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The reaction between epoxides and CO2 to yield cyclic carbonates is efficiently promoted under solvent-free and relatively mild reaction conditions (0.5 mol % catalyst loading, 0.8 MPa, 125 °C) by zinc(II) complexes of pyridine containing macrocyclic ligands (Pc−L pyridinophanes). The zinc complexes have been fully characterized, including X-ray structural determination. The [Zn(II)X(Pc−L)]X complexes showed good solubility in several polar solvents, including cyclic carbonates. The scope of the reaction under solvent-free conditions has been studied and good to quantitative conversions with excellent selectivities have been obtained, starting from terminal epoxides. When solvent-free conditions were not possible (solid epoxides or low solubility of the catalyst in the oxirane) the use of cyclic carbonates as solvents has been successfully investigated. The remarkable stability of the catalytic system has been demonstrated by a series of consecutive runs.

Summary: We propose a C++ class library developed to the purpose of making the implementation of sequence analysis algorithms easier and faster when genomic annotations and variations need to be considered. The library provides a class hierarchy to seamlessly bind together annotations of genomic elements to sequences and to algorithm results; it allows to evaluate the effect of mutations/variations in terms of both element position shifts and of algorithm results, limiting recalculation to the minimum. Particular care has been posed to keep memory and time overhead into acceptable limits.

We analyze the performance of two different core-hole potentials in the theoretical modeling of XAS of ice, liquid and gas phase water; the use of a full core-hole (FCH) in the calculations, as suggested by Hetenyi et al. [B. Hetenyi, F. De Angelis, P. Giamozzi and R. Car, J. Chem. Phys., 2004, 120(18), 8632], gives poor agreement with experiment in terms of intensity distribution as well as transition energies, while the half core hole (HCH) potential, in the case of water, provides a better compromise between initial and final state effects, leading to good agreement with the experimental data., Part of urn:nbn:se:su:diva-286

We describe the implementation of a simple technique to simulate core-level spectra within the Car-Parrinello plane-waves molecular dynamics framework. The x-ray absorption (XA) spectra are generated using the transition potential technique with the effect of the core hole included through a specifically developed pseudopotential for the core-excited atom. Despite the lack of 1s core orbitals in the pseudopotential treatment, the required transition moments are accurately calculated without reconstruction of the all-electron orbitals. The method is applied to the oxygen XA spectra of water in its various aggregation states, but it is transferable to any first-row element. The computed spectra are compared favorably with the results from all-electron cluster calculations, as well as with experimental data. The periodicity of the plane-wave technique improves the description of condensed phases. The molecular dynamics simulation enables in principle a proper treatment of thermal effects and dynamical averaging in complex systems., Part of urn:nbn:se:su:diva-286

X-ray absorption spectroscopy and x-ray Raman scattering were used to probe the molecular arrangement in the first coordination shell of liquid water. The local structure is characterized by comparison with bulk and surface of ordinary hexagonal ice Ih and with calculated spectra. Most molecules in liquid water are in two hydrogen–bonded configurations with one strong donor and one strong acceptor hydrogen bond in contrast to the four hydrogen–bonded tetrahedral structure in ice. Upon heating from 25°C to 90°C, 5 to 10% of the molecules change from tetrahedral environments to two hydrogen–bonded configurations. Our findings are consistent with neutron and x-ray diffraction data, and combining the results sets a strong limit for possible local structure distributions in liquid water. Serious discrepancies with structures based on current molecular dynamics simulations are observed, Part of urn:nbn:se:su:diva-181

Part of urn:nbn:se:su:diva-286

Part of urn:nbn:se:su:diva-294

We have studied the electronic structure of liquid water using x-ray absorption spectroscopy at the oxygen K edge. Since the x-ray absorption process takes less than a femtosecond, it allows probing of the molecular orbital structure of frozen, local geometries of water molecules at a timescale that has not previously been accessible. Our results indicate that the electronic structure of liquid water is significantly different from that of the solid and gaseous forms, resulting in a pronounced pre-edge feature below the main absorption edge in the spectrum. Theoretical calculations of these spectra suggest that this feature originates from specific configurations of water, for which the H-bond is broken on the H-donating site of the water molecule. This study provides a fingerprint for identifying broken donating H-bonds in the liquid and shows that an unsaturated H-bonding environment exists for a dominating fraction of the water molecules., QC 20100525

Part of urn:nbn:se:su:diva-286

Part of urn:nbn:se:su:diva-286

A closely integrated theoretical and experimental effort to understand chemical bonding using X-ray spectroscopic probes is presented. Theoretical techniques to simulate XAS (X-ray absorption spectroscopy), XES (X-ray emission spectroscopy), RIXS (resonant inelastic X-ray scattering) and XPS (X-ray photoelectron spectroscopy) spectra have been developed and implemented within a density functional theory (DFT) framework. In combination with new experimental techniques, such as high-resolution XAS on liquid water under ambient conditions and XES on complicated surface adsorbates, new insight into e.g. hydrogen-bonded systems is obtained. For the (3 x 2) overlayer structure of glycine/Cu(110), earlier work has been extended to include adsorbate-adsorbate interactions. Structures are optimized for large cluster models and for periodic boundary conditions. It is found that specific features in the spectra arise from hydrogen-bonding interactions, which thus have important effects at the molecular-orbital level. XAS on liquid water shows a pronounced pre-edge feature with significant intensity, while the spectrum of ice shows only little intensity in this region. Theoretical spectrum calculations, based on instantaneous structures obtained from molecular-dynamics (MD) simulations, show that the pre-edge feature in the liquid is caused by water molecules with unsaturated hydrogen bonding. Some aspects of the theoretical simulations will be briefly discussed., QC 20100525