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  • 101.
    Papadakis, Raffaello
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Preferential Solvation of a Highly Medium Responsive Pentacyanoferrate(II) Complex in Binary Solvent Mixtures: Understanding the Role of Dielectric Enrichment and the Specificity of Solute-Solvent Interactions2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 35, p. 9422-9433Article in journal (Refereed)
    Abstract [en]

    In this work, the preferential solvation of an intensely, solvatochromic ferrocyanide(II) dye involving a 4,4'-bipyridine-based ligand was examined in various binary solvent mixtures. Its solvatochromic behavior was rationalized in terms of specific and nonspecific solute-solvent interactions. An exceptional case of solvatochromic inversion was observed when going from alcohol/water to amide/water mixtures. These effects were quantified using Onsager's solvent polarity function. Furthermore, the sensitivity of the solvatochromism of the dye was determined using various solvatochromic parameters such as pi* expressing the dipolarity/polarizability of solvents and alpha expressing the hydrogen-bond-donor acidity of solvents. This analysis was useful for the rationalization of the selective solvation phenomena occurring in the three types of alcohol/water and amide/water mixtures studied. Furthermore, two preferential solvation models were employed for the interpretation of the experimental spectral results in binary solvent mixtures, namely, the model of Suppan on dielectric enrichment [J. Chem. Soc. Faraday Trans. 1 1987, 83, 495-509] and the model of Bosch, Roses, and co-workers [J. Chem. Soc., Perkin Trans. 2, 1995, 8, 1607-1615]. The first model successfully predicted the charge transfer energies of the dye in formamide/water and N-methylformamide/water mixtures, but in the case of MeOH/water mixtures, the prediction was less accurate because of the significant contribution of specific solute-solvent interactions in that case. The second model gave more insights for both specific solute-solvent as well as solvent- solvent interactions in the cybotactic region. The role of dielectric enrichment and specific interactions was discussed based on the findings.

  • 102.
    Patriksson, Alexandra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Adams, Christopher M.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
    Kjeldsen, Frank
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
    Zubarev, Roman
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    A direct comparison of protein structure in the gas and solution phase - the Trp-cage2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 46, p. 13147-13150Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location, there is significant difference in the structures, with a substantial increase in hydrogen bonds and exposure of hydrophobic parts in the gas phase. The structure of the salt bridge in the gas phase is also much more stable than in the (experimental) solution structure.

  • 103.
    Paulsson, Heléne
    et al.
    KTH, Oorganisk kemi / Inorganic Chemistry.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Kloo, Lars
    KTH, Oorganisk kemi / Inorganic Chemistry.
    Molten and Solid Trialkylsulfonium Iodides and Their Polyiodides as Electrolytes in Dye-Sensitized Nanocrystalline Solar Cells2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 49, p. 13665-13670Article in journal (Refereed)
    Abstract [en]

    Potential new electrolytes for dye-sensitized nanocrystalline solar cells (DNSCs) of Grätzel type based on trialkylsulfonium iodides have been investigated. Room temperature molten salts of (Et2MeS)I, (Bu2MeS)I, and (Bu2EtS)I, with iodine in low concentrations, revealed good conducting abilities. DNSCs using iodine-doped (Bu2MeS)I as electrolyte achieved an overall light-to-electricity conversion efficiency of 3.7% in simulated AM 1.5 solar light at a light intensity of 0.1 Sun. The effects from varying the temperature during the I/V measurements were studied, as well as the effects of 4-tert-butylpyridine treatment of the electrodes.

  • 104.
    Petersson, Jonas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Eklund, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Ultrafast Electron Transfer Dynamics of a Zn(II)porphyrin-Viologen Complex Revisited S-2 vs S-1 Reactions and Survival of Excess Excitation Energy2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 45, p. 14329-14338Article in journal (Refereed)
    Abstract [en]

    The photoinduced electron transfer reactions in a self-assembled 1 1 complex of zinc(II)tetrasulphonatophe nylporphyrin (ZnTPPS4-) and methylviologen (MV2+) in aqueous solution were investigated with transient absorption spectroscopy ZnTPPS4- was excited either in the Soret or one of the two Q-bands corresponding to excitation into the S-2 and S-1 states respectively The resulting electron transfer to MV2+ occurred surprisingly with the same time constant of tau(FET) = 180 fs from both electronic states The subsequent back electron transfer was rapid and the kinetics was independent of the initially excited state (tau(BET) = 700 fs) However ground state reactants in a set of vibrationally excited states were observed The amount of vibrationally excited ground states detected increased with increasing energy of the initial excited state showing that excess excitation energy survived a two-step electron transfer reaction in solution Differences in the ZnTPSS3-/MV+. spectra suggest that the forward election transfer from the S-2 state at least partially produces an electronically excited charge transfer state which effectively suppresses the influence of the inverted regime Other possible reasons for the similar election transfer rates for the different excited states are also discussed

  • 105.
    Petersson, Jonas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Ultrafast Electron Transfer Dynamics in a Series of Porphyrin/Viologen Complexes: Involvement of Electronically Excited Radical Pair Products2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 24, p. 7531-7540Article in journal (Refereed)
    Abstract [en]

    Ultrafast electron transfer was studied for a series of metalloporphyrin/bipyridinium complexes in aqueous solution, using laser excitation in the Soret or Q-bands of the porphyrin. Electron transfer occurred before electronic and vibrational relaxation of the initial excited state. This allowed for a thorough investigation of the dependence of electron transfer rate constants on the driving force and the nature of the product state. The driving force dependence showed that electron transfer from the S-2 state occurred to an electronically excited radical pair state, and the present results provide the most direct evidence to date for the formation of such states in photoinduced electron transfer reactions. We also found that subsequent recombination of the radical pair produced vibrationally excited ground states; the excess energy of the radical pair generated from the initial state is not completely dissipated during the lifetime of the radical pair. The porphyrin/bipyridinium complexes where recombination lies deeper in the Marcus inverted region show less formation of unrelaxed ground states, contrary to what is expected from equilibrium electron transfer theories. Instead, the rate of the electron transfer, which competes with vibrational relaxation, was the main parameter controlling the relative yield of unrelaxed ground states within this series of complexes.

  • 106.
    Poberznik, Matic
    et al.
    Jozef Stefan Inst, Dept Phys & Organ Chem, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia..
    Purg, Miha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Repic, Matej
    Natl Inst Chem, Lab Biocomp & Bioinformat, Hajdrihova Ulica 19, SI-1000 Ljubljana, Slovenia..
    Mavri, Janez
    Natl Inst Chem, Lab Biocomp & Bioinformat, Hajdrihova Ulica 19, SI-1000 Ljubljana, Slovenia..
    Vianello, Robert
    Rudjer Boskovic Inst, Computat Organ Chem & Biochem Grp, Bijenicka Cesta 54, HR-10000 Zagreb, Croatia..
    Empirical Valence Bond Simulations of the Hydride-Transfer Step in the Monoamine Oxidase A Catalyzed Metabolism of Noradrenaline2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 44, p. 11419-11427Article in journal (Refereed)
    Abstract [en]

