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  • 251.
    Ye, Weihua
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Liebau, Jobst
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Mäler, Lena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    New Membrane Mimetics with Galactolipids: Lipid Properties in Fast-Tumbling Bicelles2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 4, s. 1044-1050Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Galactolipids are the main structural component of plant chloroplastic (thylakoid) membranes and of blue-green algae cell membranes. The predominant lipids in this class are monogalactosyl-diacylglycerol (MGDG) and digalactosyl-diacylglycerol (DGDG). We here present a method for the preparation of bicelles that contain these galactolipids together with a characterization of the bicelles, and the lipids within the bicelles. NMR diffusion data show that up to 3096 of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) in a q = 0.5 DMPC/DHPC lipid matrix can be replaced with either monogalactosyl-diacylglycerol or digalactosyl-diacylglycerol and that these lipids incorporate into the bicelles. No evidence for phase separation is observed. Bicelles made with monogalactosyl-diacylglycerol are significantly larger than bicelles containing only DMPC, already with only 1096 of the DMPC replaced with the galactolipid. The effect of digalactosyl-diacylglycerol on bicelle size is much smaller. These observations are likely to be correlated with the different bilayer-forming properties of the lipids. Monogalactosyl-diacylglycerol is a non-bilayer-forming lipid, while digalactosyl-diacylglycerol is a bilayer-forming lipid. Both galactolipids display extensive local motion within the bilayer, as evidenced by natural abundance carbon-13 relaxation of the lipid molecules. The sugar headgroup regions are motionally restricted and cannot be described by a model that does not take into account anisotropic reorientation of the sugar units. No significant effect of the galactolipids on DMPC dynamics was observed. Our results indicate that these bicelles may become useful as model membrane mimetic media for studies of galactolipid-protein interactions.

  • 252.
    Yousif, Rafat
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Investigating the influence of water in lysozyme structure and dynamics using FT-IR and XRD2019Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Water is “the matrix of life” for its fascinating properties. The well-known simple water molecule consists of one oxygen atom and two hydrogen atoms, covering most of planet earth’ssurface. It is the most studied element in science; however, its properties are still not fully understood. Another essential building block of life is proteins, which manifest naturally in aqueous environments. The protein activity is controlled by the protein folding process that is dependent on the surrounding environment. It is hypothesized that the hydrogen bond network of water plays an important role in the folding process. Here, we investigate the protein lysozyme in liquid water as well as in the crystalline state ice Ih, exploring various temperatures, using FT-IR and XRD. Our main finding is that a transition occurs at approximately T=210 K, indicative of the hypothesised protein dynamic “glass” transitionobserved by previous studies in supercooled water at similar temperatures.

  • 253.
    Yu, Yang
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Understanding Composition–Structure–Bioactivity Correlations in Bioactive Glasses2018Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Bioactive glasses integrate with bone/tooth tissues by forming a layer of hydroxy-carbonate apatite (HCA), which mimics the composition of bone mineral. In the current thesis, we investigated composition–structure–bioactivity correlations of phosphosilicate and borophosphosilicate (BPS) glasses. Bioactive phosphosilicate glasses extend the compositional space of the ”45S5 Bioglass®”, which has been in clinical use for decades. Recently developed bioactive BPS glasses with SiO2→B2O3 substitutions transform more completely into HCA and their glass dissolution behaviors can be tuned by varying the relative contents of B and Si. 

    It is known that the average silicate network connectivity NSi and the phosphate content (x(P2O5)) affect the apatite formation (in vitro bioactivity) of phosphosilicate glasses, but the details remain poorly explored. Three series of phosphosilicate glasses were designed by independently varying NSi and x(P2O5). After immersion of the glasses in a simulated body fluid (SBF) for 24 hours, different degrees of their apatite formation were quantified by Fourier-transform infrared (FTIR) spectroscopy. The results revealed that a high P content widened the NSi range that generated optimum amounts of apatite and also mitigated the detrimental effects associated with using glass particles with < 50 μm. The amounts of apatite derived from FTIR agreed with those from 31P magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. The growth of apatite at bioactive glass surfaces was found to follow a sigmoidal growth model, in which the precursor phase, amorphous calcium phosphate (ACP), formed in the induction period and then crystallized into HCA in the following proliferation period, with an improvement in the structural ordering of HCA in the maturation period. This formation process closely resembles the apatite precipitated spontaneously from supersaturated Ca/P-containing solutions. The simultaneous growth of ACP and HCA is discussed in conjunction with a previously proposed mechanism for explaining in vitro bioactivity and apatite growth from bioactive glasses. 

