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  • 1. Agrell, H. G.
    et al.
    Boschloo, Gerrit
    Hagfeldt, Anders
    Conductivity studies of nanostructured TiO2 films permeated with electrolyte2004Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, nr 33, s. 12388-12396Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Charge transport in nanostructured TiO2 films permeated with an electrolyte was studied, using temperature-dependent conductivity and electron accumulation measurements. Two regions for charge transport were distinguished from the relationship between conductivity and electron concentration. In the first region (similar to1-20 electrons per TiO2 particle), the effective electron mobility is dependent on the electron concentration and values between 7 x 10(-4) and 78 x 10(-4) cm(2) V-1 s(-1) were determined. The activation energy of the mobility was similar to0.3 eV. The charge transport can be described with a trapping/detrapping model that involves localized band-gap states. In the second region (> 20 electrons per TiO2 particle), the effective electron mobility is independent of electron concentration and values of similar to150 x 10(-4) cm(2) V-1 s(-1) are calculated. The activation energy of mobility is in the range of 0-0.15 eV, depending on the electrolyte. Transport of electrons in the conduction band seems to be the most applicable model.

  • 2.
    Ai, Yue-Jie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Liao, Rongzhen
    Stockholm University.
    Chen, Shilu
    Beijing Institute of Technology.
    Hua, Wei-Jie
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fang, Wei-Hai
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase2011Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, nr 37, s. 10976-10982Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.

  • 3.
    Ai, Yue-Jie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Liao, Rong-zhen
    Chen, Shu-feng
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Fang, Wei-Hai
    Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 44, s. 14096-14102Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.

  • 4. Aidas, Kestutis
    et al.
    Olsen, Jogvan Magnus H.
    Kongsted, Jacob
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 7, s. 2069-2080Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.

  • 5. Alarcon, H.
    et al.
    Boschloo, Gerrit
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Mendoza, P.
    Solis, J. L.
    Hagfeldt, Anders
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Dye-sensitized solar cells based on nanocrystalline TiO2 films surface treated with Al3+ ions: Photovoltage and electron transport studies2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 39, s. 18483-18490Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Nanocrystalline TiO2 films, surface modified with Al3+, were manufactured by depositing a TiO2 suspension containing small amounts of aluminum nitrate or aluminum chloride onto conducting glass substrates, followed by drying, compression, and finally heating to 530 degrees C. Electrodes prepared with TiO2 nanoparticles coated with less than 0.3 wt % aluminum oxide with respect to TiO2 improved the efficiency of the dye sensitized solar cell. This amount corresponds to less than a monolayer of aluminum oxide. Thus, the Al ions terminate the TiO2 surface rather than form a distinct aluminum oxide layer. The aluminum ion surface treatment affects the solar cell in different ways: the potential of the conduction band is shifted, the electron lifetime is increased, and the electron transport is slower when aluminum ions are present between interconnected TiO2 particles.

  • 6. Amira, S.
    et al.
    Spangberg, D.
    Probst, M.
    Hermansson, Kersti
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Molecular dynamics simulation of Fe2+(aq) and Fe3+(aq)2004Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, nr 1, s. 496-502Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular dynamics simulations of single-ion Fe2+(aq) and Fe3+(aq) solutions have been performed with two rigid-water models (SPC and SPC/E) and a newly constructed SPC-based flexible-water model (SPC+CCL). The SPC+CCL water model in combination with effective Fe2+ and Fe3+ ion-water potentials manages to reproduce many experimental structural and dynamical properties of the solutions. Special attention is given to the large ion-induced frequency shifts of the OH stretching bands, which are also well reproduced by the SPC+CCL model.

  • 7. Amira, S.
    et al.
    Spangberg, D.
    Zelin, V.
    Probst, M.
    Hermansson, Kersti
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Car-Parrinello molecular dynamics simulation of Fe3+(aq)2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 29, s. 14235-14242Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The optimized geometry and energetic properties of Fe(D2O)(n)(3+) clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fell ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell(...)second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.

  • 8. Baev, A.
    et al.
    Salek, Pawel
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Gel'mukhanov, Faris
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Quantum-classical modeling of nonlinear pulse propagation in a dissolved two-photon active chromophore2006Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 11, s. 5379-5385Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the present work we outline the implications of a quantum-classical approach for modeling two-photon absorption of organic chromophores in solution. The approach joins many-photon absorption dynamic simulations with quantum chemical first principles calculations of corresponding excitation energies and transition matrix elements. Among a number of conclusions of the study, we highlight three: (i) The use of either short- or long-pulse excitation is demonstrated to switch the absorptive capacity of the nonlinear medium owing to enhancement of the nonlinear stepwise processes; (ii) The two-photon cross section strongly depends on the way in which the dephasing rate decays when the laser frequency is tuned off-resonant with the corresponding molecular transition; (iii) The results of the pulse propagation simulations based on electronic structure data obtained with a new Coulomb attenuated functional is shown to be in much better agreement with the experimental results than those based on data received with traditional density functionals.

  • 9. Baev, Alexander
    et al.
    Norman, Patrick
    Henriksson, Johan
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Theoretical Simulations of clamping levels in optical power limiting2006Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 42, s. 20912-20916Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Multiphysics modeling, combining quantum mechanical and classical wave mechanical theories, of clamping levels has been performed for a platinum(II) organic compound in a sol-gel glass matrix. A clamping level of 2.5 mu J is found for a pulse duration of 10 ns. The excited-state absorption in the triplet manifold is shown to be crucial for clamping to occur.

  • 10. Banerjee, S.
    et al.
    Sarkar, S.
    Lakshman, K.
    Dutta, Joydeep
    Water Research Center, Sultan Qaboos University, P.O. Box 17, 123 Al-Khoudh, Oman.
    Pal, S. K.
    UVA radiation induced ultrafast electron transfer from a food carcinogen benzo[a]pyrene to organic molecules, biological macromolecules, and inorganic nano structures2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 14, s. 3726-3737Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reactions involving electron transfer (ET) and reactive oxygen species (ROS) play a pivotal role in carcinogenesis and cancer biochemistry. Our present study emphasizes UVA radiation induced ET reaction as one of the key aspects of a potential carcinogen, benzo[a]pyrene (BP), in the presence of a wide variety of molecules covering organic p-benzoquinone (BQ), biological macromolecules like calf-thymus DNA (CT-DNA), human serum albumin (HSA) protein, and inorganic zinc oxide (ZnO) nanorods (NRs). Steady-state and picosecond-resolved fluorescence spectroscopy have been used to monitor such ET reactions. Physical consequences of BP association with CT-DNA have been investigated through temperature-dependent circular dichroism (CD) spectroscopy. The temperature-dependent steady-state, picosecond-resolved fluorescence lifetime and anisotropy studies reveal the effect of temperature on the perturbation of such ET reactions from BP to biological macromolecules, highlighting their temperature-dependent association. Furthermore, the electron-donating property of BP has been corroborated by measuring wavelength-dependent photocurrent in a BP-anchored ZnO NR-based photodevice, offering new physical insights for the carcinogenic study of BP.

