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  • 1.
    Dziedzic, Pawel
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Schyman, Patric
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Kullberg, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Córdova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Highly enantioselective organocatalytic addition of aldehydes to N-(phenylmethylene)benzamides: Asymmetric synthesis of the paclitaxel side chain and its analogues2009Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, nr 16, 4044-4048 s.Artikkel i tidsskrift (Fagfellevurdert)
  • 2.
    Eden, Mattias
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Grins, Jekabs
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för oorganisk kemi.
    Jansson, Kjell
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Shen, Zhijian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    Al and O substitutions in BaS-phases, Ba2AlxSi12-xN16-xO2+x: A TEM, XRD and solid-state NMR study2008Inngår i: Solid State Sciences, ISSN 1293-2558, E-ISSN 1873-3085, Vol. 10, nr 1, 50-60 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In a series of Ba-based oxonitrido-silicate S-phases (Ba2AlxSi12-xN16-xO2+x) spanning a compositional range up to x approximate to 3, we examine the incorporation of Al and O by Si-29 and Al-27 magic-angle spinning (MAS) solid state nuclear magnetic resonance (NMR) and Al-27 triple-quantum MAS (3QMAS). The 3QMAS spectra reveal Al-27 signals from two distinct structural environments, assigned to AlN4 or AlN3O tetrahedra, respectively, and with their relative amounts depending on the S-phase substitution parameter x. Si-29 NMR show variable fractions of SiN4 and SiN3O environments. The NMR results accord overall with a structural substitution model for which O enters at one crystallographic position (occupied according to N4-xOx), in conjunction with a random Al for Si substitution at two distinct crystallographic positions. This leads to S-phase frameworks built from SiN4, SiN3O, AlN4 and AlN3O tetrahedra.

  • 3. Huang, Congcong
    et al.
    Wikfeldt, K. Thor
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Tokushima, Takashi
    Nordlund, Dennis
    Harada, Yoshi
    Bergmann, Uwe
    Niebuhr, Marc
    Weiss, T. M.
    Horikawa, Yoshi
    Leetmaa, Mikael
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Ljungberg, Mathias P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Takahashi, Osamu
    Lenz, Annika
    Ojamäe, Lars
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Shin, Shik
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nilsson, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    The Inhomogeneous Structure of Water at Ambient Conditions2009Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, 15214-15218 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Small-angle X-ray scattering (SAXS) is used to demonstrate the presence of density fluctuations in ambient water on a physical length-scale of ≈1 nm; this is retained with decreasing temperature while the magnitude is enhanced. In contrast, the magnitude of fluctuations in a normal liquid, such as CCl4, exhibits no enhancement with decreasing temperature, as is also the case for water from molecular dynamics simulations under ambient conditions. Based on X-ray emission spectroscopy and X-ray Raman scattering data we propose that the density difference contrast in SAXS is due to fluctuations between tetrahedral-like and hydrogen-bond distorted structures related to, respectively, low and high density water. We combine our experimental observations to propose a model of water as a temperature-dependent, fluctuating equilibrium between the two types of local structures driven by incommensurate requirements for minimizing enthalpy (strong near-tetrahedral hydrogen-bonds) and maximizing entropy (nondirectional H-bonds and disorder). The present results provide experimental evidence that the extreme differences anticipated in the hydrogen-bonding environment in the deeply supercooled regime surprisingly remain in bulk water even at conditions ranging from ambient up to close to the boiling point.

  • 4.
    Högberg, Carl-Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Effect of Local Anesthetic Lidocaine on Electrostatic Properties of a Lipid Bilayer2008Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 94, 525-531 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 5.
    Högberg, Carl-Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Nikitin, Alexei
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Modification of the CHARMM force field for DMPC lipid bilayer2008Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, nr 14, 2359-2369 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 6. Mayerhoefer, Thomas G.
    et al.
    Shen, Zhijian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi.
    SUBLeonova, Ekaterina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Eden, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Kriltz, Antje
    Popp, Juergen
    Consolidated silica glass from nanoparticles2008Inngår i: Journal of Solid State Chemistry, ISSN 0022-4596, E-ISSN 1095-726X, Vol. 181, nr 9, 2442-2447 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A dense silica glass was prepared by consolidating a highly dispersed silicic acid powder (particle size < 10 nm) with the Spark Plasma Sintering (SPS) technique. The glass was characterized by ellipsometry, transmission electron microscopy (TEM), infrared reflectance and transmittance spectroscopy, as well as by Raman, UV-Vis-NIR and solid-state nuclear magnetic resonance (NMR) spectroscopy. The prototypic sample showed a transmittance of about 63% compared to silica glass in the UV-Vis spectral range. Based on the results of infrared transmittance spectroscopy this lower transparency is due to the comparably high water content, which is about 40 times higher than that in silica glass. H-1 magic-angle spinning (MAS) NMR confirmed an increase in hydroxyl groups in tie sample prepared by SPS relative to that of the conventional SiO2 reference glass. Aside from the comparably high water content, we conclude from the similarity of the IR-reflectance and the Si-29 MAS NMR spectra of the SPS sample and the corresponding spectra of the conventionally prepared silica glass, that the short- and medium-range order is virtually the same in both materials. Raman spectroscopy, however, Suggests that the number of three- and four-membered rings is significantly smaller in the SPS sample compared to the conventionally prepared sample. Based on these results we conclude that it is possible to prepare glasses by compacting amorphous powders by the SPS process. The SPS process may therefore enable the preparation of glasses with compositions inaccessible by conventional methods. 

