DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the “classical” B conformation (BI‐form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence‐dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII‐like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548–2559, 2010     

Experimental methodology for precise determination of density of RTILs as a function of temperature and pressure using vibrating tube densimeters

A specific calibration procedure that allows the accurate determination of densities of room temperature ionic liquids, RTILs, as a function of temperature and pressure using vibrating tube densimeters is presented. This methodology overcomes the problems of common calibration methods when they are used to determine the densities of high density and high viscosity fluids such as RTILs. The methodology is applied for the precise density determination of RTILs 1-ethyl-3-methylimidazolium tetrafluoroborate [Emim][BF₄], 1-butyl-3-methylimidazolium tetrafluoroborate [Bmim][BF₄], 1-hexyl-3-methylimidazolium tetrafluoroborate [Hmim][BF₄], and 1-octyl-3-methylimidazolium tetrafluoroborate [Omim][BF₄] in the temperature and pressure intervals (283.15 to 323.15) K and (0.1 to 60) MPa, respectively. The viscosities of these substances, needed for the estimation of the viscosity-induced errors, were estimated at the same conditions from the experimental measurements in the intervals (283.15 to 323.15) K and (0.1 to 14) MPa and from a specific extrapolation procedure. The uncertainty in the density measurements was estimated in ±0.30 kg · m^?3 which is an excellent value in the working intervals. The results of these RTILs have demonstrated that viscosity-induced errors are relevant and they must be taken into account for a precise density determination. Finally, an alternative tool for a simpler application of this procedure is presented.     

Single crystal EPR study of the dinuclear Cu(II) complex [Cu(tda)(phen)](2)·H(2)tda (tda = thiodiacetate, phen = phenanthroline): influence of weak interdimeric magnetic interactions

We report powder and single crystal EPR measurements of [Cu(tda)(phen)](2)·H(2)tda (tda = thiodiacetate, phen = phenanthroline) at 9.7 GHz. This compound consists of centrosymmetric copper(II) ion dimers, weakly ferromagnetically exchange-coupled (J = +3.2 cm(-1)), in which the dimeric units are linked by hydrophobic chemical paths involving the phen molecules. EPR revealed that the triplet spectra are collapsed by interdimeric exchange interactions mediated by that chemical path. Analysis and simulation of the single crystal EPR spectra were performed using Anderson's exchange narrowing model, together with statistical arguments. This approach allowed us to interpret the spectra modulated by the interdimeric interactions in situations of weak, intermediate, and strong exchange. We evaluated an interdimeric exchange constant J' = 0.0070(3) cm(-1), indicating that hydrophobic paths can transmit weak exchange interactions between centers at relatively long distances of the order of ～10 ?.     

Synthesis of comb type and semi-interpenetrating networks of acryloyl-l-proline methyl ester and poly (acrylic acid) for Cu (II) immobilization

Graft copolymer hydrogels and semi-interpenetrating networks (s-IPN) of acryloyl-l-proline methyl ester (A-ProOMe) and poly (acrylic acid) (PAAc) were synthesized in methanol solutions, by ionizing radiation (γ rays from a Co⁶⁰ source at room temperature). These systems are thermo and pH-sensitive and the pH sensitivity increases from acidic to basic solutions. The Lower Critical Solution Temperature (LCST), due to presence of poly (acryloyl-l-proline methyl ester) (PA-ProOMe) has been found between 18 and 20 °C and an unexpected Upper Critical Solution Temperature (UCST) due to poly acrylic acid (PAAc) has been found between 21 and 22 °C. Preliminary studies on the immobilization of Cu²⁺ for both hydrogels were done at several pH values at room temperature. Other techniques employed to characterize the comb type hydrogels and sIPN included scanning electronic microscopy (SEM) and infrared (FTIR-ATR).     

Comparison Between Different Syntesis Methods of PMMA/HA Using Ultrasonic Radiation

Summary: The use of PMMA as dental and osseous cement and also in the fabrication of intraocular lenses has been widely reported. The combination of its excellent properties with those of hydroxyapatite (HA) to form a composite material, can result in very interesting properties as a biomaterial. The key is to obtain a good filler dispersion and interface bonding. Ultrasonic radiation seems to be a very versatile method for the synthesis of these materials, since the use of conventional initiators can be avoided, the filler dispersion improved and the interface interaction can be promoted. In the present work PMMA/HA composite materials were prepared by three different synthesis routes using ultrasonic radiation, in order to study the effect of the synthesis method on the final microstructure. Method I : in situ synthesis of PMMA and HA, under ultrasonic radiation by emulsion polymerization of MMA and HA precursors. Method II : in situ synthesis of HA, (from its precursors) by high frequency ultrasound in commercial PMMA solution Method III : in situ polymerization of MMA under high frequency ultrasonic radiation and adding HA to the solution and Method IV Mixing of hydroxyapatite nanocrystals, in different proportions, in a solution of commercial PMMA, by different periods from 10 min to 7 h, under low frequency (conventional) ultrasonic radiation, to compare the effect of high frequency and conventional ultrasound radiation. The different materials were characterized by FTIR, SEM, TEM, DRX, ¹H NMR and TGA. The results showed that, all the composites prepared by in situ synthesis showed an interaction between HA and PMMA, manifested by a bonding of the phosphate groups with the polar groups of the polymer matrix observed by FTIR. On the other hand, when the synthesis was carried out simultaneously adding HA and PMMA precursors a inhibition of the polymerization reaction of MMA was observed.     

