ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions

A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self-Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins 1999, 35, 133). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an alpha-helix and a beta-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5-5.0 with respect to gas-phase calculations.     

Understanding the role of surfactants on the preparation of ZnS nanocrystals

We have synthesized surface modified ZnS nanoparticles of size 2-3 nm using non-ionic surfactant-stabilized reverse emulsions. The non-ionic surfactants in the Span series, i.e. sorbitan monolaurate (Span 20) and sorbitan monooleate (Span 80) of hydrophilic-lipophilic balance (HLB) values of 8.6 and 4.3, respectively, have been used for the stabilization of emulsions. The role of these surfactants in controlling the size and properties of the ZnS nanoparticles has been discussed. The triethylamine (TEA) has been proved to be the effective surface modifying (capping) agent for the preparation of free-standing ZnS nanoparticles. The Span 20 with the higher HLB value of 8.6 has been found to be highly suitable in synthesizing TEA-capped ZnS nanoparticles of smaller size and higher photophysical characteristics compared to that of the Span 80 of lower HLB value of 4.3. A mechanism for the formation of TEA-capped ZnS nanoparticles from the surfactant-stabilized reverse emulsions has been proposed.     

Spectroscopic properties of the molecular ions BeX+ (X=Na,K, Rb): forming cold molecular ions from an ion–atom mixture by stimulated Raman adiabatic process

In this theoretical work, we calculate potential energy curves, spectroscopic parameters and transition dipole moments of molecular ions BeX⁺ (X=Na, K, Rb) composed of alkaline ion Be and alkali atom X with a quantum chemistry approach based on the pseudopotential model, Gaussian basis sets, effective core polarisation potentials and full configuration interaction. We study in detail collisions of the alkaline ion and alkali atom in quantum regime. Besides, we study the possibility of the formation of molecular ions from the ion–atom colliding systems by stimulated Raman adiabatic process and discuss the parameters regime under which the population transfer is feasible. Our results are important for ion–atom cold collisions and experimental realisation of cold molecular ion formation.     

Facile extraction,processing and characterization of biorenewable sisal fibers for multifunctional applications

Synthetic fibers based materials have replaced most of the traditional metallic/ceramic materials for a number of applications owing to their enormous properties such as light weight, specific strength and modulus to name a few. Unfortunately, the traditional synthetic fibers are not desired from the health and environmental point of view. So, in this work, we have carried out the isolation, processing and characterization of cellulosic sisal fibers. These fibers were extracted for the first time by a simple and new unique mechanical extraction technique without affecting the quality of fibers. Subsequently these cellulosic sisal fibers were thoroughly characterized for their physicochemical, microstructure and mechanical properties. These fibers were then converted into fine textured sisal textile yarn made out of 3–6 sisal fibers in continuous operation and used for the preparation of new green materials. Different properties of fine textured sisal textile and the impact of sisal fine textile on the physical, microstructural, thermal and mechanical characteristics of the green materials were studied and discussed in detail.     

Solution behavior of normal and reverse triblock copolymers (pluronic L44 and 10R5) individually and in binary mixture

Solution properties of pluronics L44 or L [(PEO)(10)(PPO)(23)(PEO)(10)] and 10R5 or R [(PPO)(8)(PEO)(22)(PPO)(8)] were studied individually as well in their binary mixtures in aqueous medium. The critical micelle concentration (CMC), critical micelle temperature, and cloud point (CP) were determined. Ideal and nonideal behaviors of their mixtures in the formation of CMC and CP were observed; the energetics of the studied processes were determined. Spectrophotometry, isothermal titration calorimetry and dynamic light scattering (DLS) methods were used for evaluations. Morphologies of the dispersed L, R, and their mixtures along with their polydispersities were determined from DLS measurements. Atomic force microscopy was also employed. The interfacial properties of L and R were investigated forming Langmuir monolayers in a surface balance. The surface pressures (π) generated by the compounds were moderate, the area per molecule was higher for R than L. R has shown antibacterial activity against both gram positive and gram negative bacteria whereas L was inactive in this respect.     