  • 7.
    Nordenskiöld, Lars
    et al.
    Nanyang Technological University, Singapore.
    Korolev, Nikolai
    Nanyang Technological University, Singapore.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    DNA-DNA Interactions2008Inngår i: DNA interactions with polymers and surfactants / [ed] Rita Dias and Björn Lindman, Hoboken, N.J.: Willey Interscience , 2008, 209-238 s.Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 8. Smith, M. Schwenker
    et al.
    Lee, S. A.
    Rupprecht, A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    The Stability of the B Conformation in Wet-spun Films of CaDNA: A Raman Study as a Function of Water Content2009Inngår i: Journal of Biomolecular Structure and Dynamics, ISSN 0739-1102, E-ISSN 1538-0254, Vol. 27, nr 1, 105-110 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Raman spectra from 600 to 1150 cm(-1) have been collected from wet-spun films of highly oriented CaDNA as a function of relative humidity (rh). Particular attention was paid to the Raman modes at 834 and 807 cm(-1); the presence of these modes indicates that the DNA backbone is in the B or A conformations. Though the B conformation is usually found only under conditions of high hydration in such wet-spun films, CaDNA is found to remain in the B conformation down to 75% rh. These results are consistent with the hypothesis that intermolecular bonds in ordered samples of DNA are critical for the stabilization of the A conformation of DNA.

  • 9.
    Tu, Yaoquan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Towards the understanding of molecular properties in condensed phases from computer simulations and quantum mechanical calculations: methodological investigation and applications to water and related systems2002Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The present thesis summarizes some aspects in the studies of molecular properties by combining molecular dynamics computer simulations and quantum mechanical calculations. Applications to water and related system are overviewed. 

    First, method of combined quantum mechanical and molecular mechanical (QM/MM) calculations is outlined. Molecular dynamics simulations on water systems using combined QM/MM potentials are reviewed. In the simulations, the QM calculations are carried out at the ab initio Hartree-Fock level and TIP3P water models are used to represent the MM water molecules. The main focus of the studies is on the combined QM/MM coupling potentials. The simulation results show that the QM/MM coupling is very sensitive to the Lennard-Jones parameters used on the QM atoms. When the TIP3P Lennard-Jones parameters are used for the QM atoms, the QM/MM coupling is found to be too strong. However, when the LennardJones parameters on the QM atoms are optimized according to the corresponding QM/MM calculations of water dimer, the QM/MM coupling seems to be too weak. Therefore, we believe that the Lennard-Jones parameters on the QM atoms optimized from the corresponding QM/MM calculations for some molecular complexes cannot reliably be used in the simulation of the condensed phases. A modified QM/MM coupling for water systems is found by scaling down the MM charges appearing in the coupling potential. Studies show that the new QM/MM coupling potentials can be used satisfactorily in the combined Hartree-Fock QM/MM molecular simulations of water from ambient to supercritical conditions.

    In the thesis, a self-consistent charge approach developed for the study of the electronic properties of a single molecule in condensed phases is also outlined. In the approach, only the Coulomb interaction between the molecules is considered. Therefore, it is suitable for the study of molecular properties in systems where Coulomb interaction is predominant, such as liquid water, methanol, etc. As an application, the electronic properties of water molecules in water clusters and liquid water are studied. The average water dipole moment in liquid water is found to be 2.65 D. Significant changes in quadrupole moment and polarizability are also found along the water plane in the direction perpendicular to the axis bisecting the H-O-H bond angle. A further theoretical derivation based on the interaction model is presented to find the atomic charge model suitable for the MM force fields. The derived charge model shows that the appropriate atomic charge corresponds to the average value of the electrostatic potential derived charge for an isolated molecule and that obtained for the molecule in the interaction system. Applications to liquid water and methanol show that the obtained charges are similar to those found in the widely used MM force field models, such as SPC, TIP3P, OPLS, etc.   

