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  • 101.
    Klingstedt, Miia
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Miyasaka, Keiichi
    Kimura, Kosuke
    Gu, Dong
    Wan, Ying
    Zhao, Dongyuan
    Terasaki, Osamu
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Advanced electron microscopy characterization for pore structure of mesoporous materials; a study of FDU-16 and FDU-182011Inngår i: Journal of Materials Chemistry, ISSN 0959-9428, E-ISSN 1364-5501, Vol. 21, nr 35, s. 13664-13671Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a comprehensive analysis for pore structures of cage-type ordered mesoporous carbons (OMCs) using various electron microscopy techniques in addition to conventional nitrogen adsorption isotherm studies. The benefits and drawbacks of these techniques are evaluated, and it is shown that they are complementary to each other. Knowledge of the structural properties, pore sizes, and connectivity gives insight into the synthesis strategies and how they are affecting the material properties that are useful within the possible applications. Herein, focus is put on the two OMCs with Im (3) over barm and Fm (3) over barm symmetries specified by FDU-16 and FDU-18. The central techniques used in this study are high resolution scanning electron microscopy combined with cross-section polisher and three-dimensional reconstruction methods (electron tomography and electron crystallography) based on transmission electron microscopy observations.

  • 102. Koppisetty, Chaitanya A. K.
    et al.
    Frank, Martin
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Nyholm, Per-Georg
    Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations2015Inngår i: Journal of Computer-Aided Molecular Design, ISSN 0920-654X, E-ISSN 1573-4951, Vol. 29, nr 1, s. 13-21Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Accurate estimation of protein-carbohydrate binding energies using computational methods is a challenging task. Here we report the use of expanded ensemble molecular dynamics (EEMD) simulation with double decoupling for estimation of binding energies of hevein, a plant lectin with its monosaccharide and disaccharide ligands GlcNAc and (GlcNAc)(2), respectively. In addition to the binding energies, enthalpy and entropy components of the binding energy are also calculated. The estimated binding energies for the hevein-carbohydrate interactions are within the range of +/- 0.5 kcal of the previously reported experimental binding data. For comparison, binding energies were also estimated using thermodynamic integration, molecular dynamics end point calculations (MM/GBSA) and the expanded ensemble methodology is seen to be more accurate. To our knowledge, the method of EEMD simulations has not been previously reported for estimating biomolecular binding energies.

  • 103.
    Korolev, Nikolai
    et al.
    Nanyang Technological University, Singapore.
    Allahverdi, Abdollah
    Nanyang Technological University, Singapore.
    Yang, Ye
    Nanyang Technological University, Singapore.
    Fan, Yanping
    Nanyang Technological University, Singapore.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Nordenskiöld, Lars
    Nanyang Technological University, Singapore.
    Electrostatic Origin of Salt-induced Nucleosome Array Compaction2010Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 99, s. 1896-1905Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The physical mechanism of the folding and unfolding of chromatin is fundamentally related to transcription but is incompletely characterized and not fully understood. We experimentally and theoretically studied chromatin compaction by investigating the salt-mediated folding of an array made of 12 positioning nucleosomes with 177 bp repeat length. Sedimentation velocity measurements were performed to monitor the folding provoked by addition of cations Na+, K+, Mg2+, Ca2+, spermidine3+, Co(NH3)63+, and spermine4+. We found typical polyelectrolyte behavior, with the critical concentration of cation needed to bring about maximal folding covering a range of almost five orders of magnitude (from 2 μM for spermine4+ to 100 mM for Na+). A coarse-grained model of the nucleosome array based on a continuum dielectric description and including the explicit presence of mobile ions and charged flexible histone tails was used in computer simulations to investigate the cation-mediated compaction. The results of the simulations with explicit ions are in general agreement with the experimental data, whereas simple Debye-Hückel models are intrinsically incapable of describing chromatin array folding by multivalent cations. We conclude that the theoretical description of the salt-induced chromatin folding must incorporate explicit mobile ions that include ion correlation and ion competition effects.

  • 104. Kotsyubynskyy, Dmytro
    et al.
    Zerbetto, Mirco
    Šoltésová, Mária
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Charles University Prague .
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Polimeno, Antonin
    Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: 2. Interpretation of Complex Dynamics in Linear Oligosaccharides2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 50, s. 14541-14555Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters.

  • 105.
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Nuclear spin relaxation in liquids and gases2014Inngår i: Nuclear Magnetic Resonance: Volume 43 / [ed] K. Kamienska-Trela, Royal Society of Chemistry, 2014, s. 230-285Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    The review covers the progress in the field of NMR relaxation in fluids during the period from June 2012 through May 2013. The emphasis is on comparatively simple liquids and solutions of physico-chemical and chemical interest, in analogy with the previous periods, but selected biophysics-related topics and relaxation-related work on more complex systems (macromolecular solutions, liquid crystalline systems, glassy and porous materials) are also covered. The first part of the chapter is concerned with general, physical and experimental aspects of nuclear spin relaxation, while the second part is concentrated on applications.

  • 106.
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Nuclear spin relaxation in liquids and gases2012Inngår i: Nuclear Magnetic Resonance: Volume 41 / [ed] Krystyna Kamienska-Trela, Jacek Wojcik, Royal Society of Chemistry, 2012, Vol. 40, s. 196-243Kapittel i bok, del av antologi (Fagfellevurdert)
  • 107.
    Kowalewski, Josef
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Kruk, Danuta
    Paramagnetic Relaxation in Solution2011Inngår i: Encyclopedia of Magnetic Resonance / [ed] R.K. Harris and R.E. Wasylishen, John Wiley & Sons, 2011Kapittel i bok, del av antologi (Annet vitenskapelig)
    Abstract [en]

    Relaxation theory for paramagnetic systems is reviewed in a historical perspective and different principal aspects covered. The emphasis is on the post-Solomon–Bloembergen–Morgan developments of the last two decades. Experimental methods and protocols are presented briefly. Illustrative examples of experimental spin-lattice and spin-spin relaxation rates as a function of temperature and magnetic field are provided for transition metal and lanthanide complexes. Novel experiments and applications for metalloproteins are also mentioned. Finally, some joint investigations of variable-field paramagnetic relaxation enhancement and ESR spectral lineshapes are presented

  • 108.
    Krivova, Maryna G.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Grinshpan, Dmitrij D.
    Hedin, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Adsorption of C(n)TABr surfactants on activated carbons2013Inngår i: Colloids and Surfaces A: Physicochemical and Engineering Aspects, ISSN 0927-7757, E-ISSN 1873-4359, Vol. 436, s. 62-70Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cationic surfactants of the quaternary ammonium bromide type C(16)TABr, C(14)TABr, C(12)TABr, and C(10)TABr were adsorbed from aqueous solutions onto three different types of activated carbons and compared with the adsorption of the anionic surfactant sodium dodecyl benzene sulfonate. The concentrations of both cationic and anionic surfactants in aqueous solutions were determined by UV spectroscopy. In the case of anionic surfactants, a linear dependence of UV absorbance on the surfactant concentration at 200 nm can be related to the benzene fragment of the molecule. The UV sensitivity of C(n)TABr solutions is controlled by the hydration of bromide counterions, the electron dense nature of bromine, and a charge-transfer-to-solvent phenomenon. Changes in the textural properties of the activated carbons after adsorption of surfactants were studied by N-2 adsorption and mercury intrusion porosimetry, and could be correlated to surface characteristics and adsorptive capacity. The mechanism of adsorption was found to be complex, but the porous structure of the carbon exerted a critical role and the cationic surfactants were adsorbed step-by-step. At low surfactant concentrations, adsorption occurred in micropores. We conclude that surfactants are adsorbed as individual molecules. Adsorption from more concentrated solutions occurs in meso- and macropores, and resembles surfactant adsorption on flat carbon surfaces. The carbons display somewhat different tendencies to adsorb C(n)TABr. Activated carbons with small pores of 0.56-0.77 nm appear to be most effective for surfactant removal. A negative electrostatic potential on the interface of the carbons appears to enhance the adsorption of cationic surfactants, as would be expected. Controlling the electrostatic potential and pore size distribution of the activated carbons would be beneficial in the application of activated carbons for removal of surfactants from wastewater.

