Thermodynamic properties of RhO2

A solid-state electrochemical cell, with yttria-stabilized zirconia as the electrolyte and pure O-2 gas at 0.1 MPa as the reference electrode, has been used to measure the oxygen chemical potential corresponding to the equilibrium between beta-Rh2O3 and RhO2 in the temperature range from 850 to 1050K. Using standard Gibbs energy of formation of beta-Rh2O3 available in the literature and the measured oxygen potential, the standard Gibbs free energy of formation of RhO2 is derived as a function of temperature: Delta G(f)degrees(RhO2)(+/- 71)/J mol(-1) = 238,418 + 179.89T Using an estimated value of Delta C-p degrees; for the formation reaction of RhO2 from its elements, the standard enthalpy of formation, standard entropy and isobaric heat capacity of RhO2 at 298.15 K are evaluated: Delta H-f degrees (298.15 K)(+/- 164)/kJ mol(-1) = -244.94, S degrees (298.15 K)(+/- 3.00)/J mol(-1) K-1 = 45.11 and C-p degrees(298.15 K)(+/- 2.6)1mol(-1) K-1 =64.28. (C) 2010 Elsevier B.V. All rights reserved.

Optimization of two-dimensional NMR by matched accumulation

It is well known that in the time-domain acquisition of NMR data, signal-to-noise (S/N) improves as the square root of the number of transients accumulated. However, the amplitude of the measured signal varies during the time of detection, having a functional form dependent on the coherence detected. Matching the time spent signal averaging to the expected amplitude of the signal observed should also improve the detected signal-to-noise. Following this reasoning, Barna et al. (J Magn. Reson.75, 384, 1987) demonstrated the utility of exponential sampling in one- and two-dimensional NMR, using maximum-entropy methods to analyze the data. It is proposed here that for two-dimensional experiments the exponential sampling be replaced by exponential averaging. The data thus collected can be analyzed by standard fast-Fourier-transform routines. We demonstrate the utility of exponential averaging in 2D NOESY spectra of the protein ubiquitin, in which an enhanced SIN is observed. It is also shown that the method acquires delayed double-quantum-filtered COSY without phase distortion.

Playing Games on Sets and Models

The most prominent objective of the thesis is the development of the generalized descriptive set theory, as we call it. There, we study the space of all functions from a fixed uncountable cardinal to itself, or to a finite set of size two. These correspond to generalized notions of the universal Baire space (functions from natural numbers to themselves with the product topology) and the Cantor space (functions from natural numbers to the {0,1}-set) respectively. We generalize the notion of Borel sets in three different ways and study the corresponding Borel structures with the aims of generalizing classical theorems of descriptive set theory or providing counter examples. In particular we are interested in equivalence relations on these spaces and their Borel reducibility to each other. The last chapter shows, using game-theoretic techniques, that the order of Borel equivalence relations under Borel reduciblity has very high complexity. The techniques in the above described set theoretical side of the thesis include forcing, general topological notions such as meager sets and combinatorial games of infinite length. By coding uncountable models to functions, we are able to apply the understanding of the generalized descriptive set theory to the model theory of uncountable models. The links between the theorems of model theory (including Shelah's classification theory) and the theorems in pure set theory are provided using game theoretic techniques from Ehrenfeucht-Fraïssé games in model theory to cub-games in set theory. The bottom line of the research declairs that the descriptive (set theoretic) complexity of an isomorphism relation of a first-order definable model class goes in synch with the stability theoretical complexity of the corresponding first-order theory. The first chapter of the thesis has slightly different focus and is purely concerned with a certain modification of the well known Ehrenfeucht-Fraïssé games. There we (me and my supervisor Tapani Hyttinen) answer some natural questions about that game mainly concerning determinacy and its relation to the standard EF-game

Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis

Background. Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. Methodology/Principal Findings. Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. Conclusions. We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a broad overview of the similarities and differences between organisms, taking comparative genomics studies to a higher dimension.

