Thermodynamic basis of the enhanced specificity of structured DNA probes

Molecular beacons are DNA probes that form a stem-and-loop structure and possess an internally quenched fluorophore. When they bind to complementary nucleic acids, they undergo a conformational transition that switches on their fluorescence. These probes recognize their targets with higher specificity than probes that cannot form a hairpin stem, and they easily discriminate targets that differ from one another by only a single nucleotide. Our results show that molecular beacons can exist in three different states: bound to a target, free in the form of a hairpin structure, and free in the form of a random coil. Thermodynamic analysis of the transitions between these states reveals that enhanced specificity is a general feature of conformationally constrained probes.

Pore size characterization of mesoporous materials by a thermodynamic approach: A curvature-dependent solid-fluid potential

A thermodynamic analysis of nitrogen adsorption in cylindrical pores of MCM-41 and SBA-15 samples at 77 K is presented within the framework of the Broekhoff and de Boer (BdB) theory. We accounted for the effect of the solid surface curvature on the potential exerted by the pore walls. The developed model is in quantitative agreement with the non-local density functional theory (NLDFT) for pores larger than 2 tun. This modified BdB theory accounting for the Curvature Dependent Potential (CDP-BdB) was applied to determine the pore size distribution (PSD) of a number of MCM-41 and SBA-15 samples on the basis of matching the equilibrium theoretical isotherm against the adsorption branch of the experimental isotherm. In all cases investigated the PSDs determined with the new approach are very similar to those determined with the non-local density functional theory also using the same basis of matching of theoretical isotherm against the experimental adsorption branch. The developed continuum theory is very simple in its utilization, suggesting that CDP-BdB could be used as an alternative tool to obtain PSD for mesoporous solids from the analysis of adsorption branch of adsorption isotherms of any sub-critical fluids.

Application of a generalized thermodynamic approach to characterize mesoporous materials

Equilibrium adsorption and desorption in mesoporous adsorbents is considered on the basis of rigorous thermodynamic analysis, in which the curvature-dependent solid-fluid potential and the compressibility of the adsorbed phase are accounted for. The compressibility of the adsorbed phase is considered for the first time in the literature in the framework of a rigorous thermodynamic approach. Our model is a further development of continuum thermodynamic approaches proposed by Derjaguin and Broekhoff and de Boer, and it is based on a reference isotherm of a non-porous material having the same chemical structure as that of the pore wall. In this improved thermodynamic model, we incorporated a prescription for transforming the solid-fluid potential exerted by the flat reference surface to the potential inside cylindrical and spherical pores. We relax the assumption that the adsorbed film density is constant and equal to that of the saturated liquid. Instead, the density of the adsorbed fluid is allowed to vary over the adsorbed film thickness and is calculated by an equation of state. As a result, the model is capable to describe the adsorption-desorption reversibility in cylindrical pores having diameter less than 2 nm. The generalized thermodynamic model may be applied to the pore size characterization of mesoporous materials instead of much more time-consuming molecular approaches. (c) 2005 Elsevier B.V. All rights reserved.

Concentrating solar power + desalination plants (CSP+D): models and performance analysis

Tese submetida à Universidade de Lisboa, Instituto Superior Técnico e aprovada em provas públicas para a obtenção do Grau de Doutor em Sistemas Sustentáveis de Energia.

Congo Red adsorption by ball-milled sugarcane bagasse

The adsorption of Congo Red (CR) by ball-milled sugarcane bagasse was evaluated in an aqueous batch system. CR adsorption capacity increased significantly with small changes in bagasse surface area. CR removal decreased with increasing solution pH from 5.0 to 10.0. Maximum adsorption capacity was 38.2 mg/g bagasse at a CR concentration of 500 mg/L. The equilibrium isotherm fitted the Freundlich model and the adsorption kinetics obeyed pseudo-second order equation. CR adsorption obeyed the intra-particle diffusion model very well with bagasse surface area in the range of 0.58–0.66 m2/g, whereas it was controlled by multi-adsorption stages with bagasse surface area in the range of 1.31–1.82 m2/g. Thermodynamic analysis indicated that the adsorption process is an exothermic and spontaneous process. Fourier transform infrared analysis of bagasse containing adsorbed CR indicated interactions between the carboxyl and hydroxyl groups of bagasse and CR function groups.

