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  • 51.
    Eremina, Nadejda
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Use of Creatine Kinase To Induce Multistep Reactions in Infrared Spectroscopic Experiments2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 48, s. 14967-14972Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An extension of current approaches to trigger enzymatic reactions in reaction-induced infrared difference spectroscopy experiments is described. A common procedure is to add a compound that induces a reaction in the protein of interest. To be able to induce multistep reactions, we explored here the use of creatine kinase (CK) for the study of phosphate transfer mechanisms. The enzymatic reaction of CK could be followed using bands at 1614 and 979 cm(-1) for creatine phosphate consumption, at 944 cm(-1) for ADP consumption, and at 1243, 992, and 917 cm(-1) for ATP formation. The potential of CK to induce multistep reactions in infrared spectroscopic experiments was demonstrated using the sarcoplasmic reticulum Ca2+-ATPase (SERCA1a) as the protein of interest. ADP binding to the ATPase was triggered by photolytic release of ADP from P-3-1-(2-nitro)phenylethyl ADP (caged ADP). CK added in small amounts converted the released ADP to ATP on the time scale of minutes. This phosphorylated the ATPase and led to the formation of the first phosphoenzyme intermediate Ca(2)E1P. Thus a difference spectrum could be obtained that reflected the reaction from the ADP ATPase complex to the first phosphoenzyme intermediate. Comparison with a phosphorylation spectrum obtained when the initial state was the ATP ATPase complex revealed the contribution of ATP's gamma-phosphate to the conformational change of the ATPase upon nucleotide binding: gamma-phosphate binding modifies the structure of a beta-sheet, likely in the phosphorylation domain, and shifts its spectral position from similar to 1640 to similar to 1630 cm(-1). Upon phosphorylation of the ATPase, the beta-sheet relaxes back to a structure that is intermediate between that adopted in the ADP bound state and that in the ATP bound state.

  • 52.
    Ermilova, Inna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Modeling of biomembranes: from computational toxicology to simulations of neurodegenerative diseases2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    It was known from the middle of the last century that a cell-membrane is a lipid bilayer. Since that time a large number of experimental studies has been done in order to see how a certain molecule can penetrate through a membrane. Due to the complexity of laboratory experiments computational chemistry became a convenient tool for investigations involving this process. In a real life a compound has to pass through several membranes of different chemical composition before reaching the actual target. Such a diversity in constitution gives a various selectivity to cell-membranes: some molecules will penetrate through them and others will not. That is why the development and a choice of suitable models for lipid bilayers are important steps in such a research. In this thesis new all-atomistic models for polyunsaturated phospholipids in cis conformations have been derived and added to the SLipids force field. After a successful force field validation, the new lipid models were used in molecular dynamics and well-tempered metadynamics simulations of several problems, such as toxicity of hydroxylated polybrominated diphenyl ethers (OH-PBDE), behavior of cholesterol in various membranes, an aggregation of amyloid-β (Aβ) peptides. The significance of the presence of lipid unsaturation has been demonstrated by all computations. 2’-OH-BDE68 (ortho) showed the affinity to saturated lipid bilayer, but had more conformational variations in the center of the unsaturated membrane. Cholesterol did not exhibit the preference to polynsaturated lipid bilayers from free energy calculations, but the diversity in orientations of this molecule, depending on its locations was observed. The behavior of Aβ peptides was dependent on membrane saturation as well. The insertion of Aβ peptides was detected in lipid bilayers containing higher amounts of polyunsaturated phospholipids, while in systems with more saturated membranes amyloids aggregated on membrane surfaces. Moreover, a comparison of simulations for quadro- and mono-component lipid bilayers showed that the membrane built of 18:0-22:6 PC can serve as a good model for the ’healthy’ tissue of a human brain. Also the lipid bilayer built of 14:0-14:0 PC exhibited similar features as the quadro-lipid membrane representing the brain tissue affected by Alzheimer’s disease. Good agreement of some computational results with available experimental findings demonstrated the applicability of computer simulations to real life problems.

  • 53.
    Ermilova, Inna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Modelling of interactions between Aβ(25-35) peptide and phospholipid bilayers: effects of cholesterol and lipid saturation2019Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Artikkel i tidsskrift (Fagfellevurdert)
  • 54.
    Ermilova, Inna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Cholesterol in phospholipid bilayers: positions and orientations inside membranes with different unsaturation degrees2019Inngår i: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 15, nr 1, s. 78-93Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cholesterol is an essential component of all animal cell membranes and plays an important role in maintaining the membrane structure and physical–chemical properties necessary for correct cell functioning. The presence of cholesterol is believed to be responsible for domain formation (lipid rafts) due to different interactions of cholesterol with saturated and unsaturated lipids. In order to get detailed atomistic insight into the behaviour of cholesterol in bilayers composed of lipids with varying degrees of unsaturation, we have carried out a series of molecular dynamics simulations of saturated and polyunsaturated lipid bilayers with different contents of cholesterol, as well as well-tempered metadynamics simulations with a single cholesterol molecule in these bilayers. From these simulations we have determined distributions of cholesterol across the bilayer, its orientational properties, free energy profiles, and specific interactions of molecular groups able to form hydrogen bonds. Both molecular dynamics and metadynamics simulations showed that the most unsaturated bilayer with 22:6 fatty acid chains shows behaviour which is most different from other lipids. In this bilayer, cholesterol is relatively often found in a “flipped” configuration with the hydroxyl group oriented towards the membrane middle plane. This bilayer has also the highest (least negative) binding free energy among liquid phase bilayers, and the lowest reorientation barrier. Furthermore, cholesterol molecules in this bilayer are often found to form head-to-tail contacts which may lead to specific clustering behaviour. Overall, our simulations support ideas that there can be a subtle interconnection between the contents of highly unsaturated fatty acids and cholesterol, deficiency or excess of each of them is related to many human afflictions and diseases.

  • 55.
    Feng, Xiaolong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Estimating molecular conformations by solid-state NMR spectroscopy1998Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Our understanding of structure-function relationships in biological systems demands new and more sophisticated methods for examining molecular structure. This thesis presents an effort of methodology development for molecular structure determination by solid-state NMR spectroscopy and applications to biological systems.

    Rotational Resonance NMR is established as a major tool for extracting molecular structural information in solids. Some further aspects of the technique are explored. The technique is applied to obtain the binding conformation of an inhibitor, TMPIP, bound to gastric H+/K+-ATPase, an ab heterodimer with a molecular weight of over 150 kDa.

    A novel solid-state NMR method for the determination of the torsional angle of a 13C-labeled H-C-C-H moiety is developed. A detailed theoretical introduction of the method is presented. The technique has been applied to determine the H-C10-C11-H torsional angle of the retinylidene chromophore in bovine rhodopsin, a 41 kDa integral membrane protein, and its photo-intermediate metarhodopsin-I.

    A new solid-state NMR method is developed. It may be used to estimate the Ramachandran ( angle in a protein backbone chain. A detailed theory is presented. It is demonstrated on an isotopically labeled tripeptide.

