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  • 151. Napolsky, Ph S.
    et al.
    Drozhzhin, O. A.
    Istomin, S. Ya
    Kazakov, S. M.
    Antipov, E. V.
    Galeeva, A. V.
    Gippius, A. A.
    Svensson, Gunnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Abakumov, A. M.
    Van Tendeloo, G.
    Structure and high-temperature properties of the (Sr,Ca,Y)(Co, Mn)O3-y perovskites - perspective cathode materials for IT-SOFC2012Inngår i: Journal of Solid State Chemistry, ISSN 0022-4596, E-ISSN 1095-726X, Vol. 192, s. 186-194Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Oxygen deficient perovskites Sr0.75Y0.25Co1-xMnxO3-y, x=0.5 and 0.75, were prepared by using the citrate route at 1373-1573 K for 48 h. The cubic Pm-3m perovskite structure for x=0.5 was confirmed by electron diffraction study and refined using neutron powder diffraction (NPD) data. For x=0.75, the superstructure corresponding to a=root 2 x a(per), b=2 x a(per), c=root 2 x a(per) (a(0)b(-)b(-) tilt system, space group Imma) was revealed by electron diffraction. The solid solution Sr0.75-xCaxY0.25Co0.25Mn0.75O3-y, 0.1 <= x <= 0.6 and compound Ca0.75Y0.25Mn0.85Co0.15O2.92 were prepared in air at 1573 K for 48 h. The crystal structure of Ca0.75Y0.25Mn0.85Co0.15O2.92 was refined using NPD data (S.G. Pnma, a=5.36595(4), b=7.5091(6), c=5.2992(4) angstrom, R-p=0.057, R-wp=0.056, chi(2)=4.26). High-temperature thermal expansion properties of the prepared compounds were studied in air using both dilatometry and high-temperature X-ray powder diffraction data (HTXRPD). They expanding non-linearly at 298-1073 K due to the loss of oxygen at high temperatures. Calculated average thermal expansion coefficients (TECs) for Sr0.75Y0.25Co1-xMnxO3-y, x=0.5, 0.75 and Ca0.75Y0.25Mn0.85Co0.15O2.92(1) are 15.5, 15.1, and 13.8 ppm K-1, respectively. Anisotropy of the thermal expansion along different unit cell axes was observed for Sr0.15Ca0.6Y0.25Co0.25Mn0.75O3-y, and Ca0.75Y0.25Mn0.85Co0.15O2.92. Conductivity of Sr0.75Y0.25Co1-xMnxO3-y, x=0.5 and 0.75 increases with the temperature reaching 110 S/cm for x=0.5 and 44 S/cm for x=0.75 at 1173 K. Samples of Sr0.75-xCaxY0.25Co0.25Mn0.75O3-y, 0.1 <= y <= 0.6 were found to be n-type conductors at room temperature with the similar temperature dependence of the conductivity and demonstrated the increase of the sigma value from similar to 1 to similar to 50 S/cm as the temperature increases from 300 to 1173 K. Their conductivity is described in terms of the small polaron charge transport with the activation energy (E-p) increasing from 340 to 430 meV with an increase of the calcium content from x=0 to x=0.6.

  • 152. Narangifard, A.
    et al.
    den Hollander, L.
    Wennberg, C. L.
    Lundborg, M.
    Lindahl, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
    Iwai, I.
    Han, H.
    Masich, S.
    Daneholt, B.
    Norlen, L.
    Human skin barrier formation takes place via a cubic to lamellar lipid phase transition as analyzed by cryo-electron microscopy and EM-simulation2018Inngår i: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 366, nr 2, s. 139-151Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The skin's permeability barrier consists of stacked lipid sheets of splayed ceramides, cholesterol and free fatty acids, positioned intercellularly in the stratum corneum. We report here on the early stage of skin barrier formation taking place inside the tubuloreticular system in the secretory cells of the topmost viable epidermis and in the intercellular space between viable epidermis and stratum corneum. The barrier formation process was analysed in situ in its near-native state, using cryo-EM combined with molecular dynamics modeling and EM simulation. Stacks of lamellae appear towards the periphery of the tubuloreticular system and they are closely associated with granular regions. Only models based on a bicontinuous cubic phase organization proved compatible with the granular cryo-EM patterns. Only models based on a dehydrated lamellar phase organization agreed with the lamellar cryo-EM patterns. The data support that human skin barrier formation takes place via a cubic to lamellar lipid phase transition.

  • 153.
    Nikitin, Alexei
    et al.
    Institute of molecular biology, Moscow.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures2007Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, nr 12, s. 2020-2026Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new six site flexible acetonitrile molecular model is developed. The AMBER force field was used for description of intramolecular parameters, the atomic charges were calculated from a high level ab initio theory and finally the Lennard-Jones parameters were tuned to fit the experimental density and evaporation heat. The obtained in this way model reproduces correctly densities of water-acetonitrile mixtures as well as provides qualitative description of the dielectric permittivity and self-diffusion coefficients.

  • 154.
    Nikkhou Aski, Sahar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    NMR Studies of Inclusion Compounds2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis presents the application of some of the NMR methods in studying host-guest complexes, mainly in solution. The general focus of the work is on investigating the reorientational dynamics of some small molecules that are bound inside cavities of larger moieties. In the current work, these moieties belong to two groups: cryptophanes and cyclodextrins. Depending on the structure of the cavities, properties of the guest molecules and the formed complexes vary. Chloroform and dichloromethane are in slow exchange between the cage-like cavity of the cryptophanes and the solvent, on the chemical shift time scale, whereas adamantanecarboxylic acid, quinuclidine and 1,7-heptanediol in complex with cyclodextrins are examples of fast exchange. Kinetics and thermodynamics of complexation are studied by measuring exchange rates and translational self-diffusion coefficients by means of 1-dimenssional exchange spectroscopy and pulsed-field gradient (PFG) NMR methods, respectively. The association constants, calculated using the above information give estimates of the thermodynamic stability of the complexes. Carbon-13 spin relaxation data were obtained using conventional relaxation experiments, such as inversion recovery and dynamic NOE, and in some cases HSQC-type (Hetereonuclear Single Quantum Correlation Spectroscopy) experiments. Motional parameters for the free and bound guest, and the host molecules were extracted using different motional models, such as Lipari-Szabo, axially symmetric rigid body, and Clore models. Comparing the overall correlation times and the order parameters of the free and bound guest with the overall correlation time of the host molecule one can estimate the degree of the motional restriction, brought by the complexation, and the coupling between the motion of the bound guest and the reorientation of the host molecule. In one case, the guest motions were also investigated inside the cavities of a solid host material.

  • 155.
    Nilsson, Anders
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Huang, Congcong
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Fluctuations in ambient water2012Inngår i: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 176, nr SI, s. 2-16Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We emphasize the importance in simulations of water of reproducing the isothermal compressibility, dependent on density fluctuations in the liquid, for a correct description of structural fluctuations in simulated water. From x-ray spectroscopy a strict bimodality in terms of fluctuations between high- (HDL) and low-density (LDL) forms of the liquid has been reported. The inherent structure in simulations, i.e. the structure quenched to 0 K, is found to be bimodal in terms of HDL and LDL in close correspondence to x-ray spectroscopy. This is, however, smeared out in the real structure where temperature is included. We suggest that the local minima for the HDL and LDL local structures in the simulation need to be deeper and propose that many-body electronic structure effects and non-local van der Waals interactions will be important in this respect. Much larger simulations than hitherto considered are likely necessary to catch the effects of both thermal and structural fluctuations in the simulated liquid. Since structural fluctuations can be expected to significantly affect the dynamics in the liquid it is important that these are taken properly into account when discussing hydrogen-bond breaking and reformation. Here it is essential that the model used correctly reproduces the temperature and pressure dependence in thermodynamic response functions.

  • 156.
    Nilsson, Anders
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    The structural origin of anomalous properties of liquid water2015Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Water is unique in its number of unusual, often called anomalous, properties. When hot it is a normal simple liquid; however, close to ambient temperatures properties, such as the compressibility, begin to deviate and do so increasingly on further cooling. Clearly, these emerging properties are connected to its ability to form up to four well-defined hydrogen bonds allowing for different local structural arrangements. A wealth of new data from various experiments and simulations has recently become available. When taken together they point to a heterogeneous picture with fluctuations between two classes of local structural environments developing on temperature-dependent length scales.

