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  • 1. Agrell, H. G.
    et al.
    Boschloo, Gerrit
    Hagfeldt, Anders
    Conductivity studies of nanostructured TiO2 films permeated with electrolyte2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 33, p. 12388-12396Article in journal (Refereed)
    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.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chen, Shi-Lu
    Hua, Wei-Jie
    Fang, Wei-Hai
    Luo, Yi
    Repair of DNA Dewar Photoproduct to (6-4) Photoproduct in (6-4) Photolyase2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 37, p. 10976-10982Article in journal (Refereed)
    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, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liao, Rongzhen
    Stockholm University.
    Chen, Shilu
    Beijing Institute of Technology.
    Hua, Wei-Jie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fang, Wei-Hai
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 37, p. 10976-10982Article in journal (Refereed)
    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.

  • 4. Ai, Yue-Jie
    et al.
    Liao, Rong-zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chen, Shu-feng
    Luo, Yi
    Fang, Wei-Hai
    Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 44, p. 14096-14102Article in journal (Refereed)
    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.

  • 5.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Liao, Rong-zhen
    Chen, Shu-feng
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fang, Wei-Hai
    Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 44, p. 14096-14102Article in journal (Refereed)
    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.

  • 6. Aidas, Kestutis
    et al.
    Olsen, Jogvan Magnus H.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 7, p. 2069-2080Article in journal (Refereed)
    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.

  • 7. Ainalem, M. L.
    et al.
    Campbell, R. A.
    Khalid, S.
    Gillams, R .J.
    Rennie, Adrian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Nylander, T.
    On the Ability of PAMAM Dendrimers and Dendrimer/DNA Aggregates To Penetrate POPC Model Biomembranes2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 21, p. 7229-7244Article in journal (Refereed)
    Abstract [en]

    Poly(amido amine) (PAMAM) dendrimers have previously been shown, as cationic condensing agents of DNA, to have high potential for nonviral gene delivery. This study addresses two key issues for gene delivery: the interaction of the biomembrane with (i) the condensing agent (the cationic PAMAM dendrimer) and (ii) the corresponding dendrimer/DNA aggregate. Using in situ null ellipsometry and neutron reflection, parallel experiments were carried out involving dendrimers or generations 2 (G2), 4 (G4), and 6 (G6). The study demonstrates that free dendrimers of all three generations were able to traverse supported palmitoyloleoylphosphatidylcholine (POPC) bilayers deposited on silica surfaces. The model biomembranes were elevated front the solid surfaces upon dendrimer penetration, which offers a promising new way to generate more realistic model biomembranes where the contact with the supporting surface is reduced and where aqueous cavities are present beneath the bilayer. The largest dendrimer (GO) induced partial bilayer destruction directly upon penetration, whereas the smaller dendrimers (G2 and G4) leave the bilayer intact, so we propose that lower generation dendrimers have greater potential as transfection mediators. In addition to the experimental observations, coarse-grained simulations on the interaction between generation 3 (03) dendrimers and POPC bilayers were performed in the absence and presence of a bilayer-supporting negatively charged surface that emulates the support. The simulations demonstrate that G3 is transported across free-standing POPC bilayers by direct penetration and not by endocytosis. The penetrability was, however, reduced in the presence of a surface, indicating that the membrane transport observed experimentally was not driven solely by the surface. The experimental reflection techniques were also applied to dendrimer/DNA aggregates of charge ratio = 0.5, and while G2/DNA and G4/DNA aggregates interact with POPC bilayers. G6/DNA displays no such interaction. These results indicate that, in contrast to free dendrimer molecules, dendrimer/DNA aggregates of low charge ratios are not able to traverse a membrane by direct penetration.