    Monoamine oxidases (MAOs) A and B are flavoenzymes responsible for the metabolism of biogenic amines, such as dopamine, serotonin, and noradrenaline (NA), which is why they have been extensively implicated in the etiology and course of various neurodegenerative disorders and, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. The precise chemical mechanism through which MAOs regulate the amine Concentration, which is vital for the development of novel inhibitors, is still not unambiguously determined in the literature. In this work, we present atomistic empirical valence bond simulations of the rate-limiting step of the MAO-A-catalyzed NA (norepinephrine) degradation, involving hydride transfer from the substrate alpha-methylene group to the flavin moiety of the flavin adenine dinucleotide prosthetic group, employing the full dimensionality and thermal fluctuations of the hydrated enzyme, with extensive configurational sampling. We show that MAO-A lowers the free energy of activation by 14.3 kcal mol(-1) relative to that of the same reaction in aqueous solution, whereas the calculated activation free energy of Delta G(double dagger) = 20.3 +/- 1.6 kcal mori is found to be in reasonable agreement with the correlated experimental value of 16.5 kcal mol(-1). The results presented here strongly support the fact that both MAO-A and MAO-B isoforms function by the same hydride-transfer mechanism. We also considered a few point mutations of the "aromatic cage" tyrosine residue (Tyr444Phe, Tyr444Leu, Tyr444Trp, Tyr444His, and Tyr444Glu), and the calculated changes in the reaction barriers are in agreement with the experimental values, thus providing further support to the proposed mechanism.

  • 107.
    Pokapanich, Wandared
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Ottosson, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Svensson, Svante
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Öhrwall, Gunnar
    MAX-lab, Lund UniVersity.
    Winter, Bernd
    Helmholtz-Zentrum Berlin fur Materialien und Energie, and BESSY,.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Bond Breaking, Electron Pushing and Proton Pulling: Active and Passive Roles in the Interaction between Aqueous Ions and Water as Manifested in the O 1s Auger Decay2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 1, p. 3-8Article in journal (Refereed)
    Abstract [en]

    A core-ionized H2O molecule in liquid water primarily relaxes through normal Auger decay, leading to a two-hole final state in which both valence holes are localized on the same water molecule. Electronic coupling to the environment, however, allows for alternative decays resembling Intermolecular Coulombic Decay (ICD), producing final states with one of the holes delocalized on a neighboring water molecule. Here we present an experimental study of such minority processes, which adds to our understanding of dynamic interactions of electronically excited H2O molecules with their local surrounding in liquid water and aqueous solution. We show that the solvation of metal-halide salts considerably influences these minority decay channels from the water 0 1s-1 state. By breaking water-water bonds, both the metal cations and halide anions are found to reduce the decay into water-water delocalized states, thus having a "passive" effect on the Auger spectrum. The halide anions also play an "active" role by opening a new ICD-like decay pathway into water-halide delocalized states. The importance of this contribution increases from F- to I-, which we suggest to be caused by a directional polarization of the halide anion toward the core-ionized H2O+ cation in the intermediate state of the Auger process. This increases the electronic overlap between the two centers and makes delocalized decays more probable. We furthermore show that F-, the smallest and most strongly hydrated of the halides, plays an additional role as proton puller during the core-hole lifetime, resulting in proton dynamics on the low femtosecond time scale. Our results represent a step forward toward a better understanding of how aqueous solutions, when exposed to soft X-rays, channel excess energy. This has implications for several aspects of physical and radiation chemistry, as well as biology.

  • 108.
    Qazi, S. Junaid S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Rennie, Adrian R.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Tucker, Ian
    Penfold, Jeff
    Grillo, Isabelle
    Alignment of Dispersions of Plate-Like Colloidal Particles of Ni(OH)(2) Induced by Elongational Flow2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 13, p. 3271-3280Article in journal (Refereed)
    Abstract [en]

    Small-angle neutron scattering, SANS, has been used to study the alignment of a sterically stabilized colloidal dispersion of nickel hydroxide induced by elongational flow. Two different concentrations, 20 and 23 wt %, of well-defined hexagonal platelets have been studied. Significant anisotropy in the scattering patterns has been observed for the higher concentration dispersion that increases with increasing elongational strain rate. The effect of pipe flow (shear flow) on the orientational ordering at the inlets is also described. Near the outlets there is also a shear stress and this tends to increase the alignment. The orientational distribution of the particles under flow is described in terms of an order parameter calculated with respect to an individual director for each scattering pattern. The experimental measurements are supported by comparison with computer simulations which help to explain the effects of local velocity on the alignment induced by elongational flow. A slight decrease in the observed alignment was found after continuous flow for approximately 30 min and possible reasons are discussed.

  • 109.
    Qazi, S. Junaid S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Rennie, Adrian R.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Tucker, Ian
    Penfold, Jeff
    Grillo, Isabelle
    Impact of Ni(OH)(2) Platelike Particles on Lamellar Surfactant Mesophases and the Orientation of Their Mixtures under Elongational Flow2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 35, p. 10413-10424Article in journal (Refereed)
    Abstract [en]

    This article describes the behavior under elongational flow of mixtures of lamellar fragments and platelike colloidal particles. Mixtures of a dialkyl chain cationic surfactant, DHTAC (15 wt %), and the nonionic surfactant Brij 97 (0.5 wt %) form dispersions of lamellar phase fragments, and these were studied in the presence of smaller platelike colloidal particles of Ni(OH)(2) stabilized with sodium polyacrylate. Small-angle neutron scattering was used to follow the changes in the lamellar phase fragments in the mixture under elongational flow. The addition of a small fraction of the Ni(OH)(2) dispersion resulted in significantly increased viscosity and reduced the structure and size of the lamellar fragments, and this effect was further enhanced because of the flow induced alignment. The behavior of the mixture under elongational flow is described, and the induced orientation is discussed in terms of order parameters at the different positions using spatially resolved small-angle scattering. The effect of flow rate on the orientational alignment in the mixture is also described.

  • 110. Rapatskiy, Leonid
    et al.
    Ames, William M.
    Pérez-Navarro, Montserrat
    Savitsky, Anton
    Griese, Julia J.
    Stockholms universitet, Institutionen för biokemi och biofysik.
    Weyhermüller, Thomas
    Shafaat, Hannah S.
    Högbom, Martin
    Stockholms universitet, Institutionen för biokemi och biofysik.
    Neese, Frank
    Pantazis, Dimitrios A.
    Cox, Nicholas
    Characterization of Oxygen Bridged Manganese Model Complexes Using Multifrequency (17)O-Hyperfine EPR Spectroscopies and Density Functional Theory2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 43, p. 13904-13921Article in journal (Refereed)
    Abstract [en]

    Multifrequency pulsed EPR data are reported for a series of oxygen bridged (μ-oxo/μ-hydroxo) bimetallic manganese complexes where the oxygen is labeled with the magnetically active isotope (17)O (I = 5/2). Two synthetic complexes and two biological metallocofactors are examined: a planar bis-μ-oxo bridged complex and a bent, bis-μ-oxo-μ-carboxylato bridge complex; the dimanganese catalase, which catalyzes the dismutation of H2O2 to H2O and O2, and the recently identified manganese/iron cofactor of the R2lox protein, a homologue of the small subunit of the ribonuclotide reductase enzyme (class 1c). High field (W-band) hyperfine EPR spectroscopies are demonstrated to be ideal methods to characterize the (17)O magnetic interactions, allowing a magnetic fingerprint for the bridging oxygen ligand to be developed. It is shown that the μ-oxo bridge motif displays a small positive isotropic hyperfine coupling constant of about +5 to +7 MHz and an anisotropic/dipolar coupling of -9 MHz. In addition, protonation of the bridge is correlated with an increase of the hyperfine coupling constant. Broken symmetry density functional theory is evaluated as a predictive tool for estimating hyperfine coupling of bridging species. Experimental and theoretical results provide a framework for the characterization of the oxygen bridge in Mn metallocofactor systems, including the water oxidizing cofactor of photosystem II, allowing the substrate/solvent interface to be examined throughout its catalytic cycle.

