Understanding thermodynamic properties at the molecular level: multiple temperature charge density study of ribitol and xylitol

X-ray diffraction data of high quality measured to high resolution on crystals of the two pentitol epimers ribitol (centric) and xylitol (acentric) at 101, 141, and 181 K and data on the two compounds previously recorded at 122 K have formed the basis for multipole refinements with the VALRAY system. Our analysis showed that it is possible to obtain a reliable crystal electron density for an acentric compound (xylitol) from X-ray diffraction data and that the thermal motion can be deconvoluted from the static density in this temperature range. The Bader-type topological analysis of the static electron densities revealed virtually identical intramolecular interactions as well as very similar hydrogen bond interactions of ribitol and xylitol; the only minor differences are found in the weaker intermolecular interactions. The high-level periodic DFT calculations are in accordance with the thermodynamic measurements that show that the two pentitols have identical sublimation energies. A rigid body normal coordinate analysis was performed on the atomic displacement parameters obtained at the four different temperatures. The translational and librational mean square deviations derived through this analysis were used in a quantum statistical approach to derive frequencies of the corresponding harmonic oscillators. The analysis showed a consistent vibrational model for all temperatures. The frequencies were subsequently used to calculate crystal entropies assuming an Einstein-type behavior. These calculations show that the crystal entropy of ribitol is 8 J K(-1) mol(-1) higher than the crystal entropy of xylitol, confirming that it is a difference in the entropy of the two compounds that causes the difference in their free energy. Our results presented in this Article show the potential to use X-ray diffraction data to obtain physicochemical properties of crystals.     

Simulating the formation of sodium:electron tight-contact pairs: watching the solvation of atoms in liquids one molecule at a time

The motions of solvent molecules during a chemical transformation often dictate both the dynamics and the outcome of solution-phase reactions. However, a microscopic picture of solvation dynamics is often obscured by the concerted motions of numerous solvent molecules that make up a condensed-phase environment. In this study, we use mixed quantum/classical molecular dynamics simulations to furnish the molecular details of the solvation dynamics that leads to the formation of a sodium cation-solvated electron contact pair, (Na(+), e(-)), in liquid tetrahydrofuran following electron photodetachment from sodide (Na(-)). Our simulations reveal that the dominant solvent response is comprised of a series of discrete solvent molecular events that work sequentially to build up a shell of coordinating THF oxygen sites around the sodium cation end of the contact pair. With the solvent response described in terms of the sequential motion of single molecules, we are then able to compare the calculated transient absorption spectroscopy of the sodium species to experiment, providing a clear microscopic interpretation of ultrafast pump-probe experiments on this system. Our findings suggest that for solute-solvent interactions similar to the ones present in our study, the solvation dynamics is best understood as a series of kinetic events consisting of reactions between chemically distinct local structures in which key solvent molecules must be considered to be part of the identity of the reacting species.     

Protein kinase A type I activates a CRE-element more efficiently than protein kinase A type II regardless of C subunit isoform

Background  

Protein kinase A type I (PKAI) and PKAII are expressed in most of the eukaryotic cells examined. PKA is a major receptor for cAMP and specificity is achieved partly through tissue-dependent expression and subcellular localization of subunits with different biochemical properties. In addition posttranslational modifications help fine tune PKA activity, distribution and interaction in the cell. In spite of this the functional significance of two forms of PKA in one cell has not been fully determined. Here we have tested the ability of PKAI and PKAII formed by expression of the regulatory (R) subunits RIα or RIIα in conjunction with Cα1 or Cβ2 to activate a co-transfected luciferace reporter gene, controlled by the cyclic AMP responsive element-binding protein (CREB) in vivo.     

A Monte Carlo calculation of thermodynamic properties for the liquid NaCl+KCl mixture

The mixing process NaCl+KCl →(Na, K)Cl in the liquid state at T=1083 K and zero pressure is simulated by means of Monte Carlo calculations. A cubic box with periodic boundary conditions containing 216 ions interacting according to a pair potential of the Huggins-Mayer form served as a model of the system. Thermodynamic properties are calculated for the mixture and the pure salt models and compared with experiments. Radial and angular distribution functions are obtained. A perturbation theory of the heats of mixing of molten salts and the ‘random mixture approximation’ are commented on in the light of the Monte Carlo results.     

Rapidity dependence of charged antihadron to hadron ratios in Au+Au collisions at sqrt[s(NN)]=200 GeV

We present ratios of the numbers of charged antihadrons to hadrons (pions, kaons, and protons) in Au+Au collisions at sqrt[s(NN)]=200 GeV as a function of rapidity in the range y=0-3. While the ratios at midrapidity are approaching unity, the K(-)/K(+) and p;/p ratios decrease significantly at forward rapidities. An interpretation of the results within the statistical model indicates a reduction of the baryon chemical potential from mu(B) approximately 130 MeV at y=3 to mu(B) approximately 25 MeV at y=0.     

Alternating-Sign Matrices and Domino Tilings (Part II)

We continue the study of the family of planar regions dubbed Aztec diamonds in our earlier article and study the ways in which these regions can be tiled by dominoes. Two more proofs of the main formula are given. The first uses the representation theory of GL(n). The second is more combinatorial and produces a generating function that gives not only the number of domino tilings of the Aztec diamond of order n but also information about the orientation of the dominoes (vertical versus horizontal) and the accessibility of one tiling from another by means of local modifications. Lastly, we explore a connection between the combinatorial objects studied in this paper and the square-ice model studied by Lieb.     

Finding the best visualization of an ontology

An ontology is a classification model for a given domain. In information retrieval, ontologies are used to perform broad searches. An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology becomes easier with a visual representation. An idea is to use the expressive power of 3D representation to provide visualization for the user. In this paper, we propose a new method for positioning the elements of the visualized concept lattice in the 3D world based on operations research (OR) methods. One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version should be feasible for on-line processing and what-if analysis of ontologies.     

Structural and magnetic investigations of the mixed-valence Fe(II,III) two-dimensional layer complex, [Fe2(II) Fe2(III)(HCOO)10(C6H7N)6]n.

The structure of the complex, [Fe2(II)Fe2(III)(HCOO)10(C6H7N6)n, (1) exhibits a neutral two-dimensional layer network of alternating iron(II) and iron(III) ions, bridged equatorially by formate groups. All iron atoms are octahedrally coordinated, with iron(III) coordinating axially to one gamma-picoline and one formate group, while the iron(II) centers interact axially with two gamma-picoline groups, above and below the layer plane. The complex crystallizes in the triclinic space group P1 at all studied temperatures [at 120 K, the cell dimensions are: a = 10.228(1), b = 12.071(1), c = 12.072(1) A, alpha = 89.801(2), beta = 71.149(2), gamma = 73.371(2) degrees]. An intralayer antiferromagnetic exchange interaction of J = -2.8 cm(-1) between iron(II) and iron(III) was observed in the magnetic studies. Decreasing the temperature to close to 20 K causes a magnetic-ordering phenomenon to occur and a low-temperature phase with a long-range antiferromagnetic spin orientation appears. The magnetic phase transition was confirmed by M?ssbauer spectroscopic studies at temperatures above and below the critical temperature. Structural information of 1 from synchrotron X-ray diffraction data collected at room temperature and 16 K suggests that the antiferromagnetic ordering is caused by an enhanced pi-pi interaction between chi-picoline groups from adjacent layers.