Deformation and structural densification in Al2O3-Y2O3 glass

In this article, we examine the unusual plastic deformation under uniaxial compression of an Al2O3-15 mol % Y2O3 (A15Y) glass synthesized by a wet chemical route At a low temperature of 650-725 degrees C, plastic deformation of this glass is largely non-viscous through shear instabilities In contrast deformation near the crystallization temperature (850 degrees C) occurs homogeneously with work hardening and with a monotonic increase in the true density of the glass by 10-12% accompanied by an increase in hardness (H) and elastic modulus (E) of up to 100% We hypothesize a phenomenon of molecular densification of the amorphous structure through a hierarchy of multiple phases, analogous to density- or entropy-driven amorphous to-amorphous phase transitions (polyamorphism) These results suggest that the present method of preparation and the unusual behavior can trigger a search for many more systems that display such behavior (C) 2010 Acta Materialia Inc Published by Elsevier Ltd All rights reserved

Phenyl-Ring-Bearing Cationic Surfactants: Effect of Ring Location on the Micellar Structure

A series of isomeric cationic surfactants (S1-S5) bearing a long alkyl chain that carries a 1,4-phenylene unit and a trimethyl ammonium headgroup was synthesized; the location of the phenyl ring within the alkyl tail was varied in an effort to understand its influence on the amphiphilic properties of the surfactants. The cmc's of the surfactants were estimated using ionic conductivity measurements and isothermal calorimetric titrations (ITC); the values obtained by the two methods were found to be in excellent agreement. The ITC measurements provided additional insight into the various thermodynamic parameters associated with the micellization process. Although all five surfactants have exactly the same molecular formula, their micellar properties were seen to vary dramatically depending on the location of the phenyl ring; the cmc was seen to decrease by almost an order of magnitude when the phenyl ring was moved from the tail end (cmc of S1 is 23 mM) to the headgroup region (cmc of S5 is 3 mM). In all cases, the enthalpy of micellization was negative but the entropy of micellization was positive, suggesting that in all of these systems the formation of micelles is both enthalpically and entropically favored. As expected, the decrease in cmc values upon moving the phenyl ring from the tail end to he headgroup region is accompanied by an increase in the thermodynamic driving force (Delta G) for micellization. To understand further the differences in the micellar structure of these surfactants, small-angle neutron scattering (SANS) measurements were carried out; these measurements reveal that the aggregation number of the micelles increases as the cmc decreases. This increase in the aggregation number is also accompanied by an increase in the asphericity of the micellar aggregate and a decrease in the fractional charge. Geometric packing arguments are presented to account for these changes in aggregation behavior as a function of phenyl ring location.

Probing of unusual DNA structures in topologically constrained form V DNA: use of restriction enzymes as structural probe

The ability of DNA sequences to adopt unusual structures under the superhelical torsional stress has been studied. Sequences that are forced to adopt unusual conformation in topologically constrained pBR322 form V DNA (Lk=0) were mapped using restriction enzymes as probes. Restriction enzymes such as BamHI, Pstl, Aval and HindIII could not cleave their recognition sequences. The removal of topological constraint relieved this inhibition. The influence of neighbouring sequences on the ability of a given sequence to adopt unusual DNA structure, presumably left handed Z conformation, was studied through single hit analysis. Using multiple cut restriction enzymes such as Narl and Fspl, it could be shown that under identical topological strain, the extent of structural alteration is greatly influenced by the neighbouring sequences. In the light of the variety of sequences and locations that could be mapped to adopt non-6 conformation in pBR322 form V DNA, restriction enzymes appear as potential structural probes for natural DNA sequences.