  • 111.
    Razaq, Aamir
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Mihranyan, Albert
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Welch, Ken
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Nyholm, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Inorganic Chemistry.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Influence of the type of oxidant on anion exchange properties of fibrous Cladophora cellulose/polypyrrole composites2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 2, p. 426-433Article in journal (Refereed)
    Abstract [en]

    The electrochemically controlled anion absorption properties of a novel large surface area composite paper material composed of polypyrrole (PPy) and cellulose derived from Cladophora sp. algae, synthesized with two oxidizing agents, iron(III) chloride and phosphomolybdic acid (PMo), were analyzed in four different electrolytes containing anions (i.e., chloride, aspartate, glutamate, and p-toluenesulfonate) of varying size. The composites were characterized with scanning and transmission electron microscopy, N2 gas adsorption, and conductivity measurements. The potential-controlled ion exchange properties of the materials were studied by cyclic voltammetry and chronoamperometry at varying potentials. The surface area and conductivity of the iron(III) chloride synthesized sample were 58.8 m2/g and 0.65 S/cm, respectively, while the corresponding values for the PMo synthesized sample were 31.3 m2/g and 0.12 S/cm. The number of absorbed ions per sample mass was found to be larger for the iron(III) chloride synthesized sample than for the PMo synthesized one in all four electrolytes. Although the largest extraction yields were obtained in the presence of the smallest anion (i.e., chloride) for both samples, the relative degree of extraction for the largest ions (i.e., glutamate and p-toluenesulfonate) was higher for the PMo sample. This clearly shows that it is possible to increase the extraction yield of large anions by carrying out the PPy polymerization in the presence of large anions. The results likewise show that high ion exchange capacities, as well as extraction and desorption rates, can be obtained for large anions with high surface area composites coated with relatively thin layers of PPy.

  • 112.
    Rensmo, Håkan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Keis, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Lindström, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Södergren, Sven
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Solbrand, Anita
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Lindquist, Sten-Eric
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Wang, Lingna
    Muhammed, M
    High light-to-energy conversion efficiencies for solar cells based on nanostructured ZnO electrodes1997In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 101, no 14, p. 2598-2601Article in journal (Other academic)
    Abstract [en]

    Photoelectrochemical properties of nanostructured ZnO thin film electrodes have been investigated in the UV and visible regions. For films consisting of 15 nm large undoped crystallites a maximum monochromatic current conversion efficiency of 58% was obtained in the visible using a ruthenium-based dye as a sensitizer. The overall solar energy conversion efficiency for this film was 2%. In comparison, sensitized films consisting of 150 nm large Al-doped crystallites yield a monochromatic current conversion efficiency of 31% and an overall solar energy conversion efficiency of 0.5%. The study also shows that nanostructured ZnO may give high efficiencies in the UV region, approaching unity for the Al-doped films.

  • 113. Romualdo Torres, Gemma
    et al.
    Lindgren, Torbjörn
    Fasta tillståndets fysik. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Experimental Physics.
    Lu, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Experimental Physics.
    Granqvist, Claes-Göran
    Fasta tillståndets fysik. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Experimental Physics.
    Lindquist, Sten-Eric
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Experimental Physics.
    Photoelectrochemical Study of Nitrogen-Doped Titanium Dioxide for Water Oxidation2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 19, p. 5995-6003Article in journal (Refereed)
  • 114.
    Rubino, Stefano
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Razaq, Aamir
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Nyholm, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Leifer, Klaus
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Mihranyan, Albert
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Spatial Mapping of Elemental Distributions in Polypyrrole-Cellulose Nanofibers using Energy-Filtered Transmission Electron Microscopy2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 43, p. 13644-13649Article in journal (Refereed)
    Abstract [en]

    The energy-filtered transmission electron microscopy (EFTEM) technique has been used to study ion-exchange processes in conductive polymer composite nanofibers. The elemental distributions of carbon, nitrogen, oxygen, chlorine, boron, phosphorus, molybdenum, and sulfur within polypyrrole-cellulose nanofibers, used as potential controlled electrochemical solid phase extraction media, have been studied by EFTEM. The distribution of ions within the polypyrrole-cellulose nanofibers and the penetration depth of ions into the material as a function of the size and charge of the latter were investigated. Further, the spatial distribution of single stranded DNA hexamers inside polypyrrole-cellulose nanofibers was mapped subsequent to the electrochemically controlled extraction of DNA from a borate buffer solution. The results show that the EFTEM mapping technique provides unpreceded possibilities for studies of the distribution of ions inside conductive polymer composites.

  • 115. Ryan, D
    et al.
    Nagle, L
    Rensmo, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Fitzmaurice, D
    Programmed assembly of binary nanostructures in solution2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 21, p. 5371-5377Article in journal (Refereed)
    Abstract [en]

    Near size-monodisperse silver nanocrystals and silica nanospheres have been prepared and surface-modified with the [2]pseudorotaxane recognition motifs, dibenzo[24]crown-8 and dibenzylammonium cation, respectively. The silver nanocrystals, 7 nm in diameter, are shown to recognize and bind to the silica nanospheres, 180 nm in diameter, via pseudorotaxane formation. The result is the templated assembly of silver nanocrystals at the surface of the larger silica nanosphere core. This composite material exhibits optical properties that are a consequence of localizing silver nanocrystals at the surface of the silica nanospheres. The templating process is also shown to be reversible. This noncovalent recognition-directed templating strategy represents a novel metallization process resulting in the formation of composite media whose collective properties can be controlled.

  • 116. Saethre, Bjorn Steen
    et al.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Hoffmann, Alex C.
    Free Energy of Separation of Structure II Clathrate Hydrate in Water and a Light Oil2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 20, p. 5933-5940Article in journal (Refereed)
    Abstract [en]

    The adhesion forces and free energies of separation of structure II clathrate hydrates in vacuum and submerged in water and a model oil are investigated by molecular dynamics simulation. The water molecules are modeled by the TIP4P/ice model and the alkanes by the OPLS_AA force field. The results are compared with theory and earlier work. It is observed that the adhesive forces between the simulated surfaces have an effective range of no more than 1.5-2 nm. The hydrate hydrate interaction force is attractive in vacuum and oil, larger in vacuum. In water the interaction force is very slightly repulsive on average and much weaker than in the two other systems with a larger uncertainty. In all cases the interaction is largely entropically driven. The separation energies in vacuum and oil (octane) are stronger than predicted by theory, with free energies of approximately 4 and 0.7 aJ, respectively, likely due to lack of polarization effects. The hydrate hydrate interaction in water is too weak for quantitative comparisons to be made.