  • 8.
    Akhtar, Sultan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Experimental Physics.
    Strömberg, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Zardán Gómez de la Torre, Teresa
    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.
    Gunnarsson, Klas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    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.
    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, Experimental Physics.
    Real-Space Transmission Electron Microscopy Investigations of Attachment of Functionalized Magnetic Nanoparticles to DNA-Coils Acting as a Biosensor2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 41, p. 13255-13262Article in journal (Refereed)
    Abstract [en]

    The present work provides the first real-space analysis of nanobead-DNA coil interactions. Immobilization of oligonucleotide-functionalized magnetic nanobeads in rolling circle amplified DNA-coils was studied by complex magnetization measurements and transmission electron microscopy (TEM), and a statistical analysis of the number of beads hybridized to the DNA-coils was performed. The average number of beads per DNAcoil using the results from both methods was found to be around 6 and slightly above 2 for samples with 40 and 130 nm beads, respectively. The TEM analysis supported an earlier hypothesis that 40 nm beads are preferably immobilized in the interior of DNA-coils whereas 130 nm beads, to a larger extent, are immobilized closer to the exterior of the coils. The methodology demonstrated in the present work should open up new possibilities for characterization of interactions of a large variety of functionalized nanoparticles with macromolecules, useful for gaining more fundamental understanding of such interactions as well as for optimizing a number of biosensor applications.

  • 9. Alarcon, H.
    et al.
    Boschloo, Gerrit
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Mendoza, P.
    Solis, J. L.
    Hagfeldt, Anders
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Dye-sensitized solar cells based on nanocrystalline TiO2 films surface treated with Al3+ ions: Photovoltage and electron transport studies2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 39, p. 18483-18490Article in journal (Refereed)
    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.

  • 10.
    Ali, Ehesan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Oppeneer, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Datta, Sambhu N.
    Influence of Solute-Solvent Hydrogen Bonding on Intramolecular Magnetic Exchange Interaction in Aminoxyl Diradicals: A QM/MM Broken-Symmetry DFT Study2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 16, p. 5545-5548Article in journal (Refereed)
    Abstract [en]

    We have investigated the effect of nitroxide radical-water hydrogen bonding (NO center dot center dot center dot center dot H2O) on the intramolecular magnetic exchange interaction (J) for biologically relevant aminoxyl diradicals. We adopt a combination of broken-symmetry density functional theory and the quantum mechanics/molecular mechanics (QM/MM) approach. We find that the presence of hydrogen bonding reorients the radical spin density on -NO center dot. This phenomenon reduces the effective distance between the two interacting localized spin centers that eventually increases the intramolecular magnetic exchange interaction. We have also investigated the functional variation of the magnetic exchange interaction, using various GGA (BLYP, PBE, HCTH407), meta-GGA (TPSS, VXSC), and hybrid (O3LYP, B3LYP, B3P86, B3PW91, and PBE0) functionals.

  • 11. Ali, Md. Ehesan
    et al.
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Oppeneer, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Electronic Structure, Spin-States, and Spin-Crossover Reaction of Heme-Related Fe-Porphyrins: A Theoretical Perspective2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 20, p. 5849-5859Article in journal (Refereed)
    Abstract [en]

    The electronic structures, spin-states, and geometrical parameters of tetra-, penta-, and hexa-coordinated iron-porphyrins are investigated applying density functional theory (DFT) based calculations, utilizing the plane-wave pseudopotential as well as localized basis set approaches. The splitting of the spin multiplet energies are investigated applying various functionals including recently developed hybrid meta-GGA (M06 family) functionals. Almost all of the hybrid functionals accurately reproduce the experimental ground state spins of the investigated Fe-porphyrins. However, the energetic ordering of the spin-states and the energies between them are still an issue. The widely used B3LYP provides consistent results for all chosen systems. The GGA+U functionals are found to be equally competent. After assessing the performance of various functionals in spin-state calculations, the potential energy surfaces of the oxygen binding process by heme is investigated. This reveals a "double spin-crossover" feature for the lowest energy reaction path that is consistent with previous CASPT2 calculations but predicting a lowest energy singlet state. The calculations have hence captured the spin-crossover as well as spin-flip processes. These are driven by the intra-atomic orbital polarization on the central metal atom due to the atomic and orbitals rearrangements. The nature of the chemical bonding and a molecular orbital analysis are also performed for the geometrically simple but electronic structurally complicated system tetra-coordinated planar Fe porphyrin in comparison to the penta-coordinated systems. This analysis explains the observed paradoxical appearance of certain peaks in the local density of states (DOS).

