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  • 201.
    Stevensson, Baltzar
    et al.
    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.
    Interpolation by fast Wigner transform for rapid calculations of magnetic resonance spectra from powders2011Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, nr 12, s. 124104-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We introduce a novel interpolation strategy, based on nonequispaced fast transforms involving spherical harmonics or Wigner functions, for efficient calculations of powder spectra in (nuclear) magnetic resonance spectroscopy. The fast Wigner transform (FWT) interpolation operates by minimizing the time-consuming calculation stages, by sampling over a small number of Gaussian spherical quadrature (GSQ) orientations that are exploited to determine the spectral frequencies and amplitudes from a 10-70 times larger GSQ set. This results in almost the same orientational averaging accuracy as if the expanded grid was utilized explicitly in an order of magnitude slower computation. FWT interpolation is applicable to spectral simulations involving any time-independent or time-dependent and noncommuting spin Hamiltonian. We further show that the merging of FWT interpolation with the well-established ASG procedure of Alderman, Solum and Grant [J. Chem. Phys. 134, 3717 (1986)] speeds up simulations by 2-7 times relative to using ASG alone (besides greatly extending its scope of application), and between 1-2 orders of magnitude compared to direct orientational averaging in the absence of interpolation. Demonstrations of efficient spectral simulations are given for several magic-angle spinning scenarios in NMR, encompassing half-integer quadrupolar spins and homonuclear dipolar-coupled (13)C systems.

  • 202.
    Stevensson, Baltzar
    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.
    Edén, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Assessing the Phosphate Distribution in Bioactive Phosphosilicate Glasses by P-31 Solid-State NMR and Molecular Dynamics Simulations2014Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, nr 29, s. 8863-8876Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Melt-derived bioactive phosphosilicate glasses are widely utilized as bone-grafting materials for various surgical applications. However, the insight into their structural features over a medium-range scale up to similar to 1 nm remains limited. We present a comprehensive assessment of the spatial distribution of phosphate groups across the structures of 11 Na2O-CaO-SiO2-P2O5 glasses that encompass both bioactive and nonbioactive compositions, with the P contents and silicate network connectivities varied independently. Both parameters are known to strongly influence the bioactivity of the glass in vitro. The phosphate distribution was investigated by double-quantum 3113 nuclear magnetic resonance (NMR) experiments under magic-angle spinning (MAS) conditions and by molecular dynamics (MD) simulations. The details of the phosphate-ion dispersion were probed by evaluating the MD-derived glass models against various scenarios of randomly distributed, as well as clustered, phosphate groups. From comparisons of the P-P interatomic-distance spreads and the statistics of small phosphate clusters assessed for variable cutoff radii, we conclude that the spatial arrangement of the P atoms in phosphosilicate glasses is well-approximated by a statistical distribution, particularly across a short-range scale of <= 450 pm. The primary distinction is reflected in slightly closer P-P interatomic contacts in the MD-derived structures over the distance span of 450-600 pm relative to that of randomly distributed phosphate groups. The nature of the phosphate-ion dispersion remains independent of the silicate network polymerization and nearly independent of the P content of the glass throughout our explored parameter space of 1-6 mol % P2O5 and silicate network connectivities up to 2.9.

  • 203.
    Sun, Junliang
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Bonneau, Charlotte
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för strukturkemi.
    Cantín, Á
    Corma, A
    Díaz-Cabanas, M.J
    Moliner, M
    Zhang, Daliang
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Li, Mingrun
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Avdelningen för strukturkemi.
    Zou, Xiaodong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    The ITQ-37 mesoporous chiral zeolite2009Inngår i: Nature, Vol. 458, s. 1154-1157Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The synthesis of crystalline molecular sieves with pore dimensions that fill the gap between microporous and mesoporous materials is a matter of fundamental and industrial interest. The preparation of zeolitic materials with extralarge pores and chiral frameworks would permit many new applications. Two important steps in this direction include the synthesis of ITQ-33, a stable zeolite with 18 × 10 × 10 ring windows, and the synthesis of SU-32, which has an intrinsically chiral zeolite structure and where each crystal exhibits only one handedness. Here we present a germanosilicate zeolite (ITQ-37) with extralarge 30-ring windows. Its structure was determined by combining selected area electron diffraction (SAED) and powder X-ray diffraction (PXRD) in a charge-flipping algorithm. The framework follows the SrSi2 (srs) minimal net and forms two unique cavities, each of which is connected to three other cavities to form a gyroidal channel system. These cavities comprise the enantiomorphous srs net of the framework. ITQ-37 is the first chiral zeolite with one single gyroidal channel. It has the lowest framework density (10.3 T atoms per 1,000 Å3) of all existing 4-coordinated crystalline oxide frameworks, and the pore volume of the corresponding silica polymorph would be 0.38 cm3 g-1.

    Keywords: srs-net, powder X-ray, charge flipping, electron microscopy

  • 204. Sun, Lu
    et al.
    Hede, Thomas
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU).
    Tu, Yaoquan
    Leck, Caroline
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU).
    Ågren, Hans
    Combined Effect of Glycine and Sea Salt on Aerosol Cloud Droplet Activation Predicted by Molecular Dynamics Simulations2013Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, nr 41, s. 10746-10752Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The present study illustrates the combined effect of organic and inorganic compounds on cloud droplet nucleation and activation processes representative for the marine environment. Amino acids and sea salt are common marine cloud condensation nuclei (CCN) which act as a prerequisite for growth of cloud droplets. The chemical and physical properties of these CCN play a key role for interfacial properties such as surface tension, which is important for the optical properties of clouds and for heterogeneous reactions. However, there is a lack of detailed information and in situ measurements of surface tension of such nanosized droplets. Here we present a study of the combined effect of zwitterionic glycine (ZGLY) and sea salt in nanosized water droplets using molecular dynamics simulations, where particular emphasis is placed on the surface tension for the nanosized droplets. The critical supersaturation is estimated by the Kohler equation. It is found that dissolved sea salt interacts with ZGLY through a water bridge and weakens the hydrogen bonds among ZGLYs, which has a significant effect on both surface tension and water vapor supersaturation. Clusters of glycine mixed with sea salt deliquesce more efficiently and have higher growth factors.

  • 205.
    Säwén, Elin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Östervall, Jennie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. 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.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Molecular conformations in the pentasaccharide LNF-1 derived from NMR spectroscopy and molecular dynamics simulations2011Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, nr 21, s. 7109-7121Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), α-l-Fucp-(1 → 2)-β-d-Galp-(1 → 3)-β-d-GlcpNAc-(1 → 3)-β-d-Galp-(1 → 4)-d-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard 13C-excitation technique and the J-HMBC experiment, 1H,13C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional 1H,1H T-ROESY experiments, proton–proton cross-relaxation rates were determined in isotropic D2O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D2O, 1H, 1H and one-bond 1H, 13C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, τN, was calculated for transitions at the ψ torsion angle of the β-(1 → 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, τM, of 0.6 ns determined experimentally in D2O solution, the time constant for the isomerization relaxation process, τN(scaled), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous 13C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of 30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.

