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  • 1.
    Ben-Naim, Arieh
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    The Kirkwood-Buff integrals for one-component liquids2008Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, nr 23, 234501- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Kirkwood-Buff integrals (KBIs) for one-component systems are calculated from either the pair correlation functions or from experimental macroscopic quantities. As in the case of mixtures, the KBIs provide important information on the local densities around a molecule. In the low density limit (rho -> 0) one can extract from the KBI some information on the strength of the intermolecular forces. No such information may be extracted from the KBIs at higher densities. We used experimental data on densities and isothermal compressibilities to calculate the KBIs for various liquids ranging from inert molecules, to hydrocarbons, alcohols, and liquid water.

  • 2.
    Brandt, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Fluctuating hydrodynamics simulations of coarse-grained lipid membranes under steady-state conditions and in shear flow2013Inngår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 88, nr 1, 012714- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The stochastic Eulerian-Lagrangian method (SELM) is used to simulate coarse-grained lipid membrane models under steady-state conditions and in shear flow. SELM is an immersed boundary method which combines the efficiency of particle-based simulations with the realistic solvent dynamics provided by fluctuating hydrodynamics. Membrane simulations in SELM are shown to give structural properties in accordance with equilibrium statistical mechanics and dynamic properties in agreement with previous simulations of highly detailed membrane models in explicit solvent. Simulations of sheared membranes are used to calculate surface shear viscosities and inter-monolayer friction coefficients. The membrane models are shown to be shear thinning under a wide range of applied shear rates.

  • 3. Brinkmann, Andreas
    et al.
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Estimating internuclear distances between half-integer quadrupolar nuclei by central-transition double-quantum sideband NMR spectroscopy2011Inngår i: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 89, nr 7, 892-899 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We demonstrate the estimation of homonuclear dipolar couplings, and thereby internuclear distances, between half-integer spin quadrupolar nuclei by central-transition (CT) double-quantum (2Q) sideband nuclear magnetic resonance (NMR) spectroscopy. It is shown that the rotor-encoded sideband amplitudes from CT 2Q coherences in the indirect dimension of the two-dimensional NMR spectrum are sensitive probes of the magnitude of the homonuclear dipolar coupling, but are significantly less affected by other NMR parameters such as the magnitudes and orientations of the electric field gradient tensors. Experimental results of employing the R2(2)(1)R2(2)(-1) recoupling sequence to the (11)B spin pair of bis(catecholato)diboron resulted in an estimation of the internuclear B-B distance as (169.6 +/- 3) pm, i.e., with a relative uncertainty of +/- 2%, and in excellent agreement with the distance of 167.8 pm determined by single-crystal X-ray diffraction.

  • 4.
    Cheung, Ocean
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Bacsik, Zoltán
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Krokidas, Panagiotis
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Mace, Amber
    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.
    Hedin, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    K+ Exchanged Zeolite ZK-4 as a Highly Selective Sorbent for CO22014Inngår i: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 30, nr 32, 9682-9690 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Adsorbents with high capacity and selectivity for adsorption of CO2 are currently being investigated for applications in adsorption-driven separation of CO2 from flue gas. An adsorbent with a particularly high CO2-over-N-2 selectivity and high capacity was tested here. Zeolite ZK-4 (Si:Al similar to 1.3:1), which had the same structure as zeolite A (LTA), showed a high CO2 capacity of 4.85 mmol/g (273 K, 101 kPa) in its Na+ form. When approximately 26 at % of the extraframework cations were exchanged for K+ (NaK-ZK-4), the material still adsorbed a large amount of CO2 (4.35 mmol/g, 273 K, 101 kPa), but the N-2 uptake became negligible (<0.03 mmol/g, 273 K, 101 kPa). The majority of the CO2 was physisorbed on zeolite ZK-4 as quantified by consecutive volumetric adsorption measurements. The rate of physisorption of CO2 was fast, even for the highly selective sample. The molecular details of the sorption of CO2 were revealed as well. Computer modeling (Monte Carlo, molecular dynamics simulations, and quantum chemical calculations) allowed us to partly predict the behavior of fully K+ exchanged zeolite K-ZK-4 upon adsorption of CO2 and N-2 for Si:Al ratios up to 4:1. Zeolite K-ZK-4 with Si:Al ratios below 23:1 restricted the diffusion of CO2 and N-2 across the cages. These simulations could not probe the delicate details of the molecular sieving of CO2 over N-2. Still, this study indicates that zeolites NaK-ZK-4 and K-ZK-4 could be appealing adsorbents with high CO2 uptake (similar to 4 mmol/g, 101 kPa, 273 K) and a kinetically enhanced CO2-over-N-2 selectivity.

