Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

A systematic approach to construct a low-dimensional free energy landscape from a classical molecular dynamics (MD) simulation is presented. The approach is based on the recently proposed dihedral angle principal component analysis (dPCA), which avoids artifacts due to the mixing of internal and overall motions in Cartesian coordinates and circumvents problems associated with the circularity of angular variables. Requiring that the energy landscape reproduces the correct number, energy, and location of the system's metastable states and barriers, the dimensionality of the free energy landscape (i.e., the number of essential components) is obtained. This dimensionality can be determined from the distribution and autocorrelation of the principal components. By performing an 800 ns MD simulation of the folding of hepta-alanine in explicit water and using geometric and kinetic clustering techniques, it is shown that a five-dimensional dPCA energy landscape is a suitable and accurate representation of the full-dimensional landscape. In the second step, the dPCA energy landscape can be employed (e.g., in a Langevin simulation) to facilitate a detailed investigation of biomolecular dynamics in low dimensions. Finally, several ways to visualize the multidimensional energy landscape are discussed.     

Concise synthesis of enantiopure erythro-saccharinic acid lactone and potassium (2R,3R)-2,3,4-trihydroxy-2-methylbutanoate

A short and efficient approach was applied to the total synthesis of erythro-saccharinic acid lactone and the leaf-closing substance potassium (2R,3R)-2,3,4-trihydroxy-2-methylbutanoate from a 2-C-hydroxymethyl-d-erythrose derivative, using a combined strategy.     

Carbon-13 and proton magnetic resonance spectra of 2,4-disubstituted 3,3-diphenyltetrahydrofurans derived from isomethadone and isomethadol

Proton and carbon-13 nmr spectra for cis- and trans-2-ethyl-3,3-diphenyl-4-methyltetrahydrofurans and 2-ethylidene-3,3-diphenyl-4-methyltetrahydrofuran, derived from the pyrolysis of the quaternary ammonium salts of the diastereomeric isomethadols and isomethadone, respectively, are reported. ¹H and ¹³C chemical shifts and ¹H-¹H coupling constants have been assigned in each case. The isomeric teterahydrofurans have been analyzed in terms of a half-chair conformation, and an envelope conformation for the ethylidene derivative.     

Influence of the flow history on stress growth and structure changes in the thermotropic liquid crystalline polymer Vectra B950

The structure changes in the start-up flow of the thermotropic liquid crystalline polymer Vectra 8950 are probed by performing transient experiments after various flow histories. The shear and normal stress growth curves of a squeezed sample and of a randomly oriented sample show a pronounced overshoot at low strains, whereas the stress growth curve of a sample pre-sheared until steady state shows a gradual increase. This first peak is associated with the re-orientation of the director into the shearing plane. All stress transients show a second broad maximum at large strains that results from the generation of a steady defect network. The effect of varying the relaxation period after pre-shearing is reflected in the appearance of two peaks in the subsequent stress growth curves. One of these peaks shifts linearly with re laxation period and the other is more or less fixed in position. The orientation of the molecules during steady shear flow is on average in the flow direction. Intermediate orientation levels may exist in the transient depending on the amount of strain. The material is able to maintain the flow-induced orientation distribution for a long time after cessation of flow. This is reflected in a similar fashion in the initial magnitudes of the stresses and the dynamic moduli after various preshear strains. Moreover, the dynamic moduli decrease with time after cessation of steady shear flow, indicating that the orientation increases during relaxation.     