  • 206. Taborda, Farlán
    et al.
    Willhammar, Tom
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Wang, Zhengyang
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Montes, Consuelo
    Zou, Xiaodong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Synthesis and characterization of pure silica zeolite beta obtained by an aging-drying method2011Inngår i: Microporous and Mesoporous Materials, ISSN 1387-1811, E-ISSN 1873-3093, Vol. 143, nr 1, s. 196-205Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pure silica zeolite beta materials were synthesized by an unconventional method of aging and drying the starting gels at room temperature followed by the conventional hydrothermal treatment. In addition, organic solvents were added to selected samples as complementary structure directing agents (SDA). The influence of the aging-drying method, complementary SDA addition and crystallization time upon the synthesis of pure silica zeolite beta were studied. Samples were characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM), thermogravimetric analyses (TGA) and nitrogen adsorption. Results revealed that the aging-drying process increased crystallization rate, produced crystals with unique morphology and scaled-surface and allowed polymorph A enrichments to about 68-70%. It was also found that addition of organic solvents during the thermal treatment tunes the crystal morphology but, does not affect the polymorphic enrichment.

  • 207.
    Takacs, Zoltan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Chloromethane Complexation by Cryptophanes: Host-Guest Chemistry Investigated by NMR and Quantum Chemical Calculations2012Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Host–guest complexes are widely investigated because of their importance in many industrial applications. The investigation of their physico–chemical properties helps understanding the inclusion phenomenon. The hosts investigated in this work are cryptophane molecules possessing a hydrophobic cavity. They can encapsulate small organic guests such as halo–methanes (CH2Cl2, CHCl3). The encapsulation process was investigated from both the guest and the host point of view. With the help of Nuclear Magnetic Resonance (NMR), the kinetics of complex formation was determined. The information was further used to obtain the activation energies of the processes. Having done this on five different cryptophanes, it is possible to relate the energies to structural differences between the hosts. Via the dipolar interaction between the guest’s and host’s protons, one can get information on the orientation of the guest inside the cavity. Moreover, the dynamics of the guest can be further investigated by its relaxation properties. This revealed restricted motion of the guest inside the host cavity. Not only the nature of the guest plays an important role. The host is also changing its properties upon encapsulation. All the cryptophanes investigated here can exchange rapidly between many conformers. These conformers have different–sized cavities. Quantum chemical optimization of the structure of the conformers makes volume estimation possible. Not only the cavity volumes, but also the quantum-chemically obtained energies and the calculated chemical shifts of the carbon–13 atoms can be helpful to follow the changes of the host upon complex formation. The host cannot be considered as a rigid entity. Analysis of variable temperature proton and carbon-13 spectra shows that the encapsulation can be considered as a mixture of conformational selection and induced fit. The structures of the formed complexes are further investigated by means of two-dimensional nuclear Overhauser spectroscopy (NOESY). The complex formation, its kinetics and thermodynamics are found to be a complicated function of structure elements of the host, the cavity size and the guest size and properties.

  • 208.
    Takacs, Zoltan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Brotin, Thierry
    Chloromethane complexes of cryptophane-A and its analogue with butoxy groupsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Host-guest complexes between cryptophane-A as host and dichloromethane and chloroformas guests are investigated using 1H and13C NMR spectroscopy. Moreover, a relatedcryptophane, with the methoxy groups replaced by butoxy units (cryptophane-But), and itscomplexes with the same guests were also studied. Variable temperature spectra showedeffects of chemical exchange between the free and bound guests, as well as of conformationalexchange of the host. The guest exchange was studied quantitatively by exchangespectroscopy or line shape analysis. In the case of CHCl3@cryptophane-A, carbon-13relaxation of the guest was also investigated. Structural information was obtained throughmeasurements of cross-relaxation rates, both within the host and between the host and guestprotons. The NMR results were supported by DFT calculations.1

  • 209.
    Takacs, Zoltan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Šoltésová, Mária
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Charles University Prague .
    Kotsyubynskyy, Dmytro
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lang, Jan
    Brotin, Thierry
    Dutasta, Jean-Pierre
    NMR Investigation of Guest–Host Complex between Chloroform and Cryptophane C2010Inngår i: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 48, nr 8, s. 623-629Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Guest–host complex between cryptophane C, possessing two non-equivalent caps, and chloroform is investigated by NMR spectroscopy. The kinetics of the chloroform exchange between the bound and free sites is determined by 1H exchange spectroscopy. Moreover, the preferential orientation of chloroform molecule with respect to the cryptophane C frame is examined by the NOESY and ROESY experiments. The experimental findings are compared to the results of quantum chemical calculations.

  • 210.
    Takacs, Zoltan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Šoltésová, Mária
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Charles University Prague .
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lang, Jan
    Host-Guest Complexes between Cryptophane-C and Chloromethanes Revisited2013Inngår i: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 51, nr 1, s. 19-31Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cryptophane-C is composed of two nonequivalent cyclotribenzylene caps, one of which contains methoxy group substituents on the phenyl rings. The two caps are connected by three OCH2CH2O linkers in an anti arrangement. Host-guest complexes of cryptophane-C with dichloromethane and chloroform in solution were investigated in detail by nuclear magnetic resonance techniques and density functional theory (DFT) calculations. Variable temperature proton and carbon-13 spectra show a variety of dynamic processes, such as guest exchange and host conformational transitions. The guest exchange was studied quantitatively by exchange spectroscopy measurements or by line-shape analysis. The conformational preferences of the guest-containing host were interpreted through cross-relaxation measurements, providing evidence of the gauche+2 and gauche-2 conformations of the linkers. In addition, the mobility of the chloroform guest inside the cavity was studied by carbon-13 relaxation experiments. Combining different types of evidence led to a detailed picture of molecular recognition, interpreted in terms of conformational selection.

  • 211.
    Takács, Zoltan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Brotin, Thierry
    Dutasta, Jean-Pierre
    Lang, Jan
    Todde, Guido
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Inclusion of Chloromethane Guests Affects Conformation and Internal Dynamics of Cryptophane-D Host2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 27, s. 7898-7913Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cryptophane-D is composed of two nonequivalent cyclotribenzylene caps bound together by three OCH2CH2O bridges in a syn arrangement. Host-guest complexes with chloroform and dichloromethane were investigated in solution by NMR spectroscopy. Variable temperature NMR. H-1 and C-13 spectra showed effects of chemical exchange between the free and bound guest and of conformational exchange for the host, strongly and specifically affected by guest binding. We found in particular that the carbon-13 chemical shifts for the linkers connecting the two cyclotribenzylene units are very informative. The NMR results were supported by DFT calculations. The guest exchange was also studied quantitatively, either by EXSY measurements (for chloroform as guest) or by line-shape analysis (for dichloromethane as guest). In the case of chloroform guest, we also investigated cross relaxation between the guest and host protons, as well as carbon 13 longitudinal relaxation and heteronuclear NOE at three different fields. The results were interpreted in terms of orientation and dynamics of the guest inside the host cavity. Putting together various types of evidence resulted in remarkably detailed insight into the process of molecular recognition of the two guests by cryptophane-D host.

  • 212.
    Takács, Zoltan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Steiner, Emelie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Kowalewski, Josef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Brotin, T.
    NMR Investigation of Chloromethane Complexes of Cryptophane-A and Its Analogue with Butoxy Groups2014Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, nr 8, s. 2134-2146Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Host guest complexes between cryptophane-A as host and dichloromethane and chloroform as guests are investigated using H-1 and C-13 NMR spectroscopy. Moreover, a related cryptophane, with the methoxy groups replaced by butoxy units (cryptophane-But), and its complexes with the same guests were also studied. Variable temperature spectra showed effects of chemical exchange between the free and bound guests, as well as of conformational exchange of the host. The guest exchange was studied quantitatively by exchange spectroscopy or line shape analysis. Extraction of kinetic and thermodynamic parameters led to the characterization of the affinity between guests and hosts. On the other hand, the host exchange was investigated by means of C-13 Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion which aims at the determination of the transverse relaxation rate R-2, the inverse of the transverse relaxation time T-2, as a function of the repetition of the pi pulses in a CPMG train. The variation of the measured transverse relaxation rate with the repetition rate nu(CPMG) indicated conformational exchange occurring on the microsecond millisecond time scale. Structural information was obtained through measurements of cross-relaxation rates, both within the host and between the host and the guest protons. The NMR results were supported by DFT calculations.