Chemical potential of oxygen for iron-rutile-ilmenite and iron-ilmenite-ulvospinel equilibria

The chemical potential of oxygen corresponding to the iron-rutile-ilmenite (IRI) and iron-ilmenite-ulvospinel (IIU) equilibria has been measured employing solid-state galvanic cells,$$Pt, Fe + TiO_2 + FeTiO_3 //(Y_2 O_3 ) ZrO_2 //Fe + FeO, Pt$$ and $${\text{Pt, Fe + FeTiO}}_{\text{3}} {\text{ + Fe}}_{\text{2}} {\text{TiO}}_{\text{4}} {\text{//(Y}}_{\text{2}} {\text{0}}_{\text{3}} {\text{) ZrO}}_{\text{2}} {\text{//Fe + FeO, Pt}}$$ in the temperature range of 875 to 1275 K and 900 to 1373 K, respectively. The cells are written such that the right-hand electrodes are positive. The electromotive force (emf) of both the cells was found to be reversible and to vary linearly with temperature over the entire range of measurement. The chemical potential of oxygen for IRI equilibrium is represented by Δμo2(IRI) = -550,724 - 29.445T + 20.374T InT(±210) J mol−1 (875 <-T<- 1184 K) = -620,260 + 369.593T - 27.716T lnT(±210) J mol−1 (1184 <-T<- 1275 K) and that for IIU equilibrium by Δμo2(IIU) = -501,800 - 49.035T + 20.374T lnT(±210) J mol−1 (900 <-T<- 1184 K) = -571,336 + 350.003T− 27.716T lnT(=−210) J mol-1 (1184 <-T<- 1373 K) The standard Gibbs energy changes for IRI and IIU equilibria have been deduced from the measured oxygen potentials. Since ilmenite contains small amounts of Ti³+ ions, a correction for the activity of FeTiO3 has been incorporated by assuming ideal mixing on each cation sublattice in the FeTiO3-Ti2O3 system. Similarly, the ulvospinel contains some Fe³+ ions and a correction for the activity of Fe2TiO4 has been included by modeling the Fe2TiO4-Fe3O4 system. The third-law analysis of the results obtained for IRI equilibrium gives ΔH 298 0 = -575 (±1.0) kJ mol-1 and for IIU equilibrium yields ΔH 298 0 = -523.7 (±0.7) kJ mol−1}. The present results suggest that Fe2+ and Ti4+ cations mix almost ideally on the octahedral site of spinel lattice in Fe2TiO4, giving rise to a configurational contribution of 2R In 2 (11.5256 J mol-1 K-1) to the entropy of Fe2TiO4.

Two forms of Pf1 Inovirus: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit

Inovirus is a helical array of alpha-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

Nature of Cl center dot center dot center dot Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis:Correlation of Polar Flattening Effects with Geometry

The experimental charge density distribution in three compounds, 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine, and 2-chloro-3-chloromethyl-8-methylquinoline, has been obtained using high-resolution X-ray diffraction data collected at 100 K based on the aspherical multipole modeling of electron density. These compounds represent type I (cis), type I (trans), and type II geometries, respectively, as defined for short Cl center dot center dot center dot Cl interactions. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from a periodic quantum calculation at the B3LYP/6-31G** level. The topological features derived from the Bader's theory of atoms in molecules (AIM) approach unequivocally suggest that both cis and trans type I geometries show decreased repulsion, whereas type II geometry is attractive based on the nature of polar flattening of the electron density around the Cl atom.

Criteria for prediction of flow instabilities and microstructural manifestations during warm working of AISI 304L stainless steel

The deformation characteristics of 304L stainless steel in compression in the temperature range 20–700°C and strain rate range 0·001–100 s−1 have been studied with the aim of characterising the .flow instabilities occurring in the microstructure. At higher temperatures and strain rates the stainless steel exhibits flow localisation, whereas at temperatures below 500°C and strain rates lower than 0·1 s−1 the flow instabilities are due to dynamic strain aging. Strain induced martensite formation is responsible for the flow instabilities at room temperature and low strain rates (0·01 s−1). In view of the occurrence of these instabilities, cold working is preferable to warm working to achieve dimensional tolerance and reproducible properties in the product. Among the different criteria tested to explain the occurrence of instabilities, the continuum criterion, developed on the basis of the principles of maximum rate of entropy production and separability of the dissipation function, predicts accurately all the above instability features.