  • 109.
    Krogh Andersen, A.M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Norby:, P.
    Ab Initio Structure Determination and Rietveld Refinement of a High-Temperature Phase of Zirconium Hydrogen Phosphate and a New Polymorph of Zirconium Pyrophosphate from In-Situ Temperature-Resolved Powder Diffraction Data.2000Inngår i: Acta Crystallographica Section B, ISSN 0108-7681, Vol. 56, nr 4, s. 618-625Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The collected in situ temperature-resolved synchrotron powder data revealed that the transformation of the recently reported three-dimensional τ-Zr(HPO4)2 to cubic ZrP2O7 goes through two intermediate phases. The first intermediate phase, ρ-Zr(HPO4)2, is formed in a reversible phase transition at 598  K, which involves both rearrangement and disordering of the hydrogen phosphate groups of τ-Zr(HPO4)2. At 688  K condensation of the hydrogen phosphate groups leads to the formation of the second intermediate, a new polymorph of zirconium pyrophosphate (β-ZrP2O7). Heating above 973  K results in the gradual transformation of β-ZrP2O7 to cubic zirconium pyrophosphate (α-ZrP2O7). The crystal structures of the two intermediate phases were solved from the in situ powder diffraction data using direct methods and refined using the Rietveld method. Both phases are orthorhombic, space group Pnnm and Z = 2. The lattice parameters for the two phases are: ρ-Zr(HPO4)2: a = 8.1935  (2), b = 7.7090  (2), c = 5.4080  (1)  Å; β-ZrP2O7: a = 8.3127  (5), b = 6.6389  (4), c = 5.3407  (3)  Å. The formation mechanism for the new zirconium pyrophosphate polymorph, β-ZrP2O7, is discussed in relation to structurally restricted soft chemistry

  • 110.
    Krogh Andersen, A.M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Norby, P.
    Structural Aspects of the Dehydration and Dehydroxylation of Layered γ-Titanium Phosphate, γ-Ti(PO4)(H2PO4)⋅2H2O.1998Inngår i: Inorganic chemistry, ISSN 1520-510X, Vol. 37, nr 17, s. 4313-4320Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The thermal transformations of γ-titanium phosphate, γ-Ti(PO4)(H2PO4)·2H2O, have been studied using thermogravimetric analysis, differential scanning calorimetry, X-ray powder diffraction, and temperature-resolved in-situ powder diffraction. The transformation sequence goes from γ-Ti(PO4)(H2PO4)·2H2O over a new partially dehydrated form γ‘-Ti(PO4)(H2PO4)·(2−x)H2O (x 1) to the anhydrous form β-Ti(PO4)(H2PO4) and then through a two-step condensation process where layered titanium pyrophosphate, Ti(PO4)(H2P2O7)0.5, is formed first and finally cubic titanium pyrophosphate TiP2O7. The dehydration of γ-Ti(PO4)(H2PO4)·2H2O and the dehydroxylation/condensation process from β-Ti(PO4)(H2PO4) to layered titanium pyrophosphate,Ti(PO4)(H2P2O7)0.5, was followed in-situ. A new partially dehydrated phase, γ‘-Ti(PO4)(H2PO4)·(2−x)H2O (x 1), which forms at approximately 50 °C has been detected and characterized. The unit cell is monoclinic with the lattice parameters a = 23.670(1) Å, b = 6.264(1) Å, c = 5.036(1) Å, β = 102.41(1)°, and Z = 4. Layered titanium pyrophosphate, Ti(PO4)(H2P2O7)0.5, which forms at 375 °C has been characterized. The unit cell is monoclinic with lattice parameters a = 16.271(3) Å, b = 6.319(1) Å, c = 5.122(1) Å, β = 90.59(2)°, and Z = 4.

  • 111.
    Krogh Andersen, A.M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Norby, Poul
    Vogt, Tom
    Determination of the Formation Regions of Titanium Phosphates. Determination of the Crystal Structure of β-Titanium Phosphate, Ti(PO4)(H2PO4), from Neutron Powder Data.1998Inngår i: Journal of solid state chemistry, ISSN 1095-726X, Vol. 140, nr 2, s. 266-271Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The formation region of the various types of layered titanium hydrogen phosphate hydrates was investigated. The materials were prepared by hydrothermal methods, treating amorphous titanium phosphate with phosphoric acid (8 to 16M) in the temperature range 175 to 250°C. The materials obtained were:α-Ti(HPO4)2·H2O,γ-Ti(PO4)(H2PO4)·2H2O, and its anhydrous formβ-Ti(PO4)(H2PO4). The structure ofβ-Ti(PO4)(H2PO4) has been determined by Rietveld powder refinement of high resolution neutron diffraction data. The structure is refined in the monoclinic space groupP21/n(No. 14). The unit cell parameters are:a=18.9503(4) Å,b=6.3127(1) Å,c=5.1391(1) Å,β=105.366(2)°;Z=4. The final agreement factors were:Rp=2.9% andRwp=3.8%. The structure ofβ-Ti(PO4)(H2PO4) is built from TiO6octahedra linked together by tertiary phosphate (PO4) and dihydrogen phosphate ((OH)2PO2) tetrahedra. The layers are held together by hydrogen bonds.

  • 112. Kruk, D
    et al.
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    General treatment of paramagnetic relaxation enhancement associated with translational diffusion2009Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, s. -174104Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A theory of nuclear spin relaxation in isotropic liquids for nuclear spins interacting with electron spins, residing in other molecules (the outer-sphere relaxation), is presented. The approach, valid outside of the Redfield limit for electron spin relaxation, is an extension of the Swedish slow motion theory [ Benetis et al., Mol. Phys. 48, 329 (1983) ; Nilsson and Kowalewski, J. Magn. Reson. 146, 345 (2000) ] for inner-sphere relaxation. It is demonstrated that the outer-sphere relaxation rate can be expressed as an integral of a product of a translational diffusion correlation function and a function analogous to the inner-sphere spectral density. A numerical implementation of the theory is described and applied to a large number of realistic parameter sets for S = 7/2 and S = 1, which may correspond to Gd(III) and Ni(II) systems. It is shown that the outer-sphere contribution is relevant and should be included into the analysis of nuclear magnetic relaxation dispersion relaxation profiles, especially for slow relative translational diffusion and fast molecular tumbling

  • 113. Krycka, Kathryn L.
    et al.
    Borchers, Julie A.
    Salazar-Alvarez, German
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lopez-Ortega, Alberto
    Estrader, Marta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Estrade, Sonia
    Winkler, Elin
    Daniel Zysler, Roberto
    Sort, Jordi
    Peiro, Francesca
    Dolors Baro, Maria
    Kao, Chi-Chang
    Nogues, Josep
    Resolving Material-Specific Structures within Fe3O4 vertical bar gamma-Mn2O3 Core vertical bar Shell Nanoparticles Using Anomalous Small-Angle X-ray Scattering2013Inngår i: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 7, nr 2, s. 921-931Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Here it is demonstrated that multiple-energy, anomalous small-angle X-ray scattering (ASAXS) provides significant enhancement in sensitivity to internal material boundaries of layered nanoparticles compared with the traditional modeling of a single scattering energy, even for cases in which high scattering contrast naturally exists. Specifically, the material-specific structure of monodispersed Fe3O4 vertical bar gamma-Mn2O3 core vertical bar shell nanoparticles is determined, and the contribution of each component to the total scattering profile is identified with unprecedented clarity. We show that Fe3O4 vertical bar gamma-Mn2O3 core vertical bar shell nanoparticles with a diameter of 8.2 +/- 0.2 nm consist of a core with a composition near Fe3O4 surrounded by a (MnxFe1-x)(3)O-4 shell with a graded composition, ranging from x approximate to 0.40 at the Inner shell toward x approximate to 0.46 at the surface. Evaluation of the scattering contribution arising from the interference between material-specific layers additionally reveals the presence of Fe3O4 cores without a coating shell. Finally, it is found that the material-specific scattering profile shapes and chemical compositions extracted by this method are independent of the original input chemical compositions used in the analysis, revealing multiple-energy ASAXS as a powerful tool for determining internal nanostructured morphology even if the exact composition of the individual layers is not known a priori.

