Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated-B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP-and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, s(R), scaling globally the vdW radii. For good results, a basis set of at least triple-zeta quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively.     

Particle assembly on surface features (patterned surfaces)

Irreversible adsorption (deposition) of spherical particles on surface features of various shapes (collectors) was studied using the random sequential adsorption (RSA) model. The collectors in the form of linear line segments, semicircles, and circles were considered. Numerical simulation of the Monte Carlo type enabled one to determine particle configurations, the jamming coverage, and the end to end length of particle monolayers for various collector length (L) to particle size (d) ratio L = L/d. It was revealed that the jamming coverage for linear collectors Theta'(infinity) increases for L > 2 according to a linear dependence with respect to 1/L. For 2 > L > 1, a parabolic dependence of Theta'(infinity) on 1/L was predicted, characterized by the maximum value of Theta'(infinity) = 1.125 for L = 4/3. These dependencies allowed one to formulate an equation determining the length of nanostructures on surfaces if the averaged number of adsorbed particles is known. It was also predicted that the end to end length of the monolayer on a linear collector /L increased linearly with 1/L for L > 2. For 2 > L > 1 the dependence of /L on L was approximated by a polynomial expression, exhibiting a maximum of /L = 1.17 for L = 1.45. In the case of circular collectors, the jamming coverage was found to be substantially smaller for the same value of 1/L. It was demonstrated that the theoretical results are in agreement with our preliminary experimental data obtained for latex particles adsorbing on polyelectrolyte modified mica and on patterned surfaces obtained by a polymer-on-polymer stamping technique of gold covered silicon (Zheng et al. Langmuir 2002, 18, 4505).     

Total synthesis of iejimalide A-D and assessment of the remarkable actin-depolymerizing capacity of these polyene macrolides

A concise and convergent total synthesis of the highly cytotoxic marine natural products iejimalide A-D (1-4) is reported, which relies on an effective ring-closing metathesis (RCM) reaction of a cyclization precursor containing no less than 10 double bonds. Because of the exceptional sensitivity of this polyunsaturated intermediate and its immediate precursors toward acid, base, and even gentle warming, the assembly process hinged upon the judicious choice of protecting groups and the careful optimization of all individual transformations. As a consequence, particularly mild protocols for Stille as well as Suzuki reactions of elaborate coupling partners have been developed that hold considerable promise for applications in other complex settings. Moreover, a series of non-natural "iejimalide-like" compounds has been prepared, differing from the natural lead in the polar head groups linked to the macrolide's N-terminus. With the aid of these compounds it was possible to uncover the hitherto unknown effect of iejimalide and analogues on the actin cytoskeleton. Their capacity to depolymerize this microfilament network rivals that of the latrunculins which constitute the standard in the field. Structural modifications of the peptidic terminus in 2 are thereby well accommodated, without compromising the biological effects. The iejimalides hence constitute an important new class of probe molecules for chemical biology in addition to their role as promising lead structures for the development of novel anticancer agents.     

Brdicka-type processes of cysteine and cysteine-containing peptides on silver amalgam electrodes

Silver solid amalgam electrode (AgSAE) was used for differential pulse voltammetric (DPV) measurements of cysteine and cysteine-containing peptides, glutathione, gamma-Glu-Cys-Gly and phytochelatin (gamma-Glu-Cys)(3)-Gly (PC3), in the presence of Co(II) ions. It had been established earlier that cysteine-containing peptides and proteins catalyze hydrogen evolution at mercury electrodes in presence of cobalt salts; these processes are known as the Brdicka reaction. DPV signals measured with the AgSAE, the surfaces of which had been modified by mercury meniscus or mercury film, were qualitatively the same as those obtained with the hanging mercury drop electrode (HMDE). With these electrodes the number and the intensity of Brdicka signals of cysteine, glutathione and PC3 differed, making a distinction among them possible. On the other hand, with the polished silver solid amalgam electrode (the surface of which was completely free of liquid mercury) all three compounds produced only one but strikingly intense peak in the region of Brdicka reaction. Using this signal, cysteine, glutathione as well as PC3 could be determined at 10(-8)M level, representing sensitivity up to 2 orders of magnitude better than attained with the mercury-modified AgSAEs or HMDE.     

High-performance liquid chromatography with nuclear magnetic resonance detection applied to organosilicon polymers. Part 2. Comparison with other methods

LC-NMR utilizing (1)H and (29)Si NMR spectroscopy is ideally suited for the analysis of silicones. It is shown that reversed phase gradient LC-NMR surpasses standard gel permeation chromatography (GPC) and diffusion ordered spectroscopy (DOSY) in the analysis of model hydride terminated polydimethylsiloxane. (1)H and (29)Si NMR in the stopped-flow arrangement leads to full identification of the components. Concentration gradient introduces a dependence of the (29)Si shifts on solvent composition, this dependence can be substantially reduced by a proposed method of referencing. It is shown that the ADEQUATE version of powerful but insensitive 2D INADEQUATE experiment can be used for complete line assignment.     