  • 11.
    Bastardo Zambrano, Luis Alejandro
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Ytkemi.
    Garamus, V. M.
    GKSS Research Centre, Geesthacht.
    Bergström, Lars Magnus
    KTH, Skolan för kemivetenskap (CHE), Kemi, Ytkemi.
    Claesson, Per M.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Ytkemi.
    The structures of complexes between polyethylene imine and sodium dodecyl sulfate in D2O: a scattering study2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 1, s. 167-174Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The association between a highly branched polyelectrolyte with ionizable groups, polyethylene imine (PEI), and an anionic surfactant, sodium dodecyl sulfate (SDS), has been investigated at two pH values, using small-angle neutron and light scattering. The scattering data allow us to obtain a detailed picture of the association structures formed. Small-angle neutron scattering (SANS) measurements in solutions containing highly charged PEI at low pH and low SDS concentrations indicate the presence of disklike aggregates. The aggregates change to a more complex three-dimensional structure with increasing surfactant concentration. One pronounced feature in the scattering curves is the presence of a Bragg-like peak at high q-values observed at a surfactant concentration of 4.2 mM and above. This scattering feature is attributed to the formation of a common well-ordered PEI/SDS structure, in analogue to what has been reported for other polyelectrolyte-surfactant systems. Precipitation occurred at the charge neutralization point, and X-ray diffraction measurements on the precipitate confirmed the existence of an ordered structure within the PEI/SDS aggregates, which was identified as a lamellar internal organization. Polyethylene imine has a low charge density in alkaline solutions. At pH 10.1 and under conditions where the surfactant was contrast matched, the SANS scattering curves showed only small changes with increasing surfactant concentration. This suggests that the polymer acts as a template onto which the surfactant molecules aggregate. Data from both static light scattering and SANS recorded under conditions where SDS and to a lower degree PEI contribute to the scattering were found to be consistent with a structure of stacked elliptic bilayers. These structures increased in size and became more compact as the surfactant concentration was increased up to the charge neutralization point.

  • 12.
    Bastardo Zambrano, Luis Alejandro
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Ytkemi.
    Mészaros, R.
    Department of Colloid Chemistry, Eötvös Loránd University, Budapest.
    Varga, I.
    Department of Colloid Chemistry, Eötvös Loránd University, Budapest.
    Gilanyi, T.
    Department of Colloid Chemistry, Eötvös Loránd University, Budapest.
    Claesson, Per Martin
    KTH, Skolan för kemivetenskap (CHE), Kemi, Ytkemi.
    Deuterium isotope effects on the interaction between hyperbranched polyethylene imine and an anionic surfactant2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 33, s. 16196-16202Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Solvent isotope effects on the interaction between the hyperbranched cationic polyelectrolyte, polyethylene imine (PEI), and the anionic surfactant sodium dodecyl sulfate (SDS) were investigated using potentiometric titration and eletrophoretic mobility measurements. In the basic pH range, a significantly higher fraction of the amine groups was found to be protonated when the PEI was dissolved in D2O compared to H2O at the same pH/pD. The difference in polymer charge in the two solvents decreases gradually with decreasing pH, and it completely diminishes at around pH = 4. Electrophoretic mobility measurements of PEI/SDS complexes at different pH values correlated very well with these observations. At pH/pD approximate to 9 a much higher mobility of the PEI/SDS complexes was found in D2O than in H2O at low surfactant concentrations, and the charge neutralization point shifted to a considerably larger surfactant concentration in heavy water. These results can be explained by the significantly higher charge density of the PEI in D2O compared to H2O. However, at the natural pH/pD as well as at pH = 4 and pD = 4 conditions the PEI molecules have roughly equal charge densities, which result in very similar charged characteristics (mobilities) of the PEI/SDS complexes as well as the same charge neutralization SDS concentration. It can be concluded that extreme care must be taken in the general analysis of those experiments in which weak polyelectrolyte/surfactant aggregates are investigated in heavy water, and then these observations are correlated with structures of the same system in water.

  • 13. Bauer, C.
    et al.
    Boschloo, Gerrit
    Mukhtar, E.
    Hagfeldt, A.
    Interfacial electron-transfer dynamics in Ru(tcterpy)(NCS)(3)-sensitized TiO2 nanocrystalline solar cells2002Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, nr 49, s. 12693-12704Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The anchoring of the ruthenium dye {(C4H9)(4)N}[Ru(Htcterpy)(NCS)(3)] (with tcterpy = 4,4',4-tricarboxy2,2':6',2-terpyridine), the so-called black dye, onto nanocrystalline TiO2 films has been characterized by UV-vis and FT-IR spectroscopies. FT-IR spectroscopy data suggest that dye molecules are bound to the surface by a bidentate binuclear coordination mode. The interfacial electron-transfer (ET) dynamics has been investigated by femtosecond pump-probe transient absorption spectroscopy and nanosecond laser flash photolysis. The electron-injection process from the dye excited state into the TiO2 conduction band is biexponential with a fast component (200 +/- 50 fs) and a slow component (20 ps). These two components can be attributed to the electron injection from the initially formed and the relaxed dye excited states, respectively. Nanosecond kinetic data suggest the existence of two distinguishable regimes (I and II) for the rates of reactions between injected electrons and oxidized dye molecules or oxidized redox species (D+ or I-2(.-)). The frontier between these two regimes is defined by the number of injected electrons per particle (Ne), which was determined to be about 1. The present kinetic study was undertaken within regime I (N-e > 1). Under these conditions, the back-electron-transfer kinetics is comparable to that in systems with other ruthenium complexes adsorbed onto TiO2. The reduction of oxidized dye molecules by iodide results in the formation of I-2(.-) on a very fast time scale (<20 ns). Within regime 1, the decay of I-2(.-) occurs in similar to100 ns via reaction with injected electrons (I-2(.-) + e(-) --> 2I(-)). In regime II (N-e less than or equal to 1), which corresponds to the normal operating conditions of dye-sensitized solar cells, the decay of I-2(.-) is very slow and likely occurs via the dismutation reaction (2I(2)(.-) --> I- + I-3(-)). Our results predict that, under high light intensity (N-e > 1), the quantum efficiency losses in dye-sensitized solar cells will be important because of the dramatic acceleration of the reaction between I-2(.-) and injected electrons. Mechanisms for the ET reactions involving injected electrons are proposed. The relevance of the present kinetic studies for dye-sensitized nanocrystalline solar cells is discussed.

  • 14. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Odelius, Michael
    Elucidating the Mechanism of Zn2+ Sensing by a Bipyridine Probe Based on Two-Photon Absorption2016Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, nr 34, s. 9067-9075Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this work, we examine, by means of computational methods, the mechanism of Zn2+ sensing by a bipyridine-centered, D-pi-A-pi-D-type-ratiometric molecular probe. According to recently published experimental data [Divya, K. P.; Sreejith, S.; Ashokkumar, P.; Yuzhan, K.; Peng, Q; Maji, S. K.; Tong, Y.; Yu, H.; Zhao, Y.; Ramamurthy, P.; Ajayaghosh, A. A ratiometric fluorescent molecular -probe with enhanced two-photon response upon Zn2+ binding for in vitro and in vivo: bioimaging.= Chem. Sci. 2014, S, 3469-3474], after coordination to zinc ions the -probe exhibits a large enhancement of the two -photon absorption cross section. The goal of our investigation was to elucidate the mechanism behind this phenomenon. For this purpose, linear and nonlinear optical properties of -the unbound (cation-free) and bound probe were calculated, including the influence of solute Solvent interactions, implicitly using a polarizable continuum model and exp-licitely employing the QM/MM approach. Because the results of the calculations indicate that many conformers of the probe are energetically accessible at room temperature in solution and hence contribute to the Signal, structurepteperty relationships were also taken into account. Results of our simulations-demonstrate that the one-photon absorption bands for both the unbound -and bound forms correspond to the bright pi -> pi* transition to the first excited state; which, on the other hand,. exhibits negligible two-photon activity. On the basis of the results of the quadratic respOnse calculations, we put forward-notion that it is the second excited state that gives the strong signal in the experimental nonlinear spectrum. To explain the differenCes in the two-photon absorption activity for the two lowest-lying excited states and nonlinear response enhancement upon binding, we employed the generalized few -state model including the ground, first, and- second excited states. The analysis of the optical channel suggests that the large two-photon response is due to the coordination -induced increase of the, transition- moment from the first to the second excited state.