  • 114.
    Kumar, Saroj
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Infrared spectroscopy: Method development and ligand binding studies2010Licentiatavhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Infrared spectroscopy detects molecular vibrations and assesses the properties of molecules and their environment. It is a powerful technique to detect ligand induced changes in biomolecules as it has distinct signals and provides different levels of structural information. An addition of a dialysis accessory to attenuated total reflection infrared spectroscopy makes this technique more universal for ligand binding studies. It facilitates to study ligand binding of substrates, activators, inhibitors and ions to macromolecules as well as effect of pH, ionic strength or denaturants on the structure of macromolecules, which play an important role in drug development. This method was tested with two proteins cyt c and calcium ATPase. We studied phosphoenol pyruvate (PEP) in different ionization states by infrared spectroscopy combined with theoretical analysis. Theoretical calculations helped to assign the bands. The infrared spectrum of labeled PEP and infrared measurement in D2O also helped in band assignment. We used the method dialysis accessory to attenuated total reflection infrared spectroscopy to investigate the binding of PEP and Mg2+ to pyruvate kinase (PK), where conformational changes of PK were revealed upon binding of PEP and Mg2+. Isotopic labeled PEP helped to assign and evaluate the infrared absorption bands. The difference spectrum of bound and free PEP indicates specific interactions between ligand and protein. The quantitative evaluation revealed that the enzyme environment has little influence on the P-O bond strengths, which are weakened by less than 3% upon binding. The carboxylate absorption bands indicate shortening of the C-O bond by as little as 1.3 pm. The binding of PEP to PK in presence of monovalent cations K+ and Na+ showed that the binding interactions are very similar.

  • 115.
    Laaksonen, Aatto
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Mocci, Francesca
    Cagliary University, Italy.
    M.DynaMix Studies of Solvation, Solubility and Permeability2012Inngår i: Molecular Dynamics - Studies of Synthetic and Biological Macromolecules / [ed] Lichang Wang, InTech, 2012, s. 85-106Kapittel i bok, del av antologi (Fagfellevurdert)
  • 116. Laarz, Eric
    et al.
    Carlsson, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Vivien, Benoit
    Johnsson, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Nygren, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Bergström, Lennart
    Colloidal processing of Al2O3-based composites reinforced with TiN and TiC particulates, whiskers and nanoparticles2001Inngår i: Journal of the European Ceramic Society, ISSN 0955-2219, E-ISSN 1873-619X, Vol. 21, nr 8, s. 1027-1035Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A colloidal processing route has been developed for the preparation of dense and homogeneous Al2O3–TiN/TiC composites. The dispersion and rheological properties of mixtures of TiN or TiC particulates and Al2O3 particles were investigated using electrokinetics and steady-shear rheology. We found that well-dispersed aqueous suspensions with low viscosity could be prepared by adding a poly(acrylic acid) dispersant and controlling pH in the alkaline range. This processing scheme was also suitable for preparation of whisker and nanoparticle composite suspensions. The alumina-based composite suspensions with a secondary-phase concentration of 25 vol.% were freeze-granulated and hot-pressed, and the resulting bodies were fully densified with well-dispersed secondary phases. Homogeneous Al2O3–TiN nanoparticle composites could only be prepared with additions of up to 5 vol.% nanoparticles; higher additions resulted in agglomeration and subsequent grain growth of the nanoparticles. 

  • 117.
    Landersjö, Clas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Eklund, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Östervall, Jennie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Söderman, Peter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Molecular conformations of a disaccharide investigated using NMR spectroscopy2006Inngår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 35, s. 89-101Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The molecular structure of -l-Rhap-(1→ 2)--l-Rhap-OMe has been investigated using conformation sensitive NMR parameters: cross-relaxation rates, scalar 3 J CH couplings and residual dipolar couplings obtained in a dilute liquid crystalline phase. The order matrices of the two sugar residues are different, which indicates that the molecule cannot exist in a single conformation. The conformational distribution function, , related to the two glycosidic linkage torsion angles and was constructed using the APME method, valid in the low orientational order limit. The APME approach is based on the additive potential (AP) and maximum entropy (ME) models. The analyses of the trajectories generated in molecular dynamics and Langevin dynamics (LD) computer simulations gave support to the distribution functions constructed from the experimental NMR parameters. It is shown that at least two conformational regions are populated on the Ramachandran map and that these regions exhibit very different molecular order. Electronic Supplementary Material  Supplementary material is available for this article at http://www.dx.doi.org/10.1007/s10858-006-9006-0 and is accessible for authorized users.

  • 118.
    Larsson, Per Tomas
    Stockholms universitet, Naturvetenskapliga fakulteten.
    Proton spin-lattice relaxation in paramagnetic nickel(II) complexes in solutions: a theoretical and experimental study1994Doktoravhandling, med artikler (Annet vitenskapelig)
  • 119. Lehtipalo, Katrianne
    et al.
    Rondo, Linda
    Kontkanen, Jenni
    Schobesberger, Siegfried
    Jokinen, Tuija
    Sarnela, Nina
    Kürten, Andreas
    Ehrhart, Sebastian
    Franchin, Alessandro
    Nieminen, Tuomo
    Riccobono, Francesco
    Sipilä, Mikko
    Yli-Juuti, Taina
    Duplissy, Jonathan
    Adamov, Alexey
    Ahlm, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Almeida, Joao
    Amorim, Antonio
    Bianchi, Federico
    Breitenlechner, Martin
    Dommen, Josef
    Downard, Andrew J.
    Dunne, Eimear M.
    Flagan, Richard C.
    Guida, Roberto
    Hakala, Jani
    Hansel, Armin
    Jud, Werner
    Kangasluoma, Juha
    Kerminen, Veli-Matti
    Keskinen, Helmi
    Kim, Jaeseok
    Kirkby, Jasper
    Kupc, Agnieszka
    Kupiainen-Määttä, Oona
    Laaksonen, Ari
    Lawler, Michael J.
    Leiminger, Markus
    Mathot, Serge
    Olenius, Tinja
    Ortega, Ismael K.
    Onnela, Antti
    Petäjä, Tuukka
    Praplan, Arnaud
    Rissanen, Matti P.
    Ruuskanen, Taina
    Santos, Filipe D.
    Schallhart, Simon
    Schnitzhofer, Ralf
    Simon, Mario
    Smith, James N.
    Tröstl, Jasmin
    Tsagkogeorgas, Georgios
    Tome, Antonio
    Vaattovaara, Petri
    Vehkamäki, Hanna
    Vrtala, Aron E.
    Wagner, Paul E.
    Williamson, Christina
    Wimmer, Daniela
    Winkler, Paul M.
    Virtanen, Annele
    Donahue, Neil M.
    Carslaw, Kenneth S.
    Baltensperger, Urs
    Riipinen, Ilona
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Curtius, Joachim
    Worsnop, Douglas R.
    Kulmala, Markku
    The effect of acid-base clustering and ions on the growth of atmospheric nano-particles2016Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, artikkel-id 11594Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The growth of freshly formed aerosol particles can be the bottleneck in their survival to cloud condensation nuclei. It is therefore crucial to understand how particles grow in the atmosphere. Insufficient experimental data has impeded a profound understanding of nano-particle growth under atmospheric conditions. Here we study nano-particle growth in the CLOUD (Cosmics Leaving OUtdoors Droplets) chamber, starting from the formation of molecular clusters. We present measured growth rates at sub-3 nm sizes with different atmospherically relevant concentrations of sulphuric acid, water, ammonia and dimethylamine. We find that atmospheric ions and small acid-base clusters, which are not generally accounted for in the measurement of sulphuric acid vapour, can participate in the growth process, leading to enhanced growth rates. The availability of compounds capable of stabilizing sulphuric acid clusters governs the magnitude of these effects and thus the exact growth mechanism. We bring these observations into a coherent framework and discuss their significance in the atmosphere.

