An estimation method of binding free energy in terms of ABEEMσπ/MM and continuum electrostatics fused into LIE method

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. The linear interaction energy method is combined with atom‐bond electronegativity equalization method at σπ level Force field (fused into molecular mechanics) and generalized Born continuum model calculation of electrostatic solvation for the estimation of the absolute free energy of binding. The parameters of this method are calibrated by using a training set of 24 HIV‐1 protease–inhibitor complexes (PDB entry 1AAQ). A correlation coefficient of 0.93 was obtained with a root mean square deviation of 0.70 kcal mol^?1. This approach is further tested on seven inhibitor and protease complexes, and it provides small root mean square deviation between the calculated binding free energy and experimental binding free energy without reparametrization. By comparing the radii of gyration and the hydrogen bond distances between ligand and protein of three training model molecules, the consistent comparison result of binding free energy is obtained. It proves that this method of calculating the binding free energy with appropriate structural analysis can be applied to quickly assess new inhibitors of HIV‐1 proteases. To test whether the parameters of this method can apply to other drug targets, we have validated this method for the drug target cyclooxygenase‐2. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Effects of amorphous poly(vinyl acetate) on crystalline morphology of poly(3-hydroxybutyric acid-co-3-hydroxyvaleric acid)

The amorphous and crystalline phase behavior, spherulite morphology, and interactions between amorphous poly(vinyl acetate) (PVAc) and poly(3-hydroxybutyric acid-co-3-hydroxyvaleric acid) (PHBV) were examined using differential scanning calorimetry, polarized-light optical and scanning electron, atomic-force microscopy (DSC, POM, SEM, AFM), and small-angle X-ray scattering (SAXS). The PHBV/PVAc blend was found to be miscible with an almost linear T _g-composition relationship, indicating perfect homogeneity. Interaction parameter by melting point depression is a negative value of χ = −0.32, suggesting quite favorable interaction strength. With the intimate interaction between the amorphous PVAc and crystalline PHBV polymers, effects of PVAc on the spherulitic morphology of PHBV are quite significant. Owing to the higher T _g of PVAc (than that of PHBV), the spherulite growth rate of PHBV was depressed by increasing PVAc content in blends. Neat PHBV exhibits ring-banded spherulites when crystallized at T_c = 60 ~ 110^° C {T_{\rm{c}}} = {6}0\sim {11}0^\circ {\hbox{C}} ; however, with increasing PVAc content in the blends, the temperature range at which the PHBV/PVAc blends exhibit ring-banded spherulites remains similar but the regularity increases, and the inter-ring spacing significantly decreases. In addition, the spherulite size and ring-band patterns therein are strongly dependent on T _max (190 vs. 220 °C, respectively, for erasing prior nuclei), from which the blends were quenched to a T _c (60–110 °C) for crystallization. For PHBV/PVAc blends crystallized at the same T _c from different T _max, higher T _max tends to erase nuclei, leading to larger spherulites. However, such larger spherulites owing to higher T _max are not necessarily packed with thicker lamellae.     

Increased stability and size of a bubble on a superhydrophobic surface

Computational and theoretical models of millimeter-sized bubbles placed on upright hydrophobic and superhydrophobic surfaces are compared with experimental data here. Although the experimental data for a hydrophobic surface corroborated the computational and theoretical data, the case of a superhydrophobic surface showed the bubbles to be able to contain significantly larger volumes than predicted. This is attributed to the greater ability of the bubble contact line to advance compared with its tendency to detach from the surface because of buoyancy. We surmise that a static model therefore describes only an unstable equilibrium for these bubbles, which unless heavily isolated from external influences are more likely to assume a larger stable size.     

Two-dimensional solvent-mediated phase transformation in lipid membranes induced by sphingomyelinase

The spatial pattern changes in model raft membranes during sphingomyelinase (SMase)-induced solvent-mediated phase transformation are characterized in terms of a model that combines three major kinetic processes suggested by experimental observations: the release of sphingomyelin (SM) by the dissolution of SM-enriched domains within the raft membrane, the diffusion of SM from the dissolution sites to the reaction site in a solvent-like fluid lipid phase, and the consumption of SM by the enzymatic reaction at this reaction site, termed an SMase feature. Such processes may be responsible for the control of morphological changes in cell membrane organization, which are suggested to influence the signal transduction through the cell membrane walls. The model predictions are shown to be consistent with our previously reported experimental results. We numerically evaluated the range of possible scenarios of spatial pattern change and provide analytical expressions for SM-domain-area change rates and total dissolution times for several limiting cases. The model results suggest that it may be possible to tune the pattern changes by adjusting the relative importance of each of the three kinetic processes, which can be discriminated through experimentally measurable time-dependent SM concentration distributions or SM-domain-area variations with time.     