  • 157.
    Nilsson, Tomas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Nuclear spin relaxation in paramagnetic complexes in solution2000Doktoravhandling, med artikler (Annet vitenskapelig)
  • 158.
    Noack, Holger
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Theoretical investigation on the oxidative chlorination performed by a biomimetic non-heme iron catalyst2007Inngår i: Journal of Biological Inorganic Chemistry, ISSN 0949-8257, E-ISSN 1432-1327, Vol. 12, s. 1151-1162Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The present study is a part of an effort to understand the mechanism of the oxidative chlorination, as performed by a biomimetic non-heme iron complex. This catalytically active complex is generated from a peroxide and [(TPA)FeIIICl2]+ [TPA is tris(2-pyridylmethyl)amine]. The reaction catalyzed by [(TPA)FeCl2]+/ROOH involves either [(TPA)ClFeV=O]2+ or [(TPA)ClFeIV=O]+ as an intermediate. On the basis of density functional theory the reaction of these two possible catalysts with cyclohexane is investigated. A question addressed is how the competing hydroxylation of the substrate is avoided. It is demon- strated that the high-valent iron complex [(TPA)Cl– FeV=O]2+ is capable of stereospecific alkane chlorination, based on an ionic rather than on a radical pathway. In contrast, the results found for [(TPA)ClFeIV=O]+ cannot explain the experimental findings. In this case the transition states for chlorination and hydroxylation are energetically too close. The exclusive chlorination of the substrate by Cl–FeIV=O may be explained by an indirect or a direct effect, altering the position of the competing rebound barriers.

  • 159. Norberg, Stefan T.
    et al.
    Hull, Stephen
    Eriksson, Sten G.
    Ahmed, Istaq
    Kinyanjui, Francis
    Biendicho, Jordi Jacas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Pyrochlore to fluorite transition: the y 2(ti1 xzrx)(2)o 7 (0.0 <= x <= 1.0) system2012Inngår i: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 24, nr 22, s. 4294-4300Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structural properties of the system Y-2(Ti1-xZrx)(2)O-7 have been investigated using the neutron powder diffraction technique, including a detailed analysis of the total scattering using reverse Monte Carlo modeling to probe the short-range ion-ion correlations over sample range 0.0 <= x <= 1.0. The average crystal structure shows a continuous transformation from the long-range ordered pyrochlore structure (Fd (3) over barm, a = 10.0967(1) angstrom, Z = 8, for x = 0.00, Y2Ti2O7) to a disordered fluorite structure (Fm (3) over barm, a = 5.2042(1) angstrom, Z = 1, for x = 1.00, Zr2Y2O7) in agreement with previous reports. However, on increasing x the disordering of both the cation and the anion sublattices occurs in stages, with the Zr4+ initially only substituting onto the Ti4+ site and adopting a cubic, rather than octahedral, local anion environment. At concentrations in excess of x approximate to 0.4 there is a gradual disordering of the Y3+, Ti4+, and Zr4+ species over all the cation sites, coupled with a redistribution of the O2- which initially only involves those anions on the O1 sites. The relationship between the composition dependences of the structure properties and the ionic conductivity is discussed.

  • 160.
    Nordlund, Gustav
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Ng, Jovice Boon Sing
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Bergström, Lennart
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Brzezinski, Peter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    A Membrane-reconstituted Multisubunit Functional Proton Pump on Mesoporous Silica Particles2009Inngår i: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 3, nr 9, s. 2639-2646Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have investigated formation of a proteolipid membrane surrounding mesoporous silica particles with a diameter of 550 nm and pore sizes of 3.0 nm. A multisubunit redox-driven proton pump, cytochrome c oxidase, was incorporated into the membrane and we show that the enzyme is fully functional, both with respect to catalysis of O2 reduction to water, and charge separation across the membrane. The orientation of cytochrome c oxidase in the membrane was found to be the same (~70/30 %) in the lipid vesicles and in the silica-particle supported lipid membrane, which provides information on the mechanism by which the vesicles adsorb to the surface. Furthermore, cytochrome c oxidase could maintain a proton electrochemical gradient across the supported proteomembrane, i.e. the membrane system was proton tight, defining an interior particle compartment that is separated from the surrounding aqueous media. Such a biofunctional cellular interface, supported onto a colloid that has a connected interior cytoskeleton-like pore structure, provides a basis for functional studies of membrane-bound transport proteins, and also for applications within pharmaceutical drug delivery.

  • 161.
    Nozière, Barbara
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU).
    Córdova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    A Kinetic and Mechanistic Study of the Amino Acid Catalyzed Aldol Condensation of Acetaldehyde in Aqueous and Salt Solutions2008Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 13, s. 2827-2837Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The amino acid-catalyzed aldol condensation is of great interest in organic synthesis and natural environments such as atmospheric particles. But kinetic and mechanistic information on these reactions is limited. In this work, the kinetics of the aldol condensation of acetaldehyde in water and aqueous salt solutions (NaCl, CaCl2, Na2SO4, MgSO4), catalyzed by five amino acids (glycine, alanine, serine, arginine, and proline) at room temperature (295 ± 2K) has been studied. Monitoring the formation of three products, crotonaldehyde, 2,4-hexadienal, and 2,4,6-octatrienal by UV-Visible absorption over 200 – 1100 nm revealed two distinct kinetic regimes: at low amino acid concentrations (in all cases, below 0.1 M) the overall reaction was first order with respect to acetaldehyde and kinetically limited by the formation of the enamine intermediate. At larger amino acid concentrations (at least 0.3 M) the kinetics was second order and controlled by the C-C bond-forming step. The first-order rate constants increased linearly with amino acid concentration, consistent with the enamine formation. Inorganic salts further accelerated the enamine formation according to their pKb plausibly by facilitating the iminium and/or enamine formation. The rate constant of the C-C bond-forming step varied with the square of amino acid concentration, suggesting the involvement of two amino acid molecules. Thus, the reaction proceeded via a Mannich pathway. However, the contribution of an aldol pathway, first-order in amino acid, could not be excluded. Our results show that the rate constant for the self-condensation of acetaldehyde in aqueous atmospheric aerosols (up to 10 of mM of amino acids) is identical as in sulfuric acid 10 - 15 M (kI ~ 10-7 - 10-6 s-1), clearly illustrating the potential importance of amino acid catalysis in natural environments. This work also demonstrates that under usual laboratory conditions and in natural environments aldol condensation is likely to be kinetically controlled by the enamine formation. Notably, kinetic investigations of the C-C bond-forming addition step would only be possible with high concentrations of amino acids.

  • 162.
    Nozière, Barbara
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Dziedzic, Pawel
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Córdova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Products and Kinetics of the Liquid-Phase Reaction of Glyoxal Catalyzed by Ammonium Ions (NH4+)2009Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, Vol. 113, nr 1, s. 231-237Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Glyoxal, a common atmospheric gas, has been reported to be depleted in some regions of the atmosphere. The corresponding sink could be accounted for by reactions in or at the surface of atmospheric particles, but these reactions were not identified. Recently, we showed that inorganic ammonium ions, NH4+, are efficient catalysts for reactions of carbonyl compounds, including glyoxal, in the liquid phase. To determine whether ammonium-catalyzed reactions can contribute to depletion of glyoxal in the atmosphere, the reactivity of this compound in aqueous solutions containing ammonium salts (ammonium sulfate, chloride, fluoride, and phosphate) at 298 K has been studied. The products identified by LC-HRMS and UV absorption revealed a mechanism involving two distinct pathways: a Bronsted acid pathway and an iminium pathway. The kinetics of the iminium pathway was studied by monitoring formation of a specific product. This pathway was second order in glyoxal in most of the solutions studied and should therefore be second order in most ammonium containing aerosols in the atmosphere. The corresponding rate constant, kII (M-1 s-1), increased strongly with ammonium ion activity, aNH4+, and pH:

    kII (M-1 s-1) ) (2 ( 1) × 10-10 exp(1.5 ( 0.8)aNH4+ exp(2.5 ( 0.2)pH.

