An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution

Structural and dynamical properties of Zn(II) in aqueous solution were investigated, based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation at double-zeta Hartree-Fock quantum mechanical level including the first and second hydration shells into the QM region. The inclusion of the second shell in the QM region resulted in significant changes in the properties of the hydrate. The first shell coordination number was found to be 6, the second shell consists of approximately 14 water molecules. The structural properties were determined in terms of RDF, ADF, tilt and theta angle distributions, while dynamics were characterized by mean ligand residence times, ion-ligand stretching frequencies and the vibrational and librational motions of water ligands.     

Quantitative determination of the group of flavonoids and saponins from the extracts of the seeds of Glinus lotoides and tablet formulation thereof by high-performance liquid chromatography

The total flavonoids and saponins of the seeds of Glinus lotoides in the crude extracts and tablet formulation thereof were quantified by reversed-phase high-performance liquid chromatographic (RP-HPLC) methods with UV detection. The saponins were analyzed after acid hydrolysis in 3 M HCI at 100 degrees C for 1 h. Vicenin-2 and mollugogenol B were isolated and used as reference substances for the quantification of total flavonoids and saponins, respectively. The identity and purity (> 97%) of the standards were confirmed by spectroscopic (UV, MS, and NMR) and chromatographic (HPLC) methods. The flavonoids and saponins of the crude extract of the seeds and tablet formulation were separated by RP-HPLC (Nucleosil RP-18 column, 250 mm x 4.6 mm) using linear gradient elution systems of acetonitrile-water-0.1 M H3PO4 for flavonoids and methanol-water for saponins. Satisfactory separation of the compounds was obtained in less than 30 and 25 min, for the flavonoids and saponins, respectively. The methods were validated for linearity, repeatability, limits of detection (LOD) and limits of quantification (LOQ). Repeatability (inter- and intra-day, n = 6 and 9, respectively) showed less than 2% relative standard deviation (RSD). The LOD and LOQ were found to be 0.075 and 0.225 mg/mL, respectively, for vicenin-2 and 0.027 and 0.082 mg/100 mL, respectively, for mollugogenol B. The content of flavonoids and saponins of six single tablets was between 95 and 103% for flavonoids and 94-98% for saponins. The validated HPLC methods were employed to standardize a fingerprint of a laboratory produced purified extract, which could be used as a secondary standard for the routine quality control. Accordingly, the purified extract was found to contain 21.3% flavonoids (vicenin-2, 10%) and 25.4% saponins (glinuside G, 14.2%).     

Cu(II) in liquid ammonia: an approach by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulation.

To investigate the solvation structure of the Cu(II) ion in liquid ammonia, ab initio quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) simulations were carried out at Hartree Fock (HF) and hybrid density functional theory (B3 LYP) levels. A sixfold-coordinated species was found to be predominant in the HF case whereas five- and sixfold-coordinated complexes were obtained in a ratio 2:1 from the B3 LYP simulation. In contrast to hydrated Cu(II), which exhibits a typical Jahn-Teller distortion, the geometrical arrangement of ligand molecules in the case of ammonia can be described as a [2 + 4] ([2 + 3]) configuration with 4 (3) elongated copper-nitrogen bonds. First shell solvent exchange reactions at picosecond rate took place in both HF and B3 LYP simulations, again in contrast to the more stable sixfold-coordinated hydrate. NH3 ligands apparently lead to strongly accelerated dynamics of the Cu(II) solvate due to the "inverse" [2 + 4] structure with its larger number of elongated copper-ligand bonds. Several dynamical properties, such as mean ligand residence times or ion-ligand stretching frequencies, prove the high lability of the solvated complex.     

Photocatalyzed [2 + 2 + 2]-cycloaddition of nitriles with acetylene: an effective method for the synthesis of 2-pyridines under mild conditions

The photocatalyzed [2 + 2 + 2]-cycloaddition of nitriles with 2 equiv of acetylene to 2-pyridines can be carried out under mild conditions and represents a valuable extension to common synthetical methods. For the ideal wavelength range (350-500 nm), lamps as well as sunlight can be used. Working at room temperature and in organic solvents such as toluene or hexane as well as in water gives satisfying results in many cases. However, it is also possible to vary the solvent and the reaction temperature of the photocatalyzed synthesis and to choose, with respect to the specific substrate, specific requirements for this particular reaction and general requirements of the method. This simple and selective method derives its potential mainly from the large variety of applicable nitriles. Suitable substrates include (functionalized) aliphatic and aromatic nitriles as well as cyanamides derived from secondary amines.     

Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study

A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Moller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Becke's three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.     