  • 5.
    Dahlberg, Martin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Arnold, Maliniak
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Mennucci, Benedetta
    Department of Chemistry, University of Pisa.
    Marini, Alberto
    Department of Chemistry, University of Pisa.
    Quantum Chemical Modeling of the Cardiolipin Headgroup2010Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, nr 12, 4375-4387 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cardiolipin is a key lipid component in many biological membranes. Proton conduction and proton−lipid interactions on the membrane surface are thought to be central to mitochondrial energy production. However, details on the cardiolipin headgroup structure are lacking and the protonation state of this lipid at physiological pH is not fully established. Here we present ab initio DFT calculations of the cardiolipin (CL) headgroup and its 2′-deoxy derivative (dCL), with the aim of establishing a connection between structure and acid−base equilibrium in CL. Furthermore, we investigate the effects of solvation on the molecular conformations. In our model, both CL and dCL showed a significant gap between the two pKa values, with pKa2 above the physiological range, and intramolecular hydrogen bonds were found to play a central role in the conformations of both molecules. This behavior was also observed experimentally in CL. Structures derived from the DFT calculations were compared with those obtained experimentally, collected for CL in the Protein Data Bank, and conformations from previous as well as new molecular dynamics simulations of cardiolipin bilayers. Transition states for proton transfer in CL were investigated, and we estimate that protons can exchange between phosphate groups with an approximate 4−5 kcal/mol barrier. Computed NMR and IR spectral properties were found to be in reasonable agreement with experimental results available in the literature.

  • 6.
    Dahlberg, Martin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Mechanical properties of coarse grained bilayers formed by cardiolipin and zwitterionic lipids2010Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, nr 5, 1638-1649 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lipid shape and charge are connected with the physical properties and biological function of membranes. Cardiolipin, a double phospholipid with four chains and the potential of changing its charge with pH, is crucially connected with mitochondrial inner membrane shape, and recent experiments suggest that local pH changes allow highly curved local geometries. Here, we use a coarse grained molecular dynamics model to investigate the mechanical properties of cardiolipin bilayers, systematically varying the headgroup charge and composition in mixtures with zwitterionic DOPC or DOPE. Low cardiolipin charge, corresponding to low pH, was found to induce bending moduli on the order of kBT, and curved microdomains. On the length scale investigated, in contrast to continuum theoretical models, we found the area modulus and bending modulus to be inversely correlated for mixtures of cardiolipin and DOPC/DOPE, explainable by changes in the effective head group volume.

  • 7.
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    The split network analysis for exploring composition-structure correlations in multi-component glasses: I. Rationalizing bioactivity-composition trends of bioglasses2011Inngår i: Journal of Non-Crystalline Solids, ISSN 0022-3093, E-ISSN 1873-4812, Vol. 357, nr 6, 1595-1602 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a strategy, referred to as “split network” analysis, for assessing the average network polymerization (r(F)) and mean number of bridging oxygen (BO) atoms ( (N) over bar (F)(BO)) for each individual network former F in multi-component oxide-based glasses, primarily targeting those involving Al, B, P and Si. This requires a priori knowledge about the parameters (r(F), (N) over bar (F)(BO)) of all network builders, but one, whose values are deduced by the split network procedure. We illustrate split-network concepts for establishing composition/structure/bioactivity correlations in Na-Ca-Si-P-O glasses. The cooperating influences on the bioactivity from the average polymerization degree of the silicate network and the amounts of orthophosphate and sodium ions are discussed.

  • 8.
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Two-dimensional MAS NMR correlation protocols involving double-quantum filtering of quadrupolar spin-pairs2010Inngår i: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 204, nr 1, 99-110 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Three two-dimensional (2D) NMR homonuclear correlation techniques invoking double-quantum (2Q) filtration of the central transitions of half-integer spins are evaluated numerically and experimentally. They correlate directly detected single-quantum (1Q) coherences in the t(2) domain with either of 1Q, two-spin 2Q or single-spin multiple-quantum coherence-evolutions in the indirect (t(1)) dimension. We employ experimental Na-23 and Al-22 NMR on sodium sulfite and the natural mineral sillimanite (SiAl2O5), in conjunction with simulated 2D spectra from pairs of dipolar-recoupled spins-3/2 and 5/2 at different external magnetic fields, to compare the correlation strategies from the viewpoints of 2D spectral resolution, signal sensitivity, implementational aspects and their relative merits for establishing internuclear proximities and quadrupolar tensor orientations.

