Specific Polar Groups Research Articles

Risk assessment of organic aromatic compounds to Tetrahymena pyriformis in environmental protection by a simple QSAR model

A new Quantitative Structure-Activity Relationship model is introduced for reliable prediction of the toxicity of organic aromatic compounds based on the logarithm of 50 % growth inhibitory concentration of Tetrahymena pyriformis (log(IGC50−1)), which have extensive use in ecotoxicology and environmental safety applications. The largest experimental data set of log(IGC50−1) for 892 organic aromatic compounds is used to derive and test the new model. A core correlation based on additive variables is introduced by the number of nitro groups, carbon and halogen atoms as well as some specific polar groups and molecular weight. An improved correlation based on two non-additive correcting functions is developed for the increment of the reliability of the core correlation. The reliability of the improved correlation is tested and compared with two of the best available methods, which require complex descriptors. The predicted results for 661 and 231 of training and test sets have been confirmed by internal and external validations. The values of correlation coefficient (R2), mean error (ME), root mean squared error (RMSE), and maximum of errors (Max Error) for 661/231 of training/test aromatic compounds are 0.8442/0.7771, 0.0000/0.0149, 0.3166/0.3603, and 0.9732/0.9825, respectively, which are good results as compared to extra complex models with lower reported data. Various statistical parameters confirm the goodness-of-fit, high reliability, precision, and accuracy of the novel model.

New method for assessment of melting points of organic azides using their molecular structures

Organic azides are unstable chemical compounds, which can be easily decomposed or exploded. This work introduces three novel correlations for the prediction of melting point of different types of organic azides containing alkyl azides, alkenyl azides, aryl azides, acyl azides and heteroazide compounds. These models are based on the elemental composition as additive parameter and the contribution of some specific polar groups/structural moieties as non-additive functions. The new correlations have been used for 259 different organic azide compounds including complex molecular structures. The new models were validated by internal and external validation tests where their applicability domains were defined and analyzed. Third correlation, in which the contribution of Specific Polar Groups (SPG) and Inefficient Packing Factor (IPF) beside the number of carbon, hydrogen and nitrogen atoms and the number of azide groups are considered, gives the best predictions. It shows good performances in robustness and predictive power through different validation techniques. It also provides good statistical results and more reliable predictions as compared with two complex methods of the best available computer codes.

A New Model for Prediction of One Electron Reduction Potential of Nitroaryl Compounds

AbstractThis paper introduces a simple model for prediction of one electron reduction potential [E(RNO2/R•NO2–)] of various nitroaryl compounds. The new method uses energy difference between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) in gas phase at the B3LYP/6‐311++G** level (ΔEHOMO‐LUMO) and some structural parameters. It was used for 35 nitroaryl compounds including nitrobenzenes, nitrofurans, 2‐nitroimidazoles, 4‐nitroimidazoles, 5‐ninuintidazoles, nitroazaindoles, nitroacridines, and miscellaneous nitroaryl compounds. The root mean square (rms) percent deviation and the average absolute error of predictions of E(RNO2/R•NO2–) relative to experiment were decreased from 12.4 % and 0.42 V to 3.5 % and 0.11 V, respectively, upon consideration of several structural parameters. Increment of the value of ΔEHOMO‐LUMO and inclusion of specific polar groups can increase thermodynamic stability of these compounds.

An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network

Protein G is an IgG binding protein that has been widely exploited for biotechnological purposes. Rosetta protein modeling identified a set of favorable polar mutations in Protein G, at its binding interface with the Fc domain of Immunoglobulin G, that were predicted to increase the stability and tighten the binding relative to native Protein G, with only a minor perturbation of the binding mode seen in the crystal structure. This triple mutant was synthesized and evaluated experimentally. Relative to the native protein G, the mutant showed a 3.5-fold enhancement in display level on the surface of yeast and a 5-fold tighter molar affinity for rabbit and human IgG. We attribute the improved affinity to a network of hydrogen bonds exploiting specific polar groups on human and rabbit Fc. The relative specificity increased as well since there was little affinity enhancement for goat and mouse Fc, while the affinity for rat Fc was poorer by half. This designed Protein G will be useful in biotechnological applications as a recombinant protein, where its improved affinity, display and specificity will increase antibody capture sensitivity and capacity. Furthermore, the display of this protein on the surface of yeast introduces the concept of the use of yeast as an affinity matrix.

Improved method for reliable predicting enthalpy of fusion of energetic compounds

Energetic compounds are substances containing metastable molecules capable of undergoing very rapid and highly exothermic reactions and determination of their properties is likely to be expensive or dangerous with environmental problems. A simple and reliable method is introduced for desk calculations of the enthalpy of fusion of different energetic compounds with general formula CaHbNc(O or S)d(halogen)e. This method is based on two simple models, which require only elemental composition and specific polar groups or molecular fragments. The first model requires only the number of used atoms, which is improved by some molecular moieties in the second model. For 91 different energetic compounds (corresponding to 123 measured values), the predicted results of two simple models are more reliable than several of the best available methods. The second model provides more reliable results with respect to the first one and can be easily applied for energetic compounds with complex molecular structures.

