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.     

Joint characteristic functions construction via copulas

When modelling dependent risks it is important to be able to generate joint distributions with given marginals. One of the ways which may be useful in connection with using the Fast Fourier Transform is to construct joint characteristic functions from marginal characteristic functions. In this paper a class of n-dimensional continuous copulas is presented which in turn lead to a simple construction of joint characteristic functions with given marginal characteristic functions. Bounds on various measures of correlation are also given.     

Editorial

The credit crisis is a complex societal problem in which many phenomena and actors are involved. If one wants to analyze the causes of this problem, try to stabilize the situation and prevent new fall backs, a multi-disciplinary approach is prescribed. A careful analysis based on the scientific methodology of societal complexity is needed in order to find how the credit crisis happened and how new crises can be prevented. Theories of multiple disciplines must be used by a multi disciplinary team to analyze the situation and to find sustainable options. This process can be accomplished by following the Compram Methodology of DeTombe. The Compram Methodology provides a framework for policy making which includes many methods and tools. The Compram Methodology is specialized to handle complex interdisciplinary world-wide problems and to offer a step-by-step approach of analyzing the problem, finding and implementing sustainable interventions and evaluating the effects. The Compram Methodology offers a bird’s-eye view on the complexity of the problem and gives directions to policy makers to build their decisions on using a multi-disciplinary, multi-actor approach. In this article the credit crisis is discussed in relation with the Compram Methodology. Aspects of the credit crisis are described with an emphasis on the role of the actors. Based on the Compram Methodology directions can be provided for handling the credit crisis and avoiding future similar problems.     

Viscosity and electrophoretic mobility of cesium fullerenehexamalonate in aqueous solutions--comparing experiments and theories on nanometer-sized spherical polyelectrolyte

The viscosity of aqueous solutions of cesium fullerenehexamalonate T h -C 66(COOCs) 12, a rigid spherical nanometer-sized polyvalent salt, was measured by the Ubbelohde-type viscometer. The measurements were performed without added salt at 25 degrees C in the concentration range between 7 and 320 g/dm (3). THe concentration dependence of the obtained reduced viscosity was compared with the theoretical prediction, taking into account contributions stemming from the intrinsic viscosity, hydrodynamic perturbations of the hypothetically bare fullerenehexamalonate macroion, the primary electroviscous effect, and the secondary electroviscous effect. Using the geometric radius of the bare macroion from the previous measurements of the estimated effective charge of the macroion and from the small-angle X-ray scattering data of the estimated thickness of the compact shell of counterions electrostatically bound to the macroion, a good agreement between theory and the experiment was obtained in the range of the lowest and of the highest concentrations. Electrostatic interactions are identified as the main cause of the increased reduced viscosity at the lowest measured concentrations. At the highest concentrations, electrostatic interactions are effectively screened, and the influence of binary hydrodynamic interactions and perturbations of the hypothetical bare macroion prevails over electrostatic contributions to the increased viscosity. The electrophoretic mobility of the fullerenehexamalonate ion in aqueous salt-free medium was computed with the same value for the radius of the fullerenehexamalonate macroion as that used in the calculation of viscosity. The numerical solution of Ohshima's equation agreed well with the experimental values.     

Stacking and not solely topology of T3 loops controls rigidity and ammonium ion movement within d(G4T3G4)2 G-quadruplex

A solution state NMR study has shown that d(G4T3G4) in the presence of (15)NH4(+) ions folds into a single bimolecular G-quadruplex structure in which its G-tracts are antiparallel and the two T3 loops span along the edges of the outer G-quartets on the opposite sides of the G-quadruplex core. This head-to-tail topology is in agreement with the topology of the G-quadruplex recently found in the X-ray crystal structure formed by d(G4T3G4) in the presence of K(+) ions [Neidle et al. J. Am. Chem. Soc. 2006, 128, 5480]. In contrast, the presence of K(+) ions in solution resulted in a complex ensemble of G-quadruplex structures. Molecular models based on NMR data demonstrate that thymine loop residues efficiently base-base stack on the outer G-quartets and in this way stabilize a single structure in the presence of (15)NH4(+) ions. The use of heteronuclear NMR enabled us to localize three (15)NH4(+) ion binding sites between pairs of adjacent G-quartets and study the kinetics of their movement. Interestingly, no (15)NH4(+) ion movement within the G-quadruplex was detected at 25 degrees C. At 35 degrees C we were able to observe slow movement of (15)NH4(+) ions from the outer binding sites to bulk solution with the characteristic residence lifetime of 1.2 s. The slow movement of (15)NH4(+) ions from the outer binding sites into bulk solution and the absence of movement from the inner binding site were attributed to steric hindrance imposed by the T3 loops and the rigidity of the G-quadruplex.     