  • 12. Al-Manasir, Nodar
    et al.
    Zhu, Kaizheng
    Kjøniksen, Anna-Lena
    Knudsen, Kenneth D.
    Karlsson, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Nyström, Bo
    Oslo University.
    Effects of Temperature and pH on the Contraction and Aggregation of Microgels in Aqueous Suspensions2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 32, p. 11115-11123Article in journal (Refereed)
    Abstract [en]

    Chemically cross-linked poly(N-isopropylacrylamide) (PNIPAM) microgels   and PNIPAM with different amounts of acrylic acid groups   (PNIPAM-co-PAA) were synthesized and the temperature-induced   aggregation behaviors of aqueous suspensions of these microgels were   investigated mainly with the aid of dynamic light scattering (DLS) and   turbidimetry. The DLS results show that the particles at all conditions   shrink at temperatures up to approximately the lower critical solution temperature (LCST), but the relative contraction effect is larger for   the microgels without acid groups or for microgels with added anionic   surfactant (SDS). A significant depression of the cloud point is found   in suspensions of PNIPAM with very low concentrations of SDS. The   compression of the microgels cannot be traced from the turbidity   results, but rather the values of the turbidity increase in this   temperature interval. This phenomenon is discussed in the framework of   a theoretical model. At temperatures above LCST, the size of the   microgels without attached charged groups in a very dilute suspension   is unaffected by temperature, while the charged particles (pH 7 and 11)   continue to collapse with increasing temperature over the entire   domain. In this temperature range, low-charged particles of higher   concentration and particles containing acrylic acid groups at low pH   (pH 2) aggregate, and macroscopic phase separation is approached at   higher temperatures. This study demonstrates how the stabilization of   microgels can be affected by factors such as polymer concentration,   addition of ionic surfactant to particles without charged acid groups, amount of charged groups in the polymer, and pH.

  • 13.
    Almgren, Mats
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Garamus, Vasil
    Asakawa, Tsuyoshi
    Jiang, Nan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Contrast Variation SANS Investigation of Composition Distributions in Mixed Surfactant Micelles2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 25, p. 7133-7141Article in journal (Refereed)
    Abstract [en]

    Small angle neutron scattering measurements have been performed on three systems (HFDeP-d5-C (N-1(1,1,2,2-tetrahydroperfluorodecanoyl)pyridinium-d5 chloride)/C16PC in 63 mM NaCl; HFDeP-d5-C/C12PC in 200 mM NaCl, and as an example of an ideally mixed system, SDS/SDS-d25 in 200 mM NaCl) contg. micelles formed in a binary mixt. of surfactants, in order to investigate the compn. distribution of the mixed micelles. The exptl. data were collected varying the contrast between the av. scattering length d. of micelles and aq. solvent by changing the H2O/D2O ratio. Anal. of data includes a model-independent approach-the indirect Fourier transformation method and direct modeling-simultaneous fit at all contrasts by the scattering from micelles of equal size and shape with compn. distribution and an effective interaction. It has earlier been shown (Almgren, M.; Garamus, V. M. J. Phys. Chem. B 2005, 109, 11348) that for micelles of equal size, independent of the compn., and with negligible intermicellar interactions, the scattered intensity at zero angle varies quadratically with the contrast, with the min. intensity at the nominal match point proportional to s2, the variance of the micelle compn. distribution. Within the regular soln. framework, the compn. distribution and its variance are uniquely defined by the value of the interaction parameter and the micelle aggregation no. At 25 DegC, the first system gave s = 0.37, corresponding to a broad, bimodal compn. distribution, the second s = 0.22, a broad distribution with a shallow min. at the midpoint. For SDS/SDS-d25, we found s = 0.006 +- 0.030, which is a smaller value than that of the binominal compn. distribution expected for an ideally mixed system.

  • 14. Amira, S.
    et al.
    Spangberg, D.
    Probst, M.
    Hermansson, Kersti
    KTH, Superseded Departments, Biotechnology.
    Molecular dynamics simulation of Fe2+(aq) and Fe3+(aq)2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 1, p. 496-502Article in journal (Refereed)
    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.