Effect of Fe3O4 addition on removal of ammonium by zeolite NaA

Magnetic zeolite NaA with different Fe3O4 loadings was prepared by hydrothermal synthesis based on metakaolin and Fe3O4. The effect of added Fe3O4 on the removal of ammonium by zeolite NaA was investigated by varying the Fe3O4 loading, pH, adsorption temperature, initial concentration, adsorption time. Langmuir, Freundlich, and pseudo-second-order modeling were used to describe the nature and mechanism of ammonium ion exchange using both zeolite and magnetic zeolite. Thermodynamic parameters such as change in Gibbs free energy, enthalpy and entropy were calculated. The results show that all the selected factors affect the ammonium ion exchange by zeolite and magnetic zeolite, however, the added Fe3O4 apparently does not affect the ion exchange performance of zeolite to the ammonium ion. Freundlich model provides a better description of the adsorption process than Langmuir model. Moreover, kinetic analysis indicates the exchange of ammonium on the two materials follows a pseudosecond-order model. Thermodynamic analysis makes it clear that the adsorption process of ammonium is spontaneous and exothermic. Regardless of kinetic or thermodynamic analysis, all the results suggest that no considerable effect on the adsorption of the ammonium ion by zeolite is found after the addition of Fe3O4. According to the results, magnetic zeolite NaA can be used for the removal of ammonium due to the good adsorption performance and easy separation method from aqueous solution.

A new approach to prepare ZVI and its application in removal of Cr(VI) from aqueous solution

Zero valent iron (ZVI) was prepared by reducing natural goethite (NG-ZVI) and synthetic goethite (SG-ZVI) in hydrogen at 550 °C. XRD, TEM, FESEM/EDS and specific surface area (SSA) and pore analyser were used to characterize goethites and reduced goethites. Both NG-ZVI and SG-ZVI with a size of nanoscale to several hundreds of nanometers were obtained by reducing goethites at 550 °C. The reductive capacity of the ZVIs was assessed by removal of Cr(VI) at ambient temperature in comparison with that of commercial iron powder (CIP). The effect of contact time, initial concentration and reaction temperature on Cr(VI) removal was investigated. Furthermore, the uptake mechanism was discussed according to isotherms, thermodynamic analysis and the results of XPS. The results showed that SG-ZVI had the best reductive capacity to Cr(VI) and reduced Cr(VI) to Cr(III). The results suggest that hydrogen reduction is a good approach to prepare ZVI and this type of ZVI is potentially useful in remediating heavy metals as a material of permeable reaction barrier.

Removal characteristics of ammonium nitrogen from wastewater by modified Ca-bentonites

A modified inorganic bentonite (Na/Al) based on purified Ca-bentonite was prepared through exchanging Al and Na ions in the interlayer space of Ca-bentonite. The structural properties of purified and modified bentonites were characterized by XRD and SEM analysis. Batch experiments were performed for the adsorption of ammonium nitrogen and different experimental conditions were studied in order to investigate the optimum adsorption conditions. Comparative experiments were also carried out for natural Ca-bentonite (RB), unmodified purified bentonite (PB) and modified purified bentonite (MB). Through the thermodynamic analysis, the ammonium nitrogen adsorption process can be spontaneous, the standard heat was −41.46kJmol −1 , and the adsorption process based on ion exchange adsorption. The ammonium nitrogen adsorption capacity of MB (46.904mg/g) was improved compared to raw bentonite (RB) (26.631mg/g), which was among the highest values of ammonium nitrogen adsorption compared with other adsorbents according to the literatures. The described process provides a potential pathway for the removal of ammonium nitrogen at low concentrations encountered in most natural waters.