  • 9.
    Edén, Mattias
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Sundberg, Peter
    Stålhandske, Christina
    The split network analysis for exploring composition-structure correlations in multi-component glasses: II. Multinuclear NMR studies of alumino-borosilicates and glass-wool fibers2011Inngår i: Journal of Non-Crystalline Solids, ISSN 0022-3093, E-ISSN 1873-4812, Vol. 357, nr 6-7, 1587-1594 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The preceding part [M. Eden, J. Non.-Cryst. Solids, 357, (2011) 1595-1602] introduced the “split network” strategy for estimating the network polymerization degree (r(A)) and mean number of bridging oxygen (BO) atoms ((N) over bar (A)(BO)) for a network former A, given that these parameters are known for all other network builders in the multi-component oxide glass. However, as the detailed ordering of BO and non-bridging oxygen (NBO) species is often difficult to assess experimentally, we summarize some “rules of thumb” for predicting the coordination number and tendency to accept NBO ions for Al(3+), B(3+), Si(4+) and P(5+) cations: they are helpful in scenarios devoid of experimental data. Using the parameters r and (N) over bar (BO), we present expressions for the BO/NBO distributions among tetrahedrally coordinated cations, as predicted from the binary and random models. Multinuclear (11)B, (27)Al and (29)Si solid-state NMR is exploited to derive the split network representations of a set of Na-Ca-(Al)-(B)-Si-O glasses. These results are subsequently used to gain structural insight into two commercial glass-wool fibers that constitute alumino-borosilicate networks modified by Na(+), K(+), Ca(2+) and Mg(2+) ions.

  • 10. Egorov, Andrei V.
    et al.
    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.
    Molecular Dynamics Simulation Study of Glycerol-Water Liquid Mixtures2011Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, nr 49, 14572-14581 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To study the effects of water on conformational dynamics of polyalcohols, Molecular Dynamics simulations of glycerol water liquid mixtures have been carried out at different concentrations: 42.9 and 60.0 wt 96 of glycerol, respectively. On the basis of the analysis of backbone conformer distributions, it is found that the surrounding water molecules have a large impact on the populations of the glycerol conformers. While the local structure of water in the liquid mixture is surprisingly close to that in pure liquid water, the behavior of glycerols can be divided into three different categories where roughly 25% of them occur in a structure similar to that in pure liquid of glycerol, ca. 25% of them exist as monomers, solvated by water, and the remaining 50% of glycerols in the mixture form H-bonded strings as. remains of the glycerol H-bond network. The typical glycerol H-bond network still exists even at the lower concentration of 40 wt % of glycerol. The microheterogeneity of water glycerol mixtures is analyzed using time-averaged distributions of the sizes of the water aggregates. At 40 wt % of glycerol, the cluster sizes from 3 to 10 water molecules are observed. The increase of glycerol content causes a depletion of clusters leading to smaller 3-5 molecule clusters domination. Translational diffusion coefficients have been calculated to study the dynamical behavior of both glycerol and water molecules. Rotational-reorientational motion is studied both in overall and in selected substructures on the basis of time correlation functions. Characteristic time scales for different motional modes are deduced on the basis of the calculated correlation times. The general conclusion is that the presence of water increases the overall mobility of glycerol, while glycerol slows the mobility of water.

  • 11.
    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, e115856- s.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.

  • 12.
    Gebauer, Denis
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Gunawidjaja, Philips N.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Ko, J. Y. Peter
    Bacsik, Zoltan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Aziz, Baroz
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Liu, Lijia
    Hu, Yongfeng
    Bergström, Lennart
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Tai, Cheuk-Wai
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Sham, Tsun-Kong
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Hedin, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Proto-Calcite and Proto-Vaterite in Amorphous Calcium Carbonates2010Inngår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 49, nr 47, 8889-8891 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Amorphous order: Amorphous calcium carbonates (ACC) have an intrinsic structure relating to the crystalline polymorphs of calcite and vaterite. The proto-crystalline structures of calcite and vaterite (pc-ACC and pv-ACC) are analyzed by NMR (see picture), IR, and EXAFS spectroscopy, which shows that the structuring of ACC relates to the underlying pH-dependent equilibria.