  • 56. Fischer, Christian E.
    et al.
    Mink, Janos
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Hajba, Laszlo
    Bacsik, Zoltan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Nemeth, Csaba
    Mihaly, Judith
    Raith, Alexander
    Cokoja, Mirza
    Kuehn, Fritz E.
    Vibrational spectroscopic study of SiO2-based nanotubes2013Inngår i: Vibrational Spectroscopy, ISSN 0924-2031, E-ISSN 1873-3697, Vol. 66, s. 104-118Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Novel organic-inorganic hybrid nanotubes containing silica and ethane (EtSNT), ethylene (ESNT) and acetylene (ASNT) units, as well as brominated ESNT (Br-ESNT) and glycine-modified Br-ESNT (Gly-ESNT) have been studied by IR and Raman spectroscopy. The results are compared with the spectral features for conventional silica nanotubes (SNT) and amorphous silica. Bands peculiar to organic moieties have been detected and assigned. Assignment of the silicate backbone vibrations was based on the results of normal coordinate calculations. Furthermore, characteristic silicate, so-called 'nanotube' vibrations have been identified and their band positions have been summarized to serve as a future reference for such compounds. SiOSi antisymmetric stretchings were observed in the range 1000-1110 cm(-1), while the symmetric stretchings appeared between 760 and 960 cm(-1) for EtSNT, ESNT and Br-ESNT. Force constants have been refined for models of the repeating structure units: O3SiOSi(OSi)(3) for SNT and SiCHnCHnSi(OSi)(3) for organosilica nanotubes (n = 2, EtSNT: n = 1, ESNT and n = 0, ASNT). The calculated SiO stretching force constants were increased from 4.79 to 4.88 and 5.11 N cm(-1) for EtSNT, ESNT and ASNT, respectively. The force constants have been compared with those for several silicates and SiO bond length are predicted and discussed.

  • 57.
    Fossépré, Mathieu
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi. University of Namur (UNamur), Belgium.
    Leherte, Laurence
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi. Stellenbosch University, South Africa.
    Vercauteren, Daniel P.
    On the Modularity of the Intrinsic Flexibility of the mu Opioid Receptor: A Computational Study2014Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 12, s. e115856-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The mu opioid receptor (mu OR), the principal target to control pain, belongs to the G protein-coupled receptors (GPCRs) family, one of the most highlighted protein families due to their importance as therapeutic targets. The conformational flexibility of GPCRs is one of their essential characteristics as they take part in ligand recognition and subsequent activation or inactivation mechanisms. It is assessed that the intrinsic mechanical properties of the mu OR, more specifically its particular flexibility behavior, would facilitate the accomplishment of specific biological functions, at least in their first steps, even in the absence of a ligand or any chemical species usually present in its biological environment. The study of the mechanical properties of the mu OR would thus bring some indications regarding the highly efficient ability of the mu OR to transduce cellular message. We therefore investigate the intrinsic flexibility of the mu OR in its apo-form using all-atom Molecular Dynamics simulations at the sub-microsecond time scale. We particularly consider the mu OR embedded in a simplified membrane model without specific ions, particular lipids, such as cholesterol moieties, or any other chemical species that could affect the flexibility of the mu OR. Our analyses highlighted an important local effect due to the various bendability of the helices resulting in a diversity of shape and volume sizes adopted by the mu OR binding site. Such property explains why the mu OR can interact with ligands presenting highly diverse structural geometry. By investigating the topology of the mu OR binding site, a conformational global effect is depicted: the correlation between the motional modes of the extra-and intracellular parts of mu OR on one hand, along with a clear rigidity of the central mu OR domain on the other hand. Our results show how the modularity of the mu OR flexibility is related to its preability to activate and to present a basal activity.

  • 58.
    Gebauer, Denis
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Oliynyk, Vitaliy
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Salajkova, Michaela
    Sort, Jordi
    Zhou, Qi
    Bergström, Lennart
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Salazar-Alvarez, German
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    A transparent hybrid of nanocrystalline cellulose and amorphous calcium carbonate nanoparticles2011Inngår i: NANOSCALE, ISSN 2040-3364, Vol. 3, nr 9, s. 3563-3566Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Nanocellulose hybrids are promising candidates for biodegradable multifunctional materials. Hybrids of nanocrystalline cellulose (NCC) and amorphous calcium carbonate (ACC) nanoparticles were obtained through a facile chemical approach over a wide range of compositions. Controlling the interactions between NCC and ACC results in hard, transparent structures with tunable composition, homogeneity and anisotropy.

  • 59. Ghobril, Cynthia
    et al.
    Hammar, Peter
    Kodepelly, Sanjeevarao
    Spiess, Bernard
    Wagner, Alain
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Baati, Rachid
    Structure-Reactivity Relationship Studies for Guanidine-Organocatalyzed Direct Intramolecular Aldolization of Ketoaldehydes2010Inngår i: ChemCatChem, ISSN 1867-3880, E-ISSN 1867-3899, Vol. 2, nr 12, s. 1573-1581Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Structure-reactivity studies are performed to explore the reaction mechanism of the guanidine-catalyzed intramolecular aldol reaction of ketoaldehydes. A large number of guanidine and guanidine-like catalysts are synthesized and their properties studied. Kinetic profiles and pK(a) values of the catalysts are measured and correlated to reaction barriers calculated using density functional theory (DFT). The DFT calculations show that structural rigidity influences the pKa of the guanidines. Although the basicity is a very important factor in the catalysis, it is not sufficient to fully account for its catalytic efficiency. The availability of two aligned nitrogen reaction sites for proton shuttling in the transition state is an essential feature that helps to rationalize the reactivity pattern and the activation mode for this family of organocatalysts.

  • 60.
    Grippa, Alexander Yu
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Lidin, Sven
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    D'yachenko, Oleg G.
    Rupasov, Dmitry P.
    Antipov, Eugeny V.
    Synthesis and study of Sr-substituted misfit layer sulfides2005Inngår i: Materials Research Bulletin, ISSN 0025-5408, Vol. 40, nr 1, s. 79-91Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Two series of [(Ln1/3Sr2/3S)1.5]1.15NbS2 (1.5Q/1H) and (Ln1−xSrxS)1+yNbS2 (1Q/1H) misfit layer sulfides have been synthesised and studied by X-ray powder and single crystal diffraction, EDX-analysis and magnetic measurements. For the early lanthanides (Ln = La, Ce) only the (Ln1−xSrxS)1+yNbS2 (x < 0.40–0.45, y = 0.15–0.17) compounds were formed whereas for late lanthanides (Ln = Pr, Nd, Sm, Gd–Er, Yb, Lu), and yttrium, both types of phases can be obtained. The crystal structure of (Pr0.55Sr0.45S)1.15NbS2 has been refined on the basis of X-ray single crystal data using the superspace approach. It consists of double layers [Pr0.55Sr0.45S] of NaCl-type (Q-part: a = 5.799(3) Å, b = 5.810(2) Å, c = 23.331(9) Å, z = 4) and NbS2-sandwiches (H-part: a = 3.332(3) Å), z = 8, yielding a q-vector q = (α 0 0), α = 0.74) alternating along the c-direction. The superspace group pair is Fm2m (α 0 0):Fm2m (α 0 0) (No. 42.7). The refinement converged to Rw(obs) = 0.069. According to the structure refinement and EDX-analysis data in the [Pr0.55Sr0.45S]-slab almost half of the Pr-atoms are randomly replaced by Sr. The minimal formal value of charge transfer from the Q- to the H-part of the structure necessary to stabilise the misfit Nb-based layer sulfides has been estimated as about 0.6 ē per Nb atom.