Activities in the $FeTiO_{3}-NiTiO_{3}$ Solid Solution from Alloy-Oxide Equilibria at 1273 K

Nine tie-lines between Fe-Ni alloys and FeTiO3-NiTiO3 solid solutions were determined at 1273 K. Samples were equilibrated in evacuated quartz ampoules for periods up to 10 days. Compositions of the alloy and oxide phases at equilibrium were determined by energy-dispersive x-ray spectroscopy. X-ray powder diffraction was used to confirm the results. Attainment of equilibrium was verified by the conventional tie-line rotation technique and by thermodynamic analysis of the results. The tie-lines are skewed toward the FeTiO3 corner. From the tie-line data and activities in the Fe-Ni alloy phase available in the literature, activities of FeTiO3 and NiTiO3 in the ilmenite solid solution were derived using the modified Gibbs-Duhem technique of Jacob and Jeffes [K.T. Jacob and J.H.E. Jeffes, An Improved Method for Calculating Activities from Distribution Equilibria, High Temp. High Press., 1972, 4, p 177-182]. The components of the oxide solid solution exhibit moderate positive deviations from Raoult's law. Within experimental error, excess Gibbs energy of mixing for the FeTiO3-NiTiO3 solid solution at 1273 K is a symmetric function of composition and can be represented as: Delta G(E) = 8590 (+/- 200) X-FeTiO3 X-NiTiO3 J/mol Full spectrum of tie-lines and oxygen potentials for the three-phase equilibrium involving Fe-Ni alloys, FeTiO3-NiTiO3 solid solutions, and TiO2 at 1273 K were computed using results obtained in this study and data available in the literature.

Pressure dependence of 35Cl nuclear quadrupole resonance in 2,5-, 2,6- and 3,5-dichlorophenols

Pressure dependence of the 35Cl Nuclear Quadrupole Resonances (N.Q.R.) in 2,5-, 2,6- and 3,5-dichlorophenols (DCP) has been studied up to a pressure of about 6·5 kbar at room temperature. While the pressure dependence of the two resonance lines in 2,6-DCP is essentially similar, the lower frequency line in 2,5-DCP is almost pressure independent and the higher frequency line shows a linear variation with pressure upto about 3·5 kbar but shows a negative pressure coefficient beyond this pressure. The two lines in 3,5-DCP have a non-linear pressure dependence with the curvature changing smoothly with pressure. The pressure coefficient for both lines becomes negative beyond a pressure of 5 kbar. The pressure dependence of the N.Q.R. frequencies is discussed in relation to intra- and inter-molecular contacts. Also, a thermodynamic analysis of the data is carried out to determine the constant volume temperature derivative of the N.Q.R. frequency.

Activated carbon + HFC 134a based two stage thermal compression adsorption refrigeration using low grade thermal energy sources

A thermodynamic analysis is presented for the two stage thermal compression process for an adsorption refrigeration cycle with HFC-134a as the working fluid and activated carbon as the adsorbent. Three specimens of varying achievable packing densities were evaluated. The influence of evaporating, condensing/adsorption and desorption temperatures was assessed through three performance indicators, namely,the uptake efficiency, the coefficient of performance and the exergetic efficiency. Conditions under which a two stage thermal compression process performs better than the single stage unit are identified. It is concluded that two stage thermal compression will be a viable proposition when the heat source temperature is low or when adsorption characteristics are weak or when adequate packing densities are difficult to realize. (C) 2008 Elsevier Ltd. All rights reserved.

Enhanced Tetrahedral Ordering of Water Molecules in Minor Grooves of DNA: Relative Role of DNA Rigidity, Nanoconfinement, and Surface Specific Interactions

Confinement and Surface specific interactions call induce Structures otherwise unstable at that temperature and pressure. Here we Study the groove specific water dynamics ill the nucleic acid sequences, poly-AT and poly-GC, in long B-DNA duplex chains by large scale atomistic molecular dynamics simulations, accompanied by thermodynamic analysis. While water dynamics in the major groove remains insensitive to the sequence differences, exactly the opposite is true for the minor groove water. Much slower water dynamics observed in the minor grooves (especially in the AT minor) call be attributed to all enhanced tetrahedral ordering (< t(h)>) of water. The largest value of < t(h)> in the AT minor groove is related to the spine of hydration found in X-ray Structure. The calculated configurational entropy (S-C) of the water molecules is found to be correlated with the self-diffusion coefficient of water in different region via Adam-Gibbs relation D = A exp(-B/TSC), and also with < t(h)>.

