution

An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree‐Fock level in conjunction with Dunning double‐ζ plus polarization function basis sets. The simulation predicts an average H? Cl bond distance of 1.28 Å, which is in good agreement with the experimental value. The H_HCl···O_w and Cl_HCl···H_w distances of 1.84 and 3.51 Å were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure‐making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Unusual photochemical dynamics of a bridged azobenzene derivative

In a large-scale simulation study of ultrafast photochemical dynamics for an azobenzene compound with an additional ethylenic bridge we have found unexpected features: while the dynamics starting from the Z isomer follow a barrierless path with steep gradients, the dynamics starting from the E isomer proceed through a different conical intersection surrounded by a rather flat potential energy landscape and then encounter a sizeable barrier in the electronic ground state that markedly influences the reaction behavior. Direct comparisons with experimental static UV spectra, quantum yields, and transient absorption spectra show good agreement and reveal signatures of this unusual behavior.     

High resolution 1H-detected solid-state NMR spectroscopy of protein aliphatic resonances: access to tertiary structure information

Biological magic angle spinning (MAS) solid-state nuclear magnetic resonance spectroscopy has developed rapidly over the past two decades. For the structure determination of a protein by solid-state NMR, routinely (13)C,(13)C distance restraints as well as dihedral restraints are employed. In protonated samples, this is achieved by growing the bacterium on a medium which contains [1,3]-(13)C glycerol or [2]-(13)C glycerol to dilute the (13)C spin system. Labeling schemes, which rely on heteronuclei, are insensitive both for detection and in terms of quantification of distances, since they are relying on low-γ nuclei. Proton detection can in principle provide a gain in sensitivity by a factor of 8 and 31, compared to the (13)C or (15)N detected version of the experiment. We report here a new labeling scheme, which enables (1)H-detection of aliphatic resonances with high resolution in MAS solid-state NMR spectroscopy. We prepared microcrystals of the SH3 domain of chicken α-spectrin with 5% protonation at nonexchangeable sites and obtained line widths on the order of 25 Hz for aliphatic (1)H resonances. We show further that (13)C resolved 3D-(1)H,(1)H correlation experiments yield access to long-range proton-proton distances in the protein.     

Synthesis of musafluorone: a naphthoxanthenone isolated from Musa acuminata

5-Methoxy-3H-naphtho[2,1,8-mna]xanthen-3-one (musafluorone, 1), the only naphthoxanthenone reported so far from Musaceae, was synthesized starting from 2-naphthol in nine steps and resulted in an overall yield of 3%. Grignard addition of phenylmagnesium bromide to 4-methoxyperinaphthenone afforded the corresponding 4-methoxy-9-phenylphenalenone which, after epoxidation and methyl transposition, was subjected to a photochemical cyclization procedure to furnish 1.     

1,3‐Bis(trimethylsilyl)‐1,3,2‐diazaphospha‐[3]ferrocenophanes

The 2‐tert‐butyl, 2‐phenoxy, and 2‐diethylamino derivatives of 1,3‐bis(trimethylsilyl)‐1,3,2‐diazaphospha‐[3]ferrocenophane were prepared, and the molecular structure of the latter was determined by X‐ray diffraction. The phosphines could be oxidized by their slow reactions with sulfur or selenium, and the molecular structures of three sulfides and one selenide were determined. In contrast, the synthesis of oxides was less straightforward. All new compounds were characterized in solution by multinuclear magnetic resonance methods (1D and 2D ¹H, ¹³C, ¹⁵N, ²⁹Si, ³¹P, and ⁷⁷Se NMR spectroscopy).     

Intramolecular vibrational energy redistribution in aromatic molecules of type C₆H₅X (X = H, D, F, Cl, CH₃, CF₃)

Femtosecond IR pump UV probe spectroscopy was employed in the gas phase to study intramolecular vibrational energy redistribution (IVR) in benzene and five monosubstituted derivatives thereof. After selective excitation of the first overtone of the ring CH-stretch vibration, all molecules showed the same two-step redistribution dynamics characteristic for nonstatistical IVR. The nature of the substituent influences mainly the second, slower IVR component. The presence of an internal rotor does not alter the redistribution rate or pathway compared to that of a monatomic substituent of equal mass. Coupling order model calculations reflect the experimental trends well if the polyatomic substituents are regarded as decoupled from the intra-ring dynamics and modeled as point masses.     

Immunocytochemical localization of glutathione precursors in plant cells

In plant cells, the antioxidant glutathione is synthesized out of its constituents cysteine, glutamate and glycine. As information about their subcellular and cellular distribution was not available in the past, the aim of the present study was to develop a technique that would allow visualization of their distribution in plant cells. With selective antibodies against cysteine, glutamate and glycine, it was possible, for the first time, to study the relative distribution of these components in meristematic root tip cells and mesophyll cells from older and younger leaves of Cucurbita pepo plants with the transmission electron microscope. These investigations revealed that high levels of cysteine accumulated in younger leaves. However, glutamate and glycine accumulated in the older ones, where cysteine levels were found to be significantly lower. On the subcellular level, glutamate was found in similar content in all investigated cellular compartments except for the cytosol, which showed up to 49% lower glutamate content (in younger leaves) than the other cell compartments. Levels of glycine were similar in all investigated cell compartments of one organ except vacuoles, which contained the lowest amounts of glycine. Cysteine was highest in plastids, the cytosol and in nuclei. When compared with younger leaves, glutamate and glycine were found to be accumulated in plastids (180 and 83%) and the cytosol (142 and 130%) of older leaves, whereas cysteine contents were found to be very low in the glutathione producing cell compartments of the leaves. These results indicate that low levels of cysteine might be a limitation for glutathione synthesis in older leaves. Cysteine and glycine were also detected in vacuoles where glutamate was absent. None of these components were detected in the apoplast. Therefore, these results indicate that glutathione degradation occurs within vacuoles or at the tonoplast, rather than at the plasmalemma or in the apoplast. Summing up, with the methods presented in this and a previous work, it is now possible to study the subcellular distribution of glutathione and its precursors in one plant sample simultaneously. The application of these methods on plant samples during abiotic and biotic stress situations should help us reveal possible limitations of glutathione synthesis during oxidative stress.     

Modern aldol methods for the total synthesis of polyketides

The aldol reaction is one of the most important methods for the stereoselective construction of polyketide natural products, not only for nature but also for synthetic chemistry. The tremendous development in the field of aldol additions during the last 30 years has led to more and more total syntheses of complicated natural products. This Review illustrates by means of selected syntheses of natural products the new variants of the aldol addition. This includes aldol additions with various metal enolates, as well as metal-complex-catalyzed, organocatalytic, and biocatalytic methods.