  • 61.
    Grippa, Alexander Yu
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Lidin, Sven
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Svensson, Gunnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Rupasov, Dmitry P.
    Khasanova, Nellie R.
    D'yachenko, Oleg G.
    Antipov, Eugeny V.
    New strontium and rare earth-based mixed niobium misfit sulfides2003Inngår i: Solid State Sciences, Vol. 5, nr 3, s. 495-502Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    New niobium-based misfit sulfides [(Ln1/3Sr2/3S)1.5]1.15NbS2 (Ln=Sm, Tb) have been synthesized from a mixture of SrS, Ln2S3, Nb(m), and S in evacuated and sealed silica tubes by annealing at 1000 °C for 144 h under a sulfur partial pressure of 49.3 kPa. The compounds have been characterized by EDX analysis, X-ray single crystal and powder diffraction, electron diffraction, and magnetic susceptibility measurements. Both sulfides have misfit structures with orthorhombic symmetry for the (Ln1/3Sr2/3S)1.5 (Ln=Sm, Tb) and NbS2 subsystems. The lattice parameters for the different subsystems are: for the Sm-based sulfide [(Sm1/3Sr2/3S)1.5]: a=5.7953(9) Å, b=5.8007(5) Å, c=14.957(2) Å and [NbS2]: a=3.3420(7) Å, b=5.8008(5) Å, c=14.955(2) Å, and for the Tb-based sulfide [(Tb1/3Sr2/3S)1.5]: a=5.769(2) Å, b=5.7766(7) Å, c=14.906(2) Å and [NbS2]: a=3.340(1) Å, b=5.7769(8) Å, c=14.905(2) Å. The [(Sm1/3Sr2/3S)1.5]1.15NbS2 crystal structure has been refined from X-ray single crystal data. It belongs to the 1.5Q/1H homologue type where the (Sm1/3Sr2/3S)1.5 part is a three-atoms-thick slab. Sr-cations are mainly located at the exterior of the slab whereas Sm preferably occupy the positions at its center. Both compounds exhibit paramagnetic temperature dependence down to 2 K.

  • 62.
    Gunawidjaja, Philips N.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Mathew, Renny
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lo, Andy Y. H.
    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.
    Local structures of mesoporous bioactive glasses and their surface alterations in vitro: inferences from solid-state nuclear magnetic resonance2012Inngår i: Philosophical Transactions. Series A: Mathematical, physical, and engineering science, ISSN 1364-503X, E-ISSN 1471-2962, Vol. 370, nr 1963, s. 1376-1399Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We review the benefits of using Si-29 and H-1 magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for probing the local structures of both bulk and surface portions of mesoporous bioactive glasses (MBGs) of the CaO-SiO2-(P2O5) system. These mesoporous materials exhibit an ordered pore arrangement, and are promising candidates for improved bone and tooth implants. We discuss experimental MAS NMR results from three MBGs displaying different Ca, Si and P contents: the Si-29 NMR spectra were recorded either directly by employing radio-frequency pulses to Si-29, or by magnetization transfers from neighbouring protons using cross polarization, thereby providing quantitative information about the silicate speciation present in the pore wall and at the MBG surface, respectively. The surface modifications were monitored for the three MBGs during their immersion in a simulated body fluid (SBF) for intervals between 30 min and one week. The results were formulated as a reaction sequence describing the interconversions between the distinct silicate species. We generally observed a depletion of Ca2+ ions at the MBG surface, and a minor condensation of the silicate-surface network over one week of SBF soaking.

  • 63. Harper, James K.
    et al.
    Tishler, Derek
    Richardson, David
    Lokvam, John
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Solid-State NMR Characterization of the Molecular Conformation in Disordered Methyl alpha-L-Rhamnofuranoside2013Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, nr 26, s. 5534-5541Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A combination of solid-state C-13 NMR tensor data and DFT computational methods is utilized to predict the conformation in disordered methyl alpha-L-rhamnofuranoside. This previously uncharacterized solid is found to be crystalline and consists of at least six distinct conformations that exchange on the kHz time scale. A total of 66 model structures were evaluated, and six were identified as being consistent with experimental C-13 NMR data. All feasible structures have very similar carbon and oxygen positions and differ most significantly in OH hydrogen orientations. A concerted rearrangement of OH hydrogens is proposed to account for the observed dynamic disorder. This rearrangement is accompanied by smaller changes in ring conformation and is slow enough to be observed on the NMR time scale due to severe steric crowding among ring substituents. The relatively minor differences in non-hydrogen atom positions in the final structures suggest that characterization of a complete crystal structure by X-ray powder diffraction may be feasible.

  • 64.
    He, Andong
    et al.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Wettlaufer, John S.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Hertz beyond belief2014Inngår i: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 10, nr 13, s. 2264-2269Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We examine the validity of Hertz's linear elastic theory for central collisions of spheres using a viscoelastic model. This model explains why Hertz's theory is accurate in predicting the collision time and maximum contact area even when 40% of the kinetic energy is lost due to viscous dissipation. The main reason is that both the collision time and maximum contact area have a very weak dependence on the impact velocity. Moreover, we show that colliding objects exhibit an apparent size-dependent yield strength, which results from larger objects dissipating less energy at a given impact velocity.

  • 65.
    Hedin, Niklas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Ng, JBS
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Stilbs, P
    Spectral Deconvolution of NMR Cross Polarization Data Sets2009Inngår i: Solid State Nuclear Magnetic Resonance, ISSN 0926-2040, E-ISSN 1527-3326, Vol. 35, s. 208-213Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The COmponent-REsolved (CORE) strategy has been employed, for the first time to solid state NMR spectroscopy. CORE was used to extract two time-dependent spectral components in 24 Si-29(H-1) NMR spectra, recorded on a meso-structured silica material under conditions of cross polarization evolution. No prior assumptions were made about the component bandshapes, which were both found to be skewed to higher chemical shifts. For the silica fragments close to protons this skewness could be rationalized by a distribution of the degree of condensation in the silica network; however, for the other component the non-Gaussian shape was unexpected. We expect that the same strategy could be applied to a range of experiments in solid-state NMR spectroscopy, where spectral distributions or kinetic parameters need to be accurately extracted

  • 66.
    Hedin, Niklas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Rzepka, Przemyslaw
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Jasso-Salcedo, Alma Berenice
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Church, Tamara
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Bernin, Diana
    Intracrystalline Transport Barriers Affecting the Self-Diffusion of CH4 in Zeolites |Na12|-A and|Na12-xKx|-AInngår i: Artikkel i tidsskrift (Fagfellevurdert)
  • 67.
    Hedman, Fredrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Algorithms for Molecular Dynamics Simulations2006Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A perspective on the field of parallel MD simulations is given. Hardware and software aspects are characterized and the interplay between the two is briefly discussed.