  • 117.
    Schnadt, J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Henningsson, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Andersson, M. P.
    Karlsson, P. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics I.
    Uvdal, P.
    Siegbahn, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics I.
    Brühwiler, P. A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Sandell, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Adsorption and Charge-Transfer Study of Bi-isonicotinic Acid on In Situ-Grown Anatase TiO2 Nanoparticles2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 10, p. 3114-3122Article in journal (Refereed)
  • 118.
    Scholtysek, Peggy
    et al.
    Institute of Chemistry - Physical Chemistry, Martin-Luther-University Halle-Wittenberg, Germany.
    Achilles, Anja
    Institute of Physics - NMR, Martin-Luther-University Halle-Wittenberg, Germany.
    Hoffmann, Claudia-Viktoria
    Institute of Chemistry - Physical Chemistry, Martin-Luther-University Halle-Wittenberg, Germany.
    Lechner, Bob-Dan
    Institute of Chemistry - Physical Chemistry, Martin-Luther-University Halle-Wittenberg, Germany.
    Meister, Annette
    ZIK HALOmem, Martin-Luther-University Halle-Wittenberg, Germany.
    Tschierske, Carsten
    Institute of Chemistry - Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Germany.
    Saalwächter, Kay
    Institute of Physics - NMR, Martin-Luther-University Halle-Wittenberg, Germany.
    Edwards, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Blume, Alfred
    Institute of Chemistry - Physical Chemistry, Martin-Luther-University Halle-Wittenberg, Germany.
    A T-Shaped Amphiphilic Molecule Forms Closed Vesicles in Water and Bicelles in Mixtures with a Membrane Lipid2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 16, p. 4871-4878Article in journal (Refereed)
    Abstract [en]

    The T-shaped amphiphilic molecule A6/6 forms a columnar hexagonal liquid-crystalline phase between the crystalline and the isotropic liquid when studied in bulk (Chen et al., 2005). Because of the hydrophilic and flexible oligo(oxyethylene) side chain terminated by a 1-acylamino-1-deoxy-d-sorbitol moiety attached to a rigid terphenyl core with terminal hexyloxy alkyl chains, it was expected that also formation of lyotropic phases could be possible. We therefore studied the behavior of A6/6 in water and also in mixtures with bilayer-forming phospholipids, such as dipalmitoyl-phosphatidylcholine (DPPC), using differential scanning calorimetry (DSC), transmission electron microscopy (TEM), cryo-transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), and solid-state nuclear magnetic resonance (ssNMR). DSC showed for the pure A6/6 suspended in water a phase transition at ca. 23 °C. TEM and cryo-TEM showed vesicular as well as layered structures for pure A6/6 in water below and above this phase transition. By atomic force microscopy (AFM), the thickness of the layer was found to be 5?6 nm. This leads to a model for a bilayer formed by A6/6 with the laterally attached polar side chains shielding the hydrophobic layer built up by the terphenyl core with the terminal alkyl chains of the molecules. For DPPC:A6/6 mixtures (10:1), the DSC curves indicated a stabilization of the lamellar gel phase of DPPC. Negative staining TEM and cryo-TEM images showed planar bilayers with hexagonal morphology and diameters between 50 and 200 nm. The hydrodynamic radius of these aggregates in water, investigated by dynamic light scattering (DLS) as a function of time and temperature, did not change indicating a very stable aggregate structure. The findings lead to the proposition of a new bicellar structure formed by A6/6 with DPPC. In this model, the bilayer edges are covered by the T-shaped amphiphilic molecules preventing very effectively the aggregation to larger structures.

  • 119. Sitar, Simona
    et al.
    Goderis, Bart
    Hansson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Kogej, Ksenija
    Phase Diagram and Structures in Mixtures of Poly(styrenesulfonate anion) and Alkyltrimethylammonium Cations in Water: Significance of Specific Hydrophobic Interaction2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 15, p. 4634-4645Article in journal (Refereed)
    Abstract [en]

    Mixtures of polyelectrolytes and oppositely charged surfactants show very rich phase behavior that is influenced by surfactant-ion and polyion properties and by water content. A general feature is associative phase separation as a result of strong electrostatic interactions, whereas the effect of eventual more specific interactions (e.g., hydrophobic) has not been thoroughly investigated. In this paper, we report a detailed study on phase behavior and structures in poly(styrenesulfonate anion) (PSS-)-cetyltrimethylammonium cation (CTA(+))-water mixtures that are characterized by a hydrophobic interaction between the styrene groups of PSS- and the micelle interior. Structures of various phases were determined by small-angle X-ray scattering, and results indicated the presence of a disordered micellar and an ordered hexagonal phase; no cubic phase was found. The general conclusion is that the highlighted hydrophobic interaction promotes dissolution of CTAPSS when the polyion salt is added and provides further stabilization of the dense phase when the surfactant salt is added.

  • 120. Srnec, Martin
    et al.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Ryde, Ulf
    Rulisek, Lubomir
    Reaction Mechanism of Manganese Superoxide Dismutase Studied by Combined Quantum and Molecular Mechanical Calculations and Multiconfigurational Methods2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 17, p. 6074-6086Article in journal (Refereed)
    Abstract [en]

    Manganese superoxide dismutases (MnSODs) are enzymes that convert two molecules of the poisonous superoxide radical into molecular oxygen and hydrogen peroxide. During the reaction, the manganese ion cycles between the Mn2+ and Mn3+ oxidation states and accomplishes its enzymatic action in two half-cycles (corresponding to the oxidation and reduction of O-2(center dot-)). Despite many experimental and theoretical studies dealing with SODs, including quantum chemical active-site-model studies of numerous variants of the reaction mechanisms, several details of MnSOD enzymatic action are still unclear. In this study, we have modeled and compared four reaction pathways (one associative, one dissociative, and two second-sphere) in a protein environment using the QM/MM approach (combined quantum and molecular mechanics calculations) at the density functional theory level. The results were complemented by CASSCF/CASPT2/MM single-point energy calculations for the most plausible models to account properly for the multireference character of the various spin multiplets. The results indicate that the oxidation of O-2(center dot-) to O-2 most likely occurs by an associative mechanism following a two-state (quartet-octet) reaction profile. The barrier height is estimated to be less than 25 kJ.mol(-1). On the other hand, the conversion of O-2(center dot-) to H2O2 is likely to take place by a second-sphere mechanism, that is, without direct coordination of the superoxide radical to the manganese center. The reaction pathway involves the conical intersection of two quintet states, giving rise to an activation barrier of similar to 60 kJ.mol(-1). The calculations also indicate that the associative mechanism can represent a competitive pathway in the second half-reaction with the overall activation barrier being only slightly higher than the activation barrier in the second-sphere mechanism. The activation barriers along the proposed reaction pathways are in very good agreement with the experimentally observed reaction rates of SODs (k(cat) approximate to 10(4)-10(5) s(-1)).