  • 15. Amira, S.
    et al.
    Spangberg, D.
    Zelin, V.
    Probst, M.
    Hermansson, Kersti
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Car-Parrinello molecular dynamics simulation of Fe3+(aq)2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 29, p. 14235-14242Article in journal (Refereed)
    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.

  • 16.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Probst, Michael
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Molecular Dynamics simulation of Fe2+(aq) and Fe3+(aq)2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 1, p. 496-502Article in journal (Refereed)
    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.

  • 17.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Zelin, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Probst, Michael
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Car-Parrinello Molecular Dynamics simulation of Fe3+(aq)2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 29, p. 14235-14242Article in journal (Refereed)
    Abstract [en]

    The optimized geometry and energetic properties of Fe(D2O)n3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe3+ 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.

  • 18. Andersen, A.
    et al.
    Örtegren, Jonas
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Information Technology and Media.
    Koelsch, P.
    Wantke, D.
    Motschmann, H.
    Oscillating Bubble SHG on Surface Elastic and Surface Viscoelastic Systems: New Insights in the Dynamics of Adsorption Layers2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 37, p. 18466-18472Article in journal (Refereed)
    Abstract [en]

    Surface rheology governs a great variety of interfacial phenomena such as foams or emulsions and plays a dominant role in several technological processes such as high-speed coating. Its major difference with bulk rheology resides in the high compressibility of the surface phase, which is the direct consequence of the molecular exchange between adsorbed and dissolved species. In analogy to bulk rheology, a complex surface dilational modulus, ε, which captures surface tension changes upon defined area changes of the surface layer, can be defined. The module ε is complex, and the molecular interpretation of the dissipative process that gives rise to the imaginary part of the module is subject to some controversy. In this contribution, we used the oscillating bubble technique to study the surface dilational modulus in the mid-frequency range. The dynamic state of the surface layer was monitored by a pressure sensor and by surface second-harmonic generation (SHG). The pressure sensor measures the real and imaginary part of the modulus while SHG monitors independently the surface composition under dynamic conditions. The experiment allows the assessment of the contribution of the compositional term to the surface dilational modulus ε. Two aqueous surfactant solutions have been characterized:  a surface elastic and a surface viscoelastic solution. The elastic surface layer can be described within the framework of the extended Lucassen−van den Tempel Hansen model. The change in surface concentration is in phase with the relative area change of the surface layer, which is in strong contrast with the results obtained from the surface viscoelastic solution. Here, surface tension, area change, and surface composition are phase-shifted, providing evidence for a nonequilibrium state within the surface phase. The data are used to assess existing surface rheology models.

  • 19.
    Andersson, M
    et al.
    Chalmers University of Technology.
    Österlund, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Ljungstrom, S
    Chalmers University of Technology.
    Palmqvist, A E C
    Chalmers University of Technology.
    Preparation of nanosize anatase and rutile TiO2 by hydrothermal treatment of microemulsions and their activity for photocatalytic wet oxidation of phenol2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 41, p. 10674-10679Article in journal (Refereed)
    Abstract [en]

    Titanium dioxide (TiO2) nanoparticles of both anatase and rutile phases were synthesized by hydrothermal treatment of microemulsions, and their photocatalytic activity for wet oxidation of phenol was studied. The only difference between the two syntheses used was that different acids were added to the microemulsions, making direct comparison of the catalytic activity of the two polymorphs possible. If hydrochloric acid was used, the rutile structure formed, and if nitric acid was used, anatase formed. The phase stability of the microemulsion was studied and according to conductivity and turbidity measurements the idea of a direct template effect could be discarded during the hydrothermal treatment. However, an initial size-templating phenomenon is possible during the mixing step. The particles, which were in the size range of a few nanometers were characterized with N-2-adsorption; XRD, SEM, and XPS. The activity of the two polymorphs for the photocatalytic oxidation of phenol in water was examined. It was shown that the rutile phase initially decomposed phenol much faster and follows a first-order process reasonably well (k = 4 x 10(-5) s(-1)). The photodecomposition process using the anatase phase led, however, to a much more rapid overall degradation following an initial slower rate of phenol oxidation. The results indicate that the observed difference of the photodecomposition process for the two TiO2 phases is due to the formation of different intermediates.