    A method for performing ab initio MD is described; the method essentially recomputes the interaction potential at each time-step. It has been tested on a system of liquid water by comparing results with other simulation methods and experimental results. Different strategies for parallelization are explored.

    Furthermore, data-parallel methods for short-range and long-range interactions on massively parallel platforms are described and compared.

    Next, a method for treating electrostatic interactions in MD simulations is developed. It combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform---ENUF for short. The method scales as N log N, where N is the number of charges in the system. ENUF has a behavior very similar to Ewald summation and can be easily and efficiently implemented in existing simulation programs.

    Finally, an outlook is given and some directions for further developments are suggested.

  • 68.
    Hedman, Fredrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Ewald Summation Based on Nonuniform Fast Fourier Transform2006Inngår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 425, nr 1-3, s. 142-147Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a novel approach, that combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform to calculate the electrostatic energies and forces in molecular computer simulations. The method can easily be implemented in existing simulation programs. We report here some results from our implementation, where we utilize widely available libraries, and demonstrate the accuracy, and expected computational complexity of our approach.

  • 69. Henschel, Henning
    et al.
    Acosta Navarro, Juan Camilo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Yli-Juuti, Taina
    Kupiainen-Määttä, Oona
    Olenius, Tinja
    Ortega, Ismael K.
    Clegg, Simon L.
    Kurtén, Theo
    Riipinen, Ilona
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Vehkamäki, Hanna
    Hydration of Atmospherically Relevant Molecular Clusters: Computational Chemistry and Classical Thermodynamics2014Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, nr 14, s. 2599-2611Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Formation of new particles through clustering of molecules from condensable vapors is a significant source for atmospheric aerosols. The smallest clusters formed in the very first steps of the condensation process are, however, not directly observable by experimental means. We present here a comprehensive series of electronic structure calculations on the hydrates of clusters formed by up to four molecules of sulfuric acid, and up to two molecules of ammonia or dimethylamine. Though clusters containing ammonia, and certainly dimethylamine, generally exhibit lower average hydration than the pure acid clusters, populations of individual hydrates vary widely. Furthermore, we explore the predictions obtained using a thermodynamic model for the description of these hydrates. The similar magnitude and trends of hydrate formation predicted by both methods illustrate the potential of combining them to obtain more comprehensive models. The stabilization of some clusters relative to others due to their hydration is highly likely to have significant effects on the overall processes that lead to formation of new particles in the atmosphere.

  • 70. Huang, Congcong
    et al.
    Wikfeldt, Thor Kjartan
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nordlund, D.
    Bergmann, U.
    McQueen, T.
    Sellberg, Jonas
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Pettersson, Lars G.M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nilsson, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Wide-angle X-ray diffraction and molecular dynamics study of medium-range order in ambient and hot water2011Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 44, s. 19997-20007Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have developed wide-angle X-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 degrees C) under normal pressure. Using a spherically curved Ge crystal an energy resolution better than 15 eV has been achieved which eliminates influence from Compton scattering. The high quality of the data allows for a reliable Fourier transform of the experimental data resolving shell structure out to similar to 12 angstrom, i.e. 5 hydration shells. Large-scale molecular dynamics (MD) simulations using the TIP4P/2005 force-field reproduce excellently the experimental shell-structure in the range 4-12 angstrom although less agreement is seen for the first peak in the intermolecular pair-correlation function (PCF). The Shiratani-Sasai Local Structure Index [J. Chem. Phys. 104, 7671 (1996)] identifies a tetrahedral minority giving the intermediate-range oscillations in the O-O PCF and a disordered majority providing a more featureless background in this range. The current study supports the proposal that the structure of liquid water, even at high temperatures, can be described in terms of a two-state fluctuation model involving local structures related to the high-density and low-density forms of liquid water postulated in the liquid-liquid phase transition hypothesis.

  • 71.
    Högberg, Carl-Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Effect of Local Anesthetic Lidocaine on Electrostatic Properties of a Lipid Bilayer2008Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 94, s. 525-531Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The influence of local anesthetic lidocaine on electrostatic properties of a lipid membrane bilayer was studied by molecular dynamics simulations. The electrostatic dipole potential, charge densities, and orientations of the headgroup angle have been examined in presence of different amounts of charged or uncharged forms of lidocaine. Important differences of the membrane properties caused by the presence of the both forms of lidocaine are presented and discussed. Our simulations have shown that both charged and uncharged lidocaine cause almost the same increase of the dipole electrostatic potential in the middle of membrane though for different reasons. The increase, being about 90 mV for 9 mol % of lidocaine and 220 mV for 28 mol% of lidocaine, is of the size which may affect the functioning of voltage-gated ion channels.

  • 72.
    Högberg, Carl-Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Nikitin, Alexei
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Modification of the CHARMM force field for DMPC lipid bilayer2008Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, nr 14, s. 2359-2369Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids.

  • 73.
    Iftekhar, ANM Shahriar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Structure-Property-Composition Correlations in Rare-Earth Alumino-silicate Glasses2012Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Rare earth (RE) alumino-silicate (AS) glasses exhibit favorable physical, mechanical and optical properties, such as high values of the glass transition temperature, Vickers hardness, and refractive index. RE2O3-Al2O3-SiO2 glasses have found several industrial applications, for example as components of optical amplifiers and lasers. Many of these features stem from the high cation field-strength (CFS) of the trivalent RE ions (proportional to the valence of the ion divided by the square of its radius), which affects not only the physical properties of the glass, but also their structures.

    This thesis deals with investigations of four different RE2O3-Al2O3-SiO2 systems, where RE represents either of La, Y, Lu or Sc. The glass forming regions of the latter two were reported by us for the first time. Within each system, glasses were prepared for variable RE, Si and Al contents.

    The glass structures were investigated by solid-state 29Si and 27Al nuclear magnetic resonance (NMR) spectroscopy that informs about the local Si and Al environments in the glass network, which is built from interlinked SiO4 and AlO4 groups. Higher Al coordination numbers were also revealed by 27Al NMR: their amounts were observed to increase markedly as the CFS of the RE ion increases, i.e., along the series La<Y<Lu<Sc. This thesis discusses such structure/composition relationships, as well as the correlations between the glass composition and its physical properties of density, molar volume, compactness, glass transition temperature, Vickers hardness and refractive index. Some of these properties, for example the glass transition temperature and Vickers hardness, were observed to enhance as the RE3+ CFS increased.