  • 10.
    Yang, Ye
    et al.
    Nanyang Technological University, Singapore.
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Korolev, Nikolai
    Nanyang Technological University, Singapore.
    Nordenskiöld, Lars
    Nanyang Technological University, Singapore.
    Computer Modeling Reveals that Modifications of the Histone Tail Charges Define Salt-Dependent Interaction of the Nucleosome Core Particles2009Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 96, 2082-2096 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Coarse-grained Langevin molecular dynamics computer simulations were conducted for systems that mimic solutions of nucleosome core particles (NCPs). The NCP was modeled as a negatively charged spherical particle representing the complex of DNA and the globular part of the histones combined with attached strings of connected charged beads modeling the histone tails. The size, charge, and distribution of the tails relative to the core were built to match real NCPs. Three models of NCPs were constructed to represent different extents of covalent modification on the histone tails: (nonmodified) recombinant (rNCP), acetylated (aNCP), and acetylated and phosphorylated (paNCP). The simulation cell contained 10 NCPs in a dielectric continuum with explicit mobile counterions and added salt. The NCP-NCP interaction is decisively dependent on the modification state of the histone tails and on salt conditions. Increasing the monovalent salt concentration (KCl) from salt-free to physiological concentration leads to NCP aggregation in solution for rNCP, whereas NCP associates are observed only occasionally in the system of aNCPs. In the presence of divalent salt (Mg2+), rNCPs form dense stable aggregates, whereas aNCPs form aggregates less frequently. Aggregates are formed via histone-tail bridging and accumulation of counterions in the regions of NCP-NCP contacts. The paNCPs do not show NCP-NCP interaction upon addition of KCl or in the presence of Mg2+. Simulations for systems with a gradual substitution of K+ for Mg2+, to mimic the Mg2+ titration of an NCP solution, were performed. The rNCP system showed stronger aggregation that occurred at lower concentrations of added Mg2+, compared to the aNCP system. Additional molecular dynamics simulations performed with a single NCP in the simulation cell showed that detachment of the tails from the NCP core was modest under a wide range of salt concentrations. This implies that salt-induced tail dissociation of the histone tails from the globular NCP is not in itself a major factor in NCP-NCP aggregation. The approximation of coarse-graining, with respect to the description of the NCP as a sphere with uniform charge distribution, was tested in control simulations. A more detailed description of the NCP did not change the main features of the results. Overall, the results of this work are in agreement with experimental data reported for NCP solutions and for chromatin arrays.

  • 11. Zerbetto, Mirco
    et al.
    Polimeno, Antonino
    Kotsyubynskyy, Dmytro
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Ghalebani, Leila
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för fysikalisk kemi.
    Meirovitch, Eva
    Olsson, Ulrika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    An integrated approach to NMR spin relaxation in flexible biomolecules: Application to β-D-glucopyranosyl-(1→6)-α-D-mannopyranosyl-OMe2009Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, nr 23, p234501- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The description of the reorientational dynamics of flexible molecules is a challenging task, in particular when the rates of internal and global motions are comparable. The commonly used simple mode-decoupling models are based on the assumption of statistical independence between these motions. This assumption is not valid when the time scale separation between their rates is small, a situation that was found to arise in oligosaccharides in the context of certain internal motions. To make possible the interpretation of NMR spin relaxation data from such molecules, we developed a comprehensive approach generally applicable to flexible rotators with one internal degree of freedom. This approach integrates a stochastic description of coupled global tumbling and internal torsional motion, quantum chemical calculations of the local potential and the local geometry at the site of the restricted torsion, and hydrodynamics-based calculations of the diffusive properties. The method is applied to the disaccharide -D-Glcp-(16)--D-[6-13C]-Manp-OMe dissolved in a DMSO-d6/D2O cryosolvent. The experimental NMR relaxation parameters, associated with the 13CH2 probe residing at the glycosidic linkage, include 13C T1 and T2 and 13C-{1H} nuclear Overhauser enhancement (NOE) as well as longitudinal and transverse dipole-dipole cross-correlated relaxation rates, acquired in the temperature range of 253–293 K. These data are predicted successfully by the new theory with only the H–C–H angle allowed to vary. Previous attempts to fit these data using mode-decoupling models failed.

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