Modeling and predicting binding affinity of phencyclidine‐like compounds using machine learning methods

Machine learning methods have always been promising in the science and engineering fields, and the use of these methods in chemistry and drug design has advanced especially since the 1990s. In this study, molecular electrostatic potential (MEP) surfaces of phencyclidine‐like (PCP‐like) compounds are modeled and visualized in order to extract features that are useful in predicting binding affinities. In modeling, the Cartesian coordinates of MEP surface points are mapped onto a spherical self‐organizing map (SSOM). The resulting maps are visualized using electrostatic potential (ESP) values. These values also provide features for a prediction system. Support vector machines and partial least‐squares method are used for predicting binding affinities of compounds. Copyright © 2009 John Wiley & Sons, Ltd.     

Covalent immobilization of invertase on PAMAM-dendrimer modified superparamagnetic iron oxide nanoparticles

In this study, polyamidoamine (PAMAM) dendrimer was synthesized on the surface of superparamagnetite nanoparticles to enhance invertase immobilization. The amount of immobilized enzyme on the surface-hyperbranched magnetite nanoparticle was up to 2.5 times (i.e., 250%) as much as that of magnetite nanoparticle modified with only amino silane. Maximum reaction rate (V _max) and Michaelis–Menten constant (K _m) were determined for the free and immobilized enzymes. Various characteristics of immobilized invertase such as; the temperature activity, thermal stability, operational stability, and storage stability were evaluated and results revealed that stability of the enzyme is improved upon immobilization.     

Adsorption/desorption of mono- and diblock copolymers on surfaces using specific hydrogen bonding interactions

Diblock copolymers containing recognition units designed to participate in specific three-point hydrogen bonding were adsorbed onto modified gold surfaces. Self-assembled monolayers (SAMs) containing complementary recognition units were used to direct the adsorption process. The polymer-modified surfaces obtained were characterized using X-ray photoelectron spectroscopy, water contact angle, and ellipsometry. The role of individual block lengths on the adsorption process was followed by observing frequency changes of thymine-SAM-modified quartz crystal microbalance chips during adsorption of diamidopyridine-functionalized polymers from a nonpolar solvent. The renewable nature of these recognition unit functionalized surfaces was demonstrated by reversible binding of polymers. Adsorption onto fresh surfaces, followed by desorption and subsequent readsorption of monoblock and diblock copolymers was also investigated.     

Adaptive mesh redistribution method for domains with complex boundaries

An adaptive structured mesh redistribution method (ASMRM) that permits smooth transition from non-uniformly distributed boundary points to solution-adaptive interior points and enables the resolution of complex flow in the complex boundary region as well as away from the boundary is proposed. It is a variant of the traditional variational technique. It involves a combination of static and dynamic monitor functions, the former for mesh distribution in the vicinity of a complex boundary and the latter for mesh adaption with the evolving solution elsewhere. Its effectiveness is demonstrated on some example problems, and it is then applied to a chevron nozzle. The proposed method is shown to be capable of generating a mesh with a good balance of orthogonality and smoothness in the entire domain.     

Adsorption Study of Immunoglobulin G Subclasses from Different Species by Pseudobioaffinity Separation on Histidyl–Bisoxirane–Sepharose

Adsorption chromatography is increasingly used for protein separations and biomedical applications. Therapeutic molecules such as antibodies, cytokines, therapeutic DNA, and plasma proteins must be purified before characterization and utilization. Use of immunoglobulins as immunodiagnostic and therapeutic tools has initiated many attempts to develop new adsorbents for their separation. Protein A and protein G are the affinity ligands most widely used for separation of immunoglobulins. These proteins are reliable, and have good selectivity and specificity, but are very expensive. Much attention has therefore been devoted to developing alternative methods for separation of immunoglobulins. Pseudobiospecific ligands, for example metal ions and amino acids, can be used for separation of a wide range of biological molecules. In this study, IgG₁, IgG₂, and IgG₃, three subclasses of human IgG, were separated from human serum using the amino acid histidine grafted on to bisoxirane-activated Sepharose, as pseudobiospecific adsorbent. Adsorption of IgG from different animal species on the same chromatographic adsorbent was also tested. The high recovery and purification on histidyl–bisoxirane–Sepharose gel of IgG from all the sources tested compared well with results obtained by use of protein A–Sepharose gel.