  • 74.
    Iftekhar, Shahriar
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Pahari, Bholanath
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Okhotnikov, Kirill
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Jaworski, Aleksander
    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.
    Grins, Jekabs
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Eden, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Properties and Structures of RE2O3-Al2O3-SiO2 (RE=Y, Lu) Glasses Probed by Molecular Dynamics Simulations and Solid-State NMR: The Roles of Aluminum and Rare-Earth Ions for Dictating the Microhardness2012Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 116, nr 34, s. 18394-18406Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By combining molecular dynamics (MD) simulations with Si-29 and Al-27 magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy, we present a comprehensive structural report on rare-earth (RE) aluminosilicate (AS) glasses of the RE2O3-Al2O3-SiO2 (RE = Y, Lu) systems, where the latter is studied for the first time. The structural variations stemming from changes in the glass composition within each RE system as well as the effects of the increased cation field-strength (CFS) of Lu3+ relative to Y3+-are explored and correlated to measured physical properties, such as density, molar volume, glass transition temperature, and Vickers hardness (H-V). Si-29 NMR reveals a pronounced network ordering for an increase in either the RE or Al content of the glass. Al mainly assumes tetrahedral coordination, but significant AlO5 and AlO6 populations are present in all structures, with elevated amounts in the Lu-bearing glasses compared to their Y analogues. The MD-derived oxygen speciation comprises up to 3% of free O2- ions, as well as non-negligible amounts (4-19%) of O-[3] coordinations (oxygen triclusters). While the SiO4 groups mainly accommodate the nonbridging oxygen ions, a significant fraction thereof is located at the AlO4 tetrahedra, in contrast to the scenario of analogous alkali- and alkaline-earth metal-based AS glasses. The average coordination numbers (CNs) of Al and RE progressively increase for decreasing Si content of the glass, with the average CN of the RE3+ ions depending linearly on both the amount of Si and the fraction of AlO5 groups in the structure. The Vickers hardness correlates strongly with the average CN of Al, in turn dictated by the CFS and content of the RE3+ ions. This is to our knowledge the first structural rationalization of the well-known compositional dependence of H-V in RE bearing AS glasses.

  • 75. Ivanov, M. F.
    et al.
    Kiverin, A. D.
    Yakovenko, I. S.
    Liberman, Michael A.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). Russian Academy of Sciences.
    Hydrogen-oxygen flame acceleration and deflagration-to-detonation transition in three-dimensional rectangular channels with no-slip walls2013Inngår i: International journal of hydrogen energy, ISSN 0360-3199, E-ISSN 1879-3487, Vol. 38, nr 36, s. 16427-16440Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Hydrogen-oxygen flame acceleration and the transition from deflagration to detonation (DDT) in channels with no-slip walls are studied using high resolution simulations of 3D reactive Navier-Stokes equations, including the effects of viscosity, thermal conduction, molecular diffusion, real equation of state and detailed (reduced) chemical reaction mechanism. The acceleration of the flame propagating from the closed end of a channel, which is a key factor for understanding of the mechanism of DDT, is thoroughly studied. The three dimensional modeling of the flame acceleration and DDT in a semi-closed rectangular channel with cross section 10 x 10 mm and length 250 mm confirms validity of the mechanism of deflagration-to-detonation transition, which was proposed earlier theoretically and verified using 2D simulations. We show that 3D model contrary to 2D models allows to understand clearly the meaning of schlieren photos obtained in experimental studies. The numerical schlieren and numerical shadowgraph obtained using 3D calculations clarify the meaning of the experimental schlieren and shadow photos and some earlier misinterpretations of experimental data.

  • 76.
    Ivanov, Sergei
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Path Integral studies of quantum systems at finite temperatures2005Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis presents and develops the path integral simulation techniques in application to small quantum systems at finite temperatures. The first goal is to obtain exact thermodynamic expressions for systems of noninteracting

    The rest and the major part of the thesis is dedicated to the development and testing of Bead-Fourier path integral molecular dynamics. Although, path integral molecular dynamics as well as path integral Monte Carlo are well

    First, molecular dynamics under Bead-Fourier scheme was developed and tested on the examples of quantum harmonic oscillator and Hydrogen atom. The main attention was paid to ergodicity problems. Then we addressed the question,

    Later, the formalism for identical particles was developed.

    Finally, the question of molecular dynamics efficacy was raised. It was shown, that formalisms for identical and distinguishable particles, both, can be reformulated into a more efficient ones, providing all dynamical variables

  • 77.
    Jaworski, Aleksander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Structure of Rare-Earth Aluminosilicate Glasses Probed by Solid-State NMR Spectroscopy and Quantum Chemical Calculations2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Aluminosilicate glasses incorporating rare earth elements feature highly beneficial physical and chemical properties, at the level beyond that accessible for compositions based on alkali and/or alkaline earth metals. Extraordinary hardness, high glass transition temperatures and indices of refraction, favorable coefficients of thermal expansion, as well as excellent chemical durability, result in many potential technological applications. However, in contrast to the systematically explored and commercially exploited aluminosilicate glasses that contain Na, K, and Ca elements, their rare earth counterparts were sparsely investigated, although exhibit several unique structural features.

    This thesis explored the short- and medium-range structural organization of glasses belonging to the ternary RE2O3—Al2O3—SiO2 systems, where RE denotes one of the trivalent and diamagnetic rare earth metal ions of scandium (Sc), yttrium (Y), lanthanum (La), and lutetium (Lu). Comprehensive multinuclear solid-state nuclear magnetic resonance studies complemented with atomistic molecular dynamics computer simulations and quantum chemical calculations provided detailed insight into local environments of the glass networkforming elements (Si, Al), oxygen species, as well as the rare earth ions, thereby offering a deeper understanding of the glass structure.

  • 78.
    Jaworski, Aleksander
    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.
    Direct O-17 NMR experimental evidence for Al-NBO bonds in Si-rich and highly polymerized aluminosilicate glasses2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 28, s. 18269-18272Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By using solid-state O-17 NMR spectroscopy, we provide the first direct experimental evidence for bonds between Al and non-bridging oxygen (NBO) ions in aluminosilicate glasses based on rare-earth (RE) elements, where RE = {Lu, Sc, Y}. The presence of similar to 10% Al-NBO moieties out of all NBO species holds regardless of the precise glass composition, at odds with the conventional structural view that Al-NBO bonds are absent in highly polymerized and Si-rich aluminosilicate glass networks.

  • 79.
    Jaworski, Aleksander
    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.
    Sc and Y Environments in Rare-Earth Aluminosilicate Glasses Unveiled by 45Sc and 89Y NMR Spectroscopy, MD Simulations, and DFT CalculationsManuskript (preprint) (Annet vitenskapelig)
  • 80.
    Jaworski, Aleksander
    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.
    The Bearings from Rare-Earth (RE=La, Lu, Sc, Y) Cations on the Oxygen Environments in Aluminosilicate Glasses: A Study by Solid-State 17O NMR, Molecular Dynamics Simulations and DFT CalculationsManuskript (preprint) (Annet vitenskapelig)
  • 81.
    Jaworski, Aleksander
    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.
    Pahari, Bholanath
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Okhotnikov, Kirill
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Eden, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Local structures and al/si ordering in lanthanum aluminosilicate glasses explored by advanced al 27 nmr experiments and molecular dynamics simulations2012Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, nr 45, s. 15866-15878Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structures of 15 La-Al-Si-O glasses, whose compositions span 11-28 mol% La2O3, 11-30 mol% Al2O3, and 45-78 mol% SiO2, are explored over both short and intermediate length-scales by using a combination of solid-state Al-27 magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations. MAS NMR reveals Al speciations dominated by AlO4 groups, with minor but significant fractions of AlO5 (5-10%) and AlO6 (less than or similar to 3%) polyhedra present in all La2O3-Al2O3-SiO2 glasses; the amounts of Al-[5] and Al-[6] coordinations increase for decreasing molar fraction of Si. The MD simulations reproduce this compositional trend, with the fractional populations of AlOp groups (p = 4, 5, 6) according well with the experimental results. The modeled La speciations mainly involve LaO6 and LaO7 polyhedra, giving a range of average La3+ coordination numbers between 6.0 and 6.6; the latter increases slightly for decreasing Si content of the sample. Besides the expected bridging and non-bridging O species, minor contributions of oxygen triclusters (<= 9%) and free O-2(-) ions (<= 4%) are observed in all MD data. The glass structures exhibit a pronounced Al/Si disorder; the MD simulations reveal essentially random SiO4-SiO4, SiO4-AlOp and AlOp-AlOq (p, q = 4, 5, 6) associations, including significant amounts of AlO4-AlO4 contacts, regardless of the n(Al)/n(Si) molar ratio of the glass. The strong violation of Al-[4]-Al-[4] avoidance is verified by 2D Al-27 NMR experimentation that correlates double-quantum and single-quantum coherences, here applied for the first time to aluminosilicate glasses, and evidencing AlOp-AlOq connectivities dominated by AlO4-AlO4 and AlO4-AlO5 pairs. The potential bearings from distinct fictive temperatures of the experimental and modeled glass structures are discussed.