  • 20.
    Andersson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Hansson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Phase Behavior of Salt-Free Polyelectrolyte Gel-Surfactant Systems2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 24, p. 6064-6080Article in journal (Refereed)
    Abstract [en]

    Ionic surfactants tend to collapse the outer parts of polyelectrolyte gels, forming shells that can be used to encapsulate other species including protein and peptide drugs. In this paper, the aqueous phase behavior of covalently cross-linked polyacrylate networks containing sodium ions and dodecyltrimethylammonium ions as counterions is investigated by means of swelling isotherms, dye staining, small-angle X-ray scattering, and confocal Raman spectroscopy. The equilibrium state is approached by letting the networks absorb pure water. With an increasing fraction of surfactant ions, the state of the water-saturated gels is found to change from being swollen and monophasic, via multiphasic states, to collapsed and monophasic. The multiphasic gels have a swollen, micelle-lean core surrounded by a collapsed, micelle- rich shell, or a collapsed phase forming a spheroidal inner shell separating two micelle-lean parts. It is shown that the transition between monophasic and core-shell states can be induced by variation of the osmotic pressure and variation of the charge of the micelles by forming mixed micelles with the nonionic surfactant octaethyleneglycol monododecylether. The experimental data are compared with theoretical predictions of a model derived earlier. In the calculations, the collapsed shell is assumed to be homogeneous, an approximation introduced here and shown to be excellent for a wide range of compositions. The theoretical results highlight the electrostatic and hydrophobic driving forces behind phase separation.

  • 21. Andersson, Ove
    et al.
    Häussermann, Ulrich
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A Second Glass Transition in Pressure Collapsed Type II Clathrate Hydrates2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 15, p. 4376-4384Article in journal (Refereed)
    Abstract [en]

    Type II clathrate hydrates (CHs) M-17 H2O, with M = tetrahydrofuran (THF) or 1,3-dioxolane, are known to collapse, or amorphize, on pressurization to similar to 1.3 GPa in the temperature range 77-140 K. On heating at 1 GPa, these pressure-amorphized CH states show a weak, stretched sigmoid-shaped, heat-capacity increase because of a glass transition. Here we use thermal conductivity and heat capacity measurements to show that also type II CH with M = cyclobutanone (CB) collapses on isothermal pressurization and undergoes a similar, weak, glass transition upon heating at 1 GPa. Furthermore, we reveal for both THF CH and CB CH a second, much more pronounced, glass transition at temperatures above the thermally weak glass transition on heating in the 0.2-0.7 GPa range. This result suggests the general occurrence of two glass transitions in water-rich (94 mol %) pressure-collapsed CHs. Because of a large increase in dielectric permittivity concurrently as the weak heat capacity increase, the first glass transition must be due to kinetic unfreezing of water molecules. The thermal features of the second glass transition, measured on isobaric temperature cycling, are typical of a glass liquid glass transition, which suggests that pressure-amorphized CHs transform reversibly to liquids.

  • 22.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Häussermann, Ulrich
    A Second Glass Transition in Pressure Collapsed Type II Clathrate Hydrates2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 15, p. 4376-4384Article in journal (Refereed)
    Abstract [en]

    Type II clathrate hydrates (CHs) M·17 H2O, with M = tetrahydrofuran (THF) or 1,3-dioxolane, are known to collapse, or amorphize, on pressurization to ∼1.3 GPa in the temperature range 77–140 K. On heating at 1 GPa, these pressure-amorphized CH states show a weak, stretched sigmoid-shaped, heat-capacity increase because of a glass transition. Here we use thermal conductivity and heat capacity measurements to show that also type II CH with M = cyclobutanone (CB) collapses on isothermal pressurization and undergoes a similar, weak, glass transition upon heating at 1 GPa. Furthermore, we reveal for both THF CH and CB CH a second, much more pronounced, glass transition at temperatures above the thermally weak glass transition on heating in the 0.2–0.7 GPa range. This result suggests the general occurrence of two glass transitions in water-rich (94 mol %) pressure-collapsed CHs. Because of a large increase in dielectric permittivity concurrently as the weak heat capacity increase, the first glass transition must be due to kinetic unfreezing of water molecules. The thermal features of the second glass transition, measured on isobaric temperature cycling, are typical of a glass–liquid–glass transition, which suggests that pressure-amorphized CHs transform reversibly to liquids.