    This iminium pathway is a lower limit for the ammonium-catalyzed consumption of glyoxal, but the contribution of the acid pathway is expected to be small in tropospheric aerosols. With these results the reactive uptake of glyoxal on ammonium-containing aerosols was estimated and shown to be a possible explanation for the depletion of this compound in Mexico City.

  • 163.
    Ntarakas, Nikolaos
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Ermilova, Inna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Effects of lipid saturation on amyloid-beta peptides partitioning and aggregation in neuronal membranes: molecular dynamics simulations2019Inngår i: European Biophysics Journal, ISSN 0175-7571Artikkel i tidsskrift (Fagfellevurdert)
  • 164.
    Odelius, Michael
    Stockholms universitet, Naturvetenskapliga fakulteten.
    Molecular dynamics simulations of intermolecular mechanisms in nuclear spin relaxation1994Doktoravhandling, med artikler (Annet vitenskapelig)
  • 165.
    Okhotnikov, Kirill
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Eden, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    New interatomic potential parameters for molecular dynamics simulations of rare-earth (RE = La, Y, Lu, Sc) aluminosilicate glass structures: exploration of RE3+ field-strength effects2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 36, s. 15041-15055Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sets of self-consistent oxygen-rare earth (RE = La, Y, Lu, Sc) interatomic potential parameters are derived using a force-matching procedure and utilized in molecular dynamics (MD) simulations for exploring the structures of RE2O3-Al2O3-SiO2 glasses that feature a fixed molar ratio n(Al)/n(Si) = 1 but variable RE contents. The structures of RE aluminosilicate (AS) glasses depend markedly on the RE3+ cation field strength (CFS) over both short and intermediate length-scales. We explore these dependencies for glasses incorporating the cations La3+, Y3+, Lu3+ and Sc3+, whose CFSs increase due to the concomitant shrinkage of the ionic radii: R-La > R-Y > R-Lu > R-Sc. This trend is mirrored in decreasing average RE3+ coordination numbers ((Z) over bar (RE)) from (Z) over bar (La) = 6.4 to (Z) over bar (Sc) = 5.4 in the MD-derived data. However, overall the effects from RE3+ CFS elevations on the local glass structures are most pronounced in the O and {Al-[4], Al-[5], Al-[6]} speciations. The former display minor but growing populations of O-[0] (free oxygen ion) and O-[3] (oxygen tricluster) moieties. The abundance of AlO5 polyhedra increases significantly from approximate to 10% in La-based glasses to approximate to 30% in their Sc counterparts at the expense of the overall dominating AlO4 tetrahedra, whereas the amounts of AlO6 groups remain <5% throughout. We also discuss the Si-[4]/Al-[p] (p = 4, 5, 6) intermixing and the nature of their oxygen bridges, where the degree of edge-sharing increases together with the RE3+ CFS.

  • 166.
    Oliynyk, Vitaliy
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Mille, Christian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Ng, Jovice B. S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    von Ballmoos, Christoph
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Corkery, Robert W.
    Bergström, Lennart
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Selective and atp driven transport of ions across supported membranes into nanoporous carriers using gramicidin a and atp synthase2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 8, s. 2733-2740Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We report a robust and versatile membrane protein based system for selective uptake and release of ions from nanoporous particles sealed with ion-tight lipid bilayers of various compositions that is driven by the addition of ATP or a chemical potential gradient. We have successfully incorporated both a passive ion channel-type peptide (gramicidin A) and a more complex primary sodium ion transporter (ATP synthase) into the supported lipid bilayers on solid nanoporous silica particles. Protein-mediated controlled release/uptake of sodium ions across the ion-tight lipid bilayer seal from or into the nanoporous silica carrier was imaged in real time using a confocal laser scanning microscope and the intensity changes were quantified. ATP-driven transport of sodium ions across the supported lipid bilayer against a chemical gradient was demonstrated. The possibility of designing durable carriers with tight lipid membranes, containing membrane proteins for selective ion uptake and release, offers new possibilities for functional studies of single or cascading membrane protein systems and could also be used as biomimetic microreactors for controlled synthesis of inorganic multicomponent materials.

  • 167. Pai, Ranjith Krishna
    et al.
    Jansson, Kjell
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Hedin, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Transport-Mediated Control of Particles of Calcium Carbonate.      2009Inngår i: Crystal Growth & Design, ISSN 1528-7483, E-ISSN 1528-7505, Vol. 9, nr 11, s. 4581-4583Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Micrometer-sized particles of calcium carbonate were formed by adding NaHCO3 (aq) to a buffered aq. soln. of CaCl2 (aq) and polyelectrolytes.  Particle morphol. and crystal polymorphol. were tuned by varying the stirring rate.  Vigorous stirring led to the formation of micrometer-sized spherical particles of nanocryst. vaterite; slow stirring formed rhombohedral nanostructured particles of calcite.

  • 168. Pandis, Spyros N.
    et al.
    Donahue, Neil M.
    Murphy, Benjamin N.
    Riipinen, Ilona
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Fountoukis, Christos
    Karnezi, Eleni
    Patoulias, David
    Skyllakou, Ksakousti
    Introductory lecture: Atmospheric organic aerosols: insights from the combination of measurements and chemical transport models2013Inngår i: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 165, s. 9-24Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The formation, atmospheric evolution, properties, and removal of organic particulate matter remain some of the least understood aspects of atmospheric chemistry despite the importance of organic aerosol (OA) for both human health and climate change. Here, we summarize our recent efforts to deal with the chemical complexity of the tens of thousands of organic compounds in the atmosphere using the volatility-oxygen content framework (often called the 2D-Volatility Basis Set, 2D-VBS). Our current ability to measure the ambient OA concentration as a function of its volatility and oxygen to carbon (O : C) ratio is evaluated. The combination of a thermodenuder, isothermal dilution and Aerosol Mass Spectrometry (AMS) together with a mathematical aerosol dynamics model is a promising approach. The development of computational modules based on the 2D-VBS that can be used in chemical transport models (CTMs) is described. Approaches of different complexity are tested against ambient observations, showing the challenge of simulating the complex chemical evolution of atmospheric OA. The results of the simplest approach describing the net change due to functionalization and fragmentation are quite encouraging, reproducing both the observed OA levels and O : C in a variety of conditions. The same CTM coupled with source-apportionment algorithms can be used to gain insights into the travel distances and age of atmospheric OA. We estimate that the average age of OA near the ground in continental locations is 1-2 days and most of it was emitted (either as precursor vapors or particles) hundreds of kilometers away. Condensation of organic vapors on fresh particles is critical for the growth of these new particles to larger sizes and eventually to cloud condensation nuclei (CCN) sizes. The semivolatile organics currently simulated by CTMs are too volatile to condense on these tiny particles with high curvature. We show that chemical aging reactions converting these semivolatile compounds to extremely low volatility compounds can explain the observed growth rates of new particles in rural environments.

  • 169.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sørensen, Ole W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Suppressing one-bond homonuclear 13C,13C scalar couplings in the J-HMBC NMR experiment: application to 13C site-specifically labeled oligosaccharides2014Inngår i: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 52, nr 3, s. 82-86Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Site-specific C-13 isotope labeling is a useful approach that allows for the measurement of homonuclear C-13,C-13 coupling constants. For three site-specifically labeled oligosaccharides, it is demonstrated that using the J-HMBC experiment for measuring heteronuclear long-range coupling constants is problematical for the carbons adjacent to the spin label. By incorporating either a selective inversion pulse or a constant-time element in the pulse sequence, the interference from one-bond C-13,C-13 scalar couplings is suppressed, allowing the coupling constants of interest to be measured without complications. Experimental spectra are compared with spectra of a nonlabeled compound as well as with simulated spectra. The work extends the use of the J-HMBC experiments to site-specifically labeled molecules, thereby increasing the number of coupling constants that can be obtained from a single preparation of a molecule.