  • 13.
    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, 1376-1399 s.Artikkel 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.

  • 14.
    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, 142-147 s.Artikkel 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.

  • 15.
    Huang, Congcong
    et al.
    Stanford.
    Wikfeldt, Kjartan Thor
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Tokushima, Takashi
    SPring-8.
    Nordlund, Dennis
    Stanford.
    Harada, Yoshi
    Bergmann, Uwe
    Stanford.
    Niebuhr, M.
    Stanford.
    Weiss, T.M.
    Stanford.
    Horikawa, Y.
    SPring-8.
    Leetmaa, Mikael
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Ljungberg, Mathias P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Takahashi, Osamu
    University of Hiroshima.
    Lentz, Annika
    Linköpings Universitet.
    Ojamäe, Lars
    Linköpings Universitet.
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Shin, Shik
    Tokyo University.
    Pettersson, Lars G.M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nilsson, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Reply to Soper "Fluctuations in water around a bimodal distribution of local hydrogen bonded structural motifs"2010Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, nr 12, E45- s.Artikkel i tidsskrift (Fagfellevurdert)
  • 16.
    Hålenius, Ulf
    et al.
    Naturhistoriska riksmuseet.
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Skogby, Henrik
    Naturhistoriska riksmuseet.
    Nazzareni, Sabrina
    Perugia University.
    Kristiansson, Per
    Lunds universitet.
    Resmark, Jeppa
    Lunds universitet.
    Coordination of Boron in Nominally Boron-Free Rock Forming Silicates: Evidence for Incorporation of BO3 groups in Clinopyroxene2010Inngår i: Geochimica et Cosmochimica Acta, ISSN 0016-7037, E-ISSN 1872-9533, Vol. 74, 5672-5679 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To explore mechanisms of B-incorporation in common chain silicates we have investigated synthetic diopside samples produced under boron-saturated conditions by 11B and 29Si magic-angle spinning (MAS) NMR and single-crystal NRA, FTIR, EMP and XRD/SREF techniques. Our samples contain 0.14–0.65 wt.% B2O3. NMR reveals that B is predominantly present in trigonal coordination in the clinopyroxene structure. This observation is supported by vibrational bands characteristic for B–O stretching in BO3 groups in the range 1250–1400 cm−1 in polarised single crystal FTIR-spectra. Single crystal structure refinements suggest that boron replaces Si at the T site. Combined, these results suggest that boron replacement for Si at the T-site leads to disruption of one of the T–O bonds of the nominal clinopyroxene structure resulting in replacement of SiO4 tetrahedra by BO3 groups. Our results show that high concentrations of boron can be incorporated in the nominally boron-free diopside. Elevated B-concentrations in the present calcic clinopyroxenes are accompanied by modifications of the diopside crystal structure involving the breaking of one T–O bond and simultaneous formation of vacancies at the octahedral M2 site. These structural modifications destabilize the structure and constitute thereby limiting factors for incorporating higher boron concentrations in diopside.

     

     

  • 17.
    Iftekhar, Shahriar
    et al.
    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.
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Composition–property relationships of the La2O3–Al2O3–SiO2 glass system2010Inngår i: Journal of Non-Crystalline Solids, ISSN 0022-3093, E-ISSN 1873-4812, Vol. 356, nr 20-22, 1043-1048 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We report physical properties of density, glass transition temperature, Vickers hardness and refractive index for 15 La–Al–Si–O glasses within the compositional region 10–28 mol% La2O3, 11–30% Al2O3 and 45–78% SiO2. The glass transition temperature varies only slightly between 871 and 883 °C. Both the density (3.25–4.33 g cm−3) and refractive index (1.59–1.70) display similar compositional dependencies and are primarily dictated by the La2O3 content. The hardness (6.4–9.0 GPa) increases with decreasing SiO2 content and to a minor extent also with the amount of La2O3 of the glass. The physical properties, in particular the hardness, are discussed with reference to glass structure. The similarity in the observed properties between the present oxide-based glasses and those of analogous rare-earth (RE) element-containing RE–Si–(Al)–O–N oxynitride glasses is highlighted and discussed in relation to the apparent, but hitherto largely neglected, role of RE-ions to primarily control many enhanced physical properties of oxynitride glasses.