Interaction of polymyxin B with ds-DNA, and determination of DNA or polymyxin B via resonance Rayleigh scattering and resonance non-linear scattering spectra

Assays were developed for DNA or polymyxin B (PMB) based on enhanced resonance Rayleigh scattering (RRS) and resonance nonlinear scattering (including second order scattering and frequency doubling scattering) that result from the interaction of PMB with DNA. A minor-groove binding mechanism is suggested from the results obtained with RRS and from absorption and circular dichroism spectroscopy. The types of interaction and reasons of RRS enhancement are discussed. Linear relationships do exist over a wide range between the intensity of enhanced scattering and the concentrations of either DNA or PMB. When ctDNA is used as a probe to determine PMB, the detection limit (3σ) is 9.8 ng mL^?1. When PMB is used as a probe to determine DNA, the detection limit (3σ) is in the range from 3.8 to 9.0 ng mL^?1.

Native biofilm cultured under controllable condition and used in mediated method for BOD measurement

In this article, we developed a native biofilm (NBF) bioreactor used for biochemical oxygen demand mediated method (BOD_Med). There were two innovations differed from previous BOD_Med assay. Firstly, the immobilization of microorganisms was adopted in BOD_Med. Secondly, the NBF was introduced for BOD measurement. The NBF bioreactor has been characterized by optical microscopy. A culture condition of NBF with 24 h, 35 °C and pH 7 was optimized. Furthermore, a measuring condition with 35 °C, pH 7 and 55 mM ferricyanide in 1 h incubation were optimized. Based on the optimized condition, the real wastewater samples from local sewage treatment plant had been measured. Performances of the NBFs proposed at different culture conditions were recorded for 110 d, and the results indicated that long-term storage stability was obtained. With the proposed method, an uncontaminated native microbial source solution can be obtained from a wastewater treatment plant. In this way, we can ensure that the microbial species of all in the NBF are same as that in the target to be measured.     

Selective detection of dopamine in the presence of uric acid using a gold nanoparticles-poly(luminol) hybrid film and multi-walled carbon nanotubes with incorporated β-cyclodextrin modified glassy carbon electrode

Gold nanoparticles-poly(luminol) (Plu-AuNPs) hybrid film and multi-walled carbon nanotubes with incorporated β-cyclodextrin modified glassy carbon electrode (β-CD-MWCNTs/Plu-AuNPs/GCE) was successfully prepared for simultaneous determination of dopamine (DA) and uric acid (UA). The surface of the modified electrode has been characterized by X-ray photo-electron spectroscopy (XPS), energy dispersive X-ray spectroscopy (EDS), field-emission scanning electron microscope (SEM) and transmission electron microscope (TEM). Cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and differential pulse voltammetry (DPV) have been used to investigate the β-CD-MWCNTs/Plu-AuNPs composite film. Gold nanoparticles anchored into poly(luminol) film exhibited catalytic activity for DA. MWCNTs with incorporated β-CD can greatly promote the direct electron transfer. In 0.10 M phosphate buffer solution (PBS, pH 7.0), the DPV response of the β-CD-MWCNTs/Plu-AuNPs/GCE sensor to DA is about 8-fold as compared with the Plu-AuNPs/GCE sensor, and the detection limit for DA is about one order of magnitude lower than the Plu-AuNPs/GCE sensor. The steady-state current response increases linearly with DA concentration from 1.0 × 10⁻⁶ to 5.6 × 10⁻⁵ M with a low detection limit (S/N = 3) of 1.9 × 10⁻⁷ M. Moreover, the interferences of ascorbic acid (AA) and uric acid (UA) are effectively diminished. The applicability of the prepared electrode has been demonstrated by measuring DA contents in dopamine hydrochloride injection.     

Highly luminescent, polyaryl mesobenzanthrones

Several highly luminescent, aryl-substituted mesobenzanthrones (7H-benz[de]anthracen-7-ones) were prepared by a simple, two-step synthesis: addition of a carboxylated benzyne to a cyclopentadienone followed by an intramolecular Friedel-Crafts acylation. These compounds exhibit brilliant, yellow-green luminescence with quantum yields ranging from 0.01 to 1, depending on the aryl substituents present, and their photophysical behavior was elucidated by experimental and computational methods.