  • 170. Percival, Carl J.
    et al.
    Welz, Oliver
    Eskola, Arkke J.
    Savee, John D.
    Osborn, David L.
    Topping, David O.
    Lowe, Douglas
    Utembe, Steven R.
    Bacak, Asan
    McFiggans, Gordon
    Cooke, Michael C.
    Xiao, Ping
    Archibald, Alexander T.
    Jenkin, Michael E.
    Derwent, Richard G.
    Riipinen, Ilona
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Mok, Daniel W. K.
    Lee, Edmond P. F.
    Dyke, John M.
    Taatjes, Craig A.
    Shallcross, Dudley E.
    Regional and global impacts of Criegee intermediates on atmospheric sulphuric acid concentrations and first steps of aerosol formation2013Inngår i: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 165, s. 45-73Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Carbonyl oxides (Criegee intermediates), formed in the ozonolysis of alkenes, are key species in tropospheric oxidation of organic molecules and their decomposition provides a non-photolytic source of OH in the atmosphere (Johnson and Marston, Chem. Soc. Rev., 2008, 37, 699, Harrison et al., Sci. Total Environ., 2006, 360, 5, Gab et al., Nature, 1985, 316, 535, ref. 1-3). Recently it was shown that small Criegee intermediates, C.I.'s, react far more rapidly with SO2 than typically represented in tropospheric models, (Welz, Science, 2012, 335, 204, ref. 4) which suggested that carbonyl oxides could have a substantial influence on the atmospheric oxidation of SO2. Oxidation of SO2 is the main atmospheric source of sulphuric acid (H2SO4), which is a critical contributor to aerosol formation, although questions remain about the fundamental nucleation mechanism (Sipila et al., Science, 2010, 327, 1243, Metzger et al., Proc. Natl. Acad. Sci. U. S. A., 2010 107, 6646, Kirkby et al., Nature, 2011, 476, 429, ref. 5-7). Non-absorbing atmospheric aerosols, by scattering incoming solar radiation and acting as cloud condensation nuclei, have a cooling effect on climate (Intergovernmental Panel on Climate Change (IPCC), Climate Change 2007: The Physical Science Basis, Cambridge University Press, 2007, ref. 8). Here we explore the effect of the Criegees on atmospheric chemistry, and demonstrate that ozonolysis of alkenes via the reaction of Criegee intermediates potentially has a large impact on atmospheric sulphuric acid concentrations and consequently the first steps in aerosol production. Reactions of Criegee intermediates with SO2 will compete with and in places dominate over the reaction of OH with SO2 (the only other known gas-phase source of H2SO4) in many areas of the Earth's surface. In the case that the products of Criegee intermediate reactions predominantly result in H2SO4 formation, modelled particle nucleation rates can be substantially increased by the improved experimentally obtained estimates of the rate coefficients of Criegee intermediate reactions. Using both regional and global scale modelling, we show that this enhancement is likely to be highly variable spatially with local hot-spots in e. g. urban outflows. This conclusion is however contingent on a number of remaining uncertainties in Criegee intermediate chemistry.

  • 171.
    Pettersson, Lars Gunnar Moody
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nilsson, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    A Molecular Perspective on the d-Band Model: Synergy Between Experiment and Theory2014Inngår i: Topics in catalysis, ISSN 1022-5528, E-ISSN 1572-9028, Vol. 57, nr 1-4, s. 2-13Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The d-band model of Hammer and Norskov (Nature 376:238, 1995 [3]) relating adsorption energies to the d-band position, and the adsorption energies to barriers in catalytic reactions, has been extremely successful in predicting reactivities and catalysts. In the present contribution we review recent combined experimental and theoretical work on chemical bond-formation at surfaces. We focus on the adsorbate and how the adsorbate electronic structure can be rehybridized through mixing with unoccupied states to generate the radical state, real or virtual, that can then form electron pairs with the metal d-states, as described by the d-band model. We discuss five important bonding situations: (i) atomic radical, (ii) diatomics with unsaturated pi-systems (Blyholder model), (iii) unsaturated hydrocarbons (Dewar-Chatt-Duncanson model), (iv) lone-pair interactions, and (v) saturated hydrocarbons (physisorption). Where the d-band model predicts trends along the series of transition metals, the present work provides intuitive tools for predicting trends among different adsorbates.

  • 172. Piper-Feldkamp, Aundrea R.
    et al.
    Wegner, Maria
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Brzezinski, Peter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Reed, Scott M.
    Mixtures of Supported and Hybrid Lipid Membranes on Heterogeneously Modified Silica Nanoparticles2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 7, s. 2113-2122Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Simple supported lipid bilayers do not accurately reflect the complex heterogeneity of cellular membranes; however, surface modification makes it possible to tune membrane properties to better mimic biological systems. Here, 3-[2-(2-aminoethylamino)ethylamino]propyl-trimethoxysilane (DETAS), a silica modifier, facilitated formation of supported lipid bilayers on silica nanoparticles. Evidence for a stable supported bilayer came from the successful entrapment of a soluble fluorophore within an interstitial water layer. A fluorescence-quenching assay that utilized a pore-forming peptide was used to demonstrate the existence of two separate lipid leaflets. In this assay, fluorescence was quenched by dithionite in roughly equal proportions prior to and after addition of melittin. When a hydrophobic modifier, octadecyl-triethoxysilane, was codeposited on the nanoparticles with DETAS, there was a decrease in the amount of supported bilayer on the nanoparticles and an increase in the quantity of hybrid membrane. This allowed for a controlled mixture of two distinct types of membranes on a single substrate, one separated by a water cushion and the other anchored directly on the surface, thereby providing a new mimic of cellular membranes.

  • 173.
    Polyakov, Eugeny A.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Vorontsov-Velyaminov, Pavel N.
    Centroid molecular dynamics: Comparison with exact results for model systems2010Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, nr 19, s. 194103-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The relation between the accuracy of centroid molecular dynamics correlation functions, and the geometry of the centroid potential is investigated. It is shown that, depending on the temperature, there exist several regimes, and in each of them certain features of the exact Kubo correlation functions are reproduced. The change of regimes is related to the emergence of barriers in the centroid potential. In order to clarify how the above described picture of regimes is modified in real systems when dissipation is important, a methodology is developed to test the accuracy of centroid correlation functions for the model of a particle coupled to a harmonic heat bath. A modification of the centroid molecular dynamics method to include the influence of the heat bath is introduced. Preliminary results of comparison of centroid molecular dynamics with the numerically exact results of filtered propagator functional method are presented.

  • 174. Ponou, Simeon
    et al.
    Lidin, Sven
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    alpha-Cd13-xSb10 - The Devil is in the Details2009Inngår i: Zeitschrift für Anorganische und Allgemeines Chemie, ISSN 0044-2313, E-ISSN 1521-3749, Vol. 635, nr 12, s. 1747-1752Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A detailed study of the structure of α-Cd13Sb10 was performed using a high quality single crystal obtained from a cadmium-rich melt. The study clearly shows that this sample is cadmium-deficient, and should more properly be labelled α-Cd13–xSb10, but whether this is true in general for this phase, or if it is an effect of the precise conditions of synthesis remains unclear. Like for the similar zinc based compound, small differences in the cadmium (zinc) content may be crucial in determining the electronic transport properties of the material.

  • 175.
    Pu, Maoping
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Privalov, Timofei
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ab initio dynamics trajectory study of the heterolytic cleavage of H2 by a Lewis acid [B(C6F5)3] and a Lewis base [P(tBu)3]2013Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, nr 15, artikkel-id 154305Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Activation of H-2 by a frustrated Lewis pair (FLP) composed of B(C6F5)(3) and P(tBu)(3) species has been explored with high level direct ab initio molecular dynamics (AIMD) simulations at finite temperature (T = 300 K) in gas phase. The initial geometrical conditions for the AIMD trajectory calculations, i.e., the near attack conformations of FLP + H-2, were devised using the host-guest model in which suitable FLP conformations were obtained from the dynamics of the B(C6F5)(3)/P(tBu)(3) pair in gas phase. AIMD trajectory calculations yielded microscopic insight into effects which originate from nuclear motion in the reacting complex, e. g., the alternating compression/elongation of the boron-phosphorous distance and the change of the pyramidality of boron in B(C6F5)(3). The ensemble averaged trajectory analysis has been compared with the minimum energy path (MEP) description of the reaction. Similar to MEP, AIMD shows that an attack of the acid/base pair on the H-H bond gives rise to the polarization of the H-2 molecule and as a consequence generates a large dipole moment of the reacting complex. The MEP and AIMD portrayals of the reaction are fundamentally different in terms of the magnitude of the motion of nuclei in B(C6F5)(3) and P(tBu)(3) during the H-2 cleavage. In the AIMD trajectory simulations, geometries of B(C6F5)(3) and P(tBu)(3) appear as nearly frozen on the short time scale of the H-2 cleavage. This is contrary to the MEP picture. Several of the concepts which arise from this work, e. g., separation of time scales of nuclear motion and the time-dependence of the donor-acceptor interactions in the reacting complex, are important for the understanding of chemical reactivity and catalysis.