  • 120.
    Lenori, Francesca
    et al.
    Universitá di Perugia.
    Petrucci, Raffaelo
    Universitá di Perugia.
    Hickson, Kevin E.
    Université Bordeaux 1.
    Hamberg, Mathias
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Casavecchia, Piergiorgio
    Universitá di Perugia.
    Geppert, Wolf
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Crossed-Beam and Theoretical Studies of the S(1D) + C2H2 Reaction2009Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, s. 4330-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The reaction dynamics of excited sulfur atoms, S(D-1), with acetylene has been investigated by the crossed-beam scattering technique with mass spectrometric detection and time-of-flight (TOF) analysis at the collision energy of 35.6 kJ mol(-1). These studies have been made possible by the development of intense continuous supersonic beams of S(P-3,D-1) atoms. From product angular and TOF distributions, center-of-mass product angular and translational energy distributions are derived. The S(D-1) + C2H2 reaction is found to lead to formation of HCCS (thioketenyl) + H, while the only other energetically allowed channels, those leading to CCS((3)Sigma(-), Delta) + H-2, are not observed to occur to an appreciable extent. The dynamics of the H-elimination channel is discussed and elucidated. The interpretation of the scattering results is assisted by synergic high-level ab initio electronic structure calculations of stationary points and product energetics for the C2H2S ground-state singlet potential energy surface. In addition, by exploiting the novel capability of performing product detection by means of a tunable electron-impact ionizer, we have obtained the first experimental information on the ionization energy of thioketenyl radical, HCCS, as synthesized in the reactive scattering experiment. This has been complemented by ab initio calculations of the adiabatic and vertical ionization energies for the ground-state radical. The theoretically derived value of 9.1 eV confirms very recent, accurate calculations and is corroborated by the experimentally determined ionization threshold of 8.9 +/- 0.3 eV for the internally warm HCCS produced from the title reaction.

  • 121.
    Leonova, Ekaterina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Structural Investigations of Complex Glasses by Solid-state NMR2009Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This PhD thesis presents structural investigations of amorphous inorganic materials: oxide and oxynitride glasses and mesoporous bioactive glasses (MBGs), by solid-state Nuclear Magnetic Resonance (NMR).

    Lanthanum oxide and oxynitride [La-Si-(Al)-O-(N)] glasses have a large number of potential applications due to their physical properties. In our work we have studied, compared to previous investigations, significantly expanded ranges of glass compositions (for oxynitride glasses, including samples of very high nitrogen content, up to 53 % out of the anions). We have estimated local environments of 29Si and 27Al structural units (their coordination, polymerization degree and number of N incorporated into tetrahedral units) in the materials. We have suggested a random Al/Si distribution along with almost uniform non-bridging oxygen atoms distribution in aluminosilicate glasses.

    Silicon nitride was used as precursor in the oxynitride glass synthesis. We studied both α- and β-modifications of silicon nitride, 15N-enriched, as well as fully (29Si, 15N)-enriched samples. We have shown that the linewidths of 15N NMR spectra are dominated by J(29Si-15N) coupling in 29Si315N4 sample.

    Mesoporous bioactive glasses in the CaO-SiO2-P2O5 system show superior bioactivity (the ability to form a hydroxycarbonate apatite layer on the glass surface when exposed to body fluids) compared to conventional bioactive glasses due to their large surface area and uniform pore-size distribution. Previous studies suggested a homogeneous cation distribution over the MBG samples on a 10−20 nm length-scale. From our results, on the other hand, we may conclude that Si and P is not intimately mixed. We propose a structural model, in which the pore walls of MBGs are composed of a silica network, and a phosphate phase is present as nanometer-sized clusters that are dispersed on the pore wall.

  • 122.
    Li, Xichen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Sproviero, Eduardo M.
    Ryde, Ulf
    Batista, Victor S.
    Chen, Guangju
    Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach2013Inngår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, nr 4, s. 474-478Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The oxygen-evolving complex (OEC) of photosystem II is the only natural system that can form O2 from water and sunlight and it consists of a Mn4Ca cluster. In a series of publications, Siegbahn has developed a model of the OEC with the quantum mechanical (QM) cluster approach that is compatible with available crystal structures, able to form O2 with a reasonable energetic barrier, and has a significantly lower energy than alternative models. In this investigation, we present a method to restrain a QM geometry optimization toward experimental polarized extended X-ray absorption fine structure (EXAFS) data. With this method, we show that the cluster model is compatible with the EXAFS data and we obtain a refined cluster model that is an optimum compromise between QM and polarized EXAFS data.

  • 123. Li, Xin
    et al.
    Leck, Caroline
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU).
    Sun, Lu
    Hede, Thomas
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU).
    Tu, Yaoquan
    Ågren, Hans
    Cross-Linked Polysaccharide Assemblies in Marine Gels: An Atomistic Simulation2013Inngår i: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 4, nr 16, s. 2637-2642Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Marine polymeric gels or colloidal nano- and microgels have been shown to contribute significantly to the primary marine aerosol and cloud condensation nuclei over remote marine areas. A microscopic understanding of such biologically derived matter at the sea air interface is important for future development of global climate models, but unfortunately cannot be obtained from modern characterization techniques. In this contribution, we employ molecular dynamics simulations to reveal the atomistic details of marine polymeric gels represented by anionic polysaccharide assemblies. The ionic bonds formed between polysaccharides and metal ions in seawater as well as the hydrophobic contribution to surface area are investigated in detail, and destabilization of the assemblies upon removal of Ca2+ or acidification is explained. These results provide insight into physicochemical properties of polysaccharide-Ca2+ structures and enable future studies of their roles of in the wetting process of cloud droplet activation.

  • 124.
    Liljequist, David
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    On the sampling of step length in Monte Carlo simulation of trajectories with very small mean free path2012Inngår i: Radiation Physics and Chemistry, ISSN 0969-806X, E-ISSN 1879-0895, Vol. 81, nr 11, s. 1703-1709Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In an event-by-event simulation of the trajectory of a particle moving in matter it is usually assumed that the probability for the particle to travel a distance s without interaction is exp(-s/lambda), where lambda = (n . sigma)(-1) is the total mean free path, n the number of scatterers per unit volume and sigma the total cross section per scatterer. The step length s between scattering events is then generated by means of a sampling formula s = -lambda ln(1-R), where R a random number in the interval 0 < R < 1. It is here argued that this conventional sampling method, which basically assumes that the scattering medium may be regarded as a homogeneous continuum, may be erroneous unless lambda is much larger than the average distance d(nn) between nearest neighbour scatterers, estimated by d(nn) = n(-1/3). An alternative sampling method (M sampling) is proposed with a fixed step length D = d(nn) and a finite probability I = 1-exp(-D/lambda) of a single elastic or inelastic scattering event at the end of each step. According to this method, conventional sampling may exaggerate the number of events per unit path length; the corrected mean free path between events is found to be lambda(c) = D/(1-exp(-D/lambda)). The correction is substantial when lambda is comparable to or smaller than D, in practice for very low energy particles in liquids and solids. Consequently, quantities like stopping power may then be overestimated, while transport mean free path may be underestimated. In the opposite limit lambda >> D, conventional and M sampling produce the same result. Present results further indicate that conventional sampling using the corrected total mean free path lambda(c) is a good approximation to M sampling.