  • 15.
    Bergenstråhle, Malin
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik.
    Berglund, Lars
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik.
    Mazeau, Karim
    CERMAV-CNRS .
    Thermal Response in Crystalline Iβ Cellulose: A Molecular Dynamics Study2007Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, nr 30, s. 9138-9145Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The influence of temperature on structure and properties of the cellulose Iβ crystal was studied by molecular dynamics simulations with the GROMOS 45a4 force-field. At 300 K, the modeled crystal agreed reasonably with several sets of experimental data, including crystal density, corresponding packing and crystal unit cell dimensions, chain conformation parameters, hydrogen bonds, Young's modulus, and thermal expansion coefficient at room temperature. At high-temperature (500 K), the cellulose chains remained in sheets, despite differences in the fine details compared to the room-temperature structure. The density decreased while the a and b cell parameters expanded by 7.4% and 6%, respectively, and the c parameter (chain axis) slightly contracted by 0.5%. Cell angles α and β divided into two populations. The hydroxymethyl groups mainly adopted the gt orientation, and the hydrogen-bonding pattern thereby changed. One intrachain hydrogen bond, O2'H2'···O6, disappeared and consequently the Young's modulus decreased by 25%. A transition pathway between the low- and high-temperature structures has been proposed, with an initial step being an increased intersheet separation, which allowed every second cellulose chain to rotate around its helix axis by about 30°. Second, all hydroxymethyl groups changed their orientations, from tg to gg (rotated chains) and from tg to gt (non-rotated chains). When temperature was further increased, the rotated chains returned to their original orientation and their hydroxymethyl groups again changed their conformation, from gg to gt. A transition temperature of about 450 K was suggested; however, the transition seems to be more gradual than sudden. The simulated data on temperature-induced changes in crystal unit cell dimensions and the hydrogen-bonding pattern also compared well with experimental results.

  • 16.
    Bergenstråhle, Malin
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi.
    Wohlert, Jakob
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi.
    Larsson, Per Tomas
    STFI-PACKFORSK AB.
    Mazeau, Karim
    CERMAV-CNRS.
    Berglund, Lars
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi.
    Dynamics of Cellulose-Water Interfaces: NMR Spin-Lattice Relaxation Times Calculated from Atomistic Computer Simulations2008Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, nr 9, s. 2590-2595Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Solid-state nuclear magnetic resonance (CP/MAS 13C NMR) spectroscopy has often been used to study cellulose structure, but some features of the cellulose NMR spectrum are not yet fully understood. One such feature is a doublet around 84 ppm, a signal that has been proposed to originate from C4 atoms at cellulose fibril surfaces. The two peaks yield different T1, differing by approximately a factor of 2 at 75 MHz. In this study, we calculate T1 from C4-H4 vector dynamics obtained from molecular dynamics computer simulations of cellulose Iβ-water interfacial systems. Calculated and experimentally obtained T1 values for C4 atoms in surface chains fell within the same order of magnitude, 3-20 s. This means that the applied force field reproduces relevant surface dynamics for the cellulose-water interface sufficiently well. Furthermore, a difference in T1 of about a factor of 2 in the range of Larmor frequencies 25-150 MHz was found for C4 atoms in chains located on top of two different crystallographic planes, namely, (110) and (10). A previously proposed explanation that the C4 peak doublet could derive from surfaces parallel to different crystallographic planes is herewith strengthened by computationally obtained evidence. Another suggested basis for this difference is that the doublet originates from C4 atoms located in surface anhydro-glucose units with hydroxymethyl groups pointing either inward or outward. This was also tested within this study but was found to yield no difference in calculated T1.

  • 17.
    Bergström, L. M.
    et al.
    Department of Pharmacy, Pharmaceutical Physical Chemistry, Uppsala University.
    Bastardo Zambrano, Luis Alejandro
    KTH, Skolan för kemivetenskap (CHE), Kemi, Ytkemi.
    Garamus, V. M.
    GKSS Research Centre, Geesthacht.
    A small-angle neutron and static light scattering study of micelles formed in aqueous mixtures of a nonionic alkylglucoside and an anionic surfactant2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 25, s. 12387-12393Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The size and shape of micelles formed in aqueous mixtures of the anionic surfactant sodium dodecyl sulfate (SDS) and the nonionic sugar-based surfactant n-decyl beta-D-glucopyranoside (C(10)G) at different concentrations of added salt have been investigated with small-angle neutron and static light scattering. Rather small prolate ellipsoidal micelles form in the absence of added salt and at [NaCl] = 10 mM in D2O. The micelles grow considerably in length to large rods as the electrolyte concentration is raised to [NaCl] = 0.1 M. In excess of nonionic surfactant ([SDS]/[C(10)G] = 1:3) at [NaCl] = 0.1 M in D2O, several thousands of Angstroms long wormlike micelles are observed. Most interestingly, a conspicuously large isotope solvent effect was observed from static light scattering data according to which micelles formed at [SDS]/[C(10)G] = 1:3 and [NaCl] = 0.1 M in H2O are at least five times smaller than micelles formed in the corresponding samples in D2O.

  • 18.
    Bergström, Lars Magnus
    et al.
    KTH, Tidigare Institutioner, Kemi.
    Kjellin, Mikael
    KTH, Tidigare Institutioner, Kemi.
    Claesson, Per M.
    KTH, Tidigare Institutioner, Kemi.
    Grillo, I.
    Small-angle neutron scattering study of mixtures of cationic polyelectrolyte and anionic surfactant: Effect of polyelectrolyte charge density2004Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, nr 6, s. 1874-1881Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have studied mixtures of an anionic surfactant (deuterated sodium dodecyl sulfate, SDS-d) and cationic polyelectrolytes with different charge densities (10%, 30%, 60%, and 100%) using small-angle neutron scattering (SANS). Near compositions corresponding to charge neutralization, the solutions phase separate into a complex phase (precipitate) consisting of, in the cases of 30%, 60%, and 100% charge density, a two-dimensional (213) hexagonal lattice of close-packed cylindrical micelles and a clear liquid. When either polyelectrolyte with charge density less than 100% or SDS-d is present in sufficient excess, the solution becomes clear and isotropic, and from the scattering data we may conclude that prolate or rod-shaped micelles are present. The micelles are seen to grow in length with increasing SDS-d concentration and polyelectrolyte charge density from about 80 Angstrom to 550 Angstrom, whereas the cross-sectional radius is 15 Angstrom and approximately constant. The number of micelles per polyelectrolyte chain is found to be slightly larger than unity (1-6). In some of the (turbid) samples rod-shaped micelles are found to coexist with larger polyelectrolyte-surfactant complexes. Solutions consisting of 10% charged polyelectrolyte and SDS-d are very viscous and gellike, and the complex phase is much less defined with a much larger distance between adjacent aggregates in the complex phase.

  • 19.
    Bergström, Lars Magnus
    et al.
    KTH, Tidigare Institutioner                               , Kemi.
    Kjellin, U. R. M.
    Claesson, Per M
    KTH, Tidigare Institutioner                               , Kemi.
    Pedersen, J. S.
    Nielsen, M. M.
    A small-angle X-ray scattering study of complexes formed in mixtures of a cationic polyelectrolyte and an anionic surfactant2002Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, nr 44, s. 11412-11419Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The internal structure of the solid phase formed in mixtures of the anionic surfactant sodium dodecyl sulfate (SDS) and a range of oppositely charged polyelectrolytes with different side chains and charge density has been investigated using small-angle X-ray scattering. Polyelectrolytes with short side chains ([3-(2-methylpropionamido)propyl]trimethylammonium chloride, MAPTAC, and poly{[(2-propionyloxy)ethyl]-trimethylammonium chloride}, PCMA) form a 2-dimensional hexagonal structure with SDS, whereas a polyelectrolyte without side chains (poly(vinlyamine), PVAm) forms a lamellar structure. The hexagonal structure of MAPTAC is retained either when a neutral monomer (acrylamide, AM) is included in the polymer backbone to reduce the charge density or when a nonionic surfactant is admixed to the SDS/polyelctrolyte complex.. The unit cell length of AM-MAPTAC increases with decreasing charge density from a=47.7 Angstrom (MAPTAC, 100% charge density) to 58.5 Angstrom (AM-MAPTAC, 30% charge density). The unit cell length in the lamellar SDS/PVAm complex (a=36.1 Angstrom) is significantly smaller than for the different hexagonal structures. It is conjectured that the cylinders in the hexagonal structure and the bilayers in the lamellar structure are based on self-assembled surfactant aggregates with the polyelectrolyte mainly located in the aqueous region adjacent to the charged surfactant headgroups.