    The short- and medium- range structures of bioactive borophosphosilicate (BPS) glasses were investigated by solid-state MAS NMR. Two series of BPS glasses were designed by gradually replacing SiO2 with B2O3 in the 45S5 glass, as well as another base glass featuring a more condensed glass network. As the B2O3 content is increased, the glass networks become more polymerized, together with decreased fractions of the dominating BO3 and orthophosphate units. Borate groups are homogeneously mixed with the isolated orthophosphate groups, while the remaining phosphate groups exhibit a slight preference for bonding to BO4 over SiO4 units. Linkages among borate groups are dominated by B[3]–O–B[4] linkages at the expenses of B[3]–O–B[3] and B[4]–O–B[4] linkages, with the latter B[4]–O–B[4] motifs disfavored yet abundant. A similar fashion of borate mixing was observed in P-free Na/Ca-based borosilicate glasses that span a large compositional space. The content of B[4]–O–B[4] linkages was found to be controlled by the relative fractions of BO4 groups and non-bridging oxygen ions.

  • 254. Zeilinger, Michael
    et al.
    Benson, Daryn
    Haussermann, Ulrich
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Faessler, Thomas F.
    Single Crystal Growth and Thermodynamic Stability of Li17Si42013Inngår i: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 25, nr 9, s. 1960-1967Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Single crystals of Li17Si4 were synthesized from melts LixSi100-x (x > 85) at various temperatures and isolated by isothermal centrifugation. Li17Si4 crystallizes in the space group F (4) over bar 3m (a = 18.7259(1) angstrom, Z = 20). The highly air and moisture sensitive compound is isotypic with Li17Si4. represents a new compound and thus the lithium-richest phase in the binary system Li-Si superseding known Li21Si5 (Li16.8Si4). As previously shown Li22Si5 (Li17.6Si4) has been determined incorrectly. The findings are supported by theoretical calculations of the electronic structure, total energies, and structural optimizations using first-principles methods. Results from melt equilibration experiments and differential scanning calorimetry investigations suggest that Li17Si4 decomposes peritectically at 481 +/- 2 degrees C to Li4Si and melt. In addition a detailed investigation of the Li-Si phase system at the Li rich side by thermal analysis using differential scanning calorimetry is given.

  • 255. Zerbetto, Mirco
    et al.
    Kotsyubynskyy, Dmytro
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Goran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Polimeno, Antonino
    Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: I. Internal Dynamics of Cyclodextrins; y-Cyclodextrin as a Case Study2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 44, s. 13159-13171Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this work, we address the description of the dynamics of cyclodextrins in relation with nuclear magnetic resonance (NMR) relaxation data collected for hydroxymethyl groups. We define an integrated computational approach based on the definition and parametrization of a stochastic equation able to describe the relevant degrees of freedom affecting the NMR observables. The computational protocol merges molecular dynamics simulations and hydrodynamics approaches for the evaluation of most of the molecular parameters entering the stochastic description of the system. We apply the method to the interpretation of the C-13 NMR relaxation of the -CH2OH group of cyclodextrins. We use gamma-cyclodextrin as a case study. Results are in agreement with quantitative and qualitative analyses performed in the past with simpler models and molecular dynamics simulations. The element of novelty in our approach is in the treatment of the coupling of the relevant internal (glucopyranose ring twisting/tilting and hydroxymethyl group jumps) and global (molecular tumbling) degrees of freedom.

  • 256. Zhao, Xin
    Symmetry-based heteronuclear recoupling in solid-state NMR2003Doktoravhandling, med artikler (Annet vitenskapelig)
  • 257.
    Öberg, Henrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Anniyev, Toyli
    Vojvodic, Aleksandra
    Kaya, Sarp
    Ogasawara, Hirohito
    Friebel, Daniel
    Miller, Daniel J.
    Nordlund, Dennis
    Bergmann, Uwe
    Ljungberg, Mathias P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Abild-Pedersen, Frank
    Nilsson, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. SLAC Natl Accelerator Lab, Stanford Inst Mat & Energy Sci, Menlo Pk, CA 94025 USA.
    Pettersson, Lars G.M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Stability of Pt-Modified Cu(111) in the Presence of Oxygen and Its Implication on the Overall Electronic Structure2013Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, nr 32, s. 16371-16380Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The electronic structure and stability of Cu(111)-hosted Pt overlayers with and without the presence of atomic oxygen have been studied by means of core-level spectroscopy and density functional theory (DFT). Because of lattice mismatch, Pt(111) overlayers grown on Cu(111) are compressively strained, and hard X-ray photoelectron spectroscopy together with Pt L-3-edge X-ray absorption spectroscopy (XAS) reveals a pronounced downshift of the Pt d-band owing to the increased overlap of the d-orbitals, an effect also reproduced theoretically. Exposure to oxygen severely alters the surface composition; the O-Cu binding energy largely exceeds that of O-Pt, and DFT calculations predict surface segregation of Cu atoms. Comparing the adsorbate electronic structure for O on unstrained Pt(111) with that of O on Pt-modified Cu(111) using O K-edge XAS and X-ray emission spectroscopy salient differences are observed and calculations show that Cu-segregation to the topmost layer is required to reproduce the measured spectra. It is proposed that O is binding in a hollow site constituted by at least two Cu atoms and that up to 75% of the Pt atoms migrate below the surface.