  • 82.
    Julin, Jan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Shiraiwa, Manabu
    Miles, Rachael E. H.
    Reid, Jonathan P.
    Poschl, Ulrich
    Riipinen, Ilona
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Mass Accommodation of Water: Bridging the Gap Between Molecular Dynamics Simulations and Kinetic Condensation Models2013Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, nr 2, s. 410-420Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The condensational growth of submicrometer aerosol particles to climate relevant sizes is sensitive to their ability to accommodate vapor molecules, which is described by the mass accommodation coefficient. However, the underlying processes are not yet fully understood. We have simulated the mass accommodation and evaporation processes of water using molecular dynamics, and the results are compared to the condensation equations derived from the kinetic gas theory to shed light on the compatibility of the two. Molecular dynamics simulations were performed for a planar TIP4P-Ew water surface at four temperatures in the range 268-300 K as well as two droplets, with radii of 1.92 and 4.14 nm at T = 273.15 K. The evaporation flux from molecular dynamics was found to be in good qualitative agreement with that predicted by the simple kinetic condensation equations. Water droplet growth was also modeled with the kinetic multilayer model KM-GAP of Shiraiwa et al. [Atmos. Chem. Phys. 2012, 12, 2777]. It was found that, due to the fast transport across the interface, the growth of a pure water droplet is controlled by gas phase diffusion. These facts indicate that the simple kinetic treatment is sufficient in describing pure water condensation and evaporation. The droplet size was found to have minimal effect on the value of the mass accommodation coefficient. The mass accommodation coefficient was found to be unity (within 0.004) for all studied surfaces, which is in agreement with previous simulation work. Additionally, the simulated evaporation fluxes imply that the evaporation coefficient is also unity. Comparing the evaporation rates of the mass accommodation and evaporation simulations indicated that the high collision flux, corresponding to high supersaturation, present in typical molecular dynamics mass accommodation simulations can under certain conditions lead to an increase in the evaporation rate. Consequently, in such situations the mass accommodation coefficient can be overestimated, but in the present cases the corrected values were still close to unity with the lowest value at approximate to 10.99.

  • 83.
    Jämbeck, Joakim P. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Computer Simulations of Heterogenous Biomembranes2014Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Molecular modeling has come a long way during the past decades and in the current thesis modeling of biological membranes is the focus. The main method of choice has been classical Molecular Dynamics simulations and for this technique a model Hamiltonian, or force field (FF), has been developed for lipids to be used for biological membranes. Further, ways of more accurately simulate the interactions between solutes and membranes have been investigated.

    A FF coined Slipids was developed and validated against a range of experimental data (Papers I-III). Several structural properties such as area per lipid, scattering form factors and NMR order parameters obtained from the simulations are in good agreement with available experimental data. Further, the compatibility of Slipids with amino acid FFs was proven. This, together with the wide range of lipids that can be studied, makes Slipids an ideal candidate for large-scale studies of biologically relevant systems.

    A solute's electron distribution is changed as it is transferred from water to a bilayer, a phenomena that cannot be fully captured with fixed-charge FFs.  In Paper IV we propose a scheme of implicitly including these effects with fixed-charge FFs in order to more realistically model water-membrane partitioning. The results are in good agreement with experiments in terms of free energies and further the differences between using this scheme and the more traditional approach were highlighted.

    The free energy landscape (FEL) of solutes embedded in a model membrane is explored in Paper V. This was done using biased sampling methods with a reaction coordinate that included intramolecular degrees of freedom (DoF). These DoFs were identified in different bulk liquids and then used in studies with bilayers. The FELs describe the conformational changes necessary for the system to follow the lowest free energy path. Besides this, the pitfalls of using a one-dimensional reaction coordinate are highlighted.

  • 84.
    Jämbeck, Joakim P. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Eriksson, Emma S. E.
    Laaksonen, Aatto
    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.
    Eriksson, Leif A.
    Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model2014Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 1, s. 5-13Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Liposomes are proposed as drug delivery systems and can in principle be designed so as to cohere with specific tissue types or local environments. However, little detail is known about the exact mechanisms for drug delivery and the distributions of drug molecules inside the lipid carrier. In the current work, a coarse-grained (CG) liposome model is developed, consisting of over 2500 lipids, with varying degrees of drug loading. For the drug molecule, we chose hypericin, a natural compound proposed for use in photodynamic therapy, for which a CG model was derived and benchmarked against corresponding atomistic membrane bilayer model simulations. Liposomes with 21-84 hypericin molecules were generated and subjected to 10 microsecond simulations. Distribution of the hypericins, their orientations within the lipid bilayer, and the potential of mean force for transferring a hypericin molecule from the interior aqueous droplet through the liposome bilayer are reported herein.

  • 85.
    Jämbeck, Joakim P. M.
    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.
    An extension and further validation of an all atomistic force field for biological membranes2012Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, nr 8, s. 2938-2948Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Biological membranes are versatile in composition and host intriguing molecular processes. In order to be able to study these systems, an accurate model Hamiltonian or force field (FF) is a necessity. Here, we report the results of our extension of earlier developed all-atomistic FF parameters for fully saturated phospholipids that complements an earlier parameter set for saturated phosphatidylcholine lipids (J. Phys. Chem. B, 2012, 116, 3164-3179). The FF, coined Slipids (Stockholm lipids), now also includes parameters for unsaturated phosphatidylcholine and phosphatidylethanolamine lipids, e.g., POPC, DOPC, SOPC, POPE, and DOPE. As the extended set of parameters is derived with the same philosophy as previously applied, the resulting FF has been developed in a fully consistent manner. The capabilities of Slipids are demonstrated by performing long simulations without applying any surface tension and using the correct isothermal-isobaric (NPT) ensemble for a range of temperatures and carefully comparing a number of properties with experimental findings. Results show that several structural properties are very well reproduced, such as scattering form factors, NMR order parameters, thicknesses, and area per lipid. Thermal dependencies of different thicknesses and area per lipid are reproduced as well Lipid diffusion is systematically slightly underestimated, whereas the normalized lipid diffusion follows the experimental trends. This is believed to be due to the lack of collective movement in the relatively small bilayer patches used Furthermore, the compatibility with amino acid FFs from the AMBER family is tested in explicit transmembrane complexes of the WALP23 peptide with DLPC and DOPC bilayers, and this shows that Slipids can be used to study more complex and biologically relevant systems.