  • 121.
    Strambi, Angela
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Durbeej, Bo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Excited-state modeling of the astaxanthin dimer predicts a minor contribution from exciton coupling to the bathochromic shift in crustacyanin2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 15, p. 5311-5317Article in journal (Refereed)
    Abstract [en]

    The >0.50 eV bathochromic shift of the absorption by the carotenoid astaxanthin in crustacyanin, the carotenoprotein responsible for the coloration of lobster shell, is believed to result from ground-state polarization of the chromophore and/or exciton coupling between the two chromophores of each protein subunit. Here, the contribution of exciton   coupling to the shift is quantified using quantum chemical calculations that do not rely on the dipole-dipole approximation but rather consider the full astaxanthin dimer in the geometry relevant for the protein-bound state. Employing a variety of methods, it is found that the exciton coupling amounts to 0.04 eV only. Furthermore, even when more closely aggregated dimers than the one in the protein are considered, the predicted couplings remain small (0.05-0.09 eV). These findings demonstrate that the bathochromic shift cannot be explained in terms of exciton coupling. It is therefore argued that polarization is likely to be the dominant mechanism, a notion supported by the fact that calculations carried out at the same levels of theory identify a scenario (hydrogen bonding with a histidine residue) whose contribution to the shift vastly exceeds that of exciton coupling.

  • 122.
    Strömme, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Frenning, Göran
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Razaq, Aamir
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Gelin, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Nyholm, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Inorganic Chemistry.
    Mihranyan, Albert
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Ionic motion in polypyrrole-cellulose composites: Trap release mechanism during potentiostatic reduction2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 14, p. 4582-4589Article in journal (Refereed)
    Abstract [en]

    This work investigates the movement of anions during potentiostatic controlled reduction of novel compositematerials consisting of high surface area cellulose substrates, extracted from the Cladophora sp. algae, coatedwith thin (∼50 nm) layers of the intrinsically conducting polymer (ICP) polypyrrole. The coating was achievedby chemical polymerization of pyrrole on the cellulose fibers with iron(III) chloride and phosphomolybdicacid, respectively. The composites are in the form of paper sheets and can be directly immersed into anelectrolyte solution for ion absorption/desorption. The motion of glutamate and aspartate anions during cathodicpolarization was investigated as a function of preceding anodic polarization at various potentials. The compositewas found to exhibit memory effect as the response to a cathodic polarization of constant magnitude produceddifferent responses depending on the magnitude of the preceding anodic potential. After the application of acathodic potential to the composite, the reduction current curvessgenerated by anions leaving thecompositeswere found to initially increase in magnitude followed by a monotonic decay. A similar responsehas not been described and analyzed for electrochemical reduction of anion containing ICP materials earlier.A theoretical model was developed to aid the analysis of the experimental data. The model accounts for bothfreely mobile anions and anions that may be temporarily trapped in a contracting PPy network during cathodicpolarization. By fitting the recorded reduction current curves to this model, detailed information about theionic movement in the composite could be obtained, which may be used to further optimize the materialsproperties of conducting polymer systems aimed for specific electrochemical ion exchange processes.

  • 123.
    Strömme, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Mihranyan, Albert
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Ek, Ragnar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Niklasson, Gunnar A.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Fractal dimension of cellulose powders analyzed by multilayer BET adsorption of water and nitrogen2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 51, p. 14378-14382Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to show that multilayer fractal Brunauer-Emmett-Teller (mfBET) theory can be used as a tool to obtain information about the distribution of water in cellulose powder particles of varying crystallinity. Microcrystalline cellulose, agglomerated micronized cellulose, low-crystallinity cellulose, and cellulose powders from green and brown algae were characterized by scanning electron microscopy and mfBET analysis on water and nitrogen adsorption isotherms. The distribution of water in the cellulose materials was found to be characterized by a fractal dimension smaller than 1.5 for all powders. The results showed that for highly crystalline cellulose materials, such as Cladophora cellulose, the cellulose-water interactions take place mainly on cellulose fibril surfaces adjacent to open pores without causing any significant swelling of the material. For less ordered celluloses the water interaction was found to take place inside the bulk material and the water uptake process caused the pore volume to swell between 1 and 2 orders in magnitude. For the Cladophora cellulose, the thickness of the adsorbed water layer at the outer cut off of the fractal region was found to coincide very well with the average pore size obtained from nitrogen adsorption measurements. The multilayer fractal BET analysis on nitrogen adsorption isotherms showed that the particles could be characterized by fractal dimensions between 2.13 and 2.50. We conclude that water adsorption has the ability to alter the structure of the studied material and reveal a sorption-induced, "apparent" fractal structure over a relatively narrow length scale interval, while nitrogen adsorption probes the substrate morphology over a wide range of length scales and reveals the "true" fractal structure.

  • 124.
    Sund, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Lind, Christoffer
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Binding Site Preorganization and Ligand Discrimination in the Purine Riboswitch2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 3, p. 773-782Article in journal (Refereed)
    Abstract [en]

    The progress of RNA research has suggested a wide variety of RNA molecules as possible targets for pharmaceutical drug molecules. Structure-based computational methods for predicting binding modes and affinities are now important tools in drug discovery, but these methods have mainly been focused on protein targets. Here we employ molecular dynamics free-energy perturbation calculations and the linear interaction energy method to analyze the energetics of ligand binding to purine riboswitches. Calculations are carried out for 14 different purine complexes with the guanine and adenine riboswitches in order to examine their ligand recognition principles. The simulations yield binding affinities in good agreement with experimental data and rationalize the selectivity of the riboswitches for different ligands. In particular, it is found that these receptors have an unusually high degree of electrostatic preorganization for their cognate ligands, and this effect is further quantified by explicit free-energy calculations, which show that the standard electrostatic linear interaction energy parametrization is suboptimal in this case. The adenine riboswitch specifically uses the electrostatic preorganization to discriminate against guanine by preventing the formation of a G-U wobble base pair.

  • 125. Sá, Jacinto
    et al.
    Arteaga, Geomar D
    Daley, Robert A
    Bernardi, Johannes
    Anderson, James A
    Factors influencing hydride formation in a Pd/TiO2 catalyst.2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 34, p. 17090-5Article in journal (Refereed)
    Abstract [en]

    A sample containing Pd nanoparticles deposited on TiO(2) was subjected to a series of different thermal pretreatments. The range of these treatments was selected to provide a palladium surface in a number of different states, including a form where TiO(x) overlayers had been formed. Experiments were conducted to determine how the state of the Pd surface influenced the formation of Pd hydride. The amount of hydrogen released during a temperature-programmed experiment was used to quantify the extent of Pd beta-hydride formation following room-temperature exposure to hydrogen. Samples were characterized by HAADF (high-angle annular dark-field) electron microscopy with EDX (energy-dispersive X-ray) analysis and CO pulse chemisorption and FTIR (Fourier transform infrared spectroscopy) of adsorbed CO. The amount and the ease with which Pd beta-hydride was formed was found to be dependent on the metal surface area, the presence of titania overlayers, and the Pd surface roughness/defect concentration.

  • 126. Söderhjelm, Pär
    et al.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Ryde, Ulf
    Calculation of Protein-Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 32, p. 11085-11094Article in journal (Refereed)
    Abstract [en]

    We have developed a method to estimate accurate interaction energies between a full protein and a bound ligand. It is based oil the recently proposed PMISP (polarizable multipole interaction with supermolecular pairs) method (Soderhjelm, P.; Ryde, U. J. Phys. Chem. A 2009, 113. 617), which treats electrostatic interaction by multipoles up to quadrupoles, induction by anisotropic polarizabilities, and nonclassical interactions by explicit quantum mechanical (QM) calculations, using a fragmentation approach. For a whole protein, electrostatics and induction are treated the same way, but for the nonclassical interactions, a Lennard-Jones term from a standard molecular mechanics (MM) force field (e.g., Amber) is used outside a certain distance from the ligand (4-7 angstrom). This QM/MM variant of the PMISP method is carefully tested by varying this distance. Several approximations related to the classical interactions are also evaluated. It is found that one can speed up the calculation by using density functional theory to compute multipoles and polarizabilities but that a proper treatment of polarization is important. As a demonstration of the method, the interaction energies of two ligands bound to avidin are calculated at the MP2/aug-cc-pVTZ level, with an expected relative error of 1-2%.