  • 23.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Nakazawa, Yasuhiro
    Transitions in pressure collapsed clathrate hydrates2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 9, p. 3846-3853Article in journal (Refereed)
    Abstract [en]

    Type II clathrate hydrates (CHs), or ice clathrates, are inclusion compounds in which a hydrogen-bonded cage-like structure of H2O accommodates molecules of suitable size, known as guest molecules. CHs have similar local geometrical arrangements of the hydrogen-bonded water network as ice and both are known to collapse to amorphous states on isothermal pressurization at temperatures below about 140 K. Moreover, the collapsed CH states undergo a glass, or glass-like, transition at 140 K on heating at 1 GPa, which is identical to that of collapsed ice, or high density amorphous ice. Here we use thermal conductivity and dielectric measurements to study the transition behavior of two type II CHs with tetrahydrofuran and 1,3 dioxolane, respectively, as guest molecules. After their collapsed states have been heated to well above the glass transition at 1 GPa, we find transitions corresponding to the high to low density amorphous ice transition of ice with only slightly shifted temperature-pressure (T-p) coordinates compared to those of pure water. Thus, collapsed CHs show the same transition behaviors as cold water, which provide the basis for the model that explains the unusual temperature and pressure behaviors of waters properties in terms of two distinct types of liquid water. Collapsed CHs are, however, more stable than collapsed ice and can therefore be studied in a wider T-p interval. The results suggest sluggish homogenizing and phase separation processes, which affect the transition behaviors of collapsed CHs.

  • 24.
    Angles d'Ortoli, Thibault
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sjöberg, Nils A.
    Vasiljeva, Polina
    Lindman, Jonas
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bergenstråhle-Wohlert, Malin
    Wohlert, Jakob
    Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 30, p. 9559-9570Article in journal (Refereed)
    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.

  • 25.
    Arkhipov, Victor P.
    et al.
    Kazan National Research Technological University.
    Idiyatullin, Zhamil Sh
    Kazan National Research Technological University.
    Potapova, Elisaveta
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Antzutkin, Oleg
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Filippov, Andrei
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Micelles and aggregates of oxyethylated isononylphenols and their extraction properties near cloud point2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 20, p. 5480-5487Article in journal (Refereed)
    Abstract [en]

    We used nuclear magnetic resonance (NMR) spectroscopy and dynamic light scattering (DLS) techniques to study the structural and dynamic properties of micellar solutions of nonionic surfactants of a homologous series of oxyethylated isononylphenols - C9H19C6H 4O(C2H4O)nH, where n = 6, 8, 9, 10, or 12 - in a wide range of temperatures, including cloud points. The radii of the micelles and aggregates, as well as their compositions at different concentrations of surfactant, were determined. Using aqueous phenol solutions as a model, we studied the process of cloud point extraction with oxyethylated isononylphenols

  • 26. Aziz, Emad F.
    et al.
    Ottosson, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Eisebitt, Stefan
    Eberhardt, Wolfgang
    Jagoda-Cwiklik, Barbara
    Vacha, Robert
    Jungwirth, Pavel
    Winter, Bernd
    Cation-specific interactions with carboxylate in amino acid and acetate aqueous solutions: X-ray absorption and ab initio calculations2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 40, p. 12567-12570Article in journal (Refereed)
    Abstract [en]

    Relative interaction strengths between cations (X = Li+, Na+, K+, NH4+) and anionic carboxylate groups of acetate and glycine in aqueous solution are determined. These model systems mimic ion pairing of biologically relevant cations with negatively charged groups at protein surfaces. With oxygen ls X-ray absorption spectroscopy, we can distinguish between spectral contributions from H2O and carboxylate, which allows us to probe the electronic structure changes of the atomic site of the carboxylate group being closest to the countercation. From the intensity variations of the COOaq- ls X-ray absorption peak, which quantitatively correlate with the change in the local partial density of states from the carboxylic site, interactions are found to decrease in the sequence Na+ > Li+ > K+ > NH4+. This ordering, as well as the observed bidental nature of the -COOaq- and X-aq(+) interaction, is supported by combined ab initio and molecular dynamics calculations.