  • 213. Tavagnacco, Letizia
    et al.
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Schnupf, Udo
    Saboungi, Marie-Louise
    Himmel, Michael
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cesaro, Attilio
    Brady, John W.
    Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 38, s. 11701-11711Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 in solution of alpha-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 in solution of beta-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.

  • 214.
    Teymoori, Gholamhasan
    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.
    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.
    Low-power broadband homonuclear dipolar recoupling without decoupling: Double-quantum C-13 NMR correlations at very fast magic-angle spinning2012Inngår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 547, s. 103-109Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We report novel symmetry-based radio-frequency (rf) pulse sequences for efficient excitation of doublequantum (2Q) coherences under very fast (>60 kHz) magic-angle spinning (MAS) conditions. The recursively generated pulse-scheme series, R2(2p)(1)R2(2P)(-1) (p = 1; 2, 3,...), offers broadband C-13-C-13 recoupling in organic solids at a very low rf power. No proton decoupling is required. A high-order average Hamiltonian theory analysis reveals a progressively enhanced resonance-offset compensation for increasing p, as verified both by numerical simulations and 2Q filtration NMR experiments on C-13(2)-glycine, [2,3-C-13(2)] alanine, and [U-C-13] tyrosine at 14.1 T and 66 kHz MAS, where the pulse schemes with p >= 3 compare favorably to current state-of-the-art recoupling options.

  • 215.
    Teymoori, Gholamhasan
    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.
    Viswanathan, Elumalai
    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.
    Multiple-quantum spin counting in magic-angle-spinning NMR via low-power symmetry-based dipolar recoupling2013Inngår i: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 236, s. 31-40Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By using a symmetry-based R2(8)(1)S2(8)(-1) double-quantum (2Q dipolar recoupling sequence, we demonstrate high-order multiple-quantum coherence (MQC) excitation at fast magic-angle spinning (MAS) frequencies up to 34 kHz. This scheme combines several attractive features, such as a relatively high dipolar scaling factor, good compensation to rf-errors, isotropic and anisotropic chemical shifts, as well as an ultra-low radio-frequency (rf) power requirement. The latter translates into nutation frequencies below 30 kHz for MAS rates up to 60 kHz, thereby permitting rf application for very long excitation periods without risk of damaging the NMR probehead or sample, while the compensation to chemical shifts improves as the MAS rate increases. 31P MQC spin counting is demonstrated on powders of calcium hydroxyapatite (Ca-5(PO4)(3)OH) and anhydrous sodium diphosphate (Na4P2O7), from which all even coherence orders up to 30 and 14 were detected, respectively, over the respective MAS ranges of 15-24 kHz and 20-34 kHz. The amplitude distributions among the P-31 MQC orders depend on the precise nutation frequency during recoupling, despite that the highest detected order was relatively insensitive to this parameter. An observed gradual transition from a Gaussian to exponential functionality of the MQC amplitude-profile is discussed in relation to the prevailing approach to derive spin-cluster sizes by fitting the MQC amplitude-distribution to a Gaussian decay, where minor systematic deviations between the model and experimental data are frequently reported.

  • 216.
    Thaning, Johan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Molecular Structure in Liquid Crystals Studied by NMR2008Doktoravhandling, monografi (Annet vitenskapelig)
    Abstract [en]

    This thesis is focused on structure determinations of molecules in liquid crystals using NMR. The systems described here exhibit orders ranging from nearly isotropic to essentially solid. The structure is determined by interpreting, mainly dipolar couplings, but also J-couplings and NOE data using conformational distribution functions (cdfs) to capture both the structure and the flexibility of the molecules. The models used in the analysis of the NMR parameters are: a statistical approach denoted Maximum Entropy (ME), a mean field method named Additive Potential (AP) and a synthesis of the two named APME. The thesis covers some background on liquid crystals, NMR, dipolar couplings and their role in structure determination as well as the aforementioned models used for this purpose.

    The thesis also discusses four papers: 1st being a comparison of the ME, AP and APME models in the structure determination of diphenylmethane. The 2nd covering a test of the APME method, reproducing the cdf of dimyristoylphosphatidylcholine in a lipid bilayer obtained through a molecular dynamics simulation using the APME method on dipolar couplings calculated from the MD trajectory. The 3rd paper deals with a discotic molecule 2, 3, 6, 7, 10, 11-hexahexyl-thiotriphenylene, HHTT displaying a polymorphism which is investigated, using NMR, determining the characteristics of three of its phases. Finally the 4th paper is a structure investigation of α-cyclodextrin employing the ME method using experimental J-couplings, NOEs and dipolar couplings.

  • 217.
    Thaning, Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Högberg, Carl-Johan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Lyubartsev, Alexander
    Stockholms universitet, Humanistiska fakulteten, Institutionen för baltiska språk, finska och tyska, Avdelningen för nederländska. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Molecular Conformations in a Phospholipid Bilayer Extracted from Dipolar Couplings: A Computer Simulation Study2007Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, nr 48, s. 13638-13644Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper describes an analysis of NMR dipolar couplings in a bilayer formed by dimyristoylphosphatidylcholine (DMPC). The couplings are calculated from a trajectory generated in a molecular dynamics (MD) simulation based on a realistic atom−atom interaction potential. The analysis is carried out employing a recently developed approach that focuses on the construction of the conformational distribution function. This approach is a combination of two models, the additive potential (AP) model and the maximum entropy (ME) method, and is therefore called APME. In contrast to the AP model, the APME procedure does not require an intuition-based choice of the functional form of the torsional potential and is, unlike the ME method, applicable to weakly ordered systems. The conformational distribution function for the glycerol moiety of the DMPC molecule derived from the APME analysis of the dipolar couplings is in reasonable agreement with the “true” distributions calculated from the trajectory. Analyses of dipolar couplings derived from MD trajectories can, in general, serve as guidelines for experimental investigations of bilayers and other complex biological systems.

  • 218.
    Thaning, Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Molecular structure extracted from residual dipolar couplings: Diphenylmethane dissolved in a nematic liquid crystal2005Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, nr 4, s. 044507-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper describes an analysis of 1H–1H residual dipolar couplings (RDCs)in diphenylmethane (DPM) dissolved in a nematic liquid crystal, reportedby Celebre et al. [J. Chem. Phys. 118, 6417 (2003)]. Inthat article, the conformational distribution function for DPM was extractedfrom the RDCs, using the additive potential (AP) model whichis based on the molecular-field theory. The AP approach isa powerful, and frequently used, tool for analysis of thenuclear-magnetic-resonance (NMR) parameters in liquid crystals. It requires, however, apriori knowledge of the functional form of the torsional potential,which may even for a simple molecule, such as DPM,be complicated to determine. Here, we analyze the same setof the RDCs using our APME procedure, which is ahybrid model based on the AP approach and maximum entropy(ME) theory. The APME procedure does not require any assumptionsabout the functional form of the torsional potential and, incontrast with the ME method, is applicable to weakly orderedsystems. In the investigation reported in the present study, theresults from the APME analysis are in good agreement withthe AP interpretation, whereas the ME approach essentially fails inthe extraction of the conformational distribution function for DPM.

