Prediction of retention times of proteins in hydrophobic interaction chromatography using only their amino acid composition

This paper focuses on the prediction of the dimensionless retention time of proteins (DRT) in hydrophobic interaction chromatography (HIC) by means of mathematical models based, essentially, only on aminoacidic composition. The results show that such prediction is indeed possible. Our main contribution was the design of models that predict the DRT using the minimal information concerning a protein: its aminoacidic composition. The performance is similar to that observed in models that use much more sophisticated information such as the three-dimensional structure of proteins. Three models that, in addition to the amino acid composition, use different assumptions about the amino acids tendency to be exposed to the solvent, were evaluated in 12 proteins with known experimental DRT. In all the cases analyzed, the model that obtained the best results was the one based on a linear estimation of the aminoacidic surface composition. The models were adjusted using a collection of 74 vectors of aminoacidic properties plus a set of 6388 vectors derived from these using two mathematical tools: k-means and self-organizing maps (SOM) algorithms. The best vector was generated by the SOM algorithm and was interpreted as a hydrophobicity scale based partly on the tendency of the amino acids to be hidden in proteins. The prediction error (MSE(JK)) obtained by this model was almost 35% smaller than that obtained by the model that supposes that all the amino acids are completely exposed and 40% smaller than that obtained by the model that uses a simple correction factor considering the general tendency of each amino acid to be exposed to the solvent. In fact, the performance of the best model based on the aminoacidic composition was 5% better than that observed in the model based on the three-dimensional structure of proteins.     

Influence of aspect ratio and anisotropy distribution in ordered CoNi nanowire arrays

The size effects on magnetic properties of nanowires arrays were studied varying the nanowires diameter and maintaining the same periodicity among them, for two different nominal compositions of Co and Ni in the alloy form. The competition among magnetocrystalline and shape anisotropies changes drastically from smallest to biggest diameters altering the easy axis direction. In the case of 75% of Co in alloy, experimental values of the effective anisotropy constant (K_eff) vary from positive to negative depending on the diameter, which means a reversal of the easy axis direction. For 50% of Co the shape anisotropy dominates over the magnetocrystalline for all studied diameters.     

Experimental and Computational Study of the Thermal Decomposition of 3‐Methyl‐3‐buten‐1‐ol in m‐Xylene Solution

An experimental study of the thermal decomposition of a β‐hydroxy alkene, 3‐methyl‐3‐buten‐1‐ol, in m‐xylene solution, has been carried out at five different temperatures in the range of 513.15–563.15 K. The temperature dependence of the rate constants for the decomposition of this compound in the corresponding Arrhenius equation is given by ln k (s^?1) = (25.65 ± 1.52) ? (17,944 ± 814) (kJ·mol^?1)·T^?1. A computational study has been carried out at the M05–2X/6–31+G(d,p) level of theory to calculate the rate constants and the activation parameters by the classical transition state theory. There is a good agreement between the experimental and calculated rate constants and activation Gibbs energies. The bonding characteristics of reactant, transition state, and products have been investigated by the natural bond orbital analysis, which provides the natural atomic charges and the Wiberg bond indices. Based on the results obtained, the mechanism proposed is a one‐step process proceeding through a six‐membered cyclic transition state, being a concerted and slightly asynchronous process. The results have been compared with those obtained previously by us (Struct Chem 2013, 24, 1811–1816) for the thermal decomposition of 3‐buten‐1‐ol, in m‐xylene solution. We can conclude that in the compound studied in this work, 3‐methyl‐3‐buten‐1‐ol, the effect of substitution at position 3 by a weakly activating CH₃ group is the stabilization of the transition state formed in the reaction and therefore a small increase in the rate of thermal decomposition.     

Structural and Kinetic Aspects of Blood Plasma Protein Adsorption on the Surface of Hydrophobic Polymers

Abstract

Due to the wide use of polymers in medicine, researchers are required to solve a very important problem–to understand the interaction between materials of nonphysiological origin and the surrounding biological liquids, and tissues, particularly blood.     

A convective weakly viscoelastic rotating flow with pressure Neumann condition

The objective of this work is to investigate through the numeric simulation, the effects of the weakly viscoelastic flow within a rotating rectangular duct subject to a buoyancy force due to the heating of one of the walls of the duct. A direct velocity–pressure algorithm in primitive variables with a Neumann condition for the pressure is employed. The spatial discretization is made with finite central differences on a staggered grid. The pressure field is directly updated without any iteration. Numerical simulations were done for several Weissemberg numbers (We) and Grashof numbers (Gr) . The numerical results show that for high Weissemberg numbers (We>7.4 × 10^?5) and for ducts with aspect ratio 2:1 and 8:1, the secondary flow is restabilized with a stretched double vortex configuration. It is also observed that when the Grashof number is increased (Gr>17 × 10^?4) , the buoyancy force neutralizes the effects of the Coriolis force for ducts with aspect ratio 8:1. Copyright © 2008 John Wiley & Sons, Ltd.     

Vortical dynamics of spinning quantum plasmas: helicity conservation

It is shown that a vorticity, constructed from the spin field of a quantum spinning plasma, combines with the classical generalized vorticity (representing the magnetic and the velocity fields) to yield a new grand generalized vorticity that obeys the standard vortex dynamics. Expressions for the quantum or spin vorticity and for the resulting generalized helicity invariant are derived. Reduction of the rather complex spinning quantum system to a well known and highly investigated classical form opens familiar channels for the delineation of physics peculiar to dense plasmas spanning solid state to astrophysical objects. A simple example is worked out to show that the magnetics of a spinning plasma can be much richer than that of the corresponding classical system.     

A new family of "clicked" estradiol-based low-molecular-weight gelators having highly symmetry-dependent gelation ability

Reported herein is the discovery of a novel family of "clicked" estradiol-based LMWGs whose gelation ability highly depends on the gelator symmetry. These LMWGs that gel different organic solvents in the presence of H(2)O even at concentrations as low as 0.04 wt% are readily accessible using "click" chemistry.