Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg2+, presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg2+ accounts for 1/3 and all of the free energy gain in 50% and pure MgCl2 solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl2 compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg2+. In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg2+ may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Low temperature CO oxidation and water gas shift reaction over Pt/Pd substituted in Fe/TiO2 catalysts

We demonstrate the activity of Ti0.84Pt0.01Fe0.15O2-delta and Ti0.73Pd0.02Fe0.25O2-delta catalysts towards the CO oxidation and water gas shift (VMS) reaction. Both the catalysts were synthesized in the nano crystalline form by a low temperature sonochemical method and characterized by different techniques such as XRD, FT-Raman, TEM, FT-IR, XPS and BET surface analyzer. H-2-TPR results corroborate the intimate contact between noble metal and Fe ions in the both catalysts that facilitates the reducibility of the support. In the absence of feed CO2 and H-2, nearly 100% conversion of CO to CO2 with 100% H-2 selectivity was observed at 300 degrees C and 260 degrees C respectively, for Ti0.84Pt0.01Fe0.15O2-delta and Ti0.73Pd0.02Fe0.25O2-delta catalyst. However, the catalytic performance of Ti0.73Pd0.02Fe0.25O2-delta deteriorates in the presence of feed CO2 and H-2. The change in the support reducibility is the primary reason for the significant increase in the activity for CO oxidation and WGS reaction. The effect of Fe addition was more significant in Ti0.73Pd0.02Fe0.25O2-delta than Ti0.84Pt0.01Fe0.15O2-delta. Based on the spectroscopic evidences and surface phenomena, a hybrid reaction scheme utilizing both surface hydroxyl groups and the lattice oxygen was hypothesized over these catalysts for WGS reaction. The mechanisms based on the formate and redox pathway were used to fit the ldnetic data. The analysis of experimental data shows the redox mechanism is the dominant pathway over these catalysts. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Role of invariant water molecules and water-mediated ionic interactions in D-xylose isomerase from Streptomyces rubiginosus

The enzyme, D-xylose isomerase (D-xylose keto-isomerase; EC 5.3.1.5) is a soluble enzyme that catalyzes the conversion of the aldo-sugar D-xylose to the keto-sugar D-xylulose. A total of 27 subunits of D-xylose isomerase from Streptomyces rubiginosus were analyzed in order to identify the invariant water molecules and their water-mediated ionic interactions. A total of 70 water molecules were found to be invariant. The structural and/or functional roles of these water molecules have been discussed. These invariant water molecules and their ionic interactions may be involved in maintaining the structural stability of the enzyme D-xylose isomerase. Fifty-eight of the 70 invariant water molecules (83%) have at least one interaction with the main chain polar atom.

Synthesis of nanosized Ce0.85M0.1Ru0.05O2-delta (M = Si, Fe) solid solution exhibiting high CO oxidation and water gas shift activity

Nanosized Ce0.85M0.1Ru0.05O2-delta (M = Si, Fe) has been synthesized using a low temperature sonication method and characterized using XRD, TEM, XPS and H-2-TPR. The potential application of both the solid solutions has been explored as exhaust catalysts by performing CO oxidation. The addition of Si- and Fe-in Ce0.95Ru0.05O2-delta greatly enhanced the reducibility of Ce0.85M0.1Ru0.05O2-delta (M = Si, Fe), as indicated by the H-2-TPR study. The oxygen storage capacity has been used to correlate surface oxygen reactivity to the CO oxidation activity. Both the compounds reversibly release lattice oxygen and exhibit excellent CO oxidation activity with 99% conversion below 200 degrees C. A bifunctional reaction mechanism involving CO oxidation by the extraction of lattice oxygen and rejuvenation of oxide vacancy with gas feed O-2 has been used to correlate experimental data. The performance of both the solid solutions has also been investigated for energy application by performing the water gas shift reaction. The present catalysts are highly active and selective towards the hydrogen production and a lack of methanation activity is an important finding of present study.

Numerical Study of Counterflow Diffusion Flame and Water Spray Interaction

This paper reports numerical investigation concerning the interaction of a laminar methane-air counterflow diffusion flame with monodisperse and polydisperse water spray. Commercial code ANSYS FLUENT with reduced chemistry has been used for investigation. Effects of strain rate, Sauter mean diameter (SMD), and droplet size distribution on the temperature along stagnation streamline have been studied. Flame extinction using polydisperse water spray has also been explored. Comparison of monodisperse and polydisperse droplet distribution on flame properties reveals suitability of polydisperse spray in flame temperature reduction beyond a particular SMD. This study also provides a numerical framework to study flame-spray interaction and extinction.

Covalent Postassembly Modification and Water Adsorption of Pd3 Self-Assembled Trinuclear Barrels

Three new ditopic imidazole ligands (2-4) were synthesized in high yields and characterized by various spectroscopic techniques. These ligands resulted in the formation of 3 + 6] self-assembled trinuclear barrels (5-7) in quantitative yields by stoichiometric combination of individual ligands and Pd(NO3)(2) in DMSO. All the three assemblies (5-7) were characterized by `H NMR and ESI-MS analysis, and subsequently, structures of the complexes 5 and 6 were confirmed by single-crystal X-ray diffraction studies. Structure analysis reveals the presence of NO3- counter anions in the intermolecular channels/pockets, which could potentially act as H-bonding sites between adsorbed water molecules within the channels. In fact, both the assemblies (5 and 6) showed water uptake (136.58, and 123.78 cm(3) g(-1), respectively) at ambient temperature under maximum allowable humidity. In addition, free aldehyde group present in the bridging ligand in complex 7 provides reactive site for postassembly modification. Herein, Knoevenagel condensation with Meldrum's acid was utilized under mild conditions by targeting aldehyde group appended in prefabricated complex 7 and transformed into a different complex (8) with altered functional group. Such postassembly functionalization enables incorporation of a new functional group without disrupting the integrity of the trifacial structure.