  • 125.
    Lundberg, Marcus
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Siegbahn, Per E.M.
    Optimized Spin Crossings and Transition States for Short-range Electron Transfer in Transition Metal Dimers2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 20, s. 10513-10520Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Electron-transfer reactions in eight mixed-valence manganese dimers are studied using B3LYP. One of the dimers is a model of the active site of manganese catalase, while another represents a basic building block of the oxygen-evolving complex in photosystem II. The adiabatic reactions are characterized by fully optimized transition states where the single imaginary frequency represents the electron-transfer coordinate. When there is antiferromagnetic coupling between different high-spin centers, electron transfer must be accompanied by a spin transition. Spin transitions are characterized by minimum-energy crossing points between spin surfaces. Three reaction mechanisms have been investigated. First, a single-step reaction where spin flip is concerted with electron transfer. Second, an initial transition to a center with intermediate spin that can be followed by electron transfer. Third, an initial transition to a ferromagnetic state from which the electron can be transferred adiabatically. The complexes prefer the third route with rate-determining barriers ranging from 5.7 kcal/mol to 17.2 kcal/mol for different complexes. The origins of these differences are discussed in terms of oxidation states and ligand environments. Many DFT functionals overestimate charge-transfer interactions, but for the present complexes, the error should be limited because of short Mn−Mn distances

  • 126.
    Lyubartsev, Alexander
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Ben-Naim, Arieh
    The Hebrew University of Jerusalem.
    One dimensional model for water and aqueous solutions. Part V. Monte Carlo simulation of dilute solutions of hard rod in waterlike particles2009Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, s. 204507-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Wehave carried out Monte Carlo simulation on the primitive onedimensional model for water described earlier [A. Ben-Naim, J. Chem.Phys. 128, 024506 (2008)]. We show that by taking intoaccount second nearest neighbor interactions, one can obtain the characteristicanomalous solvation thermodynamic quantities of inert solutes in water. Thismodel clearly demonstrates the molecular origin of the large negativeentropy of solvation of an inert solute in water.

  • 127.
    Lyubartsev, Alexander
    et al.
    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.
    Chen, Li Jun
    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.
    Systematic coarse-graining of molecular models by the Newton inversion method2010Inngår i: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 144, s. 43-56Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Systematic construction of coarse-grained molecular models from detailed atomistic simulations, and even from ab initio simulations is discussed. Atomistic simulations are first performed to extract structural information about the system, which is then used to determine effective potentials for a coarse-grained model of the same system. The statistical-mechanical equations expressing the canonical properties in terms of potential parameters can be inverted and solved numerically according to the iterative Newton scheme. In our previous applications, known as the Inverse Monte Carlo, radial distribution functions were inverted to reconstruct pair potential, while in a more general approach the targets can be other canonical averages. We have considered several examples of coarse-graining; for the united atom water model we suggest an easy way to overcome the known problem of high pressure. Further, we have developed coarse-grained models for L- and D-prolines, dissolved here in an organic solvent (dimethylsulfoxide), keeping their enantiomeric properties from the corresponding all-atom proline model. Finally, we have revisited the previously developed coarse-grained lipid model based on an updated all-atomic force field. We use this model in large-scale meso-scale simulations demonstrating spontaneous formation of different structures, such as vesicles, micelles, and multi-lamellar structures, depending on thermodynamical conditions.

  • 128.
    Lyubartsev, Alexander P.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Rabinovich, Alexander L.
    Recent development in computer simulations of lipid bilayers2011Inngår i: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 7, nr 1, s. 25-39Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Rapid development of computer power during the last decade has made molecular simulations of lipid bilayers feasible for many research groups, which, together with the growing general interest in investigations of these very important biological systems has lead to tremendous increase of the number of research on the computational modeling of lipid bilayers. In this review, we give account of the recent progress in computer simulations of lipid bilayers covering mainly the period of the last 5 years, and covering several selected subjects: development of the force fields for lipid bilayer simulations, studies of the role of lipid unsaturation, the effect of cholesterol and other inclusions on properties of the bilayer, and use of coarse-grained models.

  • 129.
    Lyubartsev, Alexander
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Tu, Yaoquan
    Örebro university.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Hierarchical Multiscale Modelling Scheme from First Principles to Mesoscale2009Inngår i: Journal of computational and theoretical nanoscience, ISSN 1546-1963 (eISSN), Vol. 6, nr 5, s. 951-959Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a straight-forward implementation of a practical hierarchical multiscale modelling scheme which enables us to start from first-principles atomistic computer simulation and successively coarse-grain the model by leaving out uninteresting degrees of freedom. Using the Car-Parrinello method or our recently developed highly efficient tight-binding-like approximate density-functional quantum mechanical method, we first perform ab initio simulations. From these first-principles simulations we obtain a set of atomistic pair-wise effective interaction potentials to be used as a force field with no empirical data for subsequent classical all-atom simulations while scaling up the system size 2-3 orders of magnitude. The atomistic simulations similarly provide a new set of effective potentials but at a chosen coarse-grain level suitable for large-scale mesoscopic or soft-matter simulations beyond the atomic resolution. Several examples are shown of how this scheme is done based on effective interaction potentials to tie together the various scales of modelling.

  • 130.
    Mace, Amber
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Multiscale Modeling of Molecular Sieving in LTA-type Zeolites: From the Quantum Level to the Macroscopic2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    LTA-type zeolites with narrow window apertures coinciding with the approximate size of small gaseous molecules such as CO2 and N2 are interesting candidates for adsorbents with swing adsorption technologies due to their molecular sieving capabilities and otherwise attractive properties. These sieving capabilities are dependent on the energy barriers of diffusion between the zeolite pores, which can be fine-tuned by altering the framework composition. An ab initio level of theory is necessary to accurately describe specific gas-zeolite interaction and diffusion properties, while it is desirable to predict the macroscopic scale diffusion for industrial applications. Hence, a multiscale modeling approach is necessary to describe the molecular sieving phenomena exhaustively.

    In this thesis, we use several different modeling methods on different length and time scales to describe the diffusion driven uptake and separation of CO2 and N2 in Zeolite NaKA. A combination of classical force field based modeling methods are used to show the importance of taking into account both thermodynamic, as well as, kinetic effects when modeling gas uptake in narrow pore zeolites where the gas diffusion is to some extent hindered. For a more detailed investigation of the gas molecules’ pore-to-pore dynamics in the material, we present a procedure to compute the free energy barriers of diffusion using spatially constrained ab initio Molecular Dynamics. With this procedure, we seek to identify diffusion rate determining local properties of the Zeolite NaKA pores, including the Na+-to-K+ exchange at different ion sites and the presence of additional CO2 molecules in the pores. This energy barrier information is then used as input for the Kinetic Monte Carlo method, allowing us to simulate and compare these and other effects on the diffusion driven uptake using a realistic powder particle model on macroscopic timescales.

  • 131.
    Mace, Amber
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Leetmaa, Mikael
    Uppsala universitet, Institutionen för fysik och astronomi.
    Temporal coarse graining of CO2 and N2 diffusion in Zeolite NaKA; from the quantum scale to the macroscopicManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The kinetic CO2-over-N2 sieving capabilities in narrow pore zeolite are dependent on the free energy barriers of diffusion between the zeolite pores, which can be fine-tuned by altering the framework composition. An ab initio level of theory is necessary to accurately compute the energy barriers, while it is desirable to predict the macroscopic scale diffusion for industrial applications. Using spatially constrained ab initio molecu- lar dynamics on the ps time scale, the free energy barriers of diffusion can be predicted for different local pore properties in order to identify those that are rate determining for the pore-to-pore diffusion. Specifically, we investigate the effects of the Na+-to-K+ exchange at the different cation sites and the CO2 loading. These computed energy barriers are then used as input for the Kinetic Monte Carlo method, coarse-graining the dynamic simulation steps to the pore-to-pore diffusion. With this approach we simulate how the identified rate determining properties as well as the application of skin layer surface defects affect the diffusion driven uptake in a realistic powder particle model on a macroscopic time scale. Finally, we suggest a model by combining these effects, which provides an excellent agreement with the experimental CO2 and N2 uptake behaviors presented by Liu et al.