  • 18.
    Iftekhar, Shahriar
    et al.
    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.
    Gunawidjaja, Philips N.
    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.
    Glass Formation and Structure–Property–Composition Relations of theRE2O3–Al2O3–SiO2 (RE = La, Y, Lu, Sc) Systems2011Inngår i: Journal of The American Ceramic Society, ISSN 0002-7820, E-ISSN 1551-2916, Vol. 94, nr 8, 2429-2435 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We report the glass-forming regions of the ternary Lu2O3–Al2O3–SiO2 and Sc2O3–Al2O3–SiO2 systems. The density, molarvolume, compactness, Vickers hardness, refractive index, aswell as the glass transition (Tg) and crystallization temperatureare compared for two series of RE–Al–Si–O (RE=La, Y, Lu,Sc) glasses that display a constant molar ratio nAl/nSi=1.00,whereas nRE/nSi is equal to either 0.62 or 0.94. Several glassproperties scale roughly linearly with the cation field strength(CFS) of the rare-earth (RE3+) ion, except for the Tg values ofthe Sc-bearing glasses that are significantly lower than expected.Magic-angle spinning 29Si and 27Al nuclear magneticresonance (NMR) reveal enhanced network disorder and increasedrelative populations of AlO5 and AlO6 polyhedra in thealuminosilicate glasses for increasing RE3+ CFS, but overallsimilar Si and Al local environments (chemical shifts and quadrupolarcouplings) in all samples associated with a constant nRE/nSi ratio, except for unexpectedly shielded 29Si NMR signalsobserved from the Sc–Al–Si–O glasses.

  • 19.
    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, 18394-18406 s.Artikkel 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.

  • 20.
    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, 18269-18272 s.Artikkel 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.

  • 21.
    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)
  • 22.
    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)
  • 23.
    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, 15866-15878 s.Artikkel 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.

  • 24.
    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, 5-13 s.Artikkel 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.

  • 25.
    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, 2938-2948 s.Artikkel 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.

  • 26.
    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, 774-784 s.Artikkel 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.

  • 27.
    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, 3164-3179 s.Artikkel 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.

  • 28.
    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, 1781-1787 s.Artikkel 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.

  • 29.
    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, 4677-4686 s.Artikkel 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.

  • 30.
    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, 3793-3804 s.Artikkel 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.

  • 31.
    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, 187-197 s.Artikkel 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.

  • 32. 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, 13-21 s.Artikkel 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.

  • 33.
    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, 1896-1905 s.Artikkel 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.

  • 34.
    Korolev, Nikolai
    et al.
    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.
    Cation-indiced polyelectrolyte-polyelectrolyte attraction in solutions of DNA and nucleosome core particles2010Inngår i: Journal of Colloid and Interface Science, ISSN 0021-9797, E-ISSN 1095-7103, Vol. 158, 32-47 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The paper reviews our current studies on the experimentally induced cation compaction and aggregation in solutions of DNA and nucleosome core particles and the theoretical modelling of these processes using coarse-grained continuum models with explicit mobile ions and with all-atom molecular dynamics (MD) simulations. Recent experimental results on DNA condensation by cationic oligopeptides and the effects of added salt are presented. The results of MD simulations modelling DNA–DNA attraction due to the presence of multivalent ions including the polyamine spermidine and fragments of histone tails, which exhibit bridging between adjacent DNA molecules, are discussed. Experimental data on NCP aggregation, using recombinantly prepared systems are summarized. Literature data and our results of studying of the NCP solutions are compared with predictions of coarse-grained MD simulations, including the important ion correlation as well as bridging mechanisms. The importance of the results to chromatin folding and aggregation is discussed.

  • 35. Korolev, Nikolay
    et al.
    Fan, Yanping
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Nordenskioeld, Lars
    Modelling chromatin structure and dynamics: status and prospects2012Inngår i: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 22, nr 2, 151-159 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The packaging of genomic DNA into chromatin in the eukaryotic cell nucleus demands extensive compaction. This requires attractive nucleosome-nucleosome interactions to overcome repulsion between the negatively charged DNA segments as well as other constraints. At the same time, DNA must be dynamically accessible to the cellular machinery that operates on it. Recent progress in the experimental characterisation of the higher order structure and dynamics of well-defined chromatin fibres has stimulated the attempts at theoretical description of chromatin and the nucleosome. Here we review the present status of chromatin Modelling, with particular emphasis on coarse-grained computer simulation models, the role of electrostatic interactions, and discuss future perspectives in the field.