  • 219.
    Thaning, Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Östervall, Jennie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Naidoo, Kevin J.
    University of Cape Town. , CSIR Campus Rosebank..
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    NMR Studies of Molecular Conformations in α-Cyclodextrin2008Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, nr 29, s. 8434-8436Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new approach for analysis of NMR parameters is proposed. The experimental data set includes scalar couplings, NOEs, and residual dipolar couplings. The method, which aims at construction of the conformational distribution function, is applied to α-cyclodextrin in isotropic solution and dissolved in a dilute liquid crystal. An attempt to analyze the experimental data using an average molecular conformation resulted in unacceptable errors. Our approach rests on the maximum entropy method (ME), which gives the flattest possible distribution, consistent with the experimental data. Very good agreement between experimental and calculated NMR parameters was observed. In fact, two conformational states were required in order to obtain a satisfactory agreement between calculated and experimental data. In addition, good agreement with Langevin dynamics computer simulations was obtained.

  • 220.
    Thiele, Christina M.
    et al.
    Clemens Schpf Institut fr Organische Chemie und Biochemie, Technische Universitt Darmstadt, Petersenstr. 22, D-64287 Darmstadt, Germany.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Use of Local Alignment Tensors for the Determination of Relative Configurations in Organic Compounds2009Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, nr 36, s. 12878-12879Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this proof of principle the use of local alignment tensors for the determination of relative configurations in moderately flexible molecules is demonstrated. These tensors are derived from residual dipolar couplings. Two methods for the analysis of partly linearly dependent RDCs in a rigid molecular fragment are also presented.

  • 221.
    Thiele, Christina M.
    et al.
    Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Petersenstrasse 22, 64287 Darmstadt (Germany).
    Schmidts, Volker
    Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Petersenstrasse 22, 64287 Darmstadt (Germany).
    Böttcher, Benjamin
    Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Petersenstrasse 22, 64287 Darmstadt (Germany).
    Louzao, Iria
    Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Petersenstrasse 22, 64287 Darmstadt (Germany). On leave from: Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela (Spain) .
    Berger, Robert
    Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe Universität, Ruth-Moufang-Strasse 1, 60438 Frankfurt (Germany).
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    On the Treatment of Conformational Flexibility when Using Residual Dipolar Couplings for Structure Determination2009Inngår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 48, nr 36, s. 6708-6712Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mission possible! The motional averaging of NMR spectroscopic data complicates the determination of conformation and relative configuration in flexible organic molecules. Two alternative routes are discussed for the treatment of conformational equilibrium in a moderately flexible compound (see the superposition of the two conformers of the butyrolactone studied) when residual dipolar couplings are used.

  • 222. Thogersen, Jan
    et al.
    Rehault, Julien
    Odelius, Michael
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Ogden, Tom
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Jena, Naresh K.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Jensen, Svend J. Knak
    Keiding, Søren R.
    Helbing, Jan
    Hydration Dynamics of Aqueous Nitrate2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 12, s. 3376-3388Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aqueous nitrate, NO3-(aq), was studied by 2D-IR, UV-IR, and UV-UV time-resolved spectroscopies in combination with molecular dynamics (MD) simulations with the purpose of determining the hydration dynamics around the anion. In water, the D-3h symmetry of NO3- is broken, and the degeneracy of the asymmetric-stretch modes is lifted. This provides a very sensitive probe of the ion-water interactions. The 2D-IR measurements reveal excitation exchange between the two nondegenerate asymmetric-stretch vibrations on a 300-fs time scale concomitant with fast anisotropy decay of the diagonal-peak signals. The MD simulations show that this is caused by jumps of the transition dipole orientations related to fluctuations of the hydrogen bonds connecting the nitrate ion to the nearest water molecules. Reorientation of the ion, which is associated with the hydrogen-bond breaking, was monitored by time-resolved UV-IR and UV-UV spectroscopy, revealing a 2-ps time constant. These time scales are very similar to those reported for isotope-labeled water, suggesting that NO3-(aq) has a labile hydration shell.

  • 223.
    Thomas, Richard D.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Kashperka, Iryna
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Vigren, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Geppert, Wolf D.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Hamberg, Mathias
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Larsson, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    af Ugglas, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Zhaunerchyk, Vitali
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Dissociative Recombination of CH4+2013Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, nr 39, s. 9999-10005Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    CH4+ is an important molecular ion in the astrochemistry of diffuse clouds, dense clouds, cometary comae, and planetary ionospheres However, the rate of one of the common destruction mechanisms for molecular ions in these regions, dissociative recombination (DR), is somewhat uncertain. Here, we present absolute measurements for the DR of CH4+ made using the heavy ion storage ring CRYRING hi Stockholm, Sweden. From our collision energy dependent cross sections, we infer a thermal rate constant of k(T-e) = 1.71(+/- 0.02) X 10(-6)(T-e/300)(-0.66(+/- 0.02)) cm(3) s(-1) over the region of electron temperatures 10 <= T-e <= 1000 K. At low collision energies, we have measured the branching fractions of the DR products to be CH4 (0.00 +/- 0.00); CH3 + H (0.18 +/- 0.03); CH2 + 2H (0.51 +/- 0.03); CH2 + H-2 (0.06 +/- 0.01); CH + H-2 + H (0.23 +/- 0.01); and CH + 2H(2) (0.02 +/- 0.01), indicating that two or more C-H bonds are broken in similar to 80% of all collisions.

  • 224. Tokushima, Takashi
    et al.
    Horikawa, Yuka
    Arai, Hidemi
    Harada, Yoshihisa
    Takahashi, Osamu
    Pettersson, Lars G.M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nilsson, Anders
    Shin, Shik
    Polarization dependent resonant x-ray emission spectroscopy of D2O and H2O water: Assignment of the local molecular orbital symmetry2012Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 136, nr 4, s. 044517-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The polarization dependence of the split two peaks in the lone-pair region in the x-ray emission spectra has been determined at several different excitation energies for both D2O and H2O water. In contrast to predictions based on a narrow range of local water structures where the two peaks would be of different molecular orbital symmetry and arise from, respectively, intact and dissociated molecules, we show that the two peaks in the lone-pair region are both of lone-pair 1b(1) orbital symmetry. The results support the interpretation that the two peaks appear due to fluctuations between two distinct different main structural environments.

  • 225.
    Tosner, Zdenek
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    NMR Investigations of Host-Guest Complexes and Their Dynamic Properties2005Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis discusses several different methods offered by solution and solid state nuclear magnetic resonance for investigation of host-guest complexes and their constituents. The presented methods were used especially (but not exclusively) to address rotational dynamics of the bound guest in different molecular systems.

    The main part of this thesis presents results of a project that combines and compares solution and solid state NMR investigations of inclusion complexes of a spherical, cage-like molecule of cryptophane-E with small neutral guest molecules like chlorinated methanes. Strong and weak bonding of these host--guest systems is studied in solution using C-13 NMR relaxation and in the crystalline form, using advanced dipolar recoupling methods as well as deuterium NMR lineshape and spin relaxation analysis. Comparison of the results from all the techniques suggests very similar guest behaviour regardless of the physical state of the system. Residing inside the cavity, CHCl3 behaves almost as an integral part of cryptophane-E, whereas the reorientation of CH2Cl2 is influenced only slightly by weak interactions with its host.

    Molecular flexibility of thiacalix[4]arenes, a new class of the very popular calixarene family, was also studied by C-13 NMR relaxation in solution. Calixarenes are widely used in supramolecular chemistry as building blocks of receptors to many guest molecules.