  • 132. Maldonado, P.
    et al.
    Godinho, José
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Evins, L. Z.
    Oppeneeer, P. M.
    Ab Initio Prediction of Surface Stability of Fluorite Materials and Experimental Verification2013Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, nr 13, s. 6639-6650Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Utilizing first-principle simulations [based on density functional theory (DFT) corrected for on-site Coulomb interactions (DFT+U)], we develop a model to explain the experimental stability in solution of materials having the fluorite structure, such as CaF2 and CeO2. It is shown that the stability of a surface is mainly dependent on its atomic structure and the presence of sites where atoms are deficiently bonded. Using as reference planes the surfaces with low surface formation energies, viz., (111), (100), and (110), our results reveal the relation between the surface energy of any Miller-indexed plane and the surface energy of those reference planes, being dependent on the fluorite surface structure only. Therefore, they follow the same trend for CaF2 and CeO2. Comparison with experimental results shows a correlation between the trends of dry surface energies and surface stabilities during dissolution of both CaF2 and CeO2, even though the chemical processes of dissolution of CeO2 and CaF2 are different. A deviation between ab initio predictions and experiments for some surfaces highlights the sensitivity of the developed model to the treatment of surface dipolar moments.

  • 133.
    Mandal, Paulami
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Eremina, Nadejda
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Formation of Two Different Types of Oligomers in the Early Phase of pH-Induced Aggregation of the Alzheimer A beta(12-28) Peptide2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 41, s. 12389-12397Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The early phase in the aggregation process of the Alzheimer's peptide A beta(12-28) with both protected and unprotected ends was studied by time-resolved infrared spectroscopy and circular dichroism spectroscopy. Aggregation in the time-resolved experiments was initiated by a rapid pH drop caused by the photolysis of 1-(2-nitrophenyl)ethyl sulfate (caged sulfate). The infrared spectra indicate two different types of aggregates from both versions of the A beta(12-28) peptide. One type has small and/or twisted beta sheets with a beta-sheet band at 1627 cm(-1), They form fast (within 60 ms), presumably from initial aggregates, and their spectral signature is consistent with a beta-barrel structure. The other type arises relatively slowly from unstructured monomers on the seconds-to-minutes time scale and forms at lower pH than the first type. These beta sheets are antiparallel, planar, and large and show an absorption band at 1622 cm(-1) that shifts to 1617 cm(-1) in 12 min with most of the shift occurring in 10 s.

  • 134.
    Mathew, Renny
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Gunawidjaja, Philips N.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Izquierdo-Barba, Isabel
    Jansson, Kjell
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Garcia, Ana
    Arcos, Daniel
    Vallet-Regi, Maria
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Solid-State (31)P and (1)H NMR Investigations of Amorphous and Crystalline Calcium Phosphates Grown Biomimetically From a Mesoporous Bioactive Glass2011Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 115, nr 42, s. 20572-20582Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By exploiting (1)H and (31)P magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy, we explore the proton and orthophosphate environments in biomimetic amorphous calcium phosphate (ACP) and hydroxyapatite (HA), as grown in vitro at the surface of a 10CaO-85SiO(2)-5P(2)O(5) mesoporous bioactive glass (MBG) in either a simulated body fluid or buffered water. Transmission electron microscopy confirmed the presence of a calcium phosphate layer comprising nanocrystalline HA Two-dimensional (1)H-(31)P heteronudear correlation NMR established predominantly (1)H(2)O <->(31)PO(4)(3-) and O(1)H <->(31)PO(4)(3-) contacts in the amorphous and crystalline component, respectively, of the MBG surface-layer; these two pairs exhibit distinctly different (1)H <->(31)P cross-polarization dynamics, revealing a twice as large squared effective (1)H-(31)P dipolar coupling constant in ACP compared with HA. These respective observations are mirrored in synthetic (well-crystalline) HA, and the amorphous calcium orthophosphate (CaP) clusters that are present in the pristine MBG pore walls: besides highlighting very similar local (1)H and (31)P environments in synthetic and biomimetic HA, our findings evidence closely related NMR characteristics, and thereby similar local structures, of the CaP clusters in the pristine MBG relative to biomimetic ACP.

  • 135.
    Mathew, Renny
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Na/Ca Intermixing around Silicate and Phosphate Groups in Bioactive Phosphosilicate Glasses Revealed by Heteronuclear Solid-State NMR and Molecular Dynamics Simulations2015Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, nr 17, s. 5701-5715Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We characterize the intermixing of network-modifying Na+/Ca2+ ions around the silicate (QSin) and phosphate (QPn) tetrahedra in a series of 16 Na2O–CaO–SiO2–P2O5 glasses, whose P content and silicate network connectivity were varied independently. The set includes both bioactive and bioinactive compositions and also encompasses two soda-lime-silicate members devoid of P, as well as two CaO–SiO2 glasses and one Na2O–SiO2–P2O5 glass. The various Si/P↔Na/Ca contacts were probed by molecular dynamics (MD) simulations together with heteronuclear magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) experimentation utilizing 23Na{31P} and 23Na{29Si} REDOR, as well as 31P{ 23Na} and 29Si{23Na} REAPDOR. We introduce an approach for quantifying the extent of Na+/Ca2+ ordering around a given QPn or QSin group, encoded by the preference factor 0⩽ PM ⩽ 1 conveying the relative weights of a random cation intermixing (PM = 0) and complete preference/ordering (PM = 1) for one of the species M, which represents either Na+ or Ca2+. The MD-derived preference factors reveal phosphate and silicate species surrounded by Na+/Ca2+ ions intermixed nearly randomly (PM ≲ 0.15), except for the QSi4 and QSi1 groups, which manifest more significant cation ordering with preference for Na+ and Ca2+, respectively. The overall weak preferences are essentially independent of the Si and P contents of the glass, whereas PM primarily correlates with the total amount of network modifiers: as the latter is increased, the Na/Ca distribution around the {QP0, QSi1, QSi2} groups with preference for Ca2+ tend to randomize (i.e., PCa decreases), while the PNa-values grow slightly for the {QP1, QSi3, QSi4} species already preferring coordination of Na. The set of experimental preference factors {PCa} for the orthophosphate (QP0) groups extracted from 31P{23Na} REAPDOR NMR-derived M2(P–Na) dipolar second moments agrees well with the MD-generated counterparts. Our results on the Na/Ca intermixing in soda-lime-silicate glasses are discussed in relation to previous reports, highlighting the dependence of the conclusion on the approach to data evaluation.

  • 136.
    Mathew, Renny
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Tilocca, Antonio
    Eden, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Toward a Rational Design of Bioactive Glasses with Optimal Structural Features: Composition-Structure Correlations Unveiled by Solid-State NMR and MD Simulations2014Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, nr 3, s. 833-844Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The physiological responses of silicate-based bioactive glasses (BGs) are known to depend critically on both the P content (np) of the glass and its silicate network connectivity ((N) over bar (SI)(BO)). However, while the bioactivity generally displays a nonmonotonic dependence on np itself, recent work suggest that it is merely the net orthophosphate content that directly links to the bioactivity. We exploit molecular dynamics (MD) simulations combined with P-31 and Si-29 solid-state nuclear magnetic resonance (NMR) spectroscopy to explore the quantitative relationships between (N) over bar (SI)(BO), npand the silicate and phosphate speciations in a series of Na2O-CaO-SiO2-P2O5 glasses spanning 2.1 <=(N) over bar (SI)(BO) <= 2.9 and variable P2O5 contents up to 6.0 mol %. The fractional population of the orthophosphate groups remains independent of np at a fixed (N) over bar (SI)(BO)-value, but is reduced slightly as (N) over bar (SI)(BO) increases. Nevertheless, P remains predominantly as readily released orthophosphate ions, whose content may be altered essentially independently of the network connectivity, thereby offering a route to optimize the glass bioactivity. We discuss the observed composition-structure links in relation to known composition-bioactivity correlations, and define how Na2O-CaO-SiO2-P2O5 compositions exhibiting an optimal bioactivity can be designed by simultaneously altering three key parameters: the silicate network connectivity, the (ortho)phosphate content, and the n(Na)/n(ca) molar ratio.