  • 36. Korolev, Nikolay
    et al.
    Luo, Di
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Nordenskiöld, Lars
    A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo2014Inngår i: Polymers, ISSN 2073-4360, E-ISSN 2073-4360, Vol. 6, nr 6, 1655-1675 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG) approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra-and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD) simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1-100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

  • 37. Korolev, Nikolay
    et al.
    Yu, Hang
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Nordenskiöld, Lars
    Molecular Dynamics Simulations Demonstrate the Regulation of DNA-DNA Attraction by H4 Histone Tail Acetylations and Mutations2014Inngår i: Biopolymers, ISSN 0006-3525, E-ISSN 1097-0282, Vol. 101, nr 10, 1051-1064 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histone tails with DNA, all-atom molecular dynamics (MD) simulations were carried out for systems of four DNA 22-mers in the presence of 20 or 16 short fragments of the H4 histone tail (variations of the 16-23 a. a. KRHRKVLR sequence, as well as the unmodified fragment a. a. 13-20, GGAKRHRK). This setup with high DNA concentration, explicit presence of DNA-DNA contacts, presence of unstructured cationic peptides (histone tails) and K+ mimics the conditions of eukaryotic chromatin. A detailed account of the DNA interactions with the histone tail fragments, K+ and water is presented. Furthermore, DNA structure and dynamics and its interplay with the histone tail fragments binding are analysed. The charged side chains of the lysines and arginines play major roles in the tailmediated DNA-DNA attraction by forming bridges and by coordinating to the phosphate groups and to the electronegative sites in the minor groove. Binding of all species to DNA is dynamic. The structure of the unmodified fully-charged H4 16-23 a. a. fragment KRHRKVLR is dominated by a stretched conformation. The H4 tail a. a. fragment GGAKRHRK as well as the H4 Lys16 acetylated fragment are highly flexible. The present work allows capturing typical features of the histone tail-counterionDNA structure, interaction and dynamics.

  • 38.
    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

  • 39. Kruk, D.
    et al.
    Hoffmann, S. K.
    Goslar, J.
    Lijewski, S.
    Kubica-Misztal, A.
    Korpala, A.
    Oglodek, I.
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Roessler, E. A.
    Moscicki, J.
    ESR lineshape and H-1 spin-lattice relaxation dispersion in propylene glycol solutions of nitroxide radicals - Joint analysis2013Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 139, nr 24, 244502- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Electron Spin Resonance (ESR) spectroscopy and Nuclear Magnetic Relaxation Dispersion (NMRD) experiments are reported for propylene glycol solutions of the nitroxide radical: 4-oxo-TEMPO-d(16) containing N-15 and N-14 isotopes. The NMRD experiments refer to H-1 spin-lattice relaxation measurements in a broad frequency range (10 kHz-20 MHz). A joint analysis of the ESR and NMRD data is performed. The ESR lineshapes give access to the nitrogen hyperfine tensor components and the rotational correlation time of the paramagnetic molecule. The NMRD data are interpreted in terms of the theory of paramagnetic relaxation enhancement in solutions of nitroxide radicals, recently presented by Kruk et al. [J. Chem. Phys. 138, 124506 (2013)]. The theory includes the effect of the electron spin relaxation on the H-1 relaxation of the solvent. The H-1 relaxation is caused by dipole-dipole interactions between the electron spin of the radical and the proton spins of the solvent molecules. These interactions are modulated by three dynamic processes: relative translational dynamics of the involved molecules, molecular rotation, and electron spin relaxation. The sensitivity to rotation originates from the non-central positions of the interacting spin in the molecules. The electronic relaxation is assumed to stem from the electron spin-nitrogen spin hyperfine coupling, modulated by rotation of the radical molecule. For the interpretation of the NMRD data, we use the nitrogen hyperfine coupling tensor obtained from ESR and fit the other relevant parameters. The consistency of the unified analysis of ESR and NMRD, evaluated by the agreement between the rotational correlation times obtained from ESR and NMRD, respectively, and the agreement of the translation diffusion coefficients with literature values obtained for pure propylene glycol, is demonstrated to be satisfactory.

