Inner-sphere electron-transfer reorganization energies of zinc porphyrins

Inner-sphere electron-transfer reorganization energies of Zn(protoporphyrin IX) and Zn(octaethylporphyrin) are determined from band-shape analyses of the first ionization obtained by gas-phase valence photoelectron spectroscopy. The experimentally determined total inner-sphere reorganization energies for self-exchange (120-140 meV) indicate that structural changes upon oxidation are largely confined to the porphyrin ring, and substituents on the ring or solvent and other environmental factors make smaller contributions. Computational estimates by different models vary over a wide range and are sensitive to numerical precision factors for these low reorganization energies. Of current computational models that are widely available and practical for molecules of this size, functionals that contain a mixture of Hartree-Fock exchange and DFT exchange-correlation appear to be the most applicable.     

Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Thiazole orange-peptide conjugates: sensitivity of DNA binding to chemical structure

[structure: see text] Derivatives of the highly fluorescent and DNA-binding dye thiazole orange (TO) are described that feature appended peptides. Functionalization of TO can be achieved at either of the endocyclic nitrogens, and the photophysical properties and DNA-binding modes are sensitive to the position of the tethered peptide. A series of TO-peptide conjugates are described, demonstrating the utility of a solid-phase synthesis approach to their preparation and illustrating how the photophysical and DNA-binding properties of the compounds are influenced by chemical structure.     

An efficient preparation of novel 5-fluoropyrazolin-3-one derivatives from α-trifluoromethylated α-arylacetates

The reactions of α-trifluoromethylated α-arylacetates 1 with 3 equiv of hydrazine, methylhydrazine or benzylhydrazine in 1,4-dioxane at reflux for 24 h afforded the corresponding 5-fluoropyrazolin-3-one derivatives 3a-m in high yields. Similarly, treatment of 1 with 3 equiv of PhNLiNH₂ in THF at −78 °C, followed by warming to room temperature, resulted in the formation of 3n-s in high yields.     

Development and Validation of HPTLC Method for Simultaneous Determination of Quercetin and Kaempferol in Leaves of Two Chemotypes of Centella asiatica

JPC – Journal of Planar Chromatography – Modern TLC - A simple, accurate and precise high-performance thin-layer chromatography (HPTLC) method was developed and validated for the...     

Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures. For 9 of 10 predictions, the native backbone conformation is identified correctly. Electrostatic energy is modeled as a pairwise sum of interactions between anisotropic atomic charge densities. Model repulsion energy has a softness similar to that seen in ab initio data. Intrinsic torsional energy is modeled as a sum over pairs of adjacent torsion angles of 2-dimensional Fourier series. Hydrophobic energy is that of a hydration shell model. The remainder of hydration free energy is obtained as the energetic effect of a continuous dielectric medium. Parameters are adjusted to reproduce the following data: a complete set of ab initio energy surfaces, meaning one for each pair of adjacent torsion angles of each blocked amino acid; experimental crystal structures and sublimation energies for nine model compounds; ab initio energies over 1014 conformations of 15 small-molecule dimers; and experimental hydration free energies for 48 model compounds. All ab initio data is at the Hartree–Fock/6–31G* level. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 548–573, 1998     

Solid scintillation proximity membranes: I: Characterization of polysulfone-inorganic fluor morphologies precipitated from NMP solutions

Solid scintillation proximity membranes were prepared by coagulation of polysulfone polymer solutions containing cerium-activated yttrium silicate particles (CAYS) as a fluor. Membranes were formed by three different solidification processes: precipitation of the polymer-rich phase after liquid–liquid phase separation, vitrification via solvent evaporation, or rapid polymer collapse due to fast exchange between solvent in the solution and nonsolvent in the coagulation bath. The results indicate that when the coagulation process includes the liquid–liquid phase separation due to nucleation of the polymer-lean phase, the inorganic fluor particles are expressed out of the polymer-rich phase and separated from the polymer matrix. On the contrary, solidification by the vitrification of the polymer solution through solvent evaporation results in the inorganic fluors being surrounded by the polymer matrix, much like the dispersed state in the solution. In contrast, rapid collapse of the polymer also induces entrapment of the fluor in the polymer structure. However, fluor impregnation in the polymer matrix is distinguished from that in the vitrified membrane in that the impregnation is due to localized impingement of the fluor on the polymer structure rather than envelopment by polymer molecules.