Excitation and relaxation energies of trans-stilbene: Confined singlet, triplet, and charged bipolarons

The π-electronic excitations and excited-state geometries of trans-stilbene (tS) are found by combining exact solutions of the Pariser-Parr-Pople (PPP) model and semiempirical Parametric Method 3 (PM3) calculations. Comprehensive comparisons with tS spectra are obtained and related to the fluorescence and topological alternation of poly(paraphenylenevinylene) (PPV). The one-photon absorption and triplet of tS correspond, respectively, to singlet and triplet bipolarons confined to two phenyls, while the tS2- ground state is a confined charged bipolaron. Independent estimates of the relaxation energy between vertical and adiabatic excitation show the bipolaron binding energy to depend on both charge and spin, as expected for interacting π electrons in correlated or molecular states. Complete configuration interaction within the PPP model of tS accounts for the singlet-triplet gap, for the fine-structure constants and triplet-triplet spectra, for two-photon transitions and intensities, and for one-photon spectra and the radiative lifetime, although the relative position of nearly degenerate covalent and ionic singlets is not resolved. The planar PM3 geometry and low rotational barrier of tS agree with resolved rotational and vibrational spectra in molecular beams. PM3 excitation and relaxation energies for tS bipolarons are consistent with experiment and with PPP results. Instead of the exciton model, we interpret tS excitations in terms of states that are localized on each ring or extended over an alternating chain, as found exactly in Hückel theory, and find nearly degenerate transitions between extended and localized states in the singlet, triplet, and dianion manifolds. The large topological alternation of the extended system increases the ionicity and interchanges the order of the lowest one- and two-photon absorption of PPV relative to polyenes.

Two forms of PF1 INOVIRUS: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the assymetric unit

Inovirus is a helical array of agr-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

DNA Compaction by a Dendrimer

At physiological pH, a PAMAM dendrimer is positively charged and can effectively bind negatively charged DNA. Currently, there has been great interest in understanding this complexation reaction both for fundamental (as a model for complex biological reactions) as well as for practical (as a gene delivery material and probe for sensing DNA sequence) reasons. Here, we have studied the complexation between double-stranded DNA (dsDNA) and various generations of PAMAM dendrimers (G3-05) through atomistic molecular dynamics simulations in the presence of water and ions. We report the compaction of DNA on a nanosecond time scale. This is remarkable, given the fact that such a short DNA duplex with a length close to 13 nm is otherwise thought to be a rigid rod. Using several nanoseconds long MD simulations, we have observed various binding modes of dsDNA and dendrimers for various generations of PAMAM dendrimers at varying charge ratios, and it confirms some of the binding modes proposed earlier. The binding is driven by the electrostatic interaction, and the larger the dendrimer charge, the stronger the binding affinity. As DNA wraps/binds to the dendrimer, counterions originally condensed onto DNA (Na+) and the dendrimer (Cl-) get released. We calculate the entropy of counterions and show that there is gain in entropy due to counterion release during the complexation. MD simulations demonstrate that, when the charge ratio is greater than 1 (as in the case of the G5 dendrimer), the optimal wrapping of DNA is observed. Calculated binding energies of the complexation follow the trend G5 > 04 > 03, in accordance with the experimental data. For a lower-generation dendrimer, such as G3, and, to some extent, for G4 also, we see considerable deformation in the dendrimer structure due to their flexible nature. We have also calculated the various helicoidal parameters of DNA to study the effect of dendrimer binding on the structure of DNA. The B form of the DNA is well preserved in the complex, as is evident from various helical parameters, justifying the use of the PAMAM dendrimer as a suitable delivery vehicle.

Resolution of conflicting views on thermodynamics of glass transition: A unified model

Classical description of thermodynamic properties during glass transition has been questioned by the entropy-loss model. The uncompensated loss of entropy at the glass transition temperature and zero residual entropy is at the heart of the controversy. Both the models are critically reviewed. A unified model is presented which incorporates features of both entropy loss and residual entropy. It implies two different types of contributions to the entropy of the supercooled liquid, one of which vanishes at the transition and the other which contributes to residual entropy. Entropy gain during spontaneous relaxation of glass, and the nature of heat capacity `hysteresis' during cooling and heating through the glass transition range support the proposed model. Experiments are outlined for differentiating between the models.