  • 127.
    Tubasum, Sumera
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Lund Univ, Dept Chem, Div Phys Chem, Box 124, S-22100 Lund, Sweden..
    Torbjornsson, Magne
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, S-22100 Lund, Sweden..
    Yadav, Dheerendra
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, S-22100 Lund, Sweden..
    Camacho, Rafael
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, S-22100 Lund, Sweden..
    Soderlind, Gustaf
    Lund Univ, Ctr Math Sci, Div Numer Anal, Box 124, S-22100 Lund, Sweden..
    Scheblykin, Ivan G.
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, S-22100 Lund, Sweden..
    Pullerits, Tonu
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, S-22100 Lund, Sweden..
    Protein Configuration Landscape Fluctuations Revealed by Exciton Transition Polarizations in Single Light Harvesting Complexes2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 4, p. 724-732Article in journal (Refereed)
    Abstract [en]

    Protein is a flexible material with broad distribution of conformations forming an energy landscape of quasi-stationary states. Disentangling the system dynamics along this landscape is the key for understanding the functioning of the protein. Here we studied a photosynthetic antenna pigment protein complex LH2 with single molecule two-dimensional polarization imaging. Modeling based on the Redfield relaxation theory well describes the observed polarization properties of LH2 fluorescence and fluorescence excitation, strongly suggesting that at 77 K the conformational subspace of the LH2 is limited to about three configurations with relatively frequent switching among each other. At room temperature the next level of fluctuations determines the conformational dynamics. The results support the multitier model of the energy landscape of proteins and demonstrate the potential of the method for the studies of structural dynamics in proteins.

  • 128.
    Tummala, Gopi Krishna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Rojas, Ramiro
    Fibre and Polymer Technology and Wallenberg Wood Science Center, School of Chemical Science and Engineering, KTH Royal Institute of Technology, Stockholm, Sweden.
    Mihranyan, Albert
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Poly(vinyl alcohol) Hydrogels Reinforced with Nanocellulose for Ophthalmic Applications: General Characteristics and Optical Properties2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 51, p. 13094-13101Article in journal (Refereed)
    Abstract [en]

    Globally, uncorrected refractive errors are one of the main causes of visual impairment, and contact lenses form an important part of modern day eye care and culture. Several hydrogels with varying physicochemical properties are in use to manufacture soft contact lenses. Hydrogels are generally too soft and reinforcement with appropriate materials is desirable to achieve high water content without compromising mechanical properties. In this study, we have developed a highly transparent macroporous hydrogel with water content >90%, by combining poly(vinyl alcohol) with nanocellulose. Furthermore, the results show that the composite hydrogel has refractive index close to that of water and very good UV-blocking properties.

  • 129. Wang, Heli
    et al.
    Lindgren, Torbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    He, Jianjun
    Hagfeldt, Anders
    Lindquist, Sten-Eric
    Photoelectrochemistry of Nanostructured WO3 Thin Film Electrodes for Water Oxidation: Mechanism of Electron Transport2000In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 104, p. 5686-5696Article in journal (Refereed)
  • 130.
    Welch, Ken
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Burza, Matthias
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Mukhtar, Emad
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strømme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Environment-Induced Surface Dynamics of a Biomimetic Ionomer Studied Using in Situ Second Harmonic Generation2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 37, p. 11573-11579Article in journal (Refereed)
    Abstract [en]

    The environmental-induced surface dynamics of the biomimetic phosphoryl choline (PC)-functionalized poly(trimethylene carbonate) ionomer has been studied and compared to its unfunctionalized counterpart using in situ second harmonic generation measurements. Whereas the nonpolar liquid n-hexane did not induce any surface dynamic processes in the ionomer under study, the presence of water initiated a Debye-type dynamic reaction at the surface of the PC ionomer, which had no equivalent in the unfunctionalized material. This first-order reaction was attributed to a surface enrichment process of the functionalized ionomer in the hydrophilic environment involving movement of the PC endgroups from aggregates in the bulk to the surface. The time constant of the process was found to be about 6 min, and the corresponding activation energy was 0.4 eV. The dehydration process of the PC-functionalized ionomer in nitrogen gas atmosphere could be described by two time constants, one slightly below 1 min and the other one just above 13 min. The results presented in this work show that SHG measurements are well suited for the study of polymer surface restructuring dynamics in response to environmental changes. Such information is very important for the successful design and implementation of biomimetic polymers intended for biomedical applications.

  • 131.
    Werner, Josephina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Wernersson, Erik
    Ekholm, Victor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Ottosson, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Ohrwall, Gunnar
    Heyda, Jan
    Persson, Ingmar
    Söderström, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Jungwirth, Pavel
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Surface Behavior of Hydrated Guanidinium and Ammonium Ions: A Comparative Study by Photoelectron Spectroscopy and Molecular Dynamics2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 25, p. 7119-7127Article in journal (Refereed)
    Abstract [en]

    Through the combination of surface sensitive photoelectron spectroscopy and molecular dynamics simulation, the relative surface propensities of guanidinium and ammonium ions in aqueous solution are characterized. The fact that the N Is binding energies differ between these two species was exploited to monitor their relative surface concentration through their respective photoemission intensities. Aqueous solutions of ammonium and guanidinium chloride, and mixtures of these salts, have been studied in a wide concentration range, and it is found that the guanidinium ion has a greater propensity to reside at the aqueous surface than the ammonium ion. A large portion of the relative excess of guanidinium ions in the surface region of the mixed solutions can be explained by replacement of ammonium ions by guanidinium ions in the surface region in combination with a strong salting-out effect of guanidinium by ammonium ions at increased concentrations. This interpretation is supported by molecular dynamics simulations, which reproduce the experimental trends very well. The simulations suggest that the relatively higher surface propensity of guanidinium compared with ammonium ions is due to the ease of dehydration of the faces of the almost planar guanidinium ion, which allows it to approach the water-vapor interface oriented parallel to it.

  • 132.
    Westermark, K
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics II. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Tingry, S
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics II. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Persson, P
    Rensmo, Håkan
    Lunell, S
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Quantum Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics II. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics II. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Siegbahn, H
    Triarylamine on nanocrystalline TiO2 studied in its reduced and oxidized state by photoelectron spectroscopy2001In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 105, no 30, p. 7182-7187Article in journal (Refereed)
    Abstract [en]

    The electronic and molecular structures of an electrochemically reduced and oxidized triarylamine layer (((3-ethyl(p-N,N-dimethylamino)phenyl)amino)propyl-1-phosphonic acid) adsorbed on a nanocrystalline TiO2 film have been investigated. Photoelectron spe

  • 133.
    Westermark, Karin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Rensmo, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Siegbahn, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Keis, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Ojamäe, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Persson, Petter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    PES Studies of Ru(dcbpyH2)2(NCS)2 Adsorption on Nanostructured ZnO for Solar Cell Applications2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 39, p. 10102-10107Article in journal (Refereed)
    Abstract [en]

    The interaction between the dye cis-bis(4,4‘-dicarboxy-2,2‘-bipyridine)-bis(isothiocyanato)-ruthenium(II), Ru(dcbpyH2)2(NCS)2, and nanostructured ZnO was investigated by photoelectron spectroscopy (PES) using synchrotron radiation. The results are compared with those of nanostructured TiO2 sensitized with the same dye, which to date is the most efficient system for dye-sensitized photoelectrochemical solar cells. When comparing the two metal oxides, differences in the surface molecular structure were observed both for low and high dye coverages, as seen by comparing the oxygen, nitrogen and sulfur signals. The origin of these differences is discussed in terms of substrate-induced dye aggregation and in variations in surface bonding geometries. The measurements also provide information concerning the energy matching between the orbitals of the dye and the ZnO valence band, which is of importance in photoinduced charge transfer.

