Basis set and method dependence in quantum theory of atoms in molecules calculations for covalent bonds

The influence of various small- and medium-size basis sets used in Hartree-Fock (HF) and density functional theory (DFT)/B3LYP calculations on results of quantum theory of atoms in molecules based (QTAIM-based) analysis of bond parameters is investigated for several single, double, and triple covalent bonds. It is shown that, in general, HF and DFT/B3LYP methods give very similar QTAIM results with respect to the basis set. The smallest 6-31G basis set and DZ-quality basis sets of Dunning type lead to poor results in comparison to those obtained by the most reliable aug-cc-pVTZ. On the contrary, 6-311++G(2df,2pd) and in a somewhat lesser extent 6-311++G(3df,3pd) basis sets give satisfactory values of QTAIM parameters. It is also demonstrated that QTAIM calculations may be sensitive for the method and basis set in the case of multiple and more polarized bonds.     

Investigation of thermal power of reaction of titanium slag with sulphuric acid

Enriched titanium raw materials with high titanium content called titanium slags are received by the electrothermal reduction of ilmenite. Titanium slags are most frequently used in the titanium dioxide industry. The reaction of titanium slags with sulphuric acid is strongly exothermic and creates danger of thermal explosion. Kinetics of this reaction depends on the parameters such as temperature of initiation, sulphuric acid concentration and dimension of particles of titanium slag. The reaction of titanium slag with sulphuric acid was investigated at non-isothermal conditions in a special construction calorimeter. The observed thermal power changes in the calorimeter (“calorimeter run”), are the basis for estimation of reaction kinetics. A proposed model describing the thermal power changes and taking into account the moment of initiation of reaction is presented. The calorimetric investigations showed, that reaction rate of titanium slags with sulphuric acid depends on initial temperature of reaction, size of particles of titanium raw material and sulphuric acid concentration.     

Model studies of the optical rotation,and theoretical determination of its sign for β‐pinene and trans‐pinane

We have carried out extensive studies on the basis set dependence of the calculated specific optical rotation (OR) in molecules at the level of the time–dependent Hartree–Fock and density functional approximations. To reach the limits of the basis set saturation, we have devised an artificial model, the asymmetrically deformed (chiral) methane (CM) molecule. This small system permits to use basis sets which are prohibitively large for real chiral molecules and yet shows all the important features of the basis set dependence of the OR values. The convergence of the OR has been studied with n‐aug‐cc‐pVXZ basis sets of Dunning up to the 6–ζ. In a parallel series of calculations, we have used the recently developed large polarized (LPolX) basis sets. The relatively small LPolX sets have been shown to be competitive to very large n‐aug‐cc‐pVXZ basis sets. The conclusions reached in calculations of OR in CM concerning the usefulness of LPolX basis sets have been further tested on (S)‐methyloxirane and (S)‐fluoro‐oxirane. The smallest set of the LPolX family (LPol–ds) has been found to yield OR values of similar quality as those obtained with much larger Dunning's aug‐cc‐pVQZ basis set. These results have encouraged us to carry out the OR calculations with LPol–ds basis sets for systems as large as β‐pinene and trans‐pinane. In both cases, our calculations have lead to the correct sign of the OR value in these molecules. This makes the relatively small LPol–ds basis sets likely to be useful in OR calculations for large molecules. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Characterization of 1,3-alternate calix[4]arene-silica bonded stationary phases and their comparison to selected commercial columns by using principal component analysis

Twelve calix[4]arene stationary phases in 1,3-alternate conformation, synthesized in the authors’ laboratory, were characterized in terms of their surface coverage, hydrophobic selectivity, aromatic selectivity, shape selectivity, hydrogen bonding capacity and ion-exchange capacity. The set of tests commonly used for evaluation of commercially available stationary phases was applied to assess fundamental chromatographic properties of the calixarene phases. The new calixarene phases were compared to each other, to Caltrex and LiChrosorb C-18 columns. Principal component analysis has been used to provide comparison between 1,3-alternate calix[4]arene phases and commercially available phenyl, fluorophenyl and fluoroalkyl columns.     

A Spirocyclohexyl Nitroxide Amino Acid Spin Label for Pulsed EPR Spectroscopy Distance Measurements

Site‐directed spin labeling and EPR spectroscopy offer accurate, sensitive tools for the characterization of structure and function of macromolecules and their assemblies. A new rigid spin label, spirocyclohexyl nitroxide α‐amino acid and its N‐(9‐fluorenylmethoxycarbonyl) derivative, have been synthesized, which exhibit slow enough spin‐echo dephasing to permit accurate distance measurements by pulsed EPR spectroscopy at temperatures up to 125 K in 1:1 water/glycerol and at higher temperatures in matrices with higher glass transition temperatures. Distance measurements in the liquid nitrogen temperature range are less expensive than those that require liquid helium, which will greatly facilitate applications of pulsed EPR spectroscopy to the study of structure and conformation of peptides and proteins.     

Certification of reference materials for inorganic trace analysis: the INCT approach

This paper presents the work done by the Institute of Nuclear Chemistry and Technology (INCT), Warsaw on a procedure of the certification of matrix reference materials (CRMs) for inorganic trace analysis. The INCT has been involved in preparation and certification of that type of CRMs since 1986 till now. The certification of CRMs is performed on the basis of statistical evaluation of the data obtained from the worldwide interlaboratory comparison. The initially adopted certification procedure has been developed, and the final shape is presented and discussed. The modifications are connected with the new demands of the international standards. The results of analysis of candidate CRMs obtained by the potentially primary procedures based on radiochemical neutron activation analysis (RNAA) and results of analysis of CRM accompanying candidate RMs are applied in the certification process for quality assurance purpose.     

Does Maternal Treatment with Zidovudine Affect Changes in Mandibles of Newborns? Laser Induced Fluorescence Study

The influence of antiretroviral drug zidovudine treatment during pregnancy on mandible development in newborn rats was studied. The fluorescence of mandibles from 7-, 14- and 28-days old individuals was measured by means of fiber-optical fluorescence analyzer with 407 nm laser excitation. Obtained results revealed disturbing effect of maternal zidovudine administration on mandible fluorescence intensity which should decrease with bone development. Small changes in fluorescence of porphyrin forms are maintaining in the first month of newborns life while the changes observed in 440–585 nm range disappear.     

Modeling of relay helix functional dynamics and feasibility of experimental verification by neutron scattering

Cellular long-range transport involves motor proteins (MPs) (especially, kinesin and myosin) which contain a so-called relay helix. Its motion is of crucial importance to the conversion of chemical energy released in ATP hydrolysis into the coordinated mechanical movement of the entire motor protein. In this paper, we propose two combined nonlinear mechanisms for this particular functional activity and suggest the application of neutron scattering assays to experimentally determine the incoherent dynamic structure factor S(q,ω). We argue that this type of experiment is not only feasible but it could offer significant insights into the mechanism of MP function at a molecular level.