A tandem Petasis-Ugi multi component condensation reaction: solution phase synthesis of six dimensional libraries

Amino acids with three points of diversity generated from the Petasis boronic acid-Mannich reaction can be used as one of the four components of the Ugi condensation to prepare six dimensional libraries of dipeptide amides.     

Rotation sensitivity of Lau fringes: an analysis based on coherence theory

An analysis based on coherence theory is presented, which explains the experimentally observed rotation sensitivity of the contrast of Lau fringes obtained under spatially incoherent illumination.     

One pot low temperature synthesis of graphene coupled Gd-doped ZnFe<Subscript>2</Subscript>O<Subscript>4</Subscript> nanocomposite for effective removal of antibiotic levofloxacin drug

Nanocomposites of reduced graphene oxide (rGO) coupled gadolinium doped ZnFe₂O₄ (GZFG) have been successfully one pot in-situ synthesized adopting low temperature solution process from zinc nitrate, iron nitrate, gadolinium acetate and graphene oxide with varying concentrations of gadolinium (upto 10% Gd with respect to Zn) in the precursor medium. X-ray diffraction and transmission electron microscopy studies confirm the presence of single phase cubic spinel structure of ZnFe₂O₄ that uniformly distributed over the rGO layers. With increasing Gd doping concentration in precursor medium, the average crystallite size of ZnFe₂O₄ diminishes gradually from ~11 to ~5.5?nm. Raman and X-ray photoelectron spectral analyses confirm an existence of interaction between rGO and ZnFe₂O₄ in GZFG samples. Using antibiotic levofloxacin in water, the drug removal capacity (DRC) of GZFG has been performed by optimization of parameters such as gadolinium doping concentration in precursor medium, solution pH, etc. However, the gadolinium doping leads to an improvement in DRC of the nanocomposite and the 5% Gd doped sample shows about 86% DRC at the optimized condition. This simple strategy can be utilized in the synthesis of rGO coupled Gd doped other metal oxide nanocomposites for DRC application.

Open image in new window

     

Sol-Emulsion-Gel Synthesis of Shaped Powders in the System BaO-TiO2

Shaped tetragonal barium titanate (BaTiO₃) particles were prepared by the sol-emulsion-gel method with systematic variation of the concentration of a non-ionic surfactant in the organic phase (oil phase) of water-in-oil (w/o) emulsions above or below the critical micelle concentration (CMC). An acetate-based sol with equivalent oxide ratio BaO : TiO₂ = 1 : 1 was selected for the study. Micelle formation of the surfactant and their self-aggregation apparently played an important role in controlling the shape and size of the droplets and accordingly shape and size of the final barium titanate particles resulting therefrom. Transmission electron microscopy (TEM) revealed that with low concentration of the surfactant (2–5 vol%) ill-formed spheres were obtained. Spherical particles were formed with increasing the surfactant concentration to 7 vol%. At 12 vol% of the surfactant, rod-like particles were first found to form, which with further increase in surfactant concentration to 15–20 vol%, gradually transformed to cube-like/lamellar type particles. Attempts have been made to explain the various particle shapes in terms of surfactant aggregation.     

Reaction of cis-Ru(bpy)2Cl2 with 1-phenyl 5-(aminophenyl) 9-(2-pyridyl) benzimidazole derivatives: crystal structures of N-(4-chlorophenyl) imidazo[1,5a] pyridine and cis-[Ru(bpy)2(MeCN)2](ClO4)2

Reaction of 1-phenyl 5-(aminophenyl) 9-(2-pyridyl) benzimidazole derivatives (2) with cis-Ru(bpy)₂Cl₂ in MeCN results in the formation of N-(aryl) imidazo[1,5a] pyridine derivatives (4) and cis-[Ru(bpy)₂(MeCN)₂]²⁺ (5). Crystal structures of N-(4-chlorophenyl) imidazo[1,5a] pyridine (4b) and cis-[Ru(bpy)₂(MeCN)₂](ClO₄)₂ (5) are also reported.