Comparing the hydrodesulfurization reaction of thiophene on γ-Al2O3 supported CoMo, NiMo and NiW sulfide catalysts

The thiophene hydrodesulfurization (HDS) reaction on γ-Al₂O₃ supported CoMo, NiMo and NiW sulfide catalysts was compared in order to gain insight into the promoter effect on direct desulfurization (DDS) and hydrogenation (HYD) pathways. Ni-promoted Mo (or W) sulfide catalysts favor the hydrogen transfer reactions relative to CoMo sulfide catalyst, which facilitates the direct route instead. This different performance and also the dependence of the apparent Arrhenius parameters with the catalyst formulation were attributed to the major participation of Mo (or W) edge for the Ni-containing catalysts and S edge for CoMo sulfide catalyst upon the thiophene-HDS reaction.     

Indoor radon levels and gamma-radiation in dwellings of the Metropolitan Zone of Guadalajara

The present study in the Metropolitan Zone of Guadalajara (MZG) in the state of Jalisco was carried out along 2007. ²²²Rn (radon) and ²²⁰Rn (thoron) levels were measured in single-family dwellings in normal living conditions (open house condition). Measurements were accomplished by Electret Passive Environmental Radon Monitors (E-PERM) in different configurations. At the same time and for the same period, the gamma dose rate was measured by a LiF: Mg, Cu, P+PTFE thermoluminiscent dosimeter. A Quality Assurance Program was improved. Results show a lognormal distribution of annual concentrations and seasonal variations. Mean annual concentrations of radon were lower than US EPA and EEC action values. ²²⁰Rn levels appear to be higher than the typical value determined by the UNSCEAR Reports (1993 and 2000). Performance of different E-PERM configurations accomplishes the US EPA guidelines and yield useful results for diverse situations. Gamma rate dose was higher than that of the Metropolitan Zone of Mexico.     

A Molecular mechanism for the chemoselective hydrogenation of substituted nitroaromatics with nanoparticles of gold on TiO2 catalysts: a cooperative effect between gold and the support

Nanoparticles of gold on TiO2 are highly chemoselective for the reduction of substituted nitroaromatics, such as nitrostyrene. By combining kinetics and in situ IR spectroscopy, it has been found that there is a preferential adsorption of the reactant on the catalyst through the nitro group. IR studies of nitrobenzene, styrene, and nitrostyrene adsorption, together with quantum chemical calculations, show that the nitro and the olefinic groups adsorb weakly on the Au(111) and Au(001) surfaces, and that although a stronger adsorption occurs on low-coordinated atoms in gold nanoparticles, this adsorption is not selective. On the other hand, an energetically and geometrically favored adsorption through the nitro group occurs on the TiO2 support and in the interface between the gold nanoparticle and the TiO2 support. Such preferential adsorption is not observed with nanoparticles of gold on silica which, contrary to the Au/TiO2 catalyst, is not chemoselective for the reduction of substituted nitroaromatic compounds. Therefore, the high chemoselectiviy of the Au/TiO2 catalyst can be attributed to a cooperation between the gold nanoparticle and the support that preferentially activates the nitro group.     

Improvement deoxyribo nucleic acid spots classification in polyacrylamide [correction of polyacrilamide] gel images using photometric normalization algorithms

A comparative study of four enhancement algorithms traditionally used in computer vision for photometric normalization of images affected by illumination changes is presented in this paper. We experimented with the performance of these approaches to reduce the low frequency multiplicative noise that is produced as a result of a non-homogeneity illumination or a non-homogeneity developed chemical process in polyacrylamide gel electrophoresis images for the purpose of automatic classification of deoxyribo nucleic acid (DNA). The algorithms are tested on a database and their results are compared in a system for feature extraction and DNA classification.     

Feasibility of electron impact and electron capture negative ionisation mass spectrometry for the trace determination of tri- to deca-brominated diphenyl ethers in human samples

The applicability of two different MS ionisation modes (EI and ECNI) for the determination of PBDEs at low-trace levels in small-size (up to 1 mL) human samples was compared. The instrumental precision, expressed as R.S.D., obtained for both ionisation modes was similar and lower than 6% (repeatability) and 12% (intermediate precision) for all congeners investigated, except PBDE 209. The LODs obtained when using the ECNI-MS operation mode (6-507 fg) were lower than those found in EI-MS experiments (9 and 10,909 fg), mainly for those congeners with a high bromination degree, i.e., hepta- to deca-BDEs. The selectivity of the ECNI-MS method proposed in the present work was improved by using two ions of the [M−H_xBr_y]⁻ cluster as both qualifier and quantifier ions. For the final validation of the methods, serum and breast milk samples from two different inter-laboratory exercises were analysed. A good agreement was found between the results obtained using the proposed methods and the results provided by the different inter-laboratory organisations, but only ECNI-MS provided the low-LODs necessary for the quantification of high brominated congeners (mainly, PBDEs 196, 197 and 209) at low concentration levels in small-size human samples. Finally, the ECNI-MS method was applied to real-life samples obtained from the Spanish population and the preliminary results obtained were in the same range as those found in other European and Asian regions and lower than the concentrations reported in USA populations.