Quantum chemistry in parallel with PQS

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux‐based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large—by ab initio standards—molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high‐level calculations (DFT, MP2, CI, and Coupled‐Cluster) can be performed on systems with up to several thousand basis functions on small (4‐32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post‐job visualization and display. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Application of tandem column solid phase extraction and flame atomic absorption spectrometry for the determination of inorganic and organically bound forms of iron in wine

A tandem column solid phase extraction (SPE) procedure has been devised to examine the fractionation of Fe in wine. Wine was filtered through a 0.45 μm filter and then, the filtrate was driven through an adsorbing Amberlite XAD-7HP column followed by a cation exchange Dowex 50W-x8-200 column. Three different Fe groupings are discriminated and assessed, including hydrophobic species of Fe bound to phenolic substances and related species (phenolic fraction), cationic species comprising simple Fe ions and labile Fe forms (cationic fraction), in addition to anionic and/or neutral Fe complexes with organic acids (residual fraction). The suitability of the procedure has been evaluated analyzing four bottled red wines. The results obtained were verified using another tandem column assemblage in which an adsorbing Amberlite XAD-16 column was exchanged by the Amberlite XAD-7HP column. The fractionation pattern ascertained for Fe in analyzed wines is discussed in reference to previously published works. In addition, a conditioning treatment and preparation of Amberlite XAD resins have been revised.     

Electrophoretic methods for separation of nanoparticles

This article reviews progress in the application of electrophoretic techniques for the separation of nanoparticles. Numerous types of nanoparticles have recently been synthesised and integrated into different products and procedures. Consequently, analytical methods for the efficient characterisation of nanoparticles are now required. Several studies have revealed that gel electrophoresis can readily be used for separating nanoparticles according to their size or shape. However, many other studies focused on separation of nanoparticles by CE. In some cases nanoparticles could be separated by CZE, simply using pure buffer as the BGE. In other studies, buffer additives (most often SDS) were used, enabling fast separations of metallic nanoparticles by size. Other CE methods also allowed for separation of nanoparticle conjugates with biomolecules. Dielectrophoresis is yet another electrophoretic technique useful in separation and characterisation of nanoparticles; particularly nanotubes. Detection methods often used after electrophoretic separation include UV/Vis absorption and fluorescence spectroscopy. Examples of recent and relevant older reports are presented here. The authors conclude that electrophoretic methods for nanoanalysis can provide inexpensive and efficient tools for quality assurance and safety control; and as a consequence, they can augment transfer of nanotechnologies from research to industry.     

DFT analysis of co-alkyl and co-adenosyl vibrational modes in B12-cofactors

Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.     

Analysis of uncertainties in polymer viscoelastic properties obtained from equilibrium computer simulations

We critically evaluate the uncertainties in the stress autocorrelation function obtained from equilibrium molecular dynamics simulation of model polymer melts. This quantity is central to evaluating transport properties, e.g., the complex modulus and the viscosity. In contrast to the intuitive expectation that simulations have to be run five to six orders of magnitude longer than the chain relaxation time to reduce uncertainties to acceptable levels, our analysis shows that the majority of the uncertainty is associated with rapidly oscillating bonded interactions. These fluctuations occur on time scales which are approximately 10(4) times shorter than the relaxation time of a chain of length 80. Consequently, the effects of these oscillations on the stress autocorrelation function can be dramatically reduced by (i) conducting long simulations (typically 10(6) times longer than the bond relaxation times or only 10(2) chain relaxation times) and (ii) by performing running averages with time windows whose time scales are much longer than these oscillations. Conducting such long simulations also allows for the accurate determination of the melt viscosity and the low-frequency complex modulus, but performing running averages do not impact these quantities since they are time integrals of the stress autocorrelation function.     

Real space Hartree-Fock configuration interaction method for complex lateral quantum dot molecules

We present unrestricted Hartree-Fock method coupled with configuration interaction (CI) method (URHF-CI) suitable for the calculation of ground and excited states of large number of electrons localized by complex gate potentials in quasi-two-dimensional quantum dot molecules. The method employs real space finite difference method, incorporating strong magnetic field, for calculating single particle states. The Hartree-Fock method is employed for the calculation of direct and exchange interaction contributions to the ground state energy. The effects of correlations are included in energies and directly in the many-particle wave functions via CI method using a limited set of excitations above the Fermi level. The URHF-CI method and its performance are illustrated on the example of ten electrons confined in a two-dimensional quantum dot molecule.     

The sensitivity analysis of the drawpiece response on the finite element shape parameter

On this paper the numerical analysis of the drawing process is presented. The sensitivity analysis of the drawpiece response on the finite element shape parameter is realized. The sensitivity of stresses field on the edge and the round edge of drawpiece on the change sizes of the finite elements is defined. Precisely proportion between height and length of the finite element is examined. The analysis with the explicit method in the ANSYS LS–Dyna system is passed. The die and the stamp as not deformable bodies are accepted and with the shell finite elements are discretized. The drawpiece with the solid finite elements are discretized. Examples results of computer simulations are presented. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Comparison of the standard Euler-Euler and hybrid Euler-Lagrange approaches for modeling particle transport in a pilot-scale circulating fluidized bed

Particle transport phenomena in small-scale circulating fiuidized beds （CFB） can be simulated using the Euler-Euler, discrete element method, and Euler-Lagrange approaches. In this work, a hybrid Euler-Lagrange model known as the dense discrete phase model （DDPM）, which has common roots with the multiphase particle-in-cell model, was applied in simulating particle transport within a mid-sized experimental CFB facility. Implementation of the DDPM into the commercial ANSYS Fluent CFD package is relatively young in comparison with the granular Eulerian model. For that reason, validation of the DDPM approach against experimental data is still required and is addressed in this paper. Additional difficulties encountered in modeling fluidization processes are connected with long calculation times. To reduce times, the complete boiler models are simplified to include just the combustion chamber. Such simplifications introduce errors in the predicted solid distribution in the boiler. To investigate the conse- quences of model reduction, simulations were made using the simplified and complete pilot geometries and compared with experimental data. All simulations were performed using the ANSYSFLUENT 14.0 package. A set of user defined functions were used in the hybrid DDPM and Euler-Euler approaches to recirculate solid particles.     

Interactions between Diamagnetic Metal Ions and pH-Sensitive Nitroxides

Specific interactions between pH-sensitive nitroxide radicals and selected diamagnetic metal ions were investigated. To this end, the influence of different metal salts at varying concentrations on the continuous-wave electron paramagnetic resonance spectra of two imidazoline nitroxides was studied. Among the screened metal ions, Zn(II) most significantly affected the spectral profile, analogous to the effect attributed to protonation of the nitroxide imino nitrogen known from pH studies. Simulations showed the acquired spectra to result from the superposition of the signals of the coordinated and the uncoordinated species. The complex formation between Zn(II) and (4-amino-2,5-dihydro-2,2,5,5-tetramethyl-3-imidazoline-1-yloxyl) was modelled by theoretical methods revealing the rather specific selectivity of the nitroxide toward Zn(II). The results suggest imidazoline nitroxides as promising candidates for the development of new specific metal ion probes.