  • 134.
    Wiberg, Joanna
    et al.
    Chalmers University of Technology.
    Marinado, Tannia
    Physical Chemistry KTH and Division of Chemistry and Materials Shinshu University, Japan.
    Hagberg, Daniel P
    Organic Chemistry, KTH.
    Sun, Licheng
    Organic Chemistry, KTH.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Albinsson, Bo
    Chalmers University of Technology.
    Distance and driving force dependencies of electron injection and recombination dynamics in organic dye-sensitized solar cells.2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 45, p. 14358-14363Article in journal (Refereed)
    Abstract [en]

    A series of dyes based on a triphenylamine donor and a rhodanine acetic acid anchor/acceptor for solar cell application has been studied with regards to electron injection and recombination kinetics using femtosecond transient absorption. The series contains three dyes, with estimated electron transfer distances ranging from 17.2 to 11.0 Å, and which have shown significant differences in energy conversion efficiencies. The injection and recombination kinetics were studied in the NIR region where electrons in the conduction band of the TiO(2) are suggested to absorb. For all dyes, the injection rate is larger than (200 fs)(-1) which implicates a quantitative injection efficiency. Surprisingly, the subsequent recombination reaction has a rate that increases with increasing linker length. On the other hand, this behavior is consistent with the concomitant decrease in driving force for this series of dyes. Moreover, the lifetimes show exponential distance dependence when corrected for driving force and reorganization energy, which indicates a superexchange interaction between the electrons in TiO(2) and the radical cations of the dyes. A dependence on probe wavelength of the attenuation factor was found, giving a β value of 0.38 Å(-1) at 940 nm and 0.49 Å(-1) at 1040 nm. The difference is suggested to be due to the difference in electronic coupling between fully separated dye cations and injected electrons versus geminate electron-hole pairs. Addition of tert-butylpyridine, which from previous work is known to give a substantial drop in the IPCE values for the studied dyes, was found to decrease the amount of long-lived electrons in the TiO(2) without affecting the injection rate.

  • 135.
    Witte, Katharine
    et al.
    Tech Univ Berlin, Inst Opt & Atomare Phys, D-10623 Berlin, Germany.;Tech Univ Berlin, Berlin Lab Innovat Xray Technol BLiX, D-10623 Berlin, Germany.;Paul Scherrer Inst, CH-5232 Villigen, Switzerland..
    Mantouvalou, Ioanna
    Tech Univ Berlin, Inst Opt & Atomare Phys, D-10623 Berlin, Germany.;Tech Univ Berlin, Berlin Lab Innovat Xray Technol BLiX, D-10623 Berlin, Germany..
    Sanchez-de-Armas, Rocio
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Univ Seville, Dept Phys Chem, C Prof Garcia Gonzalez S-N, E-41012 Seville, Spain..
    Lokstein, Heiko
    Charles Univ Prague, Fac Math & Phys, Dept Chem Phys & Opt, Ke Karlovu 3, CR-12116 Prague, Czech Republic..
    Lebendig-Kuhla, Janina
    Tech Univ Berlin, Inst Opt & Atomare Phys, D-10623 Berlin, Germany.;Tech Univ Berlin, Berlin Lab Innovat Xray Technol BLiX, D-10623 Berlin, Germany.;Max Born Inst Nichtlineare Opt & Kurzzeitspektros, D-12489 Berlin, Germany..
    Jonas, Adrian
    Tech Univ Berlin, Inst Opt & Atomare Phys, D-10623 Berlin, Germany.;Tech Univ Berlin, Berlin Lab Innovat Xray Technol BLiX, D-10623 Berlin, Germany..
    Roth, Friedrich
    Tech Univ Bergakad Freiberg, Inst Expt Phys, Leipziger Str 23, D-09599 Freiberg, Germany..
    Kanngiesser, Birgit
    Tech Univ Berlin, Inst Opt & Atomare Phys, D-10623 Berlin, Germany.;Tech Univ Berlin, Berlin Lab Innovat Xray Technol BLiX, D-10623 Berlin, Germany..
    Stiel, Holger
    Tech Univ Berlin, Berlin Lab Innovat Xray Technol BLiX, D-10623 Berlin, Germany.;Max Born Inst Nichtlineare Opt & Kurzzeitspektros, D-12489 Berlin, Germany..
    On the Electronic Structure of Cu Chlorophyllin and Its Breakdown Products: A Carbon K-Edge X-ray Absorption Spectroscopy Study2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 6, p. 1846-1851Article in journal (Refereed)
    Abstract [en]

    Using near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, the carbon backbone of sodium copper chlorophyllin (SCC), a widely used chlorophyll derivative, and its breakdown products are analyzed to elucidate their electronic structure and physicochemical properties. Using various sample preparation methods and complementary spectroscopic methods (including UV/Vis, X-ray photoelectron spectroscopy), a comprehensive insight into the SCC breakdown process is presented. The experimental results are supported by density functional theory calculations, allowing a detailed assignment of characteristic NEXAFS features to specific C bonds. SCC can be seen as a model system for the large group of porphyrins; thus, this work provides a novel and detailed description of the electronic structure of the carbon backbone of those molecules and their breakdown products. The achieved results also promise prospective optical pump/X-ray probe investigations of dynamic processes in chlorophyll-containing photosynthetic complexes to be analyzed more precisely.

  • 136.
    Zardán Gómez de la Torre, Teresa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strömberg, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Russell, Camilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Göransson, Jenny
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Svedlindh, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Strømme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Investigation of Immobilization of Functionalized Magnetic Nanobeads in Rolling CircleAmplified DNA Coils2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 10, p. 3707-3713Article in journal (Refereed)
    Abstract [en]

    Immobilization characteristics for single-stranded oligonucleotide- functionalized magnetic beads with nominal sizes of 40, 80, 130, and 250 nm in rolling circle amplified (RCA) DNA coils is investigated by employing complex magnetization measurements, dynamic light scattering and fluorescence microscopy. It was found that larger beads in a polydisperse bead size distribution more easily immobilize in the RCA DNA coils than do smaller beads. This may be related to a higher oligonucleotide surface coverage for the larger beads. Furthermore, it was concluded that both bead size and oligonucleotide surface coverage determine whether beads immobilize to give isolated coils with beads or larger clusters of beads and coils. A small bead size and a low oligonucleotide surface coverage favor the first kind of immobilization behavior, whereas a large bead size and a high oligonucleotide surface coverage favor the other. The present findings could be used to optimize both size and surface functionalization of beads employed in substrate-free magnetic biosensors.

