Focusing of Fe3O4 nanoparticles using a rotating magnetic field in various environments

The paper shows the application of a new method – Magnetic Nanoparticles Focusing 3D, MNF-3D – for focusing of magnetic nanoparticles at any point in a three-dimensional space between the rotating magnet system. The results of focusing process of nanoparticles in water, human blood, human serum and polyurethane sponge are presented. Additionally, blood flow was also considered. The effectiveness of nanoparticle focusing was monitored optically and quantitatively by electron spin resonance method. The method enabled focusing of magnetic nanoparticles within a few minutes in different environments. A good efficiency of focusing process was observed for all the samples.     

Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues

Our Fuzzy‐Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second‐order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK _a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK _a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK _a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK _a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK _a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK _a value of 7.37 units. Thus, the presented model is capable or reproducing pK _a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc.     

Factors affecting the strengths of σ-hole electrostatic potentials

A σ-hole is a region of diminished electronic density on the extension of a covalent bond to an atom. This region often exhibits a positive electrostatic potential, which allows attractive noncovalent interactions with negative sites. In this study, we have systematically examined the dependence of σ-hole potentials upon (a) the atom having the σ-hole, and (b) the remainder of the molecule. We demonstrate that not only relative electron-attracting powers need to be considered, but also relative charge capacities (or polarizabilities), and that other factors can also have significant roles.     

Diamond kinoform hard X‐ray refractive lenses: design,nanofabrication and testing

Motivated by the anticipated advantageous performance of diamond kinoform refractive lenses for synchrotron X‐ray radiation studies, this report focuses on progress in designing, nanofabricating and testing of their focusing performance. The method involves using lift‐off and plasma etching to reproduce a planar definition of numerically determined kinoform refractive optics. Tests of the focusing action of a diamond kinoform refractive lens at the APS 8‐ID‐I beamline demonstrate angular control of the focal spot.     

PHOTOELECTRON SPECTROSCOPY STUDY OF AMMONIA-INDUCED CHANGES IN ELECTROSTATICALLY-ASSEMBLED CONJUGATED POLYMER FILMS

ABSTRACT

Exposure of electrostatically assembled polyelectrolyte films comprised of the anionic carboxylic conjugated polymer poly[2-(3-thienyl)-ethanolhydroxycarbonylmethyl-urethane], hereafter referred to as H-PURET, and polycations such as poly(diallyldimethylammonium) chloride, here after referred to as PDADMAC, to aqueous ammonia vapor leads to dra matic changes in the ultraviolet-visible absorption spectrum. In the case of H-PURET/PDADMAC, a shift from 442 to 494 nm is observed upon overnight ammonia exposure. X-ray photoelectron spectroscopy has been used to investigate the mechanism of the changes in optical properties. The C1s, O1s and S2p core levels exhibit negligible ammonia-induced changes. Two N1s peaks are observed in virgin H-PURET/PDADMAC assemblies, and ammonia exposure causes the nitrogen peak corresponding to the H-PURET side chain to become more intense relative to that of the PDADMAC layer. This selective change in the N1s feature suggests that ammonia interacts with the polythiophene side-chain, presumably by deprotonating the fraction of carboxylic acid groups that remain in the H-PURET layer. This deprotonation apparently leads to structural or single chain conformational changes in the conjugated polymer layers that alter the electronic absorption spectrum.     

Halogen Bonding: An Interim Discussion

Halogen bonding is a noncovalent interaction that is receiving rapidly increasing attention because of its significance in biological systems and its importance in the design of new materials in a variety of areas, for example, electronics, nonlinear optical activity, and pharmaceuticals. The interactions can be understood in terms of electrostatics/polarization and dispersion; they involve a region of positive electrostatic potential on a covalently bonded halogen and a negative site, such as the lone pair of a Lewis base. The positive potential, labeled a σ hole, is on the extension of the covalent bond to the halogen, which accounts for the characteristic near‐linearity of halogen bonding. In many instances, the lateral sides of the halogen have negative electrostatic potentials, allowing it to also interact favorably with positive sites. In this discussion, after looking at some of the experimental observations of halogen bonding, we address the origins of σ holes, the factors that govern the magnitudes of their electrostatic potentials, and the properties of the resulting complexes with negative sites. The relationship of halogen and hydrogen bonding is examined. We also point out that σ‐hole interactions are not limited to halogens, but can also involve covalently bonded atoms of Groups IV–VI. Examples of applications in biological/medicinal chemistry and in crystal engineering are mentioned, taking note that halogen bonding can be “tuned” to fit various requirements, that is, strength of interaction, steric factors, and so forth.     

Quantum topology phase diagrams for molecules,clusters, and solids

The need to make more quantitative use of the total electronic charge density distribution is demonstrated in this short perspective. This is framed in the perspective of the ground breaking early work of Bader and coworkers, along with mathematicians who captured the essential nature of a molecule in a suitably compact form in real space. We see that this simple form is the Poincaré–Hopf relation for molecules and clusters and the Euler–Hopf relation in solids. Thom's theory of elementary catastrophes combined with the Poincaré–Hopf relation provides the inspiration for the new quantum topology. An alternative use of the Poincaré–Hopf relation, molecular recognition, is discussed. Quantum topology is then used to create a topology phase diagram for both molecules and solids. The author adds their perspectives of the huge potential of the quantum topology approach by demonstrating the ease with which new theoretical ideas can be generated. © 2013 Wiley Periodicals, Inc.     

Comment on “Extending Hirshfeld‐I to bulk and periodic materials”

In recent years, several methods have been developed that partition the electron density among atoms using spherically symmetric atomic weights. D. E. P. Vanpoucke, P. Bultinck, and I. Van Driessche (J. Comput. Chem. 2012, doi: 10.1002/jcc.23088) recently reported a periodic implementation of the Hirshfeld‐I method that uses a combination of Becke‐style and uniform integration grids and modified atomic reference densities to compute net atomic charges in periodic materials. Herein, this method is discussed in the context of earlier periodic implementations of the Hirshfeld‐I method, the Iterated Stockholder Atoms method, and the density derived electrostatic and chemical method.     

A numerically stable restrained electrostatic potential charge fitting method

Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)‐based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER charge), and the residual part is to be determined by restrained fitting to residual ESP on grid points around the molecule. Nonuniform weighting factors as a function of the dominant charge are assigned to the atoms. Because the residual part is several folds to several orders smaller than the dominant part, the impact of ill‐conditioning is alleviated. This charge fitting method can be used in quantum mechanical/molecular mechanical (QM/MM) simulations and similar studies, where QM calculated electronic properties are frequently mapped to partial atomic charges. © 2012 Wiley Periodicals, Inc.     

Simple power supply for power load controlled isoelectric focusing

The power supply for IEF based on features of the Cockcroft‐Walton voltage multiplier (CW VM) is described in this work. The article describes a design of the IEF power supply, its electric characteristics, and testing by IEF analysis. A circuit diagram of the power supply included two opposite charged branches (each consisting of four voltage doublers). The designed CW VM was powered by 230 V/50 Hz alternate current and it generated up to 5 kV and 90 mW at the output. Voltage and current characteristics of the power supply were measured by known load resistances in the range from 10 kΩ to 1 GΩ, which is a common resistance range for IEF strip geometry. Further, the power supply was tested by a separation of a model mixture of colored pI markers using a 175 × 3 × 0.5 mm focusing bed. Automatically limited power load enabled analysis of samples without previous optimization of the focusing voltage or electric current time courses according to sample composition. Moreover, the developed power supply did not produce any intrinsic heat and was easy to set up with cheap and commonly available parts.