  • 176.
    Quinteros, Teresita B.
    Stockholms universitet, Naturvetenskapliga fakulteten.
    Ion-beam imaging and radiative recombination of light ions at CRYRING1995Doktoravhandling, med artikler (Annet vitenskapelig)
  • 177.
    Ramstadius, Clinton
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Boklund, Mikael
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conversion of fructose into a building block for the synthesis of carbocyclic mannose mimics2011Inngår i: Tetrahedron: asymmetry, ISSN 0957-4166, E-ISSN 1362-511X, Vol. 22, nr 4, s. 399-405Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fructose was converted into C-1 diastereomeric carbocyclic building blocks resembling mannose using ruthenium-catalysed ring-closing metathesis as a key step. The potential use of the compounds in the synthesis of valienamine pseudodisaccharides is demonstrated using Mitsunobu coupling chemistry directly between a carbohydrate sulfonamide and the carbasugar C-1 alcohols.

  • 178. Rebic, Matus
    et al.
    Mocci, Francesca
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). University of Cagliari, Italy.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stellenbosch University, South Africa.
    Ulicny, Jozef
    Multiscale Simulations of Human Telomeric G-Quadruplex DNA2015Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, nr 1, s. 105-113Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a coarse-grain (CG) model of human telomeric G-quadruplex, obtained using the inverse Monte Carlo (IMC) and iterative Boltzmann inversion (IBI) techniques implemented within the software package called MagiC. As a starting point, the 2HY9 human telomeric [3 + 1] hybrid, a 26-nucleobase sequence, was modeled performing a 1 mu s long atomistic molecular dynamics (MD) simulation. The chosen quadruplex includes two kinds of loops and all possible combinations of relative orientations of guanine strands that can be found in quadruplexes. The effective CG potential for a one bead per nucleotide model has been developed from the radial distribution functions of this reference system. The obtained potentials take into account explicitly the interaction with counterions, while the effect of the solvent is included implicitly. The structural properties of the obtained CG model of the quadruplex provided a perfect match to those resulting from the reference atomistic MD simulation. The same set of interaction potentials was then used to simulate at the CG level another quadruplex topology (PDB id 1KF1) that can be formed by the human telomeric DNA sequence. This quadruplex differs from 2HY9 in the loop topology and G-strand relative orientation. The results of the CG MD simulations of 1KF1 are very encouraging and suggest that the CG model based on 2HY9 can be used to simulate quadruplexes with different topologies. The CG model was further applied to a higher order human telomeric quadruplex formed by the repetition, 20 times, of the 1KF1 quadruplex structure. In all cases, the developed model, which to the best of our knowledge is the first model of quadruplexes at the CG level presented in the literature, reproduces the main structural features remarkably well.

  • 179. Rengaraj, Selvaraj
    et al.
    Venkataraj, Selvaraj
    Jee, Sun Hee
    Kim, Younghun
    Tai, Cheuk-wai
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Repo, Eveliina
    Koistinen, Arto
    Ferancova, Adriana
    Sillanpaa, Mika
    Cauliflower-like CdS Microspheres Composed of Nanocrystals and Their Physicochemical Properties2011Inngår i: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 27, nr 1, s. 352-358Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cauliflower-like cadmium sulfide (CdS) microspheres composed of nanocrystals have been successfully synthesized by a hydrothermal method using poly(ethylene glycol) (PEG) as the template coordination agent and characterized by a variety of methods. Our experiments confirmed that the size of the CdS microspheres could be easily modified by controlling the chain length of PEG. Powder X-ray diffraction and Raman spectroscopy measurements revealed the cubic structure of the CdS microspheres; morphological studies performed by HR-SEM and HR-TEM methods showed the cauliflower-like structure of the synthesized CdS microspheres. Each microsphere was identified to be created by the self-assembly of CdS nanocrystals and is attributed to the oriented aggregation of the CdS nanocrystals around a polymer-Cd(2+) complex spherical framework structure. X-ray photoelectron spectroscopy (XPS) and energy-dispersive X-ray (EDX) analysis confirmed the stoichiometries of the CdS microspheres. Diffuse reflectance spectrum (DRS) measurements showed that increasing the PEG chain length increased the band gap value of the CdS microspheres slightly, from 1.99 to 2.06 eV. The cauliflower-like CdS microspheres could be applied to photocatalytic degradation studies.

  • 180.
    Ribbing, Carl
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Spin-orbit coupling in transition metal systems: a study of octahedral Ni(II)1992Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The effects induced by spin-orbit coupling on the electronic states of Ni(II) complexes are studied with ab-initio and crystal field calculations.

    The ab-initio calculations are performed in two steps, to separate the coulomb and the spin-orbit effects. The first step is an ordinary Cl calculation which provides excited states that are spin eigenfunctions. The second step is a spin-orbit coupled Cl of a selection of the previously created states. The spin-orbit coupling is described by an effective one-electron operator. Double group symmetry is used throughout to facilitate the analysis, and the experimental comparisons, of the spin-orbit states and the matrix elements.

    The method is applied, and compared with experiments, on cubic Oh and orthorhombic Ö2h NiFg-. For the cubic form the calculated excited states are in excellent agreement. For the orthorhombic form comparison of the spin-orbit splitting, or zero field splitting, of the ground state shows that the calculated states are in correct order but a factor of two larger than the experimental energies.

    To investigate the dependence of the zero-field splitting on the degree of distortion from octahedral symmetry and the type of ligand, a series of calculations with different ligands at different distances is performed.

    Finally the possibility to parametrize the zero-field splitting as a function of the normal coordinate modes in octahedral symmetry is explored with crystal field and ab-initio calculations. The parameters for a generally distorted NiF4/6 complex are given and it is shown that crystal field calculations can be made to reproduce the ab-initio results at the expense of different scalings for the radial and the curvilinear modes.

  • 181. Risberg, Emiliana Damian
    et al.
    Jalilehvand, Farideh
    Leung, Bonnie O.
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Theoretical and Experimental Sulfur K-edge X-ray Absorption Spectroscopic Study of Cysteine, Cystine, Homocysteine, Penicillamine, Methionine and Methionine Sulfoxide2009Inngår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, s. 3542-3558Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

