Gas-phase and solution conformations of the alpha-L-iduronic acid structural unit of heparin

The IdoA2S structural unit of heparin (subunit G) may oscillate among the three conformations (4C1, 1C4, and 2So). Only the twisted boat conformation allowed the biologically active pentasaccharide unit of heparin (DEFGH) to bind to antithrombin. Our work reports, in detail, the results of systematic large-scale theoretical investigations of the three basic conformations (4C1, 1C4, and 2So) of the IdoA2S structural unit of heparin, its anionic forms, and its sodium salt using the B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d) model chemistries. According to our calculations, the most stable structure of these molecules corresponds to the 2So skew-boat conformation. This form is also the most stable in a water solution. The 2So conformation of neutral molecules is not maintained in the anionic species. With anions, both 1C4 and 4C1 conformations are present. The relative stability of individual species of the substituted iduronic acid affects extra stabilization by means of intramolecular hydrogen bonds. The calculated macroscopic pKa of 1,4-DiOMe IdoA2S are as follows: pKa = 0.25 for the terminal C(2)-OSO3H group, pKa = 3.67 for the terminal C(5)-CO2H group, and pKa = 14.00 for the C(3)-OH hydroxyl group. The computed Gibbs interaction energies, DeltaGdegrees , for the reaction 1,4-DiOMe IdoA2S(2-) + 2Na+ <==> 1,4-DiOMe IdoA2SNa2 (4C1, 1C4, and 2So conformations) are negative and span a rather small energy interval (from -1244 to -1290 kJ mol(-1)).     

Affinity liquid chromatography and capillary electrophoresis of seminal plasma proteins

Interactions of boar, bull, and human seminal plasma proteins with heparin and phosphorylcholine were studied by affinity LC using heparin immobilized to a Toyopearl support. A step gradient elution from 0.15 to 1.50 M NaCl was employed to elute the seminal plasma proteins. Relative amounts of the heparin-binding fraction of seminal plasma proteins (H+) in seminal plasma of three species were determined. Further on, the fraction of seminal plasma proteins interacting with phosphorylcholine-binding proteins (P+) was evaluated. P+ proteins were not found in human seminal plasma and their highest amount was present in bull seminal plasma. A CE method was developed for separation of seminal plasma proteins. Various capillaries and separation conditions were tested; the best resolution was obtained in a bare-silica capillary, with a micellar system consisting of a 0.02 M borate buffer and 0.05 M SDS pH 10.0. The optimized conditions were applied to the identification of the components in boar plasma.     

Copper cation interactions with biologically essential types of ligands: a computational DFT study

This work presents a systematic theoretical study on Cu(I) and Cu(II) cations in variable hydrogen sulfide-aqua-ammine ligand fields. These ligands model the biologically most common environment for Cu ions. Molecular structures of the complexes were optimized at the density functional theory (DFT) level. Subsequent thorough energy analyses revealed the following trends: (i) The ammine complexes are the most stable, followed by those containing the aqua and hydrogen sulfide ligands, which are characterized by similar stabilization energies. (ii) The most preferred Cu(I) coordination number is 2 in ammine or aqua ligand fields. A qualitatively different binding picture was obtained for complexes with H(2)S ligands where the 4-coordination is favored. (iii) The 4- and 5-coordinated structures belong to the most stable complexes for Cu(II), regardless of the ligand types. Vertical and adiabatic ionization potentials of Cu(I) complexes were calculated. Charge distribution (using the natural population analysis (NPA) method) and molecular orbital analyses were performed to elucidate the nature of bonding in the examined systems. The results provide in-depth insight into the Cu-binding properties and can be, among others, used for the calibration of bioinorganic force fields.     

Simulation Support to EPR-based Dentin Characterization

Treatment of dental caries as one of the most economically relevant human disease can rely only on the understanding of the caries progress through dentin. As it can be seen from the frequency of tooth decay among different animals, its existence and progress strongly depend on the mineral part arrangement, especially on the orientation of the hydroxyapatite (HA) crystals, which resist the mechanical and chemical stress very anisotropically. It is therefore not surprising that different attempts have been made to unravel the mystery of dentin growth and HA crystals arrangement. By dentin irradiation with gamma-rays, very stable CO₃ ^? radicals are generated within HA crystals which due to the anisotropic magnetic coupling enable detection of their orientational distribution via angular-dependent electron paramagnetic resonance spectroscopy. The latter can be significantly enhanced if the whole angular dependence can be fitted simultaneously within certain dentin structural models. As shown in this work, even subtle information like the orientation of the tubules relative to the pulp or the orientation of HA crystals relative to the tubules can be extracted. The sensitivity to different sample geometry is discussed to provide the best possible characterization.     

Generalized linear fractional programming under interval uncertainty

Data in many real-life engineering and economical problems suffer from inexactness. Herein we assume that we are given some intervals in which the data can simultaneously and independently perturb. We consider a generalized linear fractional programming problem with interval data and present an efficient method for computing the range of optimal values. The method reduces the problem to solving from two to four real-valued generalized linear fractional programs, which can be computed in polynomial time using an appropriate interior point method solver.     

On the favorable estimation for fitting heavy tailed data

Assessment of heavy tailed data and its compound sums has many applications in insurance, auditing and operational risk capital assessment among others. In this paper, we compare the classical estimators (maximum likelihood, QQ and moment estimators) with the recently introduced robust estimators of “generalized median”, “trimmed mean” and estimators based on t-score moments. We derive the exact distribution of the likelihood ratio tests of homogeneity and simple hypothesis on the tail index of a two-parameter Pareto model. Such exact tests support the assessment of the performance of estimators. In particular, we discuss some problems that one can encounter when misemploying the log-normal assumption based methods supported by the Basel II framework. Real data and simulated examples illustrate the methods.     

Theoretical study of the helio hydrogen cyanide dication HeCNH2+

The structure and stability of the helio hydrogen cyanide molecular ion, HeCNH²⁺, is investigated by standard quantum chemical methods. Single reference calculations are carried out using second-order perturbation theory (MP2), the coupled cluster expansion in the CCSD approximation, and the hybrid approach using a perturbative estimate of the triple excitation energy component designated CCSD(T). Multireference calculations using a complete active space (CASSCF) and a second-order perturbation theory estimate of correlation effects (CASPT2) are reported.     

An extremal problem for real algebraic polynomials

Let G _n be the set of all real algebraic polynomials of degree at most n, positive on the interval (?1, 1) and without zeros inside the unit circle (|z| < 1). In this paper an inequality for the polynomials from the set G _n is obtained. In one special case this inequality is reduced to the inequality given by B. Sendov [5] and in another special case it is reduced to an inequality between uniform norm and norm in the L ₂ space for the Jacobi weight.