  • 20.
    Bondesson, Laban
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Frediani, Luca
    Department of Chemistry, University of Tromsø, Norway.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Mennucci, Bendetta
    Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Italy.
    Solvation of N3- at the water surface: the Polarizable Continuum Model approach2006Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 23, s. 11361-11368Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a new quantum mechanical model to introduce Pauli repulsion interaction between a molecular solute and the surrounding solvent in the framework of the Polarizable Continuum Model. The new expression is derived in a way to allow naturally for a position-dependent solvent density. This development makes it possible to employ the derived expression for the calculation of molecular properties at the interface between two different dielectrics. The new formulation has been tested on the azide anion (N-3(-)) for which we have calculated the solvation energy, the dipole moment, and the static polarizability at the interface as a function of the ion position. The calculations have been carried out for different ion-surface orientations, and the results have also been compared with the parallel electrostatic-only solvation model.

  • 21.
    Bondesson, Laban
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Rudberg, Elias
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Salek, Pawel
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    A linear scaling study of solvent-solute interaction energy of drug molecules in aqua solution2007Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, nr 34, s. 10320-10328Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Solvent-solute interaction energies for three well-known drug molecules in water solution are computed at the Hartree-Fock and B3LYP density functional theory levels using a linear scaling technique, which allows one to explicitly include in the model water molecules up to 14 A away from the solute molecule. The dependence of calculated interaction energies on the amount of included solvent has been examined. It is found that it is necessary to account for water molecules within an 8 A radius around the drug molecule to reach the saturated solvent interaction level. Effects of electron correlation and basis set on solvent-solute interaction energies are discussed.

  • 22. Borgstrom, M.
    et al.
    Blart, E.
    Boschloo, Gerrit
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Mukhtar, E.
    Hagfeldt, Anders
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Hammarstrom, L.
    Odobel, F.
    Sensitized hole injection of phosphorus porphyrin into NiO: Toward new photovoltaic devices2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 48, s. 22928-22934Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper describes the preparation and the characterization of a photovoltaic cell based on the sensitization of a wide band gap p-type semiconductor (NiO) with a phosphorus porphyrin. A photophysical study with femtosecond transient absorption spectroscopy showed that light excitation of the phosphorus porphyrin chemisorbed on NiO particles induces a very rapid interfacial hole injection into the valence band of NiO, occurring mainly on the 2-20 ps time scale. This is followed by a recombination in which ca. 80% of the ground-state reactants are regenerated within 1 ns. A photoelectrochernical device, prepared with a nanocrystalline NiO electrode coated with the phosphorus porphyrin, yields a cathodic photocurrent indicating that electrons indeed flow from the NiO electrode toward the solution. The low incident-to-photocurrent efficiency (IPCE) can be rationalized by the rapid back recombination reaction between the reduced sensitizer and the injected hole which prevents an efficient regeneration of the sensitizer ground state from the iodide/triiodide redox mediator. To the best of our knowledge, this work represents the first example of a photovoltaic cell in which a mechanism of hole photoinjection has been characterized.

  • 23.
    Boschloo, Gerrit
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Hagfeldt, Anders
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Activation energy of electron transport in dye-sensitized TiO2 solar cells2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 24, s. 12093-12098Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Various characteristics of dye-sensitized nanostructured TiO2 solar cells, such as electron transport and electron lifetime, were studied in detail using monochromatic illumination conditions. The electron transport was found to be a thermally activated process with activation energies in the range of 0.10-0.15 eV for light intensities that varied 2 orders of magnitude. Electron lifetimes were determined using a new method and found to be significantly larger (> 1 s) than previously determined. An average potential was determined for electrons in the nanostructured TiO2 under illumination in short-circuit conditions. This potential is about 0.2 V lower than the open-circuit potential at the same light intensity. The electron transport time varies exponentially with the internal potential at short-circuit conditions, indicating that the gradient in the electrochemical potential is the driving force for electron transport in the nanostructured TiO2 film. The applicability of the conventionally used trapping/detrapping model is critically analyzed. Although experimental results can be fitted using a trapping/detrapping model with an exponential distribution of traps, the distribution parameters differ significantly between different types of experiment. Furthermore, the experimental activation energies for electron transport are smaller than those expected in a trapping/detrapping model.

  • 24.
    Boschloo, Gerrit
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Haggman, L.
    Hagfeldt, Anders
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Quantification of the effect of 4-tert-butylpyridine addition to I-/I-3(-) redox electrolytes in dye-sensitized nanostructured TiO2 solar cells2006Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 26, s. 13144-13150Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Addition of 4-tert-butylpyridine (4TBP) to redox electrolytes used in dye- sensitized TiO2 solar cells has a large effect on their performance. In an electrolyte containing 0.7 M LiI and 0.05 M I-2 in 3-methoxypropionitrile, addition of 0.5 M 4TBP gave an increase of the open-circuit potential of 260 mV. Using charge extraction and electron lifetime measurements, this increases could be attributed to a shift of the TiO2 band edge toward negative potentials (responsible for 60% of the voltage increase) and to an increase of the electron lifetime (40%). At a lower 4TBP concentration the shift of the band edge was similar, but the effect on the electron lifetime was less pronounced. The working mechanism of 4TBP can be summarized as follows: (1) 4TBP affects the surface charge of TiO2 by decreasing the amount of adsorbed protons and/or Li+ ions. ( 2) It decreases the recombination of electrons in TiO2 with triiodide in the electrolyte by preventing triiodide access to the TiO2 surface and/or by complexation with iodine in the electrolyte.

  • 25.
    Brena, Barbara
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Zhuang, G. V.
    Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley.
    Augustsson, A.
    Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley.
    Liu, G.
    Environmental Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley.
    Nordgren, J.
    Department of Physics, Uppsala University.
    Guo, J. H.
    Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley.
    Ross, P. N.
    Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Conformation dependence of electronic structures of poly(ethylene oxide)2005Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 16, s. 7907-7914Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The electronic structure of pure poly(ethylene oxide) (PEO) for four different polymeric chain conformations has been studied by Hartree-Fock (HF) and density functional theory (DFT) through the analysis of their valence band photoelectron spectroscopy (VB-PES), X-ray emission spectroscopy (XES), and resonant inelastic X-ray scattering (RIXS). It is shown that the valence band of PEO presents specific conformation dependence, which can be used as a fingerprint of the polymeric structures. The calculated spectra have been compared with experimental results for PEO powder.

  • 26. Carravetta, V.
    et al.
    De Abreu Gomes, A. H.
    Monti, S.
    Mocellin, A.
    Marinho, R. R. T.
    Björneholm, O.
    Ågren, Hans
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Naves De Brito, A.
    PH-dependent X-ray Photoelectron Chemical Shifts and Surface Distribution of Cysteine in Aqueous Solution2019Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, nr 17, s. 3776-3785Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The distribution and protonation states of amino acids in water droplets are of considerable concern in studies on the formation of clouds in the atmosphere as well as in many biological contexts. In the present work we use the amino acid cysteine as a prototypical example and explore the protonation states of this molecule in aqueous solution, which are strongly affected by the acidity of the environment and also can show different distributions between surface and bulk. We use a combination of X-ray photoelectron chemical shift measurements, density functional theory calculations of the shifts, and reactive force field molecular dynamics simulations of the underlying structural dynamics. We explore how the photoelectron spectra distinctly reflect the different protonation states that are generated by variation of the solution acidity and how the distribution of these protonation states can differ between bulk and surface regions. At specific pH values, we find that the distribution of the cysteine species at the surface is quite different from that in bulk, in particular, for the appearance in the surface region of species which do not exist in bulk. Some ramifications of this finding are discussed.