  • 86.
    Jämbeck, Joakim P. M.
    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.
    Another piece of the membrane puzzle: extending slipids further2013Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, nr 1, s. 774-784Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To be able to model complex biological membranes in a more realistic manner, the force field Slipids (Stockholm lipids) has been extended to include parameters for sphingomyelin (SM), phosphatidylglycerol (PG), phosphatidylserine (PS) lipids, and cholesterol. Since the parametrization scheme was faithful to the scheme used in previous editions of Slipids, all parameters are consistent and fully compatible. The results of careful validation of a number of key structural properties for one and two component lipid bilayers are in excellent agreement with experiments. Potentials of mean force for transferring water across binary mixtures of lipids and cholesterol were also computed in order to compare water permeability rates to experiments. In agreement with experimental and simulation studies, it was found that the permeability and partitioning of water is affected by cholesterol in lipid bilayers made of saturated lipids to the largest extent. With the extensions of Slipids presented here, it is now possible to study complex systems containing many different lipids and proteins in a fully atomistic resolution in the isothermic-isobaric (NPT) ensemble, which is the proper ensemble for membrane simulations.

  • 87.
    Jämbeck, Joakim P. M.
    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.
    Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 10, s. 3164-3179Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions.

  • 88.
    Jämbeck, Joakim P. M.
    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.
    Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers2013Inngår i: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 4, nr 11, s. 1781-1787Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.

  • 89.
    Jämbeck, Joakim P. M.
    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.
    Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 13, s. 4677-4686Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We propose an effective and straightforward way of including atomic polarization in simulations of the partitioning of small molecules in inhomogenous media based on classical molecular dynamics with non-polarizable force fields. The approach presented here takes advantage of the relatively fast sampling of phase space obtained with additive force fields by adding the polarization effects afterwards. By using pre-polarized charges for the polar and non-polar phases together with a polarization correction term the effects of atomic polarization are effectively taken into account. The results show a clear improvement compared to using the more common setup with one set of charges obtained from gas phase ab initio calculations. It is shown that when proper measures are taken into account computer simulations with non-polarizable force fields are able to accurately determine water-membrane partitioning and preferential location of small molecules in the membrane interior. We believe that the approach presented here can be useful in rational drug design and in investigations of molecular mechanisms of anesthetic or toxic action.

  • 90.
    Jämbeck, Joakim P. M.
    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.
    Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration2014Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, nr 14, s. 3793-3804Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An approach to a straightforward reparametrization of the general AMBER force field (GAFF) for small organic solutes and druglike compounds is presented. The parametrization is based on specific pair interactions between the solvent and the solute, namely, the interactions between the constituting atoms of the solute and the oxygen of water were tuned in order to reproduce experimental hydration free energies for small model compounds. The key of the parametrization was to abandon the Lorentz-Berthelot combination rules for the van der Waals interactions. These parameters were then used for larger solutes in order to validate the newly derived pair interactions. In total close to 600 hydration free energies are computed, ranging from simple alkanes to multifunctional drug compounds, and compared to experimental data. The results show that the proposed parameters work well in describing the interactions between the solute and the solvent and that the agreement in absolute numbers is good. This modified version of GAFF is a good candidate for computing and predicting hydration free energies on a large scale, which has been a long-sought goal of computational chemists and can be used in rational drug design.

  • 91.
    Jämbeck, Joakim P. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Mocci, Francesca
    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.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Partial Atomic Charges and Their Impact on the Free Energy of Solvation2013Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, nr 3, s. 187-197Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Free energies of solvation (Delta G) in water and n-octanol have been computed for common drug molecules by molecular dynamics simulations with an additive fixed-charge force field. The impact of the electrostatic interactions was investigated by computing the partial atomic charges with four methods that all fit the charges from the quantum mechanically determined electrostatic potential (ESP). Due to the redistribution of electron density that occurs when molecules are transferred from gas phase to condensed phase, the polarization impact was also investigated. By computing the partial atomic charges with the solutes placed in a conductor-like continuum, the charges were effectively polarized to take the polarization effects into account. No polarization correction term or similar was considered, only the partial atomic charges. Results show that free energies are very sensitive to the choice of atomic charges and that Delta G can differ by several k(B)T depending on the charge computing method. Inclusion of polarization effects makes the solutes too hydrophilic with most methods and in vacuo charges make the solutes too hydrophobic. The restrained-ESP methods together with effectively polarized charges perform well in our test set and also when applied to a larger set of molecules. The effect of water models is also highlighted and shows that the conclusions drawn are valid for different three-point models. Partitioning between an aqueous and a hydrophobic phase is also described better if the two environment's polarization is taken into account, but again the results are sensitive to the charge calculation method. Overall, the results presented here show that effectively polarized charges can improve the description of solvating a drug-like molecule in a solvent and that the choice of partial atomic charges is crucial to ensure that molecular simulations produce reliable results.

  • 92.
    Kadir, Abdulkarim
    Stockholms universitet, Naturvetenskapliga fakulteten.
    Studies of new ternary hydrides with different d-electron content1994Doktoravhandling, med artikler (Annet vitenskapelig)
  • 93.
    Kamerlin, Shina C. L.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Warshel, Arieh
    Multiscale modeling of biological functions2011Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 22, s. 10401-10411Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent years have witnessed a tremendous explosion in computational power, which in turn has resulted in great progress in the complexity of the biological and chemical problems that can be addressed by means of all-atom simulations. Despite this, however, our computational time is not infinite, and in fact many of the key problems of the field were resolved long before the existence of the current levels of computational power. This review will start by presenting a brief historical overview of the use of multiscale simulations in biology, and then present some key developments in the field, highlighting several cases where the use of a physically sound simplification is clearly superior to a brute-force approach. Finally, some potential future directions will be discussed.

  • 94.
    Kapla, Jon
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Computer Simulations of Membrane–Sugar Interactions2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Carbohydrate molecules are essential parts of living cells. They are used as energy storage and signal substances, and they can be found incorporated in the cell membranes as attachments to glycoproteins and glycolipids, but also as free molecules. In this thesis the effect of carbohydrate molecules on phospholipid model membranes have been investigated by the means of Molecular Dynamics (MD) computer simulations.

    The most abundant glycolipid in nature is the non-bilayer forming monogalactosyldiacylglycerol (MGDG). It is known to be important for the membrane stacking typical for the thylakoid membranes in plants, and has also been found essential for processes related to photosynthesis. In Paper I, MD simulations were used to characterize structural and dynamical changes in a lipid bilayer when MGDG is present. The simulations were validated by direct comparisons between dipolar couplings calculated from the MD trajectories, and those determined from NMR experiments on similar systems. We could show that most structural changes of the bilayer were a consequence of lipid packing and the molecular shape of MGDG.