  • 40. Kruk, D.
    et al.
    Korpala, A.
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Roessler, E. A.
    Moscicki, J.
    H-1 relaxation dispersion in solutions of nitroxide radicals: Effects of hyperfine interactions with N-14 and N-15 nuclei2012Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, nr 4, 044512- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    H-1 relaxation dispersion of decalin and glycerol solutions of nitroxide radicals, 4-oxo-TEMPO-d(16)-N-15 and 4-oxo-TEMPO-d(16)-N-14 was measured in the frequency range of 10 kHz-20 MHz (for H-1) using STELAR Field Cycling spectrometer. The purpose of the studies is to reveal how the spin dynamics of the free electron of the nitroxide radical affects the proton spin relaxation of the solvent molecules, depending on dynamical properties of the solvent. Combining the results for both solvents, the range of translational diffusion coefficients, 10(-9)-10(-11) m(2)/s, was covered (these values refer to the relative diffusion of the solvent and solute molecules). The data were analyzed in terms of relaxation formulas including the isotropic part of the electron spin - nitrogen spin hyperfine coupling (for the case of N-14 and N-15) and therefore valid for an arbitrary magnetic field. The influence of the hyperfine coupling on H-1 relaxation of solvent molecules depending on frequency and time-scale of the translational dynamics was discussed in detail. Special attention was given to the effect of isotope substitution (N-14/N-15). In parallel, the influence of rotational dynamics on the inter-molecular (radical - solvent) electron spin - proton spin dipole-dipole coupling (which is the relaxation mechanism of solvent protons) was investigated. The rotational dynamics is of importance as the interacting spins are not placed in the molecular centers. It was demonstrated that the role of the isotropic hyperfine coupling increases for slower dynamics, but it is of importance already in the fast motion range (10(-9)m(2)/s). The isotope effects is small, however clearly visible; the H-1 relaxation rate for the case of N-15 is larger (in the range of lower frequencies) than for N-14. It was shown that when the diffusion coefficient decreases below 5 x 10(-11) m(2)/s electron spin relaxation becomes of importance and its role becomes progressively more significant when the dynamics slows done. As far as the influence of the rotational dynamics is concerned, it was show that this process is of importance not only in the range of higher frequencies (like for diamagnetic solutions) but also at low and intermediate frequencies.

  • 41. Kruk, D.
    et al.
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Tipikin, S.
    Freed, J. H.
    Moscicki, M.
    Mielczarek, A.
    Port, M.
    Joint analysis of ESR lineshapes and (1)H NMRD profiles of DOTA-Gd derivatives by means of the slow motion theory2011Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, nr 2, 024508- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Swedish slow motion theory [Nilsson and Kowalewski, J. Magn. Reson. 146, 345 (2000)] applied so far to Nuclear Magnetic Relaxation Dispersion (NMRD) profiles for solutions of transition metal ion complexes has been extended to ESR spectral analysis, including in addition g-tensor anisotropy effects. The extended theory has been applied to interpret in a consistent way (within one set of parameters) NMRD profiles and ESR spectra at 95 and 237 GHz for two Gd(III) complexes denoted as P760 and P792 (hydrophilic derivatives of DOTA-Gd, with molecular masses of 5.6 and 6.5 kDa, respectively). The goal is to verify the applicability of the commonly used pseudorotational model of the transient zero field splitting (ZFS). According to this model the transient ZFS is described by a tensor of a constant amplitude, defined in its own principal axes system, which changes its orientation with respect to the laboratory frame according to the isotropic diffusion equation with a characteristic time constant (correlation time) reflecting the time scale of the distortional motion. This unified interpretation of the ESR and NMRD leads to reasonable agreement with the experimental data, indicating that the pseudorotational model indeed captures the essential features of the electron spin dynamics.

  • 42.
    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, 85-106 s.Kapittel i bok, del av antologi (Fagfellevurdert)
  • 43. Larin, Alexander V.
    et al.
    Mace, Amber
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Rybakov, Andrey A.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Carbonate "door" in the NaKA zeolite as the reason of higher CO2 uptake relative to N-22012Inngår i: Microporous and Mesoporous Materials, ISSN 1387-1811, E-ISSN 1873-3093, Vol. 162, 98-104 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Theoretical calculations are performed on a model zeolite A where sodium ions have successively been exchanged with potassium. Using both isolated cluster and periodic DFT calculations, we made an attempt to explain how the chemisorbed carbonate species in the material contribute to the exceptionally high CO2 over N-2 selectivity of nearly 200 found in recent experiments [Liu et al. [1]] with the zeolite NaKA as adsorbent to capture and separate carbon dioxide from a gas mixture containing nitrogen. We have shown that the high carbonate forming at the potassium positions in the 8R windows (KII) results in a larger 8R window diameter potentially enhancing the CO2 uptake if adsorption is measured for individual gases.