  • 27.
    Azuma, Tomoyuki
    et al.
    Univ Tokyo, Dept Bioengn, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1138656, Japan..
    Teramura, Yuji
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology. Univ Tokyo, Dept Bioengn, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1138656, Japan.
    Hoshi, Toru
    Nihon Univ, Dept Mat & Appl Chem, Coll Sci & Technol, Tokyo 1018308, Japan..
    Takai, Madoka
    Univ Tokyo, Dept Bioengn, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1138656, Japan..
    Enhancement of Cell Adhesion on a Phosphorylcholine-Based Surface through the Interaction with DNA Mediated by Ca2+ Ions2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 48, p. 12272-12278Article in journal (Refereed)
    Abstract [en]

    2-Methacryloyloxyethyl phosphorylcholine (MPC) has a PC group and is one of the most well-known bioinert polymers. In this study, we evaluated the interaction between MPC and DNA, which specifically interacts with the phospholipid head group via Ca2+ ions. A MPC monolayer and poly(MPC) brush were fabricated to observe the effect of the structure on the interaction between MPC and DNA via Ca2+ ions. The poly(MPC) brush, which shows higher MPC unit density, more efficiently interacted with DNA via Ca2+ ions. Also, serum protein could interact with the poly(MPC) brush via DNA, although the brush itself hardly interacted with serum proteins. Cell adhesion was significantly provoked on poly(MPC)/DNA compared with poly(MPC) because serum protein adsorption was induced on poly(MPC)/DNA.

  • 28.
    Bader, Reto
    Stockholm University, Faculty of Science, Department of Physics.
    Utilizing the Charge Field Effect on Amide N-15 Chemical Shifts for Protein Structure Validation2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 1, p. 347-358Article in journal (Refereed)
    Abstract [en]

    Of all the nuclei in proteins, the nuclear magnetic resonance (NMR) chemical shifts of nitrogen are the theoretically least well understood. In this study, quantum chemical methods are used in combination with polarizable-continuum models in order to show that consideration of the effective electric field, including charge screening due to solvation, improves considerably the consistencies of statistical relationships between experimental and computed amide N-15 shifts between various sets of charged and uncharged oligopeptides and small organic molecules. A single conversion scheme between shielding parameters from first principles using density functional theory (DFT) and experimental shifts is derived that holds for all classes of compounds examined here. This relationship is then used to test the accuracy of such N-15 chemical shift predictions in the cyclic decapeptide antibiotic gramicidin S (GS). GS has previously been studied in great detail, both by NMR and X-ray crystallography. It adopts a well-defined backbone conformation, and hence, only a few discrete side chain conformational states need to be considered. Moreover, a charge-relay effect of the two cationic ornithine side chains to the protein backbone has been described earlier by NMR spectroscopy. Here, DFF-derived backbone amide nitrogen chemical shifts were calculated for multiple conformations of GS. Overall, the structural dynamics of GS is revisited in view of chemical shift behavior along with energetic considerations. Together, the study demonstrates proof of concept that N-15 chemical shift information is particularly useful in the analysis and validation of protein conformational states in a charged environment.

  • 29. Baev, A.
    et al.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Quantum-classical modeling of nonlinear pulse propagation in a dissolved two-photon active chromophore2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 11, p. 5379-5385Article in journal (Refereed)
    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.

  • 30. Baev, Alexander
    et al.
    Norman, Patrick
    Henriksson, Johan
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Theoretical Simulations of clamping levels in optical power limiting2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 42, p. 20912-20916Article in journal (Refereed)
    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.

  • 31. 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 structures2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 14, p. 3726-3737Article in journal (Refereed)
    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.