     

Synthesis,characterization, optimum reaction conditions,and some polymer–metal complexes of poly(phenoxy-imine)s containing furan ring

In this study, Schiff bases containing azomethine (–HC=N–) compounds were synthesized from the condensation reaction of 4-aminophenol and 2-aminophenol and 5-methyl-2-furaldehyde. Orange-colored Schiff bases, 4-[(5-methyl- 2-furyl) methyleneamino] phenol (4MFMAP) and 2-[(5-methyl-2-furyl) methyleneamino] phenol (2MFMAP) turned to poly-4-[(5-methyl-2-furyl) methyleneamino] phenol (P-4MFMAP) and poly-2-[(5-methyl-2-furyl) methyleneamino] phenol (P-2MFMAP) polyazomethine derivatives by NaOCl oxidant in alkaline aqueous medium. In addition, poly-2-[(5-methyl-2-furyl) methyleneamino] phenol cobalt (II) and copper (II) complexes were synthesized. FTIR and NMR measurements for structural analysis of the synthesized compounds, UV–Vis analysis for optical properties, electrical conductivity measurements, and thermal analysis with the TG–DTA techniques were determined. The yield of P-4MFMAP and P-2MFMAP was found to be 84.6% and 78.6 as follows [4MFMAP] = 0.066, [KOH] = 0.198 [NaOCl] = 0.066 mol L^?1 at 60 °C for 3 h and [2MFMAP] = 0.066, [KOH] = 0.132 [NaOCl] = 0.066 mol L^?1 at 70 °C for 3 h, respectively.     

Antibacterial glass films prepared on metal surfaces by sol–gel method

This paper describes the preparation and characterization of glass films consisting of SiO₂, Li₂O, Na₂O, K₂O or MgO in varying compositions on stainless steel and aluminum substrates by sol–gel method. Silver phosphate or silver incorporated zeolite was also introduced into the sols for obtaining antibacterial effect. The SiO₂/Li₂O/Na₂O system having the composition of 85:5:10 wt% was found as the optimum for obtaining a stable sol and film formation. The films were investigated by scanning electron microscopy (SEM) and electron dispersive analysis by X-ray (EDX), Fourier transformed infrared (FTIR) spectroscopy, thermo-gravimetric analysis (TGA) and differential thermal analysis (DTA). Homogenous films having 300 ± 20 nm thicknesses were formed by spin coating and then by curing at 500 °C for 1 h. Obtained films had high adherence to the metal substrates and they were also durable in acidic, basic or NaCl environments. They also presented a powerful antibacterial effect against E. coli.     

The removal of textile dyes by diatomite earth

The adsorption of some textile dyes by diatomite was investigated using Sif Blau BRF (SB), Everzol Brill Red 3BS (EBR), and Int Yellow 5GF (IY). Adsorption of these textile dyes onto diatomite earth samples was studied by batch adsorption techniques at 30 degrees C. The adsorption behavior of textile dyes on diatomite samples was investigated using a UV-vis spectrophotometric technique. The effect of particle size of diatomite, diatomite concentration, the effect of initial dye concentrations, and shaking time on adsorption was investigated. Adsorption coverage over the surface of diatomite was studied using two well-known isotherm models: Langmuir's and Freundlich's. These results suggest that the dye uptake process mediated by diatomite has a potential for large-scale treatment of textile mill discharges. According to the equilibrium studies, the selectivity sequence can be given as IY > SB > EBR. Values of the removal efficiency of the dyes ranged from 28.60 to 99.23%. These results show that natural diatomite holds great potential to remove textile dyes from wastewater.     

Optimizing control of simulated moving beds--experimental implementation

The operation of simulated moving beds (SMBs) at their optimal operating conditions is difficult and not robust. Therefore, it is common practice to operate SMB units far from their economic optimum in order to tolerate uncertainties in the system and minimize the effect of disturbances. Recently, we have proposed an on-line optimization based SMB control scheme that allows to exploit the full economic potential of SMB technology. The goal of this work is two-fold. Firstly, to experimentally evaluate and demonstrate the capability of the controller to optimize and operate the SMB units, thus delivering the products with maximum productivity and minimum solvent consumption. Secondly, to show the suitability of the controller even using a minimum of system information, thus making the detailed isotherm measurements redundant and saving time in the separation design phase. This paper reports and discusses the first experimental implementation of the control concept on a high purity separation of nucleosides (uridine, guanosine) with an eight-column four-section SMB where the species to be separated are retained on the source 30RPC stationary phase according to a linear isotherm.