  • 27.
    Chen, Pan
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Nishiyama, Yoshiharu
    Wohlert, Jakob
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Lu, Ang
    Mazeau, Karim
    Ismail, Ahmed E.
    Translational Entropy and Dispersion Energy Jointly Drive the Adsorption of Urea to Cellulose2017Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, nr 10, s. 2244-2251Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The adsorption of urea on cellulose at room temperature has been studied using adsorption isotherm experiments and molecular dynamics (MD) simulations. The immersion of cotton cellulose into bulk urea solutions with concentrations between 0.01 and 0.30 g/mL led to a decrease in urea concentration in all solutions, allowing the adsorption of urea on the cellulose surface to be measured quantitatively. MD simulations suggest that urea molecules form sorption layers on both hydrophobic and hydrophilic surfaces. Although electrostatic interactions accounted for the majority of the calculated interaction energy between urea and cellulose, dispersion interactions were revealed to be the key driving force for the accumulation of urea around cellulose. The preferred orientation of urea and water molecules in the first solvation shell varied depending on the nature of the cellulose surface, but urea molecules were systematically oriented parallel to the hydrophobic plane of cellulose. The translational entropies of urea and water molecules, calculated from the velocity spectrum of the trajectory, are lower near the cellulose surface than in bulk. As urea molecules adsorb on cellulose and expel surface water into the bulk, the increase in the translational entropy of the water compensated for the decrease in the entropy of urea, resulting in a total entropy gain of the solvent system. Therefore, the cellulose urea dispersion energy and the translational entropy gain of water are the main factors that drive the adsorption of urea on cellulose.

  • 28.
    Chen, Shilu
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Fang, Wei-Hai
    Beijing Normal Univ, Sch Chem.
    Himo, Fahmi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Theoretical Study of the Phosphotriesterase Reaction Mechanism2007Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, nr 6, s. 1253-1255Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phosphotriesterase (PTE) is a binuclear zinc enzyme that catalyzes the hydrolysis of extremely toxic organophosphate triesters. In the present work, we have investigated the reaction mechanism of PTE using the hybrid density functional theory method B3LYP. We present a potential energy surface for the reaction and provide characterization of the transition states and intermediates. We used the high resolution crystal structure to construct a model of the active site of PTE, containing the two zinc ions and their first shell ligands. The calculations provide strong support to an associative mechanism for the hydrolysis of phosphotriesters by PTE. No protonation of the leaving group was found to be necessary. In particular, the calculations demonstrate that the nucleophilicity of the bridging hydroxide is sufficient to be utilized in the hydrolysis reaction, a feature that is of importance for a number of other di-zinc enzymes.

  • 29.
    Chen, Shilu
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Marino, Tiziana
    Università della Calabria, Dipartimento di Chimica.
    Fang, Wei-Hai
    Beijing Normal Univ, Coll Chem.
    Russo, Nino
    Università della Calabria, Dipartimento di Chimica.
    Himo, Fahmi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Peptide Hydrolysis by the Binuclear Zinc Enzyme Aminopeptidase from Aeromonas proteolytica: A Density Functional Theory Study2008Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, nr 8, s. 2494-2500Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aminopeptidase from Aeromonas proteolytica (AAP) is a binuclear zinc enzyme that catalyzes the cleavage of the N-terminal amino acid residue of peptides and proteins. In this study, we used density functional methods to investigate the reaction mechanism of this enzyme. A model of the active site was constructed on the basis of the X-ray crystal structure of the native enzyme, and a model dipeptide was used as a substrate. It was concluded that the hydroxide is capable of performing a nucleophilic attack at the peptide carbonyl from its bridging position without the need to first become terminal. The two zinc ions are shown to have quite different roles. Zn2 binds the amino group of the substrate, thereby orienting it toward the nucleophile, while Zn1 stabilizes the alkoxide ion of the tetrahedral intermediate, thereby lowering the barrier for the nucleophilic attack. The rate-limiting step is suggested to be the protonation of the nitrogen of the former peptide bond, which eventually leads to the cleavage of the C−N bond.

  • 30.
    Chmyrov, Andriy
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Sandén, Tor
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Widengren, Jerker
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Iodide as a Fluorescence Quencher and Promoter-Mechanisms and Possible Implications2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 34, s. 11282-11291Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this work, fluorescence correlation spectroscopy (FCS) was used to investigate the effects of potassium iodide (KI) on the electronic-state population kinetics of a range of organic dyes in the visible wavelength range. Apart from a heavy atom effect promoting intersystem crossing to the triplet states in all dyes, KI was also found to enhance the triplet-state decay rate by a charge-coupled deactivation. This deactivation was only found for dyes with excitation maximum in the blue range, not for those with excitation maxima at wavelengths in the green range or longer. Consequently, under excitation conditions sufficient for triplet state formation, KI can promote the triplet state buildup of one dye and reduce it for another, red-shifted dye. This anticorrelated, spectrally separable response of two different dyes to the presence of one and the same agent may provide a useful readout for biomolecular interaction and microenvironmental monitoring studies. In contrast to the typical notion of KI as a fluorescence quencher, the FCS measurements also revealed that when added in micromolar concentrations KI can act as an antioxidant, promoting the recovery of photo-oxidized fluorophores. However, in millimolar concentrations KI also reduces intact, fluorescently viable fluorophores to a considerable extent. In aqueous solutions, for the dye Rhodamine Green, an optimal concentration of KI of approximately 5 mM can be defined at which the fluorescence signal is maximized. This concentration is not high enough to allow full triplet state quenching. Therefore, as a fluorescence enhancement agent, it is primarily the antioxidative properties of KI that play a role.

  • 31. Coates, C. G.
    et al.
    Olofsson, J.
    Coletti, M.
    McGarvey, J. J.
    Önfelt, Björn
    Lincoln, P.
    Norden, B.
    Tuite, E.
    Matousek, P.
    Parker, A. W.
    Picosecond time-resolved resonance Raman probing of the light-switch states of Ru(Phen)(2)dppz (2+)2001Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 105, nr 50, s. 12653-12664Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Picosecond time-resolved resonance Raman (picosecond-TR3) spectroscopy has been used to conduct an extensive photophysical characterization of the light- switch complex [Ru(phen)(2)dppz](2+) as a function of environment, in which studies have been carried out in aqueous and nonaqueous media and in DNA. The results are considered in rotation to a previous report describing environment-sensitive lowest triplet MLCT states. Vibrational marker features and enhancement patterns were used to determine the rapid progression (< 20 ps) between two triplet MLCT states in aqueous environment, followed by subnanosecond, nonradiative deactivation to the ground state. In nonaqueous environment, the long-lived, emissive triplet MLCT state is spectrally identified as the short-lived first triplet MLCT state observed in water, in agreement with the earlier proposed mechanism. The present data are shown to correlate well with previous nanosecond RR findings for the complex in each environment. Interestingly, a precursor state has been identified upon excitation in both nonaqueous solvent and in DNA, which precedes the triplet MLCT state, and the lifetime of which appears to be environment dependent. Observation of this state is discussed in relation to other recent femtosecond spectroscopic studies on this complex.