    The thesis is completed with examination of a β-cyclodextrin (β-CD) inclusion complex with adamantanecarboxylic acid (AdCA) where changes of translational and rotational diffusion properties of the guest were monitored during complexation with the host. By means of C-13 NMR relaxation it was found that despite the high association constant (which suggests strong interactions between the two molecules) AdCA rotates fast around the β-CD symmetry axis inside the cavity. This motion is made possible by the spherical shape of the adamantyl moiety and the whole system resembles to a "molecular bearing".

  • 226. Tosner, Zdenek
    et al.
    Skoch, Antonin
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Behavior of Two Almost Identical Spins during the CPMG Pulse Sequence2010Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 11, nr 3, s. 638-645Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Multiple-spin-echo experiments have found wide use in nuclear magnetic resonance spectroscopy. In particular, the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence is used to determine transverse relaxation times T-2. Herein it is demonstrated, both theoretically and experimentally, that for a pair of almost identical spins-1/2 the experimental setup can have a profound effect on the observed spin dynamics. It is shown that, in the case of dipolar relaxation, the measured T-2 values can roughly vary between the limits of identical and unlike spins, just depending on the repetition rate of pi pulses with respect to chemical shift separation. Such an effect can, in the extreme narrowing regime, amount to a 50% difference.

  • 227.
    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.   

  • 228. Vallet, Valerie
    et al.
    Wahlgren, Ulf
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Grenthe, Ingmar
    Probing the Nature of Chemical Bonding in Uranyl(VI) Complexes with Quantum Chemical Methods2012Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, nr 50, s. 12373-12380Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To assess the nature of chemical bonds in uranyl(VI) complexes with Lewis base ligands, such as F-, Cl-, OH-, CO32-, and O-2(2-), we have used quantum chemical observables, such as the bond distances, the internal symmetric/asymmetric uranyl stretch frequencies, and the electron density with its topology analyzed using the quantum theory of atoms-in-molecules. This analysis confirms that complex formation induces a weakening of the uranium-axial oxygen bond, reflected by the longer U-O-yl bond distance and reduced uranyl-stretching frequencies. The strength of the ligand-induced effect increases in the order H2O < Cl- < F- < OH- < CO32- < O-2(2-). In-depth analysis reveals that the trend across the series does not always reflect an increasing covalent character of the uranyl-ligand bond. By using a point-charge model for the uranyl tetra-fluoride and tetra-chloride complexes, we show that a significant part of the uranyl bond destabilization arises from purely electrostatic interactions, the remaining part corresponding either to charge-transfer from the negatively charged ligands to the uranyl unit or a covalent interaction. The charge-transfer and the covalent interaction are qualitatively different due to the absence of a charge build up in the uranyl-halide bond region in the latter case. In all the charged complexes, the uranyl-ligand bond is best described as an ionic interaction. However, there are covalent contributions in the very stable peroxide complex and, to some extent, also in the carbonate complex. This study demonstrates that it is possible to describe the nature of chemical bond by observables rather than by ad hoc quantities such as atomic populations or molecular orbitals.

  • 229.
    van Dam, Lorens
    Stockholms universitet.
    NMR studies of DNA structure and counterion behaviour2000Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    DNA is a polymer of nucleotides, each nucleotide consisting of a negatively charged phosphate group, a ribose sugar unit, and a purine or pyrimidine base. The secondary structure of DNA is commonly a double-helix with Watson-Crick paired bases. Several secondary structures, all with these features, are observed for DNA. Due to the negative charge of DNA, it is always accompanied by cations, referred to as counterions. The concentration and charge, as well as the specific molecular details of the counterions, have a profound impact on the secondary structure of DNA. Also the activity of water in the system, which hydrate the molecules, comes into play. The thesis looks into some of these systems and their behavior, with nuclear magnetic resonance, NMR, as the main tool of investigation. The thesis is based on the following publications and manuscripts:Papers I-III deal with the unusual transition from the B- to the C-form of fibrous LiDNA as the water activity is lowered. A multiple-quantum NMR diffusion experiment is designed, and the diffusion of Li+ and Cs+ in oriented polymeric DNA measured using NMR. It is found that the Li+ diffusion is very slow compared to that of Cs+. Molecular dynamics simulations show strong complexation of Li+ with the charged DNA phosphate oxygens O1' and O2'. The phosphate orientations of the B- and C-forms of DNA with LiDNA are measured by 31P solid-state NMR, and a new model for the C-form is built. The new model involves a high degree of BII nucleotides, which could be of relevance to the DNA-protein recognition process.

    Papers IV-V set to investigate the behavior of the biologically interesting polyamines with oligomeric DNA in solution and oriented polymeric DNA fibers. The diffusion, measured by 1H NMR, of some polyamines with oligonucleotides in the Z-form and B-form, show a higher degree of association to the Z-form. 1H NMR NOE measurements show the association with DNA to be weak with both DNA forms, although a slightly shorter polyamine correlation time is observed with the Z-form. The transition of fibrous DNA from the B-form to the A-form with some polyamines but not with others is investigated. 1H NMR diffusion measurements show no unusual behavior, but some characteristic 2H spectral features are observed. No direct molecular reason for the differentent impacts on DNA structure by different polyamines can be isolated, and the effect is believed to be thermodynamic in origin.

    Paper VI shows that DNA complexed with the suspected intercalator bipyridyl(ethylenediamine)Pt(II)2+ remains in the B-form, meaning that the molecule does not interacalate fibrous DNA to a high degree. This is seen by application of a number of methods sensitive to the molecular conformation, amongst those extraction of the phosphate orientation using 31P solid-state NMR.

  • 230. Verchenko, V. Yu
    et al.
    Likhanov, M. S.
    Kirsanova, M. A.
    Gippius, A. A.
    Tkachev, A. V.
    Gervits, N. E.
    Galeeva, A. V.
    Buettgen, N.
    Kraetschmer, W.
    Lue, C. S.
    Okhotnikov, Kirill S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Shevelkov, A. V.
    Intermetallic solid solution Fe1-xCoxGa3: Synthesis, structure, NQR study and electronic band structure calculations2012Inngår i: Journal of Solid State Chemistry, ISSN 0022-4596, E-ISSN 1095-726X, Vol. 194, s. 361-368Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Unlimited solid solution Fe1-xCoxGa3 was prepared from Ga flux. Its crystal structure was refined for Fe0.5Co0.5Ga3 (P4(2)/mnm, a=6.2436(9), c=6.4654(13), Z=4) and showed no ordering of the metal atoms. A combination of the electronic band structure calculations within the density functional theory (DFT) approach and Ga-69,Ga-71 nuclear quadrupole resonance (NRQ) spectroscopy clearly shows that the Fe-Fe and Co-Co dumbbells are preferred to the Fe-Co dumbbells in the crystals structure. The band structure features a band gap of about 0.4 eV, with the Fermi level crossing peaks of a substantial density of electronic states above the gap for x > 0. The solid solution is metallic for x > 0.025. The study of the nuclear spin-lattice relaxation shows that the rate of the relaxation, 1/T-1, is very sensitive to the Co concentration and correlates well with the square of the density of states at the Fermi level, N-2(E-F).