Studies on a chitooligosaccharide-specific lectin from Coccinia indica. Thermodynamics and kinetics of umbelliferyl glycoside binding.

Coccinia indica agglutinin (CIA) is a chitooligosaccharide-specific lectin with two binding sites/homodimer of M(r) 32,000. Quenching studies implied tryptophan involvement in binding activity, which was confirmed by chemical modification experiments (A. R. Sanadi and A. Surolia, submitted for publication). Binding of 4-methylumbelliferyl chitooligosaccharides has been carried out to study their binding by CIA. Reversal experiments confirm the validity of the data previously obtained (A. R. Sanadi and A. Surolia, submitted for publication) from intrinsic fluorescence studies. Surprisingly, unlike wheat germ agglutinin, there is no consistent thermodynamic effect of the chromophoric label on binding activities as compared with the native sugars. From the changes in the optical properties of the chromophoric group upon binding to CIA, it has been possible to confirm that the tryptophan located in the binding site is closest to the fourth subsite. Thermodynamic analysis shows that the binding of the labeled tetrasaccharide is very strongly entropically driven, with the terminal, nonreducing sugar residue protruding from the binding pocket. The results of stopped-flow kinetic studies on the binding of the chromophoric trisaccharide by CIA show that the mechanism of binding is a one-step process.

Characterization of a continuous CO2 laser-welded Fe-Cu dissimilar couple

Continuous CO2 laser welding of an Fe-Cu dissimilar couple in a butt-weld geometry at different process conditions is studied. The process conditions are varied to identify and characterize the microstructural features that are independent of the welding mode. The study presents a characterization of the microstructure and mechanical properties of the welds. Detailed microstructural analysis of the weld/base-metal interface shows features that are different on the two sides of the weld. The iron side can grow into the weld with a local change in length scale, whereas the interface on the copper side indicates a barrier to growth. The interface is jagged, and a banded microstructure consisting of iron-rich layers could be observed next to the weld/Cu interface. The observations suggest that solidification initiates inside the melt, where iron and copper are mixed due to convective flow. The transmission electron microscopy (TEM) of the weld region also indicates the occasional presence of droplets of iron and copper. The microstructural observations are rationalized using arguments drawn from a thermodynamic analysis of the Fe-Cu system.

Temperature- and pressure-dependent study of Cl-35 NQR frequency and spin lattice relaxation time in 2,3-dichloroanisole

The temperature and pressure dependence of Cl-35 NQR frequency and spin lattice relaxation time (T-1) were investigated in 2,3-dichloroanisole. Two NQR signals were observed throughout the temperature and pressure range studied. T-1 were measured in the temperature range from 77 to 300 K and from atmospheric pressure to 5 kbar. Relaxation was found to be due to the torsional motion of the molecule and also reorientation f motion of the CH3 group. T-1 versus temperature data were analyzed on the basis of Woessner and Gutowsky model, and the activation energy for the reorientation of the CH3 group was estimated. The temperature dependence of the average torsional lifetimes of the molecules and the transition probabilities were also obtained. NQR frequency shows a nonlinear behavior with pressure, indicating both dynamic and static effects of pressure. The pressure coefficients were observed to be positive for both the lines. A thermodynamic analysis of the data was carried out to determine the constant volume temperature coefficients of the NQR frequency. The variation of spin lattice time with pressure was very small, showing that the relaxation is mainly due to the torsional motions of the molecules. Copyright (C) 2010 John Wiley & Sons, Ltd.