  • 32. Cordomi, Arnau
    et al.
    Edholm, Olle
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Perez, Juan J.
    Effect of ions on a dipalmitoyl phosphatidylcholine bilayer. A molecular dynamics simulation study2008Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, nr 5, s. 1397-1408Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effect of physiological concentrations of different chlorides on the structure of a dipalmitoyl phosphatidylcholine (DPPC) bilayer has been investigated through atomistic molecular dynamics simulations. These calculations provide support to the concept that Li+, Na+, Ca2+, Mg2+, Sr2+, Ba2+, and Ac3+, but not K+, bind to the lipid-head oxygens. Ion binding exhibits an influence on lipid order, area per lipid, orientation of the lipid head dipole, the charge distribution in the system, and therefore the electrostatic potential across the head-group region of the bilayer. These structural effects are sensitive to the specific characteristics of each cation, i.e., radius, charge, and coordination properties. These results provide evidence aimed at shedding some light into the apparent contradictions among different studies reported recently regarding the ordering effect of ions on zwitterionic phosphatidylcholine lipid bilayers.

  • 33.
    Dai, Jing
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Alaei, Zahra
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Plazzotta, Beatrice
    Pedersen, Jan Skov
    Furo, Istvan
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Release of Solubilizate from Micelle upon Core Freezing2017Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, nr 45, s. 10353-10363Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By combining NMR (yielding H-1 chemical shift, spin relaxation, and self-diffusion data) and small-angle X-ray scattering experiments, we investigate the complex temperature dependence of the molecular and aggregate states in aqueous solutions of the surfactant [CH3(CH2)(17)(OCH2CH2)(20)OH], abbreviated as C18E20, and.hexamethyldisiloxane, HMDSO. The latter molecule serves as a model for hydrophobic solubilizates. Previously, the pure micellar solution was demonstrated to exhibit core freezing at approximately 7-8 degrees C. At room temperature, we find that HMDSO solubilizes at a volume fraction of approximately 10% in the core of the C18E20 micelles, which consists of molten and thereby highly mobile alkyl chains. Upon lowering the temperature, core freezing is found, just like in pure micelles, but at a temperature shifted significantly to 3 degrees C. The frozen cores contain immobile alkyl chains and exhibit a higher density but are essentially devoid (volume fraction below 1%) of the solubilizate. The latter molecules are released, first gradually and then rather steeply, from the core in the temperature range that is roughly delimited by the two core freezing temperatures, one for pure micelles and one for micelles with solubilizates. The release behavior of systems with different initial HMDSO loading follows the same master curve. This feature is rationalized in terms of loading capacity being strongly temperature dependent: upon lowering the temperature, release commences once the loading capacity descends below the actual solubilizate content. The sharp release curves and the actual release mechanism with its molecular features shown in rich detail have some bearing on a diverse class of possible applications.

  • 34.
    Dedinaite, Andra
    et al.
    KTH, Tidigare Institutioner                               , Kemi.
    Ernstsson, M.
    Chitosan-SDS interactions at a solid-liquid interface: Effects of surfactant concentration and ionic strength2003Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, nr 32, s. 8181-8188Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effect of ionic strength on adsorption of chitosan on mica as well as the impact of addition of an anionic surfactant, SDS, on the adsorbed chitosan layers is explored. It is demonstrated by chemical surface analysis (ESCA) and surface force measurements (SFA) that an elevated salt concentration leads to larger adsorbed amounts and thicker adsorption layers of this cationic polyelectrolyte. It is also shown that in contrast to the bulk, the binding of oppositely charged surfactant to the polyelectrolyte adsorbed on a negatively charged surface is facilitated by elevated ionic strength. Thus, the association process in bulk and at solid-liquid interfaces is rather different. The main point of difference is that at the solid-liquid interface one also has to consider interactions between the polyelectrolyte and the surface as well as between the surfactant and the surface.

  • 35.
    Dedinaite, Andra
    et al.
    KTH, Tidigare Institutioner, Kemi.
    Meszaros, R.
    Claesson, Per M
    KTH, Tidigare Institutioner, Kemi.
    Effect of sodium dodecyl sulfate on adsorbed layers of branched polyethylene imine2004Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, nr 31, s. 11645-11653Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effect of an anionic surfactant, sodium dodecyl sulfate, SDS, on the properties of adsorbed layers of a cationic highly branched polyelectrolyte, polyethylene,imine, PEI, has been investigated using surface force measurements, atomic force microscopy, and ESCA. The strategy used was to preadsorb PEI on negatively charged muscovite mica surfaces from a 20 ppm polyelectrolyte solution in 10 mM NaCl. The adsorption of PEI under these conditions gives rise to a strong recharging of the surface, i.e. after adsorption of PEI the surface carries a net positive charge. This conclusion was supported by ESCA measurements. Despite the high molecular weight of PEI (1.8 x 10(5) g/mol), the adsorbed layer is found to be very flat, and a repulsive double-layer force dominates at large separations. At smaller separation a strong attractive force is the main feature. Addition of SDS to a concentration of 0.01 cmc results in a nearly complete removal of the double-layer force, an increase in compressed layer thickness, and an increase in the magnitude of the adhesion force. Hence, significant SDS incorporation in the adsorbed layer occurs already at this low surfactant concentration. A recharging of the layer occurs at higher surfactant concentrations. At 0.5 cmc, the compressed thickness of the adsorbed layer is increased significantly and the adhesion between the surfaces has disappeared. We argue that each layer now is coated with an outer SDS layer oriented with the polar groups toward solution. In fact, there are striking similarities between the interfacial association between SDS and PEI and the adsorption of an ionic surfactant to an oppositely charged mineral surface. AFM imaging reveals that the adsorbed PEI layer is somewhat nonhomogeneous and contains polyelectrolyte patches. These surface features are smoothed out by addition of SDS to a concentration of 6 mM (1 cmc in 10 mM NaCl). ESCA measurements showed that exposure of the preadsorbed PEI layer to SDS concentrations around the cmc resulted in a limited desorption; about 15% of the initially adsorbed polyelectrolyte was removed after 16 h.

  • 36. Deshpande, M. D.
    et al.
    Scheicher, R. H.
    Ahuja, Rajeev
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Pandey, R.
    Binding strength of sodium ions in cellulose for different water contents2008Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, nr 30, s. 8985-8989Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The interaction strength of sodium ions (Na+) with cellulose is investigated from first principles for varying degrees of water content. We find that the interaction of water molecules and Na+ can be studied independently at the various OH groups in cellulose which we categorize as two different types. In the absence of water, Na+ forms strong ionic bonds with the OH groups of cellulose. When water molecules are anchored to the OH groups via hydrogen bonds, Na+ can eventually no longer bind to the OH groups, but will instead interact with the oxygen atoms of the water molecules. Due to the rather weak attachment of the latter to the OH groups, Na+ becomes effectively more mobile in the fully hydrated cellulose framework. The present study thus represents a significant step toward a first-principles understanding of the experimentally observed dependence of ionic conductivity on the level of hydration in cellulose network.

  • 37. d'Ortoli, Thibault Angles
    et al.
    Sjöberg, Nils A.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Vasiljeva, Polina
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Lindman, Jonas
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Widmalm, Göran
    Bergenstråhle-Wohlert, Malin
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Wohlert, Jakob
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers2015Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, nr 30, s. 9559-9570Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model.

  • 38. Dvinskikh, Sergey V.
    et al.
    Luz, Z.
    Zimmermann, H.
    Maliniak, A.
    Sandstrom, D.
    Molecular characterization of hexaoctyloxy-rufigallol in the solid and columnar phases: A local field NMR study2003Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, nr 9, s. 1969-1976Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Separated local field NMR spectroscopy was used to obtain H-1-C-13 dipolar interactions in the solid and columnar phases of the discotic compound 1,2,3,5,6,7-hexaoctyloxy-rufigallol (RufH8O). The couplings were measured and assigned by a variety of advanced NMR techniques performed under both static and magic-angle spinning conditions. The analysis of the dipolar couplings shows that the three nonequivalent aliphatic chains in RufH8O exhibit vastly different structural and dynamical characteristics. It was also found that one of the alpha methylene signals exhibits two H-1-C-13 dipolar splittings at low temperatures in the columnar phase. Similar pairs of doublets have previously been observed in a H-2 NMR study of RufH8O-H-2(alpha) and were there interpreted in terms of dynamic packing fluctuations along the columns. We will present an alternative explanation and show that these two doublets most likely originate from nonequivalent protons (or deuterons) in the alpha methylene group and not from density modulations.