  • 231.
    Volkov, Nikolai
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Vorontsov-Velyaminov, Pavel
    Lyubartsev, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Two-Dimensional Wang–Landau Algorithm for Osmotic Pressure Calculations in a Polyelectrolyte–Membrane System2011Inngår i: Macromolecular Theory and Simulations, ISSN 1022-1344, E-ISSN 1521-3919, Vol. 20, nr 7, s. 496-509Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Monte Carlo method based on two-dimensional entropic sampling within the Wang–Landau (WL) algorithm is applied to simulation of a continuous model of a polyelectrolyte between membrane surfaces. Membranes are presented by parallel plane surfaces holding either fixed or mobile dipoles (representing lipid headgroups). A strongly charged polyion accompanied by neutralizing counterions is placed between the membranes. Periodic boundary conditions are imposed along X- and Y-axes. The volume of the main cell is varied during the simulation by shifting one of the surfaces along Z-axis. Within two-dimensional WL sampling algorithm we obtain joint density of states as a function of energy and volume in a single run. In order to increase efficiency of our calculations we introduce a number of modifications to the original WL-approach. Various properties of the system over wide temperature and volume or pressure ranges, i.e., conformational energy, heat capacity, and free energy, are obtained from the two-dimensional density of states by simple integration. The osmotic pressure is calculated as a derivative of Helmholtz free energy. Alternatively, properties of the system, including average volume, can be obtained under condition of NPT ensemble. It is shown that the both approaches produce coinciding Posm(V) isotherms. In all considered cases we observe repulsive effective interaction between the membrane surfaces, and repulsion is stronger for the surfaces with fixed dipoles.

  • 232. Waluyo, Iradwikanari
    et al.
    Huang, Congcong
    Nordlund, Dennis
    Bergmann, Uwe
    Weiss, Thomas M.
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nilsson, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    The structure of water in the hydration shell of cations from x-ray Raman and small angle x-ray scattering measurements2011Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, nr 6, s. 064513-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl2, and AlCl3 with the particular aim to provide information about the structure of the hydration shells of the cations. XRS spectra show that Na+ weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg2+ and Al3+, on the other hand, cause formation of short and strong hydrogen bonds between the surrounding water molecules. SAXS data show that Mg2+ and Al3+ form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factor extracted from the SAXS data, we found that Mg2+ and Al3+ have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg2+ and Al3+ is, respectively, ~61% and ~71% higher than in bulk water.

  • 233. Wang, Hongjing
    et al.
    Wang, Liang
    Sato, Takaaki
    Sakamoto, Yasuhiro
    Tominaka, Satoshi
    Miyasaka, Keiichi
    Miyamoto, Nobuyoshi
    Nemoto, Yoshihiro
    Terasaki, Osamu
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Yamauchi, Yusuke
    Synthesis of Mesoporous Pt Films with Tunable Pore Sizes from Aqueous Surfactant Solutions2012Inngår i: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 24, nr 9, s. 1591-1598Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Platinum (Pt) is widely used as battery electrodes, catalysts for chemicals, and catalysts for exhaust gas decomposition in industries. Increasing need and very limited supply of rare Pt is a serious problem in the world. Here, we propose new synthetic way for reducing the use of Pt in a catalytic system by increasing the surface area and modifying the Pt surface structure. Several types of mesoporous Pt films with different pore sizes ranging from 5 to 30 nm are prepared by electrochemical plating in aqueous surfactant solutions. The mesopore walls are composed of connected Pt nanoparticles with around 3 nm in diameter. The Pt atomic crystallinity is coherently extending across over several Pt nanoparticles, showing a large number of atomic steps, which can accelerate methanol oxidation reaction. As a result of a high surface area and unique Pt surface, our mesoporous Pt film exhibits high potentiality as a superior electrocatalyst.

  • 234.
    Wang, Yong-Lei
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Electrostatic Interactions in Coarse-Grained Simulations: Implementations and Applications2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Electrostatic interactions between charged species play a prominent role in determining structures and states of physical system, leading to important technological and biological applications. In coarse-grained simulations, accurate description of electrostatic interactions is crucial in addressing physical phenomena at larger spatial and longer temporal scales.

    In this thesis, we implement ENUF method, an abbreviation for Ewald summation based on non-uniform fast Fourier transform technique, into dissipative particle dynamics (DPD) scheme. With determined suitable parameters, the computational complexity of ENUF-DPD method is approximately described as O(N logN). The ENUF-DPD method is further validated by investigating dependence of polyelectrolyte conformations on charge fraction of polyelectrolyte and counterion valency of added salts, and studying of specific binding structures of dendrimers on amphiphilic membranes.

    In coarse-grained simulations, electrostatic interactions are either explicitly calculated with suitable methods, or implicitly included in effective potentials. The effect of treatment fashion of electrostatic interactions on phase behavior of [BMIM][PF6] ionic liquid (IL) is systematically investigated. Our systematic analyses show that electrostatic interactions should be incorporated explicitly in development of effective potentials, as well as in coarse-grained simulations to improve reliability of simulation results.

    Detailed image of microscopic structures and orientations of [BMIM][PF6] at graphene and vacuum interfaces are investigated by using atomistic simulations. Imidazolium rings and alkyl side chains of [BMIM] lie preferentially flat on graphene surface. At IL-vacuum interface, ionic groups pack closely together to form polar domains, leaving alkyl side chains populated at interface and imparting hydrophobic character. With the increase of IL filmthickness, orientations of [BMIM] change gradually from dominant flat distributions along graphene surface to orientations where imidazolium rings are either parallel or perpendicular to IL-vacuum interface with tilted angles. The interfacial spatial ionic structural heterogeneity formed by ionic groups also contributes to heterogeneous dynamics in interfacial regions.

  • 235.
    Wang, Yong-Lei
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stellenbosch University, South Africa.
    Interfacial structure and orientation of confined ionic liquids on charged quartz surfaces2014Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, nr 42, s. 23329-23339Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Atomistic molecular dynamics simulations have been performed to study microscopic ionic structures and orientational preferences of absorbed [BMIM] cations and four paired anions ([BF4], [PF6], [TFO] and [TF2N]) on quartz surfaces. Two chemically different quartz surface models were adopted: one is saturated with silanol Si(OH)(2) groups, and the other one is covered by silane SiH2 groups, respectively. Simulation results reveal that dense ionic layers, characterized by distinct mass, number, charge and electron densities, are formed in quartz interfacial region. The orientational preferences of confined ionic groups are characterized with different features depending on the size and shape of anionic groups, and the quartz surface charge. The [BMIM] cations attach exclusively onto the negatively charged Si(OH) (2) surface. The imidazolium rings lie preferentially perpendicular to Si(OH)(2) surface, to which the directly connected methyl and butyl chains are oriented and elongated along Si(OH)(2) surface, respectively. The anions are mainly absorbed on positively charged SiH2 surface. The main axes of asymmetric [TFO] and [TF2N] anions are perpendicular and parallel to SiH2 surface, respectively. Such distinct structural and orientational preferences of confined ionic groups attribute to the strong electrostatic interactions and the formation of hydrogen bonds between confined ionic species and quartz interfacial groups.