  • 137.
    Mathew, Renny
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Turdean-Ionescu, Claudia
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Izquierdo-Barba, Isabel
    Garcia, Ana
    Arcos, Daniel
    Vallet-Regi, Maria
    Eden, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Direct Probing of the Phosphate-Ion Distribution in Bioactive Silicate Glasses by Solid-State NMR: Evidence for Transitions between Random/Clustered Scenarios2013Inngår i: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 25, nr 9, s. 1877-1885Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By employing P-31 multiple-quantum coherence-based solid-state nuclear magnetic resonance spectroscopy, we present the first comprehensive experimental assessment of the nature of the orthophosphate ion distributions in silicate based bioactive glasses (BGs). Results are provided both from melt prepared BG and evaporation-induced self-assembly-derived mesoporous bioactive glass (MEBG) structures of distinct compositions. The phosphate species are randomly dispersed in melt-derived BGs (comprising 44-55 mol % SiO2) of the Na2O-CaO-SiO2-P2O5 system, whereas a Si-rich (86 mol % SiO2) and Ca-poor ordered MBG structure exhibits nanometer-sized amorphous calcium phosphate clusters, conservatively estimated to comprise at least nine orthophosphate groups. A Ca-richer MBG (58 mol % SiO2) reveals a less pronounced phosphate clustering. We rationalize the variable structural role of P in these amorphous biomatetials.

  • 138.
    Metere, Alfredo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    On the nature of self-assembly in low-density condensed matter: A classical molecular dynamics approach2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The study of the physics of self-assembly in low-density condensed matter is an extremely interesting, mostly unexplored field of scientific research. The contribution reported in this thesis explains how this problem can be addressed using molecular dynamics simulation of 3D systems composed by simple, identical particles, interacting via a spherically symmetric pair potential, which belongs to the class of Dzugutov potentials. Such approach resulted in four, self-assembled archetypal structures, which are reported in the included papers I, II, III, IV. In order to produce the reported results, a major effort of software development has been done by the author, both in the simulation and the analysis programs used. This thesis will start with a brief introduction to the field, highlighting the important aspects needed to have a more complete, general understanding of the reported scientific results. Some conclusions will be drawn, together with some possible future endeavors.

  • 139.
    Mirzoev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Multiscale simulations of soft matter: systematic structure-based coarse-graining approach2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The soft matter field considers a wide class of objects such as liquids, polymers, gels, colloids, liquid crystals and biological macromolecules, which have complex internal structure and conformational flexibility leading to phenomena and properties having multiple spacial and time scales. Existing computer simulation methods are able to cover these scales, but with different resolutions, and ability to link them together performing a multiscale simulation is highly desirable.

    The present work addresses systematic multiscaling approach for soft matter studies, using structure-based coarse-graining (CG) methods such as iterative Boltzmann inversion and inverse Monte Carlo. A new software package MagiC implementing these methods is introduced. The software developed for the purpose of effective CG potential derivation is applied for ionic water solution and for water solution of DMPC lipids. A thermodynamic transferability of the obtained potentials is studied.

    The effective inter-ionic solvent mediated potentials derived for NaCl successfully reproduce structural properties obtained in explicit solvent simulation, which indicates the perspectives of using the structure-based coarse-graining for studies of ion-DNA and other polyelectrolytes systems. The potentials have temperature dependence, dominated mostly by the electrostatic long-range part which can be described by temperature dependent effective dielectric permittivity, leaving the short-range part of the potential thermodynamically transferable.

    For CG simulations of lipids a 10-bead water-free model of dimyristoylphosphatidylcholine is introduced. Four atomistic reference systems, having different lipid/water ratio are used to derive the effective bead-bead potentials, which are used for subsequent coarse-grained simulations of lipid bilayer. A significant influence of lipid/water ratio in the reference system on the properties of the simulated bilayers is noted, however it can be softened by additional angle-bending interactions. At the same time the obtained bilayers have stable structure with correct density profiles. The model provides acceptable agreement between properties of coarse-grained and atomistic bilayer, liquid crystal - gel phase transition with temperature change, as well as realistic self-aggregation behavior, which results in formation of bilayer, bicell or vesicle from a dispersed lipid solution in a large-scale simulation.

  • 140.
    Mirzoev, Alexander
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Systematic implicit solvent coarse graining of DMPC lipidsArtikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A 10-site coarse-grained implicit solvent model of DMPC phospholipid is developed with effective solvent-mediated potentials derived using the inverse Monte Carlo method. The potentials providing for the coarse-grained model the same site-site RDFs, bond and angle distributions as those computed in atomistic simulations were computed for four different lipid-water molar ratios.It was shown that there is a significant concentration dependence for both effective potentials and properties of lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favour to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid-like structure. Introduction of bending angle interaction into coarse-grained model makes effective potentials somewhat less concentration-dependent. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing full hydration of DMPC lipids in bilayer. Despite theoretical limitations of the structure-based approach expressed in state point dependence of the effective potentials, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area and compressibility. Another important property demonstrated by the model is liquid/gel phase transition observed at lowering the temperature. In addition to bilayer simulations, the model has proven its robustness in modeling of self-aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicells and vesicles.

  • 141.
    Mirzoev, Alexander
    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.
    Effective solvent mediated potentials of Na+ and Cl ions in aqueous solution: temperature dependence2011Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, nr 13, s. 5722-5727Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effective solvent-mediated potentials for Na+ and Cl ions in aqueous solution were calculated in a wide range of temperatures from 0 to 100 °C. The potentials have been determined using the inverse Monte Carlo approach, from the ion–ion radial distribution functions computed in 50 ns molecular dynamics simulations of ions and explicit water molecules. We further separated the effective potentials into a short-range part and an electrostatic long-range part represented by a coulombic potential with some dielectric permittivity. We adjusted the value of the dielectric permittivity to provide the fastest possible decay of the short-range potentials at larger distances. The obtained temperature dependence of the dielectric permittivity follows well the experimental data. We show also that the largest part of the temperature dependence of the effective potentials can be attributed to the temperature-dependent dielectric permittivity.

  • 142.
    Mirzoev, Alexander
    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.
    MagiC: Software Package for Multiscale Modeling2013Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, nr 3, s. 1512-1520Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present software package MagiC, which is designed to perform systematic structure-based coarse graining of molecular models. The effective pairwise potentials between coarse-grained sites of low-resolution molecular models are constructed to reproduce structural distribution functions obtained from the modeling of the system in a high resolution (atomistic) description. The software supports coarse-grained tabulated intramolecular bond and angle interactions, as well as tabulated nonbonded interactions between different site types in the coarse-grained system, with the treatment of long-range electrostatic forces by the Ewald summation. Two methods of effective potential refinement are implemented: iterative Boltzmann inversion and inverse Monte Carlo, the latter accounting for cross-correlations between pair interactions. MagiC uses its own Metropolis Monte Carlo sampling engine, allowing parallel simulation of many copies of the system with subsequent averaging of the properties, which provides fast convergence of the method with nearly linear scaling at parallel execution.

  • 143.
    Mirzoev, Alexander
    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.
    Systematic Implicit Solvent Coarse Graining of Dimyristoylphosphatidylcholine Lipids2014Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, nr 16, s. 1208-1218Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have used systematic structure-based coarse graining to derive effective site-site potentials for a 10-site coarse-grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse-grained model the same site-site radial distribution functions, bond and angle distributions as those computed in atomistic simulations carried out at four different lipid-water molar ratios. It was shown that there is a non-negligible dependence of the effective potentials on the concentration at which they were generated, which is also manifested in the properties of the lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favor to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid-like structure. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing fully saturated hydration of DMPC lipids. Despite theoretical limitations of pairwise coarse-grained potentials expressed in their state point dependence, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area, compressibility and orientational ordering. In addition to bilayer simulations, the model has proven its robustness in modeling of self-aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicelles, and vesicles.