      The experimental sulfur K-edge X-ray absorption near-edge structure (XANES) spectra of the amino acids cysteine, homocysteine, penicillamine, methionine, including the oxidation products methionine sulfoxide and the disulfide cystine, have been analyzed by transition potential DFT calculations. The absolute energies and intensities of the main pre-edge sulfur 1s electron transitions have been computed to determine the character of the receiving unoccupied molecular orbitals (MO), and to investigate the influence of external interactions, especially by introducing water molecules hydrogen-bonded to the ionic species present in different pH ranges. When the thiol group deprotonates for cysteine, homocysteine and penicillamine and also for the cysteine residue in glutathione the energy of the main transition, to an MO with antibonding σ*(S–H) character, reduces by 1.1 eV and the receiving MO obtains σ*(S–C) character. The changes in transition energy due to hydrogen-bonding were in most cases found to be relatively small, although the transition intensities could vary significantly due to the changes induced in the molecular charge distribution, thereby affecting the shapes of the spectral features. For the cysteine and penicillamine zwitterions deconvolution of the experimental spectra allowed the microscopic acid dissociation constants to be extracted separately for the thiol and the protonated amine groups, pKaS = 8.5 ± 0.1 and 8.2 ± 0.1, and pKaN = 8.9 ± 0.1 and 8.8 ± 0.1, respectively, with the thiol group in both cases being the more acidic. Coordination of cysteine to nickel(II) or mercury(II) introduced a new low energy transition involving metal ion orbitals in the receiving LUMO. The small experimentally observed energy differences between the similar main absorption features of the cysteine and methionine zwitterions, 0.2–0.3 eV in comparable surrounding, as well as a minor difference in their intensities, are reflected in the calculated transitions. The S K-edge XANES spectrum of the disulfide cystine displays a characteristic double peak with the lower energy transition (2469.9 eV) into the antibonding σ*(S–S) MO. The second peak, at 2471.5 eV in aqueous solution, contains several transitions into MOs with σ*(S–C) character involving also charge transfer to the water molecules hydrating the protonated amine groups (NH3+) of cystine. For solid cystine without hydrogen bonding the experimental energy difference between the two peaks is 0.2 eV larger, while no such increase occurs for the oxidized disulfide of glutathione, with a similar –S–S– bond between its cysteine residues as in cystine, because the amine groups are engaged in peptide bonds. This study shows that externally induced changes in the intramolecular bonding, e.g., by coordination, conformation geometry or hydrogen-bonding, can significantly influence the S K-edge spectra, and emphasizes the importance of a similar chemical surrounding when choosing the model compounds for standard spectra of sulfur functional groups, used to deconvolute composite experimental spectra.

  • 182.
    Rudbeck, Maria E.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Blomberg, Margareta R. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Hydrolysis of the E2P Phosphoenzyme of the Ca2+-ATPase: A Theoretical Study2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 31, s. 9224-9232Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dephosphorylation of the E2P phosphoenzyme intermediate of the sarcoplasmic reticulum Ca2+-ATPase was studied using density functional theory. The hydrolysis reaction proceeds via a nucleophilic attack on the phosphorylated residue Asp351 by a water molecule, which is positioned by the nearby residue Glu183 acting as a base. The activation barrier was calculated to be 14.3 kcal/mol, which agrees well with values of 15-17 kcal/mol derived from experimentally observed rates. The optimized structure of the transition state reveals considerable bond breakage between phosphorus and the Asp351 oxygen (distance 2.19 angstrom) and little bond formation to the attacking water oxygen (distance 2.26 angstrom). Upon formation of the singly protonated phosphate product, Glu183 becomes protonated. The bridging aspartyl phosphate oxygen approaches Lys684 progressively when proceeding from the reactant state (distance 1.94 angstrom) via the transition state (1.78 angstrom) to the product state (1.58 angstrom). This stabilizes the negative charge that develops on the leaving group. The reaction was calculated to be slightly endergonic (+0.9 kcal/mol) and therefore reversible, in line with experimental findings. It is catalyzed by a preorganized active site with little movement of the nonreacting groups except for a rotation of Thr625 toward the phosphate group.

  • 183.
    Rzepka, Przemyslaw
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Bacsik, Zoltan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Pell, Andrew
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Hedin, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Jaworski, Aleksander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    The Nature of Chemisorbed CO2 in Zeolite AInngår i: Artikkel i tidsskrift (Fagfellevurdert)
  • 184.
    Rzepka, Przemyslaw
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Bacsik, Zoltán
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Smeets, Stef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Hansen, Thomas C.
    Hedin, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Wardecki, Dariusz
    Site-Specific Adsorption of CO2 in Zeolite NaK‑A2018Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, nr 47, s. 27005-27015Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Zeolite |Na12|-A is a commercial adsorbent, and its CO2-over-N2(CH4) selectivity can be further enhanced kinetically by replacing Na+ in the 8-ring windows that control gas diffusion with large cations. In this study, samples of zeolite |Na12–xKx|-A with x = 0.0, 0.8, 2.0, and 3.0 were prepared, and the positions of adsorbed CO2 molecules were determined using in situ neutron powder diffraction through profile refinement. Adsorbed CO2 molecules were located at three different sites within the large α-cavities in the zeolite structure, revealing the interaction between the adsorbed CO2 and the host framework. The number of CO2 molecules at each site depends on CO2 pressure and follows site-specific CO2 isotherms described with a Langmuir model. Most of the CO2 molecules in zeolite |Na12–xKx|-A bridge two cations at neighboring 8-ring sites. These are relatively weakly physisorbed, and therefore, most of the working capacity of CO2 adsorption is related to this site. The CO2 molecules at the second most populated site are coordinated to a cation in the 8-ring plane. Some of them seemed to form chemical bonds with the O atoms of the framework as carbonate-like species and acted as chemisorption. The remaining minor fraction of CO2 is directly attracted by Na+ at the 6-rings. The different positioning of physisorbed CO2 and the presence of chemisorbed CO2 was confirmed by in situ infrared spectroscopy.

  • 185. Santosh, Mysore S.
    et al.
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Mirzoev, Alexander A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Bhat, D. Krishna
    Molecular Dynamics Investigation of Dipeptide - Transition Metal Salts in Aqueous Solutions2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 49, s. 16632-16640Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular dynamics (MD) simulations of glycylglycine dipeptide with transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+) in aqueous solutions have been carried out to get an insight into the solvation structure, intermolecular interactions, and salt effects in these systems. The solvation structure and hydrogen bonding were described in terms of radial distribution function (RDF) and spatial distribution function (SDF). The dynamical properties of the solvation structure were also analyzed in terms of diffusion and residence times. The simulation results show the presence of a well-defined first hydration shell around the dipeptide, with water molecules forming hydrogen bonds to the polar groups of the dipeptide. This shell is, however, affected by the strong electric field of divalent metal ions, which at higher ion concentrations lead to the shift in the dipeptide−water RDFs. Higher salt concentrations lead also to increased residence times and slower diffusion rates. In general, smaller ions (Cu2+, Zn2+) demonstrate stronger binding to dipeptide than the larger ones (Fe2+, Mn2+). Simulations do not show any stronger association of peptide molecules indicating their dissolution in water. The above results may be of potential interest to future researchers on these molecular interactions.

  • 186. Santosh, Mysore Sridhar
    et al.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Mirzoev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Bhat, Denthaje Krishna
    Solute-Solvent Interactions in Aqueous Glycylglycine-CuCl(2) Solutions: Acoustical and Molecular Dynamics Perspective2011Inngår i: Journal of Solution Chemistry, ISSN 0095-9782, E-ISSN 1572-8927, Vol. 40, nr 9, s. 1657-1671Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Acoustical and molecular dynamics studies were carried out to understand the various interactions present in glycylglycine-CuCl(2) aqueous solutions. Amongst these interactions, hydrogen bonding and solute-solvent interactions have been highlighted in this study. The radial distribution function (RDF) was used to investigate solution structure and hydration parameters. Binding of Cu(2+) with various polar peptide atoms reveals the nature and degree of binding. The formation of complex clusters between glycylglycine and water molecules increases the relaxation time. The first hydration shell considerably influences the structure of the second shell, facilitating the formation of an ordered hydrogen bonded network. Both experimental and theoretical results have proved to be efficient in analyzing the behavior of molecules and to give a clear idea on molecular interactions in solutions.

  • 187.
    Sarman, Sten
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Molecular dynamics simulation of planar elongational flow in a nematic liquid crystal based on the Gay-Berne potential2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 5, s. 3332-3342Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular dynamics simulations of planar elongational flow in a nematic liquid crystal model system based on the Gay-Berne fluid were undertaken by applying the SLLOD equations of motion with an elongational velocity field or strain rate. In order to facilitate the simulation, Kraynik-Reinelt periodic boundary conditions allowing arbitrarily long simulations were used. A Lagrangian constraint algorithm was utilized to fix the director at different angles relative to the elongation direction, so that the various pressure tensor elements could be calculated as a function of this angle. This made it possible to obtain accurate values of the shear viscosities which were found to agree with results previously obtained by shear flow simulations. The torque needed to fix the director at various angles relative to the elongation direction was evaluated in order to determine the stable orientation of the director, where this torque is equal to zero. This orientation was found to be parallel to the elongation direction. It was also noted that the irreversible entropy production was minimal when the director attained this orientation. Since the simulated system was rather large and fairly long simulation runs were undertaken it was also possible to study the cross coupling between the strain rate and the order tensor. It turned out to be very weak at low strain rates but at higher strain rates it could lead to break down of the liquid crystalline order.