Infrared spectrum of 4-methoxypicolinic acid N-oxide: computation of asymmetric O-H stretching band

In this article we studied the strong intramolecularly hydrogen-bonded system 4-methoxypicolinic acid N-oxide. The potential energy surface V = V(rOH,rOO) and the corresponding dipole moment function were calculated using the DFT B3LYP/6-31+G(d,p) level of approximation. The time-independent vibrational Schr?dinger equation was solved using a rectangular grid basis set and shifted Gaussian basis set. The vibrational spectrum and metric parameters were also calculated. Effects of deuteration were considered. The calculated vibrational spectra were compared with the experimental spectra. The vibrational transition corresponding to asymmetric O-H stretching that occurs at about 1400 cm-1 compares well with the experimentally assigned O-H asymmetric stretching band centered at 1380 cm-1. The corresponding asymmetric O-D stretching band was predicted to be at 1154 cm-1, while the experimental O-D band was not assigned due to its very low intensity. Several overtones and hot transitions of significant intensities were located in the vicinity of the fundamental O-H stretching frequency, effectively broadening the infrared absorption attributed to the O-H stretching mode. This is in a good agreement with the observed broad protonic absorptions found in the infrared spectra of the title compound and its analogs. We have shown that the Gaussian basis set is the method of choice for a two-dimensional vibrational problem that requires several hundreds of vibrational basis functions and when high accuracy of the eigenvalues is required or when extending the calculations to more vibrational degrees of freedom. We have also demonstrated that for a large number of basis functions the Gramm-Schmidt orthogonalization procedure outperforms symmetric and canonical orthogonalization schemes.     

Analysis of sample of highly water-soluble Th-symmetric fullerenehexamalonic acid C66(COOH)12 by ion-chromatography and capillary electrophoresis

Ion chromatography (IC) was used to establish isomer purity of the highly water-soluble sample of fullerenehexamalonic acid, Th-symmetric hexakis-adduct C66(COOH)12. Sharp and symmetric peaks were obtained by IC using 1.0 M potassium hydroxide as eluent and applying gradient elution program. The identity of the two largest peaks in the chromatogram was assigned to Th-C66(COOH)12 and C66H(COOH)11. The developed IC procedure can be used for the semi-quantitative determination of the extent of the partial decarboxylation of the sample. As an alternative analytical technique, a CE procedure was introduced and its performance against IC was compared for this particular case.     

Approach to nonadiabatic transitions by density matrix evolution and molecular dynamics simulations

Many biological processes are characterized by an essentially quantum dynamical event, such as electron or proton transfer, in a complex classical environment. To treat such processes properly by computer simulation, allowing nonadiabatic transitions involving excited states, we recently developed a density matrix evolution (DME ) method [H. J. C. Berendsen and J. Mavri, J. Phys. Chem, 97 , 13464 (1993)] which simulates the dynamics of quantum systems embedded in a classical environment. The formalism of the method is presented and an overview of the applications ranging from collisions of a quantum harmonic oscillator with noble gas atoms to proton tunneling in a double-well hydrogen bond is given. The methodology for treatment of proton-transfer processes with inclusion of excited states is presented. Future application of the method on biologically interesting processes, such as proton transfer in enzymatic reactions, is discussed. © 1996 John Wiley & Sons, Inc.     

Thermodynamic and NMR study of aggregation of dodecyltrimethylammonium chloride in aqueous sodium salicylate solution

The complex aggregation processes of dodecyltrimethylammonium chloride (DTAC) have been studied in dilute solutions of sodium salicylate (NaSal) by isothermal titration calorimetry and electrical conductivity at temperatures between 278.15 K and 318.15 K. A structural transformation that was dependent on the concentrations of DTAC and NaSal was observed. The micellization process in dilute solutions of DTAC has been subjected to a detailed thermodynamic analysis and shown to occur at considerably lower critical micelle concentrations than reported for DTAC in water and NaCl solutions. Gibbs free energy, Δ _mic G ^o, and entropy, Δ _mic S ^o, were deduced by taking into account the degree of micelle ionization, β, estimated from conductivity measurements. From the temperature dependence of the enthalpy of micellization, Δ _mic H ^o, the heat capacities of micellization, D_mic c_p^o {\Delta_{{{\rm mic} }}}c_p^o were determined and discussed in terms of the removal of large areas of non-polar surface from contact with water upon micellization. The process is exothermic at all temperatures, indicating, in addition to the hydrophobic effect, the presence of strong interactions between surfactant and salicylate ions. These were confirmed by ¹H NMR spectroscopy and diffusion NMR experiments. Salicylate ions not only interact with the headgroups but also insert further into the micelle core. At c _NaSal/c _DTAC > 2.5, the structural rearrangements occur even at relatively low concentrations of NaSal.