  • 39.
    Dvinskikh, Sergey V.
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Yamamoto, Kazutoshi
    Scanu, David
    Deschenaux, Robert
    Ramamoorthy, Ayyalusamy
    High-resolution characterization of liquid-crystalline 60 fullerenes using solid-state nuclear magnetic resonance spectroscopy2008Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, nr 39, s. 12347-12353Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Liquid-crystalline materials containing fullerenes are valuable in the development of supramolecular switches and in solar cell technology. In this study, we characterize the liquid-crystalline and dynamic properties of fullerene-containing thermotropic compounds using solid-state natural abundance C-13 NMR experiments under stationary and magic angle spinning sample conditions. Chemical shifts spectra were measured in isotropic, liquid-crystalline nematic and smectic A and crystalline phases using one-dimensional 13C experiments, while two-dimensional separated local-field experiments were used to measure the H-1-C-13 dipolar couplings in mesophases. Chemical shift and dipolar coupling parameters were used to characterize the structure and dynamics of the liquid-crystalline dyads. NMR data of fullerene-containing thermotropic liquid crystals are compared to that of basic mesogenic unit and mesomorphic promoter compounds. Our NMR results suggest that the fullerene-ferrocene dyads form highly dynamic liquid-crystalline phases in which molecules rotate fast around the symmetry axis on the characteristic NMR time scale of similar to 10(-1) s.

  • 40. Engin, Ozge
    et al.
    Villa, Alessandra
    Sayar, Mehmet
    Hess, Berk
    Driving forces for adsorption of amphiphilic peptides to the air-water interface.2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 34, s. 11093-11101Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have studied the partitioning of amphiphilic peptides at the air-water interface. The free energy of adsorption from bulk to interface was calculated by determining the potential of mean force via atomistic molecular dynamics simulations. To this end a method is introduced to restrain or constrain the center of mass of a group of molecules in a periodic system. The model amphiphilic peptides are composed of alternating valine and asparagine residues. The decomposition of the free energy difference between the bulk and interface is studied for different peptide block lengths. Our analysis revealed that for short amphiphilic peptides the surface driving force dominantly stems from the dehydration of hydrophobic side chains. The only opposing force is associated with the loss of orientational freedom of the peptide at the interface. For the peptides studied, the free energy difference scales linearly with the size of the molecule, since the peptides mainly adopt extended conformations both in bulk and at the interface. The free energy difference depends strongly on the water model, which can be rationalized through the hydration thermodynamics of hydrophobic solutes. Finally, we measured the reduction of the surface tension associated with complete coverage of the interface with peptides.

  • 41. Engstrom, M.
    et al.
    Vaara, J.
    Schimmelpfennig, B.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Density functional theory calculations of electron paramagnetic resonance parameters of a nitroxide spin label in tissue factor and factor VIIa protein complex2002Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, nr 47, s. 12354-12360Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The electron paramagnetic resonance (EPR) g and N-14 hyperfine coupling (A) tensors of a nitroxide spin label are calculated with density-functional theory (DFT). The influence on the spin label from nearby amino acids in the extracellular part of tissue factor (sTF) and activated factor VII (FVIIa) protein complex is investigated. For that purpose, the nitroxide unit and six surrounding amino acids within 5 Angstrom are selected on the basis of a molecular mechanics structure of the protein complex. The effects of the surroundings on the EPR parameters of the spin label can be divided into indirect effects caused by the induced structure changes of the spin label and direct effects. The structural changes are larger in the present case. The experimentally measurable hyperfine tensor component perpendicular to the molecular plane of the spin label, A(zz), as well as the g tensor component along the NO direction, g,,, are significant probes of the intramolecular structure of the spin label. This indicates the possibility of relating EPR properties to the geometric structure of radical sites. The direct environmental effects on the g tensor from the surrounding amino acids mainly affect the second-order spin-orbit/orbital Zeeman cross-term contributions from the spin label itself. The direct effects originating elsewhere in the model are small. Neither the g nor A tensors display additivity of the effects of individual amino acids on the final observable. The results underline the feasibility of DFT calculations of the EPR parameters in large molecular systems, such as spin labels and other radicals in proteins.

  • 42.
    Fang, Yuan
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Giesecke, Marianne
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Furo, Istvan
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Complexing Cations by Poly(ethylene oxide): Binding Site and Binding Mode2017Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, nr 9, s. 2179-2188Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The binding of K+ and Ba2+ cations to short poly(ethylene oxide) (PEO) chains with ca. 4-25 monomeric units in methanol was studied by determining the effective charge of the polymer through a combination of electrophoretic NMR and diffusion NMR experiments. These cations were previously found to bind to long PEO chains in a similar strong manner. In addition, H-1 chemical shift and longitudinal spin relaxation rate changes upon binding were quantified. For both systems, binding was stronger for the short chains than that for the longer chains, which is attributed mainly to interactions between bound ions. For K+ ions, the equilibrium binding constant of a cation to a binding site was measured. For both cations, the binding site was estimated to consist of ca. six monomeric units that coordinated with the respective ions. For the systems with barium, a significant fraction of the bound ions are (BaAnion)(+) ion pairs. This leads to a strong anion effect in the effective charge of the oligomers acquired upon barium ion binding. For K+, the coordinating oligomer segment remains rather mobile and individual oligomers exchange rapidly (<<s) between their free and ion-complexing states. In contrast, segmental dynamics slows significantly for the oligomer section that coordinates with the barium species, and for individual oligomers, binding and nonbinding sections do not exchange on the time scale of seconds. Hence, oligomers also exchange slowly (>s) between their free and barium complexing states.

  • 43.
    Fang, Yuan
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Giesecke, Marianne
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Furo, Istvan
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Complexing Cations by Polyethylene Oxide. Binding Site and Binding Mode2017Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207Artikkel i tidsskrift (Fagfellevurdert)
  • 44.
    Frise, Anton E.
    et al.
    KTH, Skolan för kemivetenskap (CHE), Centra, Centrum för Industriell NMR-teknik.
    Dvinskikh, Sergey V.
    KTH, Skolan för kemivetenskap (CHE), Centra, Centrum för Industriell NMR-teknik.
    Ohno, Hiroyuki
    Kato, Takashi
    Furo, Istvan
    KTH, Skolan för kemivetenskap (CHE), Centra, Centrum för Industriell NMR-teknik.
    Ion Channels and Anisotropic Ion Mobility in a Liquid-Crystalline Columnar Phase As Observed by Multinuclear NMR Diffusometry2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 47, s. 15477-15482Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The anisotropic diffusion of anions and cations in the columnar and isotropic phases of a fan-shaped imidazolium hexafluorophosphate salt is measured by H-1 and F-19 diffusion NMR experiments. The macroscopic orientation of the columnar phase is investigated by H-2 NMR spectroscopy. We find that the anions, confined by the cations, diffuse faster than the cations along the columns but slowly across them, which exemplifies the ion channel model of these materials. The cations and anions are dissociated in the columnar phase but are paired or clustered in the isotropic phase.