  • 144. Mogelhoj, Andreas
    et al.
    Kelkkanen, Andre K.
    Wikfedt, K. Thor
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Schiotz, Jakob
    Mortensen, Jens Jorgen
    Pettersson, Lars G.M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Lundqvist, Bengt I.
    Jacobsen, Karsten W.
    Nilsson, Anders
    Norskov, Jens K.
    Ab Initio van der Waals Interactions in Simulations of Water Alter Structure from Mainly Tetrahedral to High-Density-Like2011Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, nr 48, s. 14149-14160Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations in the NVE ensemble using van der Waals (vdW) density-functional theory, i.e., using the new exchange-correlation functionals optPBE-vdW and vdW-DF2, where the latter has softer nonlocal correlation terms. Inclusion of the more isotropic vdW interactions counteracts highly directional hydrogen bonds, which are enhanced by standard functionals. This brings about a softening of the microscopic structure of water, as seen from the broadening of angular distribution functions and, in particular, from the much lower and broader first peak in the oxygen-oxygen pair-correlation function (PCF) and loss of structure in the outer hydration shells. Inclusion of vdW interactions is shown to shift the balance of resulting structures from open tetrahedral to more close-packed. The resulting O-O PCF shows some resemblance with experiment for high-density water (Soper, A. K.; Ricci, M.A. Phys. Rev. Lett. 2000, 84, 2881), but not directly with experiment for ambient water. Considering the accuracy of the new functionals for interaction energies, we investigate whether the simulation protocol could cause the deviation. An O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from low-density liquid water, as extrapolated from experiments, reproduces near-quantitatively the experimental O-O PCF for ambient water. This suggests the possibility that the new functionals maybe reliable and that instead larger-scale simulations in the NPT ensemble, where the density is allowed to fluctuate in accordance with proposals for supercooled water, could resolve the apparent discrepancy with the measured PCF.

  • 145.
    Mojumdar, Enamul
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Molecular Dynamics Simulations of Local Anesthetic Articaine in a Lipid Bilayer2010Inngår i: Biophysical Chemistry, ISSN 0301-4622, E-ISSN 1873-4200, Vol. 153, nr 1, s. 27-35Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In order to investigate structural and dynamical propertiesof local anesthetic articaine in a model lipid bilayer, a series ofmolecular dynamics simulations have been performed. Simulations werecarried out for neutral and charged (protonated) forms of articaine insertedin fully hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer. For comparison purpose, a fully hydrated DMPC bilayer withoutarticaine was also simulated. The length of each simulation was 200 ns. Various properties of the lipid bilayer systems in the presence of both charged and uncharged forms of articaine taken at two different concentrations have been examined: membrane area per lipid, mass density distributions, order parameters, radial distribution functions, head group tilt, diffusion coefficients, electrostatic potential, etc, and compared with results of previous simulations of DMPC bilayer in presence of lidocaine.It was shown that addition of both charged and neutral forms of articainecauses increase of the dipole electrostatic potential in the membraneinterior.

  • 146.
    Moser, D.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Haussermann, U.
    Utsumi, T.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Björling, T.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Noréus, D.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    A series of BaAl2-xSixH2-x (0.4 < x < 1.6) hydrides with compositions and structures in between BaSi2 and BaAl2H22010Inngår i: Journal of Alloys and Compounds, ISSN 0925-8388, E-ISSN 1873-4669, Vol. 505, nr 1, s. 1-5Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By substituting Si- with (Al-H)(-) in trigonal BaSi2, a series of hydrides has been synthesized with compositions BaAl2-xSixH2-x (0.4 < x < 1.6). OFF calculations show that the end compositions BaSi2 and BaAl2H2 are conductors whereas the intermediate BaAlSiH is a semiconductor. The cell parameters for the trigonal cell vary linearly as a function of the Si-/(Al-H)(-) substitution in this MgB2 related structure type, opening up the possibility of continuously tunable electric properties.

  • 147. Mucke, M.
    et al.
    Eland, J. H. D.
    Takahashi, O.
    Linusson, Per
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Lebrun, D.
    Ueda, K.
    Feifel, R.
    Formation and decay of core-orbital vacancies in the water molecule2013Inngår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 558, s. 82-87Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Primary steps in the interaction of high energy photons with water creating multiply ionised products are examined experimentally and theoretically. Double Auger decay from a 1s-hole state populates triply ionised states between 80 and 140 eV binding energy. Ejection of one 1s electron and one valence electron gives states around 570 eV which decay to triply ionised states between 75 and 110 eV. Nuclear motion in these states competes with Auger decay and substantially modifies the final state spectra. The double core-hole state from ionisation of both 1s electrons is found at 1171 +/- 1 eV and calculated at 1170.85 eV.

  • 148.
    Murtola, Teemu
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Vuorela, Timo A.
    Hyvonen, Marja T.
    Marrink, Siewert-Jan
    Karttunen, Mikko
    Vattulainen, Ilpo
    Low density lipoprotein: structure, dynamics, and interactions of apoB-100 with lipids2011Inngår i: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 7, nr 18, s. 8135-8141Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Low-density lipoprotein (LDL) transports cholesterol in the bloodstream and plays an important role in the development of cardiovascular diseases, in particular atherosclerosis. Despite its importance to health, the structure of LDL is not known in detail. This is worrying since the lack of LDL's structural information makes it more difficult to understand its function. In this work, we have combined experimental and theoretical data to construct LDL models comprised of the apoB-100 protein wrapped around a lipid droplet of about 20 nm in size. The models are considered by near-atomistic multi-microsecond simulations to unravel structural as well as dynamical properties of LDL, with particular attention paid to lipids and their interactions with the protein. We find that the distribution and the ordering of the lipids in the LDL particle are rather complex. The previously proposed 2- and 3- layer models turn out to be inadequate to describe the properties of the lipid droplet. At the surface of LDL, apoB-100 is found to interact favorably with cholesterol and its esters. The interactions of apoB-100 with core molecules, in particular cholesteryl esters, are rather frequent and arise from hydrophobic amino acids interacting with the ring of cholesteryl esters, and also in part from the rather loose packing of lipids at the surface of the lipoparticle. The loose packing may foster the function of transfer proteins, which transport lipids between lipoproteins. Finally, the comparison of the several apoB-100 models in our study suggests that the properties of lipids in LDL are rather insensitive to the conformation of apoB-100. Altogether, the findings pave the way for further studies of LDL to better understand the central steps in the emergence of atherosclerosis.

  • 149. Nakata, Yoshiki
    et al.
    Tsuchida, Kunio
    Miyanaga, Noriaki
    Furusho, Hirotoshi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Liquidly process in femtosecond laser processing2009Inngår i: Applied Surface Science, ISSN 0169-4332, E-ISSN 1873-5584, Vol. 255, nr 24, s. 9761-9763Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Nano-sized water-crown like structure in array was firstly generated onmetallic thin film by interfering femtosecond laser processing. We named the structure as ‘‘nanocrown’’. Ridges are standing on the edge of each ablated hole. The shapes of ridges are spike, nano-waterdrop and bead on column. The radius of the top of a spike was just 7 nm, which is far smaller than that of nanobump generated in the previous work. The self-rising in liquidly process result in the generation of mesoscopic nanostructure with the size between nanohorn or nanotube and micron structures processed by machining or lithography. This is a new surface modification technique in top-down technology.

  • 150.
    Naomé, Aymeric
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Schyman, Patric
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Vercauteren, Daniel P.
    Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 14, s. 4789-4801Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present results of molecular dynamics (MD) simulations of a double-stranded DNA fragment of sequence 5'-d(CGCGAGTTCGCG)-3' and 3'-d(GCGCTCAAGCGC)-5' in its native form and altered with guanine in the G6/C19 base pair replaced by 8-oxoguanine (8oxoG). DNA was simulated in solution with Na+ counterions and explicit water molecules. Trajectories were analyzed for radial distribution functions (RDFs), spatial distribution functions (SDFs), residence times, and occupancies, for both water and ions. Structural parameters of DNA fragments were also considered. Particularly, we report sensible differences in the statistical and dynamical behavior of water and ions between the healthy and lesion containing models. Structural features such as sugar phosphate backbone torsion angles also significantly differ. We conclude that 8oxoG noticeably modifies its close environment and that the observed changes in the vicinity of the lesion site might help the enzymes in charge of cleansing 8oxoG from human DNA to locate the aberration in its intrahelical context. This work supports the existence of a determinant early recognition mode of 8oxoG; for hOGG1.

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