Determination of hydrogen peroxide by using a flow injection system with immobilized peroxidase and long pathlength capillary spectrophotometry

The development of a highly sensitive method for the determination of nanomolar concentrations of hydrogen peroxide in the liquid phase is described. This paper demonstrates for the first time a flow injection analysis (FIA) system with immobilized enzyme reactor combined with a total internal reflective cell (a liquid waveguide capillary cell (LWCC)) and spectrophotometric detection, for the development of an improved procedure for the determination of hydrogen peroxide. Moreover, the newly synthesized 4-aminopyrazolone derivative, 4-amino-5-(p-aminophenyl)-1-methyl-2-phenyl-pyrazol-3-one (DAP), is used as a color coupler in its oxidative condensation with the sodium salt of N-ethyl-N-sulphopropylaniline sodium salt (ALPS) which acts as a hydrogen donor. Immobilization of peroxidase is achieved by coupling the periodate-treated enzyme to aminopropyl controlled-pore glass (CPG) beads. The determination of hydrogen peroxide is carried out in a 0.1 M phosphate buffer and the product is monitored at 590 nm with a charge-coupled device (CCD) detector equipped with fiber optics in a fully computerized system. The interference of different species, mainly ionic, was investigated.The method permits detection down to 4 nmol l⁻¹ hydrogen peroxide (signal-to-noise ratio=3). A linear calibration graph was obtained over the range 20-700 nmol l⁻¹. The relative standard deviation (R.S.D.) at 300 nmol l⁻¹ H₂O₂ is 1.7% (n=7). The method was successfully applied for the determination of hydrogen peroxide in samples from a vat-cleaning process.     

One-pot synthesis of highly crystalline mesoporous TiO2 nanoparticle assemblies with enhanced photocatalytic activity

We report an unprecedented formation of mesoporous titania via a surfactant-assisted aggregating assembly of TiO(2) nanoparticles. These mesostructures possess a highly crystalline anatase phase, large and accessible pore surface area, and exhibit superior photocatalytic performance.     

Palladium catalyzed reductive decarboxylation of allyl α-alkenyl-β-ketoesters. A new synthesis of (E)-3-alkenones

The reductive decarboxylation of α-alkenyl derivatives of allyl-β-ketoesters was achieved by use of palladium(0) catalyst generated in situ from Pd(OAc)₂ and PPh₃, with triethylammonium formate as the hydride source, in THF. The reaction proceeds smoothly and cleanly, with linear alkenyl derivatives of allyl-β-ketoesters, to afford (E)-3-alkenones in good to excellent yields (73-92%) and high stereoselectivity (>98%).     

Synthesis,characterization, crystal structures, in vitro and in vivo antitumor activity of palladium(II) and zinc(II) complexes with 2-formyl and 2-acetyl pyridine N(4)-1-(2-pyridyl)-piperazinyl thiosemicarbazone

The present paper includes synthesis and spectral characterization of the novel prepared palladium(II) and zinc(II) complexes with 2-formyl pyridine N(4)-1-(2-pyridyl)-piperazinyl thiosemicarbazone, HFo4Npypipe, 1 and the 2-acetyl pyridine N(4)-1-(2-pyridyl)-piperazinyl thiosemicarbazone, HAc4Npypipe, 2. The Pd(II) complexes [PdCl(Fo4Npypipe)], 3, [PdCl(Ac4Npypipe)], 4 and the Zn(II) complexes [ZnCl₂(Fo4Npypipe)], 5 and [ZnCl₂(Ac4Npypipe)], 6 have been characterized by elemental analyses and spectroscopic studies. The crystal structure of the complexes [PdCl(Fo4Npippy)], 3 and [PdCl(Ac4Npippy)], 4, have been solved by single-crystal X-ray diffraction. The electronic, IR, UV/Vis, and NMR spectroscopic data of the complexes are reported. The results of the cytotoxic activity of 1–6 have been evaluated in vitro against the cells of three human cancer cell lines: MCF-7, T24, A-549 and a mouse L-929 (a fibroblast-like cell line cloned from strain L). For selected compounds 2 and 6 the acute toxicity and antitumor activity were evaluated on leukemia P388-bearing mice. The Zn(II) compounds 5 and 6 are considered as agents with potential antitumor activity, and can therefore be candidates for further stages of screening in vitro and/or in vivo.