  • 137.
    Zhang, H.
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tan, T.
    Feng, W.
    Van Der Spoel, David
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Molecular recognition in different environments: β-Cyclodextrin dimer formation in organic solvents2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 42, p. 12684-12693Article in journal (Refereed)
    Abstract [en]

    Electrostatic and van der Waals interactions as well as entropy contribute to the energetics governing macromolecular complexation in biomolecules. Hydrogen bonds play a particularly important role in such interactions. Here we use molecular dynamics (MD) simulations to investigate the hydrogen bond (HB) orientations of free beta-cyclodextrin (β-CD) and head-to-head dimerization of β-CD monomers with and without guest molecules in different environments, namely, in 10 different solvents covering a wide range of polarity. Potentials of mean force for the dimer dissociation are derived from umbrella sampling simulations, allowing determination of the binding affinity between monomers. The HB orientations are in good agreement with available experimental data in water and dimethyl sulfoxide, yielding confidence in the force field used. HB exchanges at the secondary rim of β-CD are observed with a fast rate in water and with a low rate or even no exchange in other solvents. Orientational preferences of interglucopyranose HBs and their effects on the β-CD structure in these solvents are discussed in detail. Polar solvents with stronger HB accepting abilities can interrupt intermolecular HBs more easily, resulting in a less stable dimer. Guest molecules included in the channel-type cavity strengthen the binding affinity between two monomers to some extent, particularly in polar solvents. Formation of the head-to-head dimer is therefore solvent-dependent and guest-modulated. There is only limited correlation between the dimer binding energies and solvent properties like the dielectric constant. This implies that implicit solvent models will not be capable of predicting important properties like binding energy for other solvents than water without a complete reparameterization. This work provides a deeper comprehension on the properties of β-CD, and implications for the application of cyclodextrins in aqueous and nonaqueous media are discussed.

  • 138.
    Zhang, Haiyang
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Ge, Chunling
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Feng, Wei
    Tan, Tianwei
    Insight into the Structural Deformations of Beta-Cyclodextrin Caused by Alcohol Cosolvents and Guest Molecules2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 12, p. 3880-3889Article in journal (Refereed)
    Abstract [en]

    Beta-cyclodextrin (beta-CD) is an ideal candidate for a host molecule, and it is used as such in drug delivery and separation technology. The structural behavior of free beta-CD and host guest complexes of beta-CD with two isoflavonoid isomers (puerarin and daidzin) in aqueous alcohol solutions, covering methanol, ethanol, 2-propanol, and 1-propanol, was investigated through molecular dynamics (MD) simulations. The MD results highlighted aspects of the structural flexibility and rigidity of beta-CD in different alcohol solutions. The alcohol residence time within the beta-CD cavity, solvent distribution around beta-CD, and guest-induced structural changes were analyzed. Interaction with puerarin endowed beta-CD with a more rigid structure than with daidzin and a weaker ternary complex beta-CD/puerarin/alcohol was formed with a local participation of water molecules. The retention behavior of puerarin and daidzin on a beta-CD-coupled medium was determined via chromatographic experiments and simulation results provided a structural explanation for such interactions.

  • 139.
    Zhang, Haiyang
    et al.
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, Box 53, Beijing 100029, Peoples R China.;Univ Sci & Technol Beijing, Sch Chem & Biol Engn, Dept Biol Sci & Engn, Beijing 100083, Peoples R China..
    Lv, Yongqin
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, Box 53, Beijing 100029, Peoples R China..
    Tan, Tianwei
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, Box 53, Beijing 100029, Peoples R China..
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 3, p. 477-484Article in journal (Refereed)
    Abstract [en]

    Fabrication of metal organic frameworks (MOFs) with large apertures triggers a brand-new research area for selective encapsulation of biomolecules within MOF nanopores. The underlying inclusion mechanism is yet to be clarified however. Here we report a molecular dynamics study on the mechanism of protein encapsulation in MOFs. Evaluation for the binding of amino acid side chain analogues reveals that van der Waals interaction is the main driving force for the binding and that-guest size acts as a key factor predicting protein binding with MOFs. Analysis on the conformation and-thermodynamic stability of the miniprotein Trp-cage encapsulated in a series of with varying pore apertures and-surface chemistries indicates,that protein encapsulation can be achieved Vial maintaining a polar/nonpolar balance in the MOF surface through tunable modification of organic linkers and Mg-O chelating moieties. Such modifications endow MOFs with a more biocompatible confinement. This work provides guidelines for selective inclusion of biomolecules within MOFs and facilitates MOF functions as a new class of host materials and molecular chaperones.

  • 140.
    Åberg, Emma
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Karlsson, O. Andreas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Binding Kinetics of the Intrinsically Disordered p53 Family Transactivation Domains and MDM22018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 27, p. 6899-6905Article in journal (Refereed)
    Abstract [en]

    Because of their prominent roles in cell-cycle regulation and cancer, the interaction between MDM2 and the intrinsically disordered transactivation domain (TAD) of p53 is exceptionally well-studied. However, although there are numerous computational studies on the interaction mechanism, there is a paucity of experimental data regarding the kinetics and mechanism. We have used stopped flow fluorescence to investigate the binding reaction between MDM2 and TAD from p53 as well as from its paralogs p63 and p73, and in particular, focused on the salt dependence of the interaction. The observed kinetics are consistent with a two-state mechanism within the time frame of the stopped flow methodology; thus, any conformational changes including the previously identified MDM2 lid dynamics must occur on a time scale <5 ms at 10 °C. The association rate constants are similar for the three TADs, and differences in the dissociation rate constants determine the various affinities with MDM2. In contrast to previous studies, we found a relatively small ionic-strength dependence for all three interactions, highlighting the large variation in the role of electrostatics among binding reactions of intrinsically disordered proteins (IDPs). The basal association rate constants in the absence of electrostatic interactions were relatively high (≥2 × 106 M–1 s–1 at 10 °C), suggesting that a large number of initial contacts may lead to a productive complex. Our findings support an emerging picture of “conformational funneling” occurring in the initial stages of interactions involving IDPs and that these early binding events can rely on hydrophobic as well as charge–charge interactions.

  • 141.
    Öhrwall, Gunnar
    et al.
    MAX-lab, Lund UniVersity.
    Ottosson, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Pokapanich, Wandared
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Legendre, Sébastien
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Svensson, Svante
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Charge Dependence of Solvent-Mediated Intermolecular Coster-Kronig Decay Dynamics of Aqueous Ions2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 51, p. 17057-17061Article in journal (Refereed)
    Abstract [en]

    The 2s and 2p photoelectron spectra have been measured for Na+, Mg2+, and Al3+ ions in aqueous solution.In all cases, the 2s lines are significantly broader than the 2p features, which is attributed to a shorter lifetimeof the respective 2s hole. Since intraionic Coster-Kronig decay channels from the (2s)-1 state are closed forfree Na+, Mg2+, and Al3+ ions, this is evidence for an intermolecular Coster-Kronig-like process, reminiscentof intermolecular Coulombic decay (ICD), involving neighboring water solvent molecules. The observed 2s Lorentzian line widths correspond to lifetimes of the (2s)-1 state of 3.1, 1.5, and 0.98 fs for the solvated Na,Mg, and Al ions, respectively.

123 101 - 141 of 141
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