  • 188.
    Sarman, Sten
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Thermomechanical coupling, heat conduction and director rotation in cholesteric liquid crystals studied by molecular dynamics simulation2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 10, s. 3442-3453Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The lack of a centre of inversion in a cholesteric liquid crystal allows linear cross couplings between thermodynamic forces and fluxes that are polar vectors and pseudovectors, respectively. This makes it possible for a temperature gradient parallel to the cholesteric axis to induce a torque that rotates the director, a phenomenon known as the Lehmann effect or thermomechanical coupling. The converse is also possible: a torque applied parallel to the cholesteric axis rotates the director and drives a heat flow. In order to study this phenomenon, nonequilibrium molecular dynamics simulation algorithms and Green-Kubo relations evaluated by equilibrium molecular dynamics simulation have been used to calculate the Leslie coefficient, i.e. the cross coupling coefficient between the temperature gradient and the director angular velocity, for a model system composed of soft prolate ellipsoids of revolution interacting via the Gay-Berne potential augmented by a chiral interaction potential causing the formation of a cholesteric phase. It is found that the Leslie coefficient is two orders of magnitudes smaller than other transport coefficients such as the heat conductivity and the twist viscosity, so that very long simulations are required to evaluate it. The Leslie coefficient decreases with the pitch but it has not been possible to determine the exact functional dependence of this coefficient on the pitch. Since very long simulations have been performed to evaluate the Leslie coefficient, very accurate values have been obtained for the twist viscosity and the heat conductivity as a by-product and it is found that they are very similar to the values of the corresponding quantities in the achiral nematic phase that arises when the pitch goes to infinity.

  • 189.
    Sarman, Sten
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Twist viscosities and flow alignment of biaxial nematic liquid crystal phases of a soft ellipsoid string fluid studied by molecular dynamics simulation2012Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, nr 34, s. 11999-12013Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have calculated the twist viscosity and the alignment angle between the director and the stream lines in shear flow of a liquid crystal model system, which forms biaxial nematic liquid crystals, as functions of the density, from the Green-Kubo relations by equilibrium molecular dynamics simulation and by a nonequilibrium molecular dynamics algorithm, where a torque conjugate to the director angular velocity is applied to rotate the director. The model system consists of a soft ellipsoid-string fluid where the ellipsoids interact according a repulsive version of the Gay-Berne potential. Four different length-to-width-to-breadth ratios have been studied. On compression, this system forms discotic or calamitic uniaxial nematic phases depending on the dimensions of the molecules, and on further compression a biaxial nematic phase is formed. In the uniaxial nematic phase there is one twist viscosity and one alignment angle. In the biaxial nematic phase there are three twist viscosities and three alignment angles corresponding to the rotation around the various directors and the different alignments of the directors relative to the stream lines, respectively. It is found that the smallest twist viscosity arises by rotation around the director formed by the long axes, the second smallest one arises by rotation around the director formed by the normals of the broadsides, and the largest one by rotation around the remaining director. The first twist viscosity is rather independent of the density whereas the last two ones increase strongly with density. One finds that there is one stable director alignment relative to the streamlines, namely where the director formed by the long axes is almost parallel to the stream lines and where the director formed by the normals of the broadsides is almost parallel to the shear plane. The relative magnitudes of the components of the twist viscosities span a fairly wide interval so this model should be useful for parameterisation experimental data.

  • 190.
    Schlesinger, Daniel
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Wikfeldt, Kjartan Thor
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Skinner, Lawrie B.
    Nilsson, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Intermediate range molecular correlations in liquid waterManuskript (preprint) (Annet vitenskapelig)
  • 191.
    Schyman, Patric
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Modeling DNA Damage2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In this thesis methods of computational chemistry have been used to examine DNA damaging processes initiated by ionizing radiation, free radicals, or Low-Energy Electrons (LEE).

    The computational chemistry method based on quantum mechanics that has been mainly used here is the Density Functional Theory (DFT). The Car-Parrinello Molecular Dynamics (CPMD) method, which includes the dynamics of atoms, has also been used. For enabling calculations of large systems the hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) method has been applied by treating the chemically relevant part with quantum mechanics and the rest of the system with molecular mechanics.

    Herein, several types of DNA damaging processes have been examined by performing calculations on models of sections of DNA. A detailed description of how DNA becomes damaged is of major importance for understanding and treating diseases such as cancer.

    Hydrogen abstractions by nucleobase radicals have been investigated as an initial step leading to DNA strand break or base release. The nucleobase radicals that have been examined are uracil-5-yl, uracil-5-peroxyl, and hydroxyl-thymine. The uracil-5-yl radical was identified as the prominent hydrogen abstracting radical.

    Secondary electrons with low energy, LEEs, produced in the tracks of ionizing radiation can reduce nucleotides in DNA and thereby create an unstable anion nucleotide radical. The aim of these studies has been to investigate the effect of LEE attachment on cytosine and guanine nucleotides in an aqueous environment. To verify the possibility of strand break in DNA the ruptures of the phosphodiester bonds, which link the deoxyriboses and the phosphate groups, were analyzed. This study revealed that strand break most likely would occur when a guanine nucleotide, compared with other nucleotides, becomes reduced by an LEE in an aqueous environment.

  • 192. Sekikawa, Taro
    et al.
    Schalk, Oliver
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Hokkaido University.
    Wu, Guorong
    Boguslavskiy, Andrey E.
    Stolow, Albert
    Initial Processes of Proton Transfer in Salicylideneaniline Studied by Time-Resolved Photoelectron Spectroscopy2013Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, nr 14, s. 2971-2979Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Excited-state intramolecular proton transfer (ESIPT) in salicylideneaniline (SA) and selected derivatives substituted in the para position of the anilino group have been investigated by femtosecond time-resolved photoelectron spectroscopy (TRPES) and time-dependent density functional theory (TDDFT). SA has a twisted structure at the energetic minimum of the ground state, but ESIPT is assumed to take place through a planar structure, although this has not been fully established. The TRPES studies revealed that the excited-state dynamics within the S-1 band varied significantly with excitation wavelength. At finite temperatures, the ground state was found to sample a broad range of torsional angles, from planar to twisted. At lower photon energies (370 nm), only the planar ground-state molecules were excited, and the excited-state reaction took place within 50 fs. At higher energies (350 and 330 nm), predominantly twisted ground-state molecules were excited: they had to planarize before ESIPT could occur. This process was found to be slower in methylated SA but did not change significantly in the brominated and nitrated SAs. These substitution effects on the decay dynamics can be explained by modifications of the potential barriers, as predicted by the TDDFT calculations, and support the mechanism of a twisting motion of the anilino ring prior to ESIPT. The contribution of another pathway leading to internal conversion within the enol form was found to be minor at the excitation wavelengths considered here.

  • 193.
    Sellberg, Jonas A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    X-ray scattering and spectroscopy of supercooled water and ice2014Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis presents experimental studies of water and ice at near-atmospheric pressures using intense x-rays only accessible at synchrotrons and free-electron lasers. In particular, it focuses on the deeply supercooled, metastable state and its implications on ice nucleation.

    The local structure of the liquid phase was studied by x-ray scattering over a wide temperature range extending from 339 K down to 227 K. In order to be able to study the deeply supercooled liquid, micron-sized water droplets were evaporatively cooled in vacuum and probed by ultrashort x-ray pulses. This is to date the lowest temperature at which measurements of the structure have been performed on bulk liquid water cooled from room temperature. Upon deep supercooling, the structure evolved toward that of a low-density liquid with local tetrahedral coordination. At ~230 K, where the low-density liquid structure started to dominate, the number of droplets containing ice nuclei increased rapidly. The estimated nucleation rate suggests that there is a “fragile-to-strong” transition in the dynamics of the liquid below 230 K, and its implications on water structure are discussed.

