A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models

The hydration of K(+) is studied using a hierarchy of theoretical approaches, including ab initio Born-Oppenheimer molecular dynamics and Car-Parrinello molecular dynamics, a polarizable force field model based on classical Drude oscillators, and a nonpolarizable fixed-charge potential based on the TIP3P water model. While models based more directly on quantum mechanics offer the possibility to account for complex electronic effects, polarizable and fixed-charges force fields allow for simulations of large systems and the calculation of thermodynamic observables with relatively modest computational costs. A particular emphasis is placed on investigating the sensitivity of the polarizable model to reproduce key aspects of aqueous K(+), such as the coordination structure, the bulk hydration free energy, and the self diffusion of K(+). It is generally found that, while the simple functional form of the polarizable Drude model imposes some restrictions on the range of properties that can simultaneously be fitted, the resulting hydration structure for aqueous K(+) agrees well with experiment and with more sophisticated computational models. A counterintuitive result, seen in Car-Parrinello molecular dynamics and in simulations with the Drude polarizable force field, is that the average induced molecular dipole of the water molecules within the first hydration shell around K(+) is slightly smaller than the corresponding value in the bulk. In final analysis, the perspective of K(+) hydration emerging from the various computational models is broadly consistent with experimental data, though at a finer level there remain a number of issues that should be resolved to further our ability in modeling ion hydration accurately.     

Solution-based chemical synthesis of boehmite nanofibers and alumina nanorods

This article reports an easy chemical method of synthesizing boehmite nanofibers by a modified sol-gel process involving aluminum isopropoxide precursor. Nanorods of gamma-alumina have been successfully prepared after dehydration of the viscous sol at 600 degrees C for 4 h in air. The boehmite nanofibers and gamma-alumina nanorods were characterized by X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy for surface chemistry and functional groups, scanning electron microscopy, high-resolution transmission electron microscopy with selected area electron diffraction, and energy-dispersed spectroscopy for morphology and structure identification. The length of the boehmite nanofibers was found to be more than 10 mum with a crystalline lattice structure. The mechanism of formation of the boehmite nanofibers included the preferential growth along the longitudinal axis due to interaction between the solvent molecules and the surface OH- groups of hydrogen bonds. It is also suggested that the boehmite nanofibers may have formed due to the inherent instability of the planar structure of the boehmite lattice. The diameter of the gamma-alumina nanorods was found to be less than 10 nm with a varying length in the range of 50-200 nm. Boehmite to gamma-Al2O3 transformation was attributed to the loss of water molecules by internal condensation of protons and hydroxyl ions.     

Mathematical Analysis of Reaction–Diffusion Equations Modeling the Michaelis–Menten Kinetics in a Micro-Disk Biosensor

In this study, we have investigated the mathematical model of an immobilized enzyme system that follows the Michaelis–Menten (MM) kinetics for a micro-disk biosensor. The film reaction model under steady state conditions is transformed into a couple differential equations which are based on dimensionless concentration of hydrogen peroxide with enzyme reaction (H) and substrate (S) within the biosensor. The model is based on a reaction–diffusion equation which contains highly non-linear terms related to MM kinetics of the enzymatic reaction. Further, to calculate the effect of variations in parameters on the dimensionless concentration of substrate and hydrogen peroxide, we have strengthened the computational ability of neural network (NN) architecture by using a backpropagated Levenberg–Marquardt training (LMT) algorithm. NNs–LMT algorithm is a supervised machine learning for which the initial data set is generated by using MATLAB built in function known as “pdex4”. Furthermore, the data set is validated by the processing of the NNs–LMT algorithm to find the approximate solutions for different scenarios and cases of mathematical model of micro-disk biosensors. Absolute errors, curve fitting, error histograms, regression and complexity analysis further validate the accuracy and robustness of the technique.     

Polynomial Solution of Non-Central Potentials

We show that the exact energy eigenvalues and eigenfunctions of the Schrödinger equation for charged particles moving in certain class of non-central potentials can be easily calculated analytically in a simple and elegant manner by using Nikiforov and Uvarov (NU) method. We discuss the generalized Coulomb and harmonic oscillator systems. We study the Hartmann Coulomb and the ring-shaped and compound Coulomb plus Aharanov–Bohm potentials as special cases. The results are in exact agreement with other methods.     

Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions

The X-ray crystal structures of mannose trimming enzyme drosophila Golgi alpha-mannosidase II (dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E. In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements around the methionine residues in the protein. Collectively, our studies contradict the long held view that potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.     

Efficient Chemical Protein Synthesis using Fmoc-Masked N-Terminal Cysteine in Peptide Thioester Segments

We report an operationally simple method to facilitate chemical protein synthesis by fully convergent and one-pot native chemical ligations utilizing the fluorenylmethyloxycarbonyl (Fmoc) moiety as an N-masking group of the N-terminal cysteine of the middle peptide thioester segment(s). The Fmoc group is stable to the harsh oxidative conditions frequently used to generate peptide thioesters from peptide hydrazide or o-aminoanilide. The ready availability of Fmoc-Cys(Trt)-OH, which is routinely used in Fmoc solid-phase peptide synthesis, where the Fmoc group is pre-installed on cysteine residue, minimizes additional steps required for the temporary protection of the N-terminal cysteinyl peptides. The Fmoc group is readily removed after ligation by short exposure (<7 min) to 20 % piperidine at pH 11 in aqueous conditions at room temperature. Subsequent native chemical ligation reactions can be performed in presence of piperidine in the same solution at pH 7.     

Investigations into the parallel kinetic resolution of 2-phenylpropanoyl chloride using quasi-enantiomeric oxazolidinones

The resolution of 2-phenylpropanoyl chloride using an equimolar combination of quasi-enantiomeric oxazolidinones is discussed. The levels of diastereoselectivity were found to be dependent upon the structural nature of the metallated oxazolidinone, temperature and metal counter-ion.     

Comparison of the quality of aqueous dispersions of single wall carbon nanotubes using surfactants and biomolecules

The use of single wall carbon nanotubes (SWCNTs) in current and future applications depends on the ability to process SWCNTs in a solvent to yield high-quality dispersions characterized by individual SWCNTs and possessing a minimum of SWCNT bundles. Many approaches for the dispersion of SWCNTs have been reported. However, there is no general assessment which compares the relative quality and dispersion efficiency of the respective methods. Herein we report a quantitative comparison of the relative ability of "wrapping polymers" including oligonucleotides, peptides, lignin, chitosan, and cellulose and surfactants such as cholates, ionic liquids, and organosulfates to disperse SWCNTs in water. Optical absorption and fluorescence spectroscopy provide quantitative characterization (amount of SWCNTs that can be suspended by a given surfactant and its ability to debundle SWCNTs) of these suspensions. Sodium deoxy cholate (SDOCO), oligonucleotides (GT)(15), (GT)(10), (AC)(15), (AC)(10), C(10-30), and carboxymethylcellulose (CBMC-250K) exhibited the highest quality suspensions of the various systems studied in this work. The information presented here provides a good framework for further study of SWCNT purification and applications.     

Effect of β-cyclodextrin complexation on physicochemical properties of zaleplon

The physicochemical properties and dissolution profile of zaleplon (ZPN) β-cyclodextrin (βCD) inclusion complex were investigated. The phase solubility profile of ZPN with β-cyclodextrin was classified as A_L-type. Stability constant with 1:1 molar ratio was calculated from the phase solubility diagram and the aqueous solubility of ZPN was found to be enhanced by 714% (p < 0.001) for β-cyclodextrin. Binary systems of ZPN with βCD were prepared by kneading method. The solid-state properties of complex were characterized by differential scanning calorimetry, Fourier transformation-infrared spectroscopy and powder X-ray diffractometry. It could be concluded that ZPN could form inclusion complex with β-cyclodextrin. The dissolution profile of inclusion complex was determined and compared with those of ZPN alone and its physical mixture. The dissolution rate of ZPN was significantly increased by complexation with βCD, as compared with pure drug and physical mixture.