  • 45.
    Frise, Anton
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi. KTH, Skolan för kemivetenskap (CHE), Centra, Centrum för Industriell NMR-teknik.
    Pages, Guilhem
    KTH, Skolan för kemivetenskap (CHE), Kemi. KTH, Skolan för kemivetenskap (CHE), Centra, Centrum för Industriell NMR-teknik. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Shtein, M.
    Pri Bar, I.
    Regev, O.
    Furo, Istvan
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi. KTH, Skolan för kemivetenskap (CHE), Centra, Centrum för Industriell NMR-teknik.
    Polymer binding to carbon nanotubes in aqueous dispersions: Residence time on the nanotube surface As Obtained by NMR diffusometry2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 9, s. 2635-2642Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The binding of block copolymer Pluronic F-127 in aqueous dispersions of single- (SWCNT) and multiwalled (MWCNT) carbon nanotubes has been studied by pulsed-field-gradient (PFG) 1H NMR spectroscopy. We show that a major fraction of polymers exist as a free species while a minor fraction is bound to the carbon nanotubes (CNT). The polymers exchange between these two states with residence times on the nanotube surface of 24 ± 5 ms for SWCNT and of 54 ± 11 ms for MWCNT. The CNT concentration in the solution was determined by improved thermal gravimetric analysis (TGA) indicating that the concentration of SWCNT dispersed by F-127 was significantly higher than that for MWCNT. For SWCNT, the area per adsorbed Pluronic F-127 molecule is estimated to be about 40 nm 2.

  • 46. Galoppini, Elena
    et al.
    Rochford, Jonathan
    Chen, Hanhong
    Saraf, Gaurav
    Lu, Yicheng
    Hagfeldt, Anders
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Boschloo, Gerrit
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Fast electron transport in metal organic vapor deposition grown dye-sensitized ZnO nanorod solar cells2006Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 33, s. 16159-16161Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The electron transport in dye-sensitized solar cells with a MOCVD (metal organic vapor deposition)-grown ZnO nanorod array (ZnO-N) or a mesoporous film prepared from ZnO colloids (ZnO-C) as the working electrode was compared. The electrodes were of similar thickness (2 Am) and sensitized with zinc(II) mesotetrakis(3-carboxyphenyl) porphyrin, while the electrolyte was I-/I-3-in 3-methoxypropionitrile. Electron transport in the ZnO-C cells was comparable with that found for colloidal TiO2 films (transport time similar to 10 ms) and was light intensity dependent. Electron transport in solar cells with ZnO-N electrodes was about 2 orders of magnitude faster (similar to 30 mu s). Thus, the morphology of the working ZnO electrode plays a key role for the electron transport properties.

  • 47. Ganguly, Pritam
    et al.
    Schravendijk, Pim
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. Technische Universität Darmstadt, Germany; Stockholm University, Sweden .
    van der Vegt, Nico F. A.
    Ion Pairing in Aqueous Electrolyte Solutions with Biologically Relevant Anions2011Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, nr 13, s. 3734-3739Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We performed molecular simulations to study ion pairing in aqueous solutions. Our results indicate that ion specific interactions of Li+, Na+, and K+ with the dimethyl phosphate anion are solvent-mediated. The same mechanism applies to carboxylate ions, as has been illustrated in earlier simulations of aqueous alkali acetate solutions. Contact ion pairs play only a minor role or no role at all in determining the solution structure and ion specific thermodynamics of these systems. On the basis of the Kirkwood Buff theory of solution we furthermore show that the well-known reversal of the Hofmeister series of salt activity coefficients, comparing chloride or bromide with dimethyl phosphate or acetate, is caused by changing from a contact pairing mechanism in the former system to a solvent-mediated interaction mechanism in the latter system.

  • 48.
    Gao, Li
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Tu, Yaoquan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Eriksson, Leif A.
    Characterization of Agonist Binding to His524 in the Estrogen Receptor alpha Ligand Binding Domain2012Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 16, s. 4823-4830Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The bioactivities of the natural steroidal estrogen 17 beta-estradiol (E-2), the synthetic estrogen diethylstilbestrol (DES), and the phytoestrogen genistein (GEN) are intimately associated with their binding to the estrogen receptor alpha ligand binding domain (ER alpha LBD) and accordingly allostery. Molecular modeling techniques have been performed on agonists in complex with the LBD, focusing on the pivotal role of His524 modeled as the epsilon-tautomer and the protonated form (depending on pH). It is found that E-2 binds to the active LBD with the aid of Leu525, showing existing stable patterns of an H-binding network with Glu419 via His524 in all models. The main difference seen in the effect is that the full agonists E-2 and DES have higher binding energies to the protonated His524 than the partial agonists GEN and Way-169916 (W), which is in line with noted experimental transcriptional activities. In conclusion, the study demonstrates that the phytoestrogen GEN interacts differently with the LBD than what E-2 and DES do, which explains the observed signaling differences.

  • 49.
    Giesecke, Marianne
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Hallberg, Fredrik
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Fang, Yuan
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Stilbs, Peter
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Furó, István
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Binding of monovalent and multivalent metal cations to polyethylene oxide in methanol probed by electrophoretic and diffusion NMR2016Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, nr 39, s. 10358-10366Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Complex formation in methanol between monodisperse polyethylene oxide (PEO) and a large set of cations was studied by measuring the effective charge acquired by PEO upon complexation. Quantitative data were obtained at a low ionic strength of 2 mM (for some salts, also between 0.5 and 6 mM) by a combination of diffusion nuclear magnetic resonance (NMR) and electrophoretic NMR experiments. For strongly complexing cations, the magnitude of the acquired effective charge was on the order of 1 cation per 100 monomer units. For monovalent cations, the relative strength of binding varies as Na+ < K+ ≈ Rb+ ≈ Cs+, whereas Li+ exhibited no significant binding. All polyvalent cations bind very weakly, except for Ba2+ that exhibited strong binding. Anions do not bind, as is shown by the lack of response to the chemical nature of anionic species (perchlorate, iodide, or acetate). Diffusion experiments directly show that the acetate anion with monovalent cations does not associate with PEO. Considering all cations, we find that the observed binding does not follow any Hofmeister order. Instead, binding occurs below a critical surface charge density, which indicates that the degree of complexation is defined by the solvation shell. A large solvation shell prevents the binding of most multivalent ions.

  • 50. Griffiths, P. C.
    et al.
    Cheung, A. Y. F.
    Farley, C.
    Paul, A.
    Heenan, R. K.
    King, S. M.
    Pettersson, Erik
    KTH, Tidigare Institutioner, Kemi.
    Stilbs, Peter
    KTH, Tidigare Institutioner, Kemi.
    Ranganathan, R.
    Small-angle neutron scattering, electron paramagnetic resonance, electrophoretic NMR, and time-resolved fluorescence quenching studies of sodium dodecyl sulfate and tetra(ethylene oxide) dodecyl ether mixed surfactant micelles2004Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, nr 4, s. 1351-1356Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Small-angle neutron scattering (SANS), time-resolved fluorescence quenching (TRFQ), electrophoretic NMR (ENMR), and electron paramagnetic resonance (EPR) have been used to study mixed micelles formed from the two dodecyl tailed surfactants, sodium dodecyl sulfate (SDS) and tetra(ethylene oxide) dodecyl ether. By combining the TRFQ and EPR techniques, one is essentially able to calculate the SANS data, lending significant weight to the micelle characteristics thus obtained. EPR reports the degree of hydration of the surfactant headgroups; TRFQ, the micelle aggregation number and inter alia the volume of the hydrophobic core. Given the physical dimensions of the surfactant, i.e., alkyl chain length, headgroup volumes, etc., it is then possible to calculate the micelle ellipticity and shell thickness. The ENMR studies provide a rather different but complementary estimate of the ionic character of the micelle. With increasing nonionic content, the aggregation number increases, the micelle becomes more elliptical, and the headgroup region of the micelle becomes less hydrated and significantly more viscous. The degree of sodium counterion dissociation shows an initial small decrease with decreasing SDS micelle mole fraction but subsequently increases, reflecting the interplay between the electrostatic character of the micelle surface and the micelle curvature.

1234 1 - 50 of 167
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