Editor’s letter

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Editor’s letter     

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.     

Rational redesign of Candida antarctica lipase B for the ring opening polymerization of D,D-lactide

Based on molecular modelling, the enzyme Candida antarctica lipase B was redesigned as a catalyst for the ring opening polymerization of D,D-lactide. Two mutants with 90-fold increased activity as compared to the wild-type enzyme were created. In a preparative synthesis of poly(D,D-lactide) the mutants greatly improved the rate and the degree of polymerization.     

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.     

A Modular Functor Which is Universal¶for Quantum Computation

We show that the topological modular functor from Witten–Chern–Simons theory is universal for quantum computation in the sense that a quantum circuit computation can be efficiently approximated by an intertwining action of a braid on the functor's state space. A computational model based on Chern–Simons theory at a fifth root of unity is defined and shown to be polynomially equivalent to the quantum circuit model. The chief technical advance: the density of the irreducible sectors of the Jones representation has topological implications which will be considered elsewhere. Received: 4 May 2001 / Accepted: 18 February 2002     

Nonlinear optical and electrostatic force microscopy for ferroelectric polarization imaging

Second-harmonic generation (SHG)-based nonlinear optical microscopy is used for spatially resolved imaging of the polarization switching in lead zirconium titanate ferroelectric thin films. The local SHG hysteresis loops reveal a strong dependence on film composition and structure. The SHG microscopy results are in good agreement with the efficiency of electrostatic force microscopy writing and allow us to predict the microscopic dielectric memory efficiency, both in contact and contact-less ways. Received: 15 January 2001 / Revised version: 27 March 2002 / Published online: 6 June 2002