  • 236.
    Wang, Yong-Lei
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Jilin University.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lu, Zhong-Yuan
    Influence of ionic liquid film thickness on ion pair distributionsand orientations at graphene and vacuum interfaces2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 32, s. 13559-13569Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microscopic structures, orientational preferences together with mass, number and electron density distributions of 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been studied on a neutral hydrophobic graphene surface, and at the IL–vacuum interface using atomistic Molecular Dynamics simulations. At the IL–graphene interface, distinct mass, number and electron density distributions are observed oscillating into the bulk region with several compact structural layers. The imidazolium ring of [BMIM] cations lies preferentially flat on the graphene surface, with its methyl and butyl side chains elongated along the graphene surface. At the IL–vacuum interface, however, the distributions of [BMIM][PF6] ion pairs are strongly influenced by the thickness of IL film. With the increase of IL film thickness, the orientations of [BMIM] cations at the IL–vacuum interface change gradually from dominant flat distributions along the graphene surface to orientations where the imidazolium rings are either parallel or perpendicular to the IL–vacuum interface with tilted angles. The outmost layers are populated with alkyl groups and imparted with distinct hydrophobic character. The calculated radial distribution functions suggest that ionic structures of [BMIM][PF6] ion pairs in IL–graphene and IL–vacuum interfacial regions are significantly different from each other and also from that in bulk regions.

  • 237.
    Wang, Yong-Lei
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Jilin University.
    Laaksonen, Aattoo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lu, Zhong-Yuan
    Implementation of non-uniform FFT based Ewald summation in dissipative particle dynamics method2013Inngår i: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 235, s. 666-682Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The ENUF method, i.e., Ewald summation based on the non-uniform FFT technique (NFFT), is implemented in dissipative particle dynamics (DPD) simulation scheme to fast and accurately calculate the electrostatic interactions at mesoscopic level. In a simple model electrolyte system, the suitable ENUF–DPD parameters, including the convergence parameter α, the NFFT approximation parameter p, and the cut-offs for real and reciprocal space contributions, are carefully determined. With these optimized parameters, the ENUF–DPD method shows excellent efficiency and scales as O(NlogN)O(NlogN). The ENUF–DPD method is further validated by investigating the effects of charge fraction of polyelectrolyte, ionic strength and counterion valency of added salts on polyelectrolyte conformations. The simulations in this paper, together with a separately published work of dendrimer–membrane complexes, show that the ENUF–DPD method is very robust and can be used to study charged complex systems at mesoscopic level.

  • 238.
    Wang, Yong-Lei
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lu, Zhong-Yuan
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stellenbosch University, South Africa.
    Heterogeneous dynamics of ionic liquids in confined films with varied film thickness2014Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, nr 38, s. 20731-20740Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dynamical behavior and characteristics of 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) in confined films with varied film thickness have been investigated using atomistic molecular dynamics simulations. Simulation results indicate that the dynamics of confined ionic groups in interfacial regions is highly heterogeneous and depends strongly on their relative layered positions in the confined IL film. The dynamics and relaxation times of the ionic groups in the bulk region of confined IL films are very similar to that in the corresponding pure bulk simulation. In contrast, the diffusion of the corresponding ionic groups slows down and can be characterized by slaved diffusion while the corresponding relaxation times increase remarkably as these ionic groups come closer to the neutral graphene surface. While at the IL-vacuum interface, the diffusion and relaxation of terminal carbon atoms of butyl chains of [BMIM] cations are much faster than in other layers of the confined IL film and in the bulk region of the simulation system without confinement, due to their librated motion in this interfacial region. The dynamical heterogeneity of the confined ionic groups is intrinsically related to microscopic ionic structures and the orientational preference of [BMIM][PF6] ion pairs in interfacial regions.

  • 239.
    Wang, Yong-Lei
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Jilin University.
    Lyubartsev, Alexander
    Lu, Zhong-Yuan
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effectivepotentials2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 20, s. 7701-7712Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A coarse-grained model, with three sets of effective pair potentials for 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim][PF6]) ionic liquid, is introduced and used to study the structural and dynamical properties over extended length and time scales. Three sets of effective pair potentials between coarse-grained beads are obtained using the Newton Inversion and the Iterative Boltzmann Inversion methods, respectively, with different treatment of electrostatic interactions. The coarse-grained simulation results are compared systematically with corresponding atomistic simulation results on several thermodynamical and structural quantities together with charge density distributions. In addition, the scattering and dynamical properties are also calculated and compared to both atomistic simulation results and experimental measurements. While all three sets of the effective potentials provide perfect agreement with the atomistic simulation for radial distribution functions, our analysis shows that in coarse-grained simulations, the long-range electrostatic interactions between ionic groups are important and should be treated explicitly to improve the reliability of other simulation results. With explicit incorporation of electrostatic interactions derived from the Newton Inversion, the coarse-grained potentials provide the most consistent description of thermodynamical, scattering and dynamical properties including their temperature dependence as compared to atomistic simulations. We conclude also that the current atomistic force field should be further improved to meet specific requirements for studying the dynamical properties of the [Bmim][PF6] system over a large temperature range.

  • 240.
    Wang, Yong-Lei
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Shah, Faiz Ullah
    Glavatskih, Sergei
    Antzutkin, Oleg N.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stellenbosch University, South Africa.
    Atomistic Insight into Orthoborate-Based Ionic Liquids: Force Field Development and Evaluation2014Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, nr 29, s. 8711-8723Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P-6,P-6,P-6,P-14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions.

  • 241. Wennberg, Christian L.
    et al.
    Murtola, Teemu
    Hess, Berk
    Lindahl, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties2013Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, nr 8, s. 3527-3537Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The accuracy of electrostatic interactions in molecular dynamics advanced tremendously with the introduction of particle-mesh Ewald (PME) summation almost 20 years ago. Lattice summation electrostatics is now the de facto standard for most types of biomolecular simulations, and in particular, for lipid bilayers, it has been a critical improvement due to the large charges typically present in zwitterionic lipid headgroups. In contrast, Lennard-Jones interactions have continued to be handled with increasingly longer cutoffs, partly because few alternatives have been available despite significant difficulties in tuning cutoffs and parameters to reproduce lipid properties. Here, we present a new Lennard-Jones PME implementation applied to lipid bilayers. We confirm that long-range contributions are well approximated by dispersion corrections in simple systems such as pentadecane (which makes parameters transferable), but for inhomogeneous and anisotropic systems such as lipid bilayers there are large effects on surface tension, resulting in up to 5.5% deviations in area per lipid and order parameters-far larger than many differences for which reparameterization has been attempted. We further propose an approximation for combination rules in reciprocal space that significantly reduces the computational cost of Lennard-Jones PME and makes accurate treatment of all nonbonded interactions competitive with simulations employing long cutoffs. These results could potentially have broad impact on important applications such as membrane proteins and free energy calculations.

  • 242.
    Westin, Gunnar
    Stockholms universitet, Naturvetenskapliga fakulteten.
    A study of sol-gel preparation of M-SB oxides via bimetallic alkoxides or mixed acetate-alkoxide routes1994Doktoravhandling, med artikler (Annet vitenskapelig)
  • 243. Westin, Gunnar
    et al.
    Leideborg, Michael
    Lashgari, Koroush
    Coleman, Victoria A
    Jansson, Kjell
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Pohl, Annika
    Solution processing of conducting dense and porous films; doped ZnO and TiO2, and perovskites2009Inngår i: International Journal of Nanotechnology, Vol. 6, nr 9, s. 828-849Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Soln. based processing of porous and dense films by all-alkoxide based precursor systems have been investigated and compared, with a focus on the connection between the precursors and heat-treatment, and the product oxide quality and structure.  Three systems were investigated typically with TGA, DSC, XPS, IR spectroscopy, X-ray diffraction, TEM-EDS and SEM-EDS, but also with other advanced characterization techniques: (i) manganate and cobaltate perovskites of the LCMO (La0.67Ca0.33MnO3), LSMO (La0.75Sr0.25MnO3), LNCMO (La0.33Nd0.33Ca0.33MnO3), LBSM (La0.75Ba0.125Sr0.125MnO3) and LSCO (La0.50Sr0.50CoO3) compns. were investigated.  Highly epitaxial films of LCMO and LSCO were prepd., and the CMR properties of the LCMO were comparable to those of PVD derived films.  Polycryst. films were prepd. for all perovskites.  (ii) Three routes to ZnO : Co/Al were investigated and compared; an acetate based route and two alkoxide based routes with different heat-treatments.  With the acetate based and the alkoxide based route using hydrolysis in air, a max. Co doping of 6% was obtained, while in absence of CO2 and O2, the doping range could be extended to 20%Co.  Both dense films and porous nano-structured films were prepd.  The magnetic properties of the Co-doped films did not show any room-temp. ferro-magnetism.  (iii) ZrO2 and NbO2.5 doped anatase TiO2 were prepd. by heat-treatment or hydrothermal routes.  Alio-valent doping of up to more than 35% of NbO2.5 could be achieved in the anatase.  It is believed that the pentavalent metal doping is compensated by metal vacancies, and as expected from this assumption, the materials have a low d.  ZrO2 doping in titania led to an increase in the dye-sensitized solar cell efficiency and highly active and stable photo-catalysts.