Methane-to-methanol oxidation by the hydrated iron(IV) oxo species in aqueous solution: a combined DFT and car-parrinello molecular dynamics study

Previously, we have shown that the ferryl ion ([FeIVO]2+) is easily produced from Fenton's reagent (i.e., a mixture of Fe2+ ions and H2O2 in aqueous solution), using DFT and Car-Parrinello MD calculations. To verify that the ferryl ion can indeed act as the active species in oxidation reactions with Fenton's reagent, we study in the present paper the reactivity of the ferryl ion toward an organic substrate, in particular the oxidation of methane to methanol. In the first part of this paper, we perform static DFT calculations on the reaction of CH4 with the [(H2O)5FeIVO]2+ complex in vacuo that show a strong prevalence of the oxygen-rebound mechanism over the methane coordination mechanism. This is in agreement with the static DFT results for methane oxidation by biocatalysts MMO and P450, but not with those for methane oxidation by bare metal-oxo ions, where the methane coordination mechanism prevails. The highest energy barrier in the oxygen-rebound mechanism is only 3 kcal/mol in vacuo, whereas in the methane coordination mechanism the highest barrier is 23 kcal/mol. Overall the oxidation reaction energy is downhill by 47 kcal/mol. We conclude that the ferryl ion can indeed act as the oxidative intermediate in the Fenton oxidation of organic species. In the second part of this paper, we perform a preliminary assessment of solvent effects on the oxidation by the ferryl ion in aqueous solution using the method of constrained (first principles) molecular dynamics. The free energy barrier of the H-abstraction reaction from methane by the ferryl ion (i.e., the first step in the rebound mechanism) in aqueous solution is, with 22 kcal/mol in solution, significantly higher than in vacuo. Given the fact that methane has a relatively strong C-H bond (ca. 10 kcal/mol stronger than the C-H bonds in the more typical Fenton's reagent substrates), we infer that for many organic substrates oxidation with the ferryl ion as an active intermediate may be a perfectly viable route.     

Quantum pharmacological studies on antimalarial drugs

Summary Linear models for the relation between electronic structure and antimalarial activity of chloroquine drugs have been investigated, based on CNDO/2 molecular orbital calculations. The results indicate that changes in electron density on the atoms N1, N2, C4, C9, and C10 have the strongest influence on the pharmacological activity, so that these atoms can be assumed to form the main active center of these drugs. Correlations improve, if substitution on the nucleus of chloroquine and side chain variations are treated separately. The models found seem to be a useful tool for designing new drugs within the chloroquine series.

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Quantenchemisch-pharmakologische Untersuchungen von Antimalaria-Wirkstoffen

Zusammenfassung Auf der Basis von CNDO/2-Rechnungen wurden lineare Modelle für die Relation zwischen Elektronenverteilung und der Antimalaria-Aktivität von Chlorochinen untersucht. Es zeigte sich, daß Veränderungen in den Elektronendichten der Atome N1, N2, C4, C9 und C10 den stärksten Einfluß auf die pharmakologische Wirkung haben. Es kann somit angenommen werden, daß diese Atome die hauptsächlich aktiven Zentren der Verbindung sind. Die Korrelation wird verbessert, wenn die Substitution am Chlorochin-Kern und Variationen der Seitenketten separat behandelt werden. Die aufgefundenen Modellvorstellungen sollten ein nützliches Werkzeug zur gezielten Synthese neuer Wirkstoffe innerhalb der Chlorochin-Reihe darstellen.

     

Cathodoluminescence Depth Profiling in SiO2:Ge Layers

 For investigation of the luminescent center profile cathodoluminescence measurements are used under variation of the primary electron energy E ₀ = 2…30 keV. Applying a constant incident power regime (E ₀·I ₀ = const), the depth profiles of luminescent centers are deduced from the range of the electron energy transfer profiles dE/dx. Thermally grown SiO₂ layers of thickness d = 500 nm have been implanted by Ge⁺-ions of energy 350 keV and doses (0.5–5)10¹⁶ ions/cm². Thus Ge profiles with a concentration maximum of (0.4 – 4) at% at the depth of d_m≅240 nm are expected. Afterwards the layers have been partially annealed up to T _a = 1100 °C for one hour in dry nitrogen. After thermal annealing, not only the typical violet luminescence (λ = 400 nm) of the Ge centers is strongly increased but also the luminescent center profiles are shifted from about 250 nm to 170 nm depth towards the surface. This process should be described by Ge diffusion processes, precipitation and finally Ge nanocluster formation. Additionally, a Ge surface layer is piled-up extending to a depth of roughly 25 nm.