  • 44. Lee, Scott A.
    et al.
    Tao, Nong-Jian
    Rupprecht, Allan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    A Raman scattering study of the interactions of DNA with its water of hydration2013Inngår i: Journal of Biomolecular Structure and Dynamics, ISSN 0739-1102, E-ISSN 1538-0254, Vol. 31, nr 11, 1337-1342 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Raman spectroscopy is used to probe the nature of the hydrogen bonds which hold the water of hydration to DNA. The approximate to 3450cm(-1) molecular O-H stretching mode shows that the first six water molecules per base pair of the primary hydration shell are very strongly bound to the DNA. The observed shift in the peak position of this mode permits a determination of the length of the hydrogen bonds for these water molecules. These hydrogen bonds appear to be about 0.3 angstrom shorter than the hydrogen bonds in bulk water. The linewidth of this mode shows no significant changes above water contents of about 15 water molecules per base pair. This technique of using a vibrational spectroscopy to obtain structural information about the hydration shells of DNA could be used to study the hydration shells of other biomolecules.

  • 45. Lu, Hui
    et al.
    Tu, Yaoquan
    Lin, Xian
    Fang, Bin
    Luo, Duanbin
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Effects of laser irradiation on the structure and optical properties of ZnO thin films2010Inngår i: Materials letters (General ed.), ISSN 0167-577X, E-ISSN 1873-4979, Vol. 64, nr 19, 2072-2075 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effects of laser irradiation on the surface microstructure and optical properties of ZnO films deposited on glass substrates were investigated experimentally and compared with those of thermal annealing. X-ray diffraction (XRD) and atomic force microscopy (AFM) measurements showed that the irradiation treatment with an Ar+ laser of 514 nm for 5 min improves the crystalline quality of ZnO thin films through increasing the grain size and enhancing the c-axis orientation, with the effects similar to those of the thermal annealing at 500 degrees C for 1 h. Laser irradiation was found to be more effective both for the relaxation of the residual compressive stress in the as-grown films and for the modification of the surface morphology. A significant increase in the UV absorption and a widening in the optical band-gap of the films were also observed after laser irradiation.

  • 46. Lu, Hui
    et al.
    Zheng, Zhi-Jia
    Lin, Xian
    Xu, Fei
    Bi, Han
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Grain growth behavior, surface morphology evolution, structures, and optical properties of ZnO thin films prepared by RF reactive magnetron sputtering2014Inngår i: Journal of Optoelectronics and Advanced Materials, ISSN 1454-4164, E-ISSN 1841-7132, Vol. 16, nr 1-2, 170-175 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    ZnO thin films were prepared by radio frequency (RF) reactive magnetron sputtering at varying deposition conditions. The effects of RF power (from 40 to 90 W) and substrate temperature (from 100 to 200 degrees C) on the grain growth behavior, surface morphology evolution, and the structural and optical properties of the films were investigated. Atomic force microscopy (AFM) measurements confirmed that the grain size and surface roughness depend mainly on the RF power and increase with increasing it at the initial deposition stage of 5 s, and are strongly affected by the substrate temperature and increase with increasing it at the final deposition stage of 45 min. The influence of both the deposition parameters on the surface structure of the ZnO films at different deposition stages and the mechanism concerning this influence were discussed. The X-ray diffraction (XRD) and optical absorption spectra analysis indicated that all the films deposited for 45 min are in the state of the compressive stress and exhibit polycrystalline nature with the (002) preferential orientation, and they have high optical transparency in the visible range and sharp absorption edges around the wavelength 360 nm corresponding to the ZnO exciton. With the increase of the RF power and substrate temperature, the grain size increases, the residual compressive stress relaxes, and the optical band gaps broaden. In comparison with the RF power, the substrate temperature has more evident influence on the microstructure of the ZnO thin films.

  • 47.
    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, 43-56 s.Artikkel 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.

  • 48.
    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, 20572-20582 s.Artikkel 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.

  • 49.
    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, 5701-5715 s.Artikkel 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.

  • 50.
    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, 833-844 s.Artikkel 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.

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