    In certain plants and organisms, the enrichment of small sugars such as sucrose and trehalose close to the membrane interfaces, are known to be one of the strategies to survive freezing and dehydration. The cryoprotecting abilities of these sugar molecules are long known, but the mechanisms at the molecular level are still debated. In Papers II–IV, the interactions of trehalose with a lipid bilayer were investigated. Calculations of structural and dynamical properties, together with free energy calculations, were used to characterize the effect of trehalose on bilayer properties. We could show that the binding of trehalose to the lipid bilayer follows a simple two state binding model, in agreement with recent experimental investigations, and confirm some of the proposed hypotheses for membrane–sugar interactions. The simulations were validated by dipolar couplings from our NMR investigations of TRH in a dilute liquid crystal (bicelles). Furthermore, the assumption about molecular structure being equal in the ordered and isotropic phases was tested and verified. This assumption is central for the interpretation of experimentally determined dipolar couplings in weakly ordered systems.

    In addition, a coarse grain model was used to tackle some of the problems with slow dynamics that were encountered for trehalose in interaction with the bilayer. It was found that further developments of the interaction models are needed to properly describe the membrane–sugar interactions. Lastly, from investigations of trehalose curvature sensing, we concluded that it preferably interacts in bilayer regions with high negative curvature.

  • 95.
    Kapla, Jon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Wohlert, Jakob
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 34, s. 22438-22447Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.

  • 96.
    Kapla, Jon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Dahlberg, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Molecular Dynamics Simulations of Membranes Composed of Glycolipids and Phospholipids2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 1, s. 244-252Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lipid membranes composed of 1,2-di-(9Z,12Z,15Z)-octade-catrienoyl-3-O-β-D-galactosyl-sn-glycerol or monogalactosyldiacylglycerol(MGDG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were studied by means of molecular dynamics (MD) computer simulations. Three lipid compositions were considered: 0%, 20%, and 45% MGDG (by mole) denoted as MG-0, MG-20, and MG-45, respectively. The article is focused on the calculation of NMR dipolar interactions, which were confronted with previously reported experimental couplings. Dynamical processes and orientational distributions relevant for the averaging of dipolar interactions were evaluated. Furthermore, several parameters important for characterization of the bilayer structure, molecular organization, and dynamics were investigated. In general, only a minor change in DMPC properties was observed upon the increased MGDG/DMPC ratio, whereas properties related to MGDG undergo a more pronounced change. This effect was ascribed to the fact that DMPC is a bilayer (Lα) forming lipid, whereas MGDG prefers a reverse hexagonal (HII) arrangement.

  • 97.
    Kapla, Jon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Wohlert, Jakob
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Molecular Dynamics Simulations of Membrane-Sugar Interactions2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 22, s. 6667-6673Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range W-TRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane sugar interactions.

  • 98.
    Karlsson, Torgny
    Stockholms universitet.
    Rotational Resonance in the Nuclear Magnetic Resonance of solids1999Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis presents new physical phenomena in the rotational resonance NMR of magic-angle spinning solids. The theory of a new class of nuclear spin echoes is developed. These spin echoes, excited by rotational resonance, demonstrate the general physical principle that time dependent dynamics may in some circumstances be reversed by external intervention. Rotational resonance echoes reveal specific properties of the relaxation behaviour of coupled spin-1/2 nuclei.

    New methods for efficient excitation of multiple-quantum coherence by rotational resonance echoes, are presented. These experiments are extended to also work with high efficiency at spinning frequencies not satisfying a rotational resonance condition. The above methods employ modest radio-frequency irradiation of the recoupled spin species and are feasible at high magic-angle spinning frequencies. These experiments are important as central building blocks in the development of methods for structure determination, such as the determination of internuclear distances and molecular torsion angles.

  • 99. Khasanova, Nellie R.
    et al.
    Van Tandeloo, Gustaaf
    Lebedev, Oleg I.
    Amelinx, S.
    Grippa, Alexander Yu
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Abakumov, Artiom M.
    Istomin, Sergey Ya.
    D'yachenko, Oleg G.
    Antipov, Eugeny V.
    A New Structure Type of the Ternary Sulfide Eu1.3Nb1.9S52002Inngår i: Journal of Solid State Chemistry, ISSN 1095-726X, Vol. 164, nr 2, s. 345-353Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure model for the Eu1.3Nb1.9S5 compound is determined based on high-resolution electron microscopy evidence. This compound crystallizes in a hexagonal unit cell with a=8.8732(8) Å and c=23.45(1) Å. Its structure is built up as an alternating sequence of trigonal-prismatic NbS2 layers of formula [Nb7S14] and [Nb(Eu3S4)2] slabs along the c-direction. In the [Nb(Eu3S4)2] block the stacking of two close-packed (Eu3S4) layers creates octahedral interstices formed by S atoms; these cavities are occupied by Nb cations. The model is compared with structures of other Eu-containing niobium sulfides, such as Eu0.167NbS2 and the misfit compound [(EuS)1.5]1.15NbS2.

  • 100.
    Klepsch, Mirjam
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Into the Membrane and Beyond: Improving Membrane Protein Over-Expression in Escherichia coli2011Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Membrane proteins fulfil a wide variety of essential functions in the cell and many are (potential) drug targets. Since their natural abundance is usually very low, most membrane proteins have to be over-expressed for functional and structural studies. T7 RNA polymerase (T7RNAP) based Escherichia coli strains, like BL21(DE3), are very popular protein production hosts. Unfortunately, over-expression of membrane proteins in E. coli is usually toxic to the cells. During my Ph.D. I have tried to understand the reasons for this toxicity by studying the consequences of membrane protein over-expression using a combination of proteomics and more focused biochemical and genetic methods. First, we had to improve the existing 2D BN/SDS-PAGE protocol to perform reliable comparative analysis of membrane proteomes. With the new protocol I have studied the effects of the expression of membrane proteins, including the human KDEL receptor, on BL21(DE3) and its derivatives, C41(DE3) and C43(DE3) (a.k.a. the Walker strains). The latter two were isolated for their improved membrane protein over-expression characteristics. Saturation of the Sec translocon, a cytoplasmic membrane associated protein conducting channel that mediates the insertion/biogenesis of membrane proteins, appeared to be the prime reason for the toxicity of membrane protein over-expression. Therefore, it was not surprising that we have identified mutations in the promoter governing the expression of the T7RNAP in the C41(DE3) and C43(DE3) strains that weaken it compared to the one in BL21(DE3). Based on this observation, we have engineered a plasmid (pLemo) with the gene encoding the natural inhibitor of T7RNAP, T7 lysozyme, under the control of the titratable rhamnose promoter. With the help of this plasmid the activity of the T7RNAP can be precisely set thereby avoiding saturation of the Sec translocon upon membrane protein over-expression. However, we have identified more changes in the Walker strains. Notable examples are the up regulation of peptide transporters in C41(DE3) and the expression of the Lon protease in C43(DE3). To study peptide import in E. coli I have characterized the in C41(DE3) strongly up regulated periplasmic binding protein OppA using a combination of biochemical and structural methods. The obtained data have resulted in many leads and ideas to further improve membrane protein over-expression yields in E. coli.

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