    Similarly, the electronic structure of deeply supercooled water was studied by x-ray emission spectroscopy down to 222 K, but the spectral changes expected from the structural transformation remained absent and explanations are discussed. At high fluence, the non-linear dependence of the x-ray emission yield indicated that there were high valence hole densities created during the x-ray pulse length due to Auger cascades, resulting in reabsorption of the x-ray emission.

    Finally, the hydrogen-bonded network in water was studied by x-ray absorption spectroscopy and compared to various ices. It was found that the pre-edge absorption cross-section, which is associated with distorted hydrogen bonds, could be minimized for crystalline ice grown on a hydrophobic BaF2(111) surface with low concentration of nucleation centers.

  • 194.
    Sellberg, Jonas Alexander
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Huang, Congcong
    McQueen, Trevor A.
    Loh, N. Duane
    Laksmono, Hartawan
    Schlesinger, Daniel
    Sierra, Raymond G.
    Nordlund, Dennis
    Hampton, Christina H.
    Starodub, Dmitri
    DePonte, Daniel P.
    Beye, Martin
    Chen, Chen
    Martin, Andrew V.
    Barty, Anton
    Wikfeldt, Kjartan Thor
    Weiss, Thomas M.
    Caronna, Chiara
    Feldkamp, Jan
    Skinner, Lawrie B.
    Seibert, Marvin M.
    Messerschmidt, Marc
    Williams, Garth J.
    Boutet, Sebastien
    Pettersson, Lars G. M.
    Bogan, Michael J.
    Nilsson, Anders
    Experimental Observation of Bulk Liquid Water Structure in “No-man’s Land”Manuskript (preprint) (Annet vitenskapelig)
  • 195.
    Sellberg, Jonas Alexander
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Kaya, Sarp
    Segtnan, Vegard H.
    Chen, Chen
    Tyliszczak, Tolek
    Ogasawara, Hirohito
    Nordlund, Dennis
    Pettersson, Lars G. M.
    Nilsson, Anders
    Comparison of x-ray absorption spectra between water and ice: new ice data with low pre-edge absorption cross-sectionManuskript (preprint) (Annet vitenskapelig)
  • 196.
    Shafeie, Samrand
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Grins, Jekabs
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Istomin, S. Y.
    Karvonen, L.
    Chen, S. A.
    Chen, T. H.
    Chen, J. M.
    Weidenkaff, A.
    Karppinen, M.
    Sirtl, T.
    Svensson, Gunnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Phase formation, crystal structures and magnetic properties of perovskite-type phases in the system La2Co1+z(MgxTi1-x)1-zO62011Inngår i: Journal of Solid State Chemistry, ISSN 0022-4596, E-ISSN 1095-726X, Vol. 184, nr 1, s. 177-190Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Perovskite-type cobaltates in the system La(2)Co(1+z) (Mg(x)Ti(1-x))(1-z)O(6) were studied for z=0 <= x <= 0.6 and 0 <= x <= 0.9, using X-ray and neutron powder diffraction, electron diffraction (ED), magnetic susceptibility measurements and X-ray absorption near-edge structure (XANES) spectroscopy. The samples were synthesised using the citrate route in air at 1350 degrees C. The space group symmetry of the structure changes from P2(1)/n via Pbnm to R (3) over barc with both increasing Mg content and increasing Co content. The La(2)Co(Mg(x)Ti(1-x))O(6) (z=0) compounds show anti-ferromagnetic couplings of the magnetic moments for the Co below 15 K for x=0, 0.1 and 0.2. XANES spectra show for the compositions 0 <= x <= 0.5 a linear decrease in the L(3)/(L(3)+ L(2))Co-L(2.3) edge branching ratio with x, in agreement with a decrease of the average Co ion spin-state, from a high-spin to a lower-spin-state, with decreasing nominal Co(2+) ion content.

  • 197.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    The Effect of Backbone Constraints: The Case of Water Oxidation by the Oxygen-Evolving Complex in PSII2011Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, nr 17, s. 3274-3280Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The procedure for fixing atoms of amino acid residues in cluster model calculations on enzymes is reviewed. Examples from recent calculations on photosystem II (PSII) and Mo,Cu-dependent CO dehydrogenase are given. In this context, the cluster model work on finding a mechanism for O?O bond formation and a structure of the oxygen-evolving complex in PSII is also reviewed. In that work, fixing certain atoms played an important role. The main part of the present study concerns the mechanism in PSII using models based on the new high-resolution (1.9 angstrom) X-ray structure, which is compared to that using the old, theoretically suggested, structure. It is concluded that the mechanism remains the same, with a similar barrier height. Finally, a connection between the OEC structure and Mn,Ca-containing minerals is also briefly discussed.

  • 198.
    Srimanee, Artita
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi. Mahidol University, Thailand.
    Regberg, Jakob
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Hällbrink, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Vajragupta, Opa
    Langel, Ülo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi. University of Tartu, Estonia.
    Role of scavenger receptors in peptide-based delivery of plasmid DNA across a blood-brain barrier model2016Inngår i: International Journal of Pharmaceutics, ISSN 0378-5173, E-ISSN 1873-3476, Vol. 500, nr 1-2, s. 128-135Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Receptor-mediated transcytosis remains a major route for drug delivery across the blood-brain barrier (BBB). PepFect 32 (PF32), a peptide-based vector modified with targeting ligand (Angiopep-2) binding to low-density lipoprotein receptor-related protein-1 (LRP-1), was previously found to be a promising vector for plasmid delivery across an in vitro model of the BBB. Cellular uptake of PF32/plasmid DNA (pDNA) complexes was speculated the internalization via LRP-1 receptor. In this study, we prove that PF32/pDNA nanocomplexes are not only transported into brain endothelial cells via LRP-1 receptor-mediated endocytosis, but also via scavenger receptor class A and B (SCARA3, SCARA5, and SR-BI)-mediated endocytosis. SCARA3, SCARA5, and SR-BI are found to be expressed in the brain endothelial cells. Inhibition of these receptors leads to a reduction of the transfection. In conclusion, this study shows that scavenger receptors also play an essential role in the cellular uptake of the PF32/pDNA nanocomplexes.

  • 199.
    Stevens, Sam M
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Cubillas, Pablo
    Jansson, Kjell
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Terasaki, Osamu
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Anderson, Michael W
     Nanoscale Electron Beam Damage Studied by Atomic Force Microscopy2009Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, nr 43, s. 18441-18443Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    High-resoln. SEM (HRSEM) has recently been added to the arsenal of characterization tools for material scientists to observe nanoscale surface features on both conducting and insulating materials.  It is now therefore crucial to understand whether the intense electron beam will damage the features of interest.  The authors were able, for the 1st time, to measure and quantify this damage using a combination of HRSEM and at. force microscopy (AFM), and as a consequence, the bulk of the damage, expressed as a depression on the crystal surface, is confined primarily to a subsurface vol.  Simulations demonstrate that the depth of the depression is proportional to the interaction vol. of impact electrons below the crystal surface.  More importantly, the nanometer surface features are conserved, and there is negligible assocd. loss of the crit. information in nanoscopic surface topog.  These results confirm the usefulness of HRSEM as a tool for surface anal. not only for scientists studying crystal growth but also for materials scientists analyzing any surface at the nanoscale.

  • 200.
    Stevensson, Baltzar
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Efficient orientational averaging by the extension of Lebedev grids via regularized octahedral symmetry expansion2006Inngår i: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 181, nr 1, s. 162-176Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Gaussian spherical quadrature methods in the guise of the Lebedev sampling grids are highly efficient for some orientational (“powder”) averaging problems in solid state NMR. However, their applicability is currently restricted, as the sets of orientations are derived analytically and because they are not well adapted to simulate the broad peakshapes encountered, for example, in the NMR on static powders or on half-integer quadrupolar spins subject to second order quadrupolar interactions under magic-angle spinning conditions. We remedy these problems by (i) introducing the recursive procedure regularized octahedral symmetry expansion (ROSE), to which any existing Lebedev set may be subjected. Each recursive step gives a 9-fold enlarged set of orientations. (ii) We demonstrate that ROSE-expanded grids, in conjunction with spectral interpolation, is well suited for calculating broad peakshapes. These advances combine into the apparently most efficient general-purpose two-angle orientational averaging technique proposed to date for solid state NMR applications.

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