  • 258.
    Öberg, Henrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nestsiarenka, Yuliya
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Matsuda, A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Gladh, Jörgen
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Hansson, Tony
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Pettersson, Lars G.M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Öström, Henrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Adsorption and Cyclotrimerization Kinetics of C2H2 at a Cu(110) Surface2012Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 116, nr 17, s. 9550-9560Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The kinetics of acetylene adsorption and cyclotrimerization was studied by vibrational sum-frequency generation spectroscopy (SFG) and density functional theory (DFT) calculations. At low temperature, SFG shows two resonances corresponding to acetylene adsorbed in two different sites. Upon heating, two new vibrational resonances appear. We interpret these resonances as being due to C2H2 island formation and adsorbed C4H4, which is the intermediate in the subsequent cyclotrimerization reaction to form benzene. A kinetic model is applied, which allows determination of the relevant activation barriers. The barrier for C2H2 diffusion is determined to be 43 +/- 1 kJ/mol. The activation barrier for formation of the C4H4 intermediate is found to be 84 +/- 6 kJ/mol and the barrier for benzene formation 5 +/- 3 kJ/mol lower. Barriers to diffusion and formation of C4H4 and C6H6 obtained from DFT calculations are in quantitative agreement with the experiments once the locally high coverage in C2H2 islands is included.

  • 259.
    Šoltésová, Mária
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Charles University in Prague, Department of low temperature physics.
    Fast Dynamic Processes in Solution Studied by NMR Spectroscopy2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Nuclear magnetic resonance (NMR) spectroscopy is capable to deliver a detailed information about the dynamics on molecular level in a wide range of time scales, especially if accompanied by suitably chosen theoretical tools. In this work, we employed a set of high-resolution NMR techniques to investigate dynamics processes in several weakly interacting molecular systems in solution.

    Van der Waals interactions play an important role in inclusion complexes of cryptophane-C with chloroform or dichloromethane. The complex formation was thoroughly investigated by means of 1H and 13C NMR experiments along with the quantum-chemical density functional theory (DFT) calculations. We characterized kinetics, thermodynamics, as well as fine details of structural rearrangements of the complex formation.

    Internal dynamics of oligo- and polysaccharides presents a considerable challenge due to possible coupling of internal and global molecular motions. Two small oligosaccharides were investigated as test cases for a newly developed integrated approach for interpreting the dynamics of the molecules with non-trivial internal flexibility. The approach comprised advanced theoretical tools, including stochastic modeling, molecular dynamics (MD) simulations, and hydrodynamic simulations.

    A biologically important bacterial O-antigenic polysaccharide from E. Coli O91 was addressed employing selective isotope labeling and multiple-field 13C relaxation experiments. The complex dynamics of the polysaccharide is characterized by the conformational motion of the exocyclic groups of the sugars, superimposed to the breathing motion of the polymeric chain.

    Hydrogen bonding is another major non-covalent interaction. Dilute solutions of ethanol were chosen as a model of liquid systems containing extensive hydrogen-bonded networks. We developed a new methodology consisting of NMR diffusion measurements, DFT calculations, and hydrodynamic modeling and utilized it to determine average size of the molecular clusters of ethanol at given conditions.

  • 260.
    Šoltésová, Mária
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Charles University in Prague.
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Dynamics of exocyclic groups in the Escherichia coli O91 O-antigen polysaccharide in solution studied by carbon-13 NMR relaxation2013Inngår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 57, nr 1, s. 37-45Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Carbon-13 relaxation data are reported for exocyclic groups of hexopyranosyl sugar residues in the repeating unit within the Escherichia coli O91 O-antigen polysaccharide in a dilute D2O solution. The measurements of T 1, T 2 and heteronuclear nuclear Overhauser enhancements were carried out at 310 K at two magnetic fields (16.4 T, 21.1 T). The data were analyzed using the standard and extended Lipari–Szabo models, as well as a conformational jump model. The extended version of the Lipari–Szabo and the two-site jump models were most successful for the hydroxymethyl groups of Gal and GlcNAc sugar residues. Different dynamics was found for the hydroxymethyl groups associated with different configurations (d-gluco, d-galacto) of the sugar residues, the latter being faster than the former.

  • 261.
    Šoltésová, Mária
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Charles University in Prague.
    Peksa, Mikuláš
    Benda, Ladislav
    Czernek, Jiří
    Lang, Jan
    Determination of size of molecular clusters of ethanol by means of diffusion NMR and hydrodynamic calculationsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Microscopic structure of ethanol in liquid state is characterized as dynamic equilibrium of hydrogen bonded clusters of different sizes and topologies. We have developed a novel method for determination of average size of the clusters that combines measurement of diffusion coefficient by means of PFG NMR technique and hydrodynamic simulations. The approach includes the use of HydroNMR [de la Torre 2000] for small molecules, which is attained here by the calibration procedure using dilute solution of tetramethylsilane. It is thus possible to correlate the experimentally determined apparent hydrodynamic radius of ethanol with calculated hydrodynamic radii of the modeled clusters of different sizes. We found that average size of the clusters in 0.16 M solution of ethanol in hexane ranges from monomer above 300 K to hexamer below 200 K. The clusters in the case of 0.44 M are generally slightly larger – from average size of dimer at 320 K to heptamer below 210 K.

3456 251 - 261 of 261
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