A new method for predicting the heats of combustion of polynitro arene, polynitro heteroarene, acyclic and cyclic nitramine, nitrate ester and nitroaliphatic compounds

A new method is presented for estimating the gross and net heats of combustion of important classes of energetic compounds including polynitro arene, polynitro heteroarene, acyclic and cyclic nitramine, nitrate ester and nitroaliphatic compounds. Elemental compositions as well as the presence of some specific polar groups and molecular fragments are important parameters in the new model. The novel method can be easily used for any complex organic compounds with at least one nitro, nitramine or nitrate functional groups by which the predictions of their heats of combustion by the available methods are inaccurate or difficult. The predicted results show that this method gives reliable predictions of heats of combustion with respect to group additivity method and computed values based on atom-type electrotopological state indices for several energetic compounds where the models can be applied.

Solvatochromism as an alternative for contact angle measurements in the characterisation of modified polymer surfaces

Polyolefine surfaces have been pre-treated by UV/ozone and UV/water methods. The increase in polar groups on a polymer surface and the contribution of these polar groups to the adhesion of the polymer has been investigated by using contact angles and tensile strength tests. Because contact angle measurements do not give information about the specific polar groups on the surface we have used solvatochromic analyses to identify specific polar groups. The results showed that solvatochromic analyses is a promising method to discriminate between different kinds of polar groups and therefore solvatochromic surface characterisation may become an important surface analytical tool in adhesive technology.

Adhesion of vacuum-deposited thin cobalt metal film to poly(ethylene terephthalate) pretreated with RF plasma

Specific polar groups were introduced on a poly(ethylene terephthalate) (PET) film surface by radio-frequency (RF) plasma treatment. These polar groups were analyzed quantitatively by ESCA, and their effect on the adhesion strength of vacuum-deposited thin cobalt metal film on the plasma-treated PET film surface was investigated. Hydroperoxide and hydroxyl groups introduced onto the PET film surface by RF plasma under an argon or oxygen atmosphere greatly increased the adhesion strength. In particular, oxygen plasma treatment at high RF power was most effective. A large number of amino groups were introduced by the ammonia plasma treatment, but they did not increase the adhesion strength.

20] Protein chromatography on hydroxyapatite columns

The use of hydroxyapatite (HA) columns for protein chromatography has been introduced by Tiselius et al. He also proposed a mechanism for protein adsorption to and desorption from HA, since the principles of ion-exchange chromatography are not applicable to HA chromatography. Furthermore, the roles of protein fine structure and of specific polar groups have been probed. This last study included proteins in which individual polar groups were modified specifically, along with those in which very extensive numbers of amino or carboxyl groups are modified with (1) retention of the same charge, (2) inversion of the charge, or (3) annihilation of the charge. As a result of this work, a mechanism of protein-HA interaction has been deduced, which is based on three fundamental conclusions: 1. Adsorption and elution cannot be regarded as simple reversals of a single process. 2. Amino and carboxyl groups act differently in the adsorption of proteins to HA. 3. Elutions of basic and acidic proteins by different salts follow different mechanisms.

The interaction of proteins with hydroxyapatite: I. Role of protein charge and structure

The criteria for elution of proteins from hydroxyapatite columns were examined as a function of (1) protein isoelectric point (22 proteins with isoelectric points between 3.5 and 11.0); (2) ionic nature of eluant (Na salts of PO 4, F −, Cl −, SCN −, ClO 4 −, and CaCl 2); and (3) structural differences between related proteins. It was found that proteins can be classified into three groups: (1) basic proteins, which elute at similar, moderate molarities of PO 4, F −, Cl −, SCN −, and ClO 4 −, and low (<0.003 m) Ca 2+; (2) acidic proteins which elute at about equal moderate molarities of PO 4 and F −, but do not elute with Ca 2+ and usually not with Cl −; (3) neutral proteins, which elute with PO 4, F −, and Cl −, but show a strong anion specificity, and do not elute with Ca 2+ or SCN −. Furthermore, individual specific polar groups are not in general crucial to binding or desorption, and variations in structure, other than major loosening, do not influence strongly the pattern of protein-hydroxyapatite interaction.

Relation between γ- and α-chymotrypsin

The criteria for elution of proteins from hydroxyapatite columns were examined as a function of (1) protein isoelectric point (22 proteins with isoelectric points between 3.5 and 11.0); (2) ionic nature of eluant (Na salts of PO4, F−, Cl−, SCN−, ClO4−, and CaCl2); and (3) structural differences between related proteins. It was found that proteins can be classified into three groups: (1) basic proteins, which elute at similar, moderate molarities of PO4, F−, Cl−, SCN−, and ClO4−, and low (<0.003 m) Ca2+; (2) acidic proteins which elute at about equal moderate molarities of PO4 and F−, but do not elute with Ca2+ and usually not with Cl−; (3) neutral proteins, which elute with PO4, F−, and Cl−, but show a strong anion specificity, and do not elute with Ca2+ or SCN−. Furthermore, individual specific polar groups are not in general crucial to binding or desorption, and variations in structure, other than major loosening, do not influence strongly the pattern of protein-hydroxyapatite interaction.