  • 244.
    Wicklein, Bernd
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi. Wallenberg Wood Science Center, KTH, Sweden.
    Salazar-Alvarez, German
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för materialkemi. Wallenberg Wood Science Center, KTH, Sweden.
    Functional hybrids based on biogenic nanofibrils and inorganic nanomaterials2013Inngår i: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 1, nr 18, s. 5469-5478Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This feature article reviews some of the recent work on the fabrication of functional hybrids based on biogenic nanofibers and inorganic nanomaterials with an emphasis on their functional properties and suggested potential applications. We also discuss some of the work oriented towards the formation of ordered materials in the pursuit of achieving a hierarchical construction. Besides the academic interest in biogenic nanomaterials, it is anticipated that the use of natural, abundant nanomaterials, e.g., cellulose, chitin, collagen, and silk, could provide affordable functional nanomaterials in developing countries.

  • 245.
    Wikfeldt, Kjartan Thor
    et al.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). University of Iceland.
    Batista, E. R.
    Vila, F. D.
    Jonsson, H.
    A transferable H2O interaction potential based on a single center multipole expansion: SCME2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 39, s. 16542-16556Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A transferable potential energy function for describing the interaction between water molecules is presented. The electrostatic interaction is described rigorously using a multipole expansion. Only one expansion center is used per molecule to avoid the introduction of monopoles. This single center approach turns out to converge and give close agreement with ab initio calculations when carried out up to and including the hexadecapole. Both dipole and quadrupole polarizability are included. All parameters in the electrostatic interaction as well as the dispersion interaction are taken from ab initio calculations or experimental measurements of a single water molecule. The repulsive part of the interaction is parametrized to fit ab initio calculations of small water clusters and experimental measurements of ice I-h. The parametrized potential function was then used to simulate liquid water and the results agree well with experiment, even better than simulations using some of the point charge potentials fitted to liquid water. The evaluation of the new interaction potential for condensed phases is fast because point charges are not present and the interaction can, to a good approximation, be truncated at a finite range.

  • 246.
    Wikfeldt, Thor Kjartan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Nilsson, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Pettersson, Lars G.M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Spatially inhomogeneous bimodal inherent structure of simulated liquid water2011Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 44, s. 19918-19924Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the supercooled regime at elevated pressure two forms of liquid water, high-density (HDL) and low-density (LDL), have been proposed to be separated by a coexistence line ending at a critical point, but a connection to water at ambient conditions has been lacking. Here we perform large-scale molecular dynamics simulations and demonstrate that the underlying potential energy surface gives a strictly bimodal characterization of the molecules at all temperatures and pressures, including the biologically and technologically important ambient regime, as spatially inhomogeneous either LDL- or HDL-like with a 3 : 1 predominance for HDL under ambient conditions. The Widom line in the supercooled regime, where maximal structural fluctuations take place, coincides with a 1 : 1 distribution. Although our results are based on molecular dynamics force-field simulations the close agreement with recent analyses of experimental X-ray spectroscopy and scattering data indicates a unified description also of real liquid water covering supercooled to ambient conditions.

  • 247. Wolf, T. J. A.
    et al.
    Schalk, Oliver
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. University of Munich.
    Radloff, R.
    Wu, G.
    Lang, P.
    Stolow, A.
    Unterreiner, A. -N
    Ultrafast photoinduced dynamics of halogenated cyclopentadienes: observation of geminate charge-transfer complexes in solution2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 18, s. 6673-6683Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The photoinduced dynamics of the fully halogenated cyclopentadienes C5Cl6 and C5Br6 have been investigated in solution and gas phase by femtosecond time-resolved spectroscopy. Both in solution and in gas phase, homolytic dissociation into a halogen radical and a C5X5 (X = Cl, Br) radical was observed. In liquid phase, solvent-dependent formation of charge transfer complexes between geminate radicals was observed for the first time. These complexes were found to be surprisingly stable and offered the opportunity to follow the dynamics of specific radical pairs. In the case of C5Cl6 in trichloroethanol, a reaction of the chlorine radical with molecules from the solvent cage was observed.

  • 248.
    Xu, Chao
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Hedin, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Synthesis of microporous organic polymers with high CO2-over-N-2 selectivity and CO2 adsorption2013Inngår i: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 1, nr 10, s. 3406-3414Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A series of microporous organic polymers (MOPs) were synthesized by Schiff base condensation of 1,3,5-tris(4-aminophenyl)benzene and a number of dialdehyde monomers. The polymers were structurally characterized by in situ infrared and ex situ solid state C-13{H-1} nuclear magnetic resonance (NMR) spectroscopy. Synthesis conditions were optimized to enhance CO2 uptake by the MOPs. Synthesis at low temperatures results in the MOPs being linked by imine groups. Heating of the MOPs reduces the number of imine groups and after heating to >300 degrees C nitrile groups were found to be present in the MOPs. The MOPs have specific surface areas up to 614 m(2) g(-1) and narrow pore size distributions of similar to 4 to 8 angstrom. The selectivity of CO2-over-N-2 at 273 K and 1 bar was 56-77, which requires either an influence of chemisorption on CO2 or a molecular sieving (or kinetic selection) of CO2-over-N-2. The materials had also heats of adsorption typical for physisorption of CO2.

  • 249. Xu, Yunhua
    et al.
    Åkermark, Torbjörn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Gyollai, Viktor
    Zou, Dapeng
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Duan, Lele
    Zhang, Rong
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Sun, Licheng
    A New Dinuclear Ruthenium Complex as an  Efficient for Water Oxidation Catalyst2009Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 48, nr 7, s. 2717-2719Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A dinuclear ruthenium complex, which acts as a molecular catalyst for water oxidation, has been synthesized and characterized. The electronic and electrochemical properties were studied by UV−vis spectroscopy and cyclic voltammetry. The oxidation potentials of the complex are significantly lowered by introducing a negatively charged carboxylate ligand, in comparison with those of the reported complexes that have neutral ligands. The catalytic activity of the complex toward water oxidation using Ce(NH4)2(NO3)6 as a chemical oxidant was investigated by means of an oxygen electrode and mass spectrometry. The turnover number of this catalyst with CeIV as the chemical oxidant was found to be ca. 1700. The mass spectroscopic analysis of the isotopomer distribution in oxygen evolved from 18O-labeled water indicates that O atoms in the evolved oxygen originate from water

  • 250.
    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, s. 2082-2096Artikkel 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.

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