Organocatalysis with a fluorous tag: asymmetric reduction of imines with trichlorosilane catalyzed by amino acid-derived formamides

Asymmetric reduction of ketimines 1 with trichlorosilane can be catalyzed by N-methylvaline-derived Lewis-basic formamides 3a-d with high enantioselectivity (< or =95% ee) and low catalyst loading (1-5 mol %) at room temperature in toluene. Appending a fluorous tag, as in 5a-c, simplifies the isolation procedure, while preserving high enantioselectivity (< or =92% ee).     

Obesity and Energy Substrate Transporters in Ovarian Cancer—Review

Ovarian cancer is the seventh most common cancer in women. It is characterized by a high mortality rate because of its aggressiveness and advanced stage at the time of diagnosis. It is a nonhomogenous group of neoplasms and, of which the molecular basics are still being investigated. Nowadays, the golden standard in the treatment is debulking cytoreductive surgery combined with platinum-based chemotherapy. We have presented the interactions and the resulting perspectives between fatty acid transporters, glucose transporters and ovarian cancer cells. Studies have shown the association between a lipid-rich environment and cancer progression, which suggests the use of correspondent transporter inhibitors as promising chemotherapeutic agents. This review summarizes preclinical and clinical studies highlighting the role of fatty acid transport proteins and glucose transporters in development, growth, metastasizing and its potential use in targeted therapies of ovarian cancer.     

AdipoRon,an Orally Active,Synthetic Agonist of AdipoR1 and AdipoR2 Receptors Has Gastroprotective Effect in Experimentally Induced Gastric Ulcers in Mice

Introduction: Adiponectin is a hormone secreted by adipocytes, which exhibits insulin-sensitizing and anti-inflammatory properties and acts through adiponectin receptors: AdipoR1 and AdipoR2. The aim of the study was to evaluate whether activation of adiponectin receptors AdipoR1 and AdipoR2 with an orally active agonist AdipoRon has gastroprotective effect and to investigate the possible underlying mechanism. Methods: We used two well-established mouse models of gastric ulcer (GU) induced by oral administration of EtOH (80% solution in water) or diclofenac (30 mg/kg, p.o.). Gastroprotective effect of AdipoRon (dose 5 and 50 mg/kg p.o.) was compared to omeprazole (20 mg/kg p.o.) or 5% DMSO solution (control). Clinical parameters of gastroprotection were assessed using macroscopic (gastric lesion area) and microscopic (evaluation of the gastric mucosa damage) scoring. To establish the molecular mechanism, we measured: myeloperoxidase (MPO), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPX) activities; glutathione (GSH) level; and IL-1β, adenosine monophosphate-activated protein kinase (AMPK), and phosphorylated AMPK expression in gastric tissue. Results: AdipoRon produced a gastroprotective effect in both GU mouse models as evidenced by significantly lower macroscopic and microscopic damage scores. AdipoRon exhibited anti-inflammatory effect by reduction in MPO activity and IL-1β expression in the gastric tissue. Moreover, AdipoRon induced antioxidative action, as demonstrated with higher GSH levels, and increased SOD and GPX activity. Conclusions: Activation of AdipoR1 and AdipoR2 using AdipoRon reduced gastric lesions and enhanced cell response to oxidative stress. Our data suggest that AdipoR1 and AdipoR2 activation may be an attractive therapeutic strategy to inhibit development of gastric ulcers.     

Electro-optic and dielectric properties of new binary ferroelectric and antiferroelectric liquid crystalline mixtures

Several new binary liquid crystalline mixtures have been designed and their properties were studied by complementary methods. It has been shown that even both pure components used for the mixture design possess the ferroelectric behaviour; the induced antiferroelectric smectic phase has been detected for one of the prepared mixtures. The phase diagram has been constructed and the existence of the antiferroelectric phase was confirmed by switching time and dielectric spectroscopy measurements. Some of the resulted mixtures possess very high values of the tilt angle that reaches close below 45° degrees at saturation. Values of spontaneous polarisation were found within 50–200 nC/cm² in dependence of the mixture’s composition. Due to specific properties, the obtained mixtures might be interesting for further design of multicomponent mixtures and formulation of the advanced nanocomposite systems.     

DG method for numerical pricing of multi-asset Asian options—The case of options with floating strike

Option pricing models are an important part of financial markets worldwide. The PDE formulation of these models leads to analytical solutions only under very strong simplifications. For more general models the option price needs to be evaluated by numerical techniques. First, based on an ideal pure diffusion process for two risky asset prices with an additional path-dependent variable for continuous arithmetic average, we present a general form of PDE for pricing of Asian option contracts on two assets. Further, we focus only on one subclass—Asian options with floating strike—and introduce the concept of the dimensionality reduction with respect to the payoff leading to PDE with two spatial variables. Then the numerical option pricing scheme arising from the discontinuous Galerkin method is developed and some theoretical results are also mentioned. Finally, the aforementioned model is supplemented with numerical results on real market data.