  • 32.
    Bassan, Arianna
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Physics.
    Borowski, Tomasz
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Oxygen Activation by Rieske Non-Heme Iron Oxygenases, a Theoretical Insight2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 34, p. 13031-13041Article in journal (Refereed)
    Abstract [en]

    The first steps of dioxygen activation in naphthalene 1,2-dioxygenase have been investigated by means of hybrid density functional theory. Reduction of molecular oxygen by this Rieske dioxygenase occurs in the catalytic domain accommodating a mononuclear non-heme iron(II) complex, and it requires two external electrons ultimately delivered by a Rieske [2Fe−2S] cluster hosted in the neighboring domain. Theoretical tools have been applied to gain insight into the O2-binding step and into the first one-electron-transfer process involving the mononuclear and the Rieske centers, and yielding an iron(II)−superoxo intermediate. The reaction, which is mimicked with a model including both metal sites, is found to be a reversible equilibrium. Although the entropic loss associated with the binding of O2 to iron(II) is not canceled by the corresponding enthalpic binding energy, it is, however, balanced by the exothermicity of the electron transfer process from the Rieske cluster to the dioxygen-bound iron(II) complex. The rationalization for the calculated energetics is related to the values of the ionization potential (IP) of the Rieske cluster and the electron affinity (EA) of the mononuclear iron complex: the latter is computed to be higher than the former, when dioxygen is bound to the metal. The possibility that a second external electron is delivered to the mononuclear site before dioxygenation of the substrate has also been examined. It is shown that, if the second electron is available in the Rieske domain, the electron transfer process is energetically favored. The results acquired with the large model comprising the two metal centers are compared to the corresponding information collected from the study of smaller models, where either the mononuclear iron complex or the Rieske cluster is included.

  • 33. Bastardo, LA
    et al.
    Garamus, VM
    Bergström, M
    Claesson, PM
    YKI – Ytkemiska institutet.
    The structures of complexes between polyethylene imine and sodium dodecyl sulfate in D2O: A scattering study2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, p. 167-174Article in journal (Refereed)
    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 smallangle 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 wellordered 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.

  • 34. Bastardo, LA
    et al.
    Mészáros, R
    Varga, I
    Gilányi, T
    Claesson, PM
    YKI – Ytkemiska institutet.
    Deuterium isotope effects on the interaction between hyperbranched polyethylene imine and an anionic surfactant2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, p. 16196-16202Article in journal (Refereed)
    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 gradually decreases 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≈9 a much higher mobility of the PEI/SDS complexes was found at low surfactant concentrations in D2O than in H2O, 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. On the other hand, at the natural pH/pD as well as at pH=4 and pD=4 conditions the PEI molecules have roughly equal charge density which results 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 where weak polyelectrolyte/surfactant aggregates are investigated in heavy water and then these observations are correlated with structures of the same system in water.

  • 35.
    Bastardo Zambrano, Luis Alejandro
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    Garamus, V. M.
    GKSS Research Centre, Geesthacht.
    Bergström, Lars Magnus
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    Claesson, Per M.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    The structures of complexes between polyethylene imine and sodium dodecyl sulfate in D2O: a scattering study2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 1, p. 167-174Article in journal (Refereed)
    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.

  • 36.
    Bastardo Zambrano, Luis Alejandro
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    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, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    Deuterium isotope effects on the interaction between hyperbranched polyethylene imine and an anionic surfactant2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 33, p. 16196-16202Article in journal (Refereed)
    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.

  • 37. Battistel, Marcos D.
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Freedberg, Daron I.
    Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 17, p. 4860-4869Article in journal (Refereed)
    Abstract [en]

    We introduce the abundant hydroxyl groups of glycans as NMR handle's and structural probes to expand the repertoire of tools for structure function studies on glycans in solution. To this end, we present the facile detection and assignment of hydroxyl groups in a Wide range of sample concentrations (0.5-1700 mM) and temperatures, ranging from -5 to 25 degrees C.,We then exploit this information to directly detect hydrogen bonds, well-known for their importance in molecular structural determination through NMR. Via HSQC-TOCSY, we were able to determine the directionality; of these hydrogen bonds in sucrose Furthermore, by means Of molecular dynamics simulations in conjunction with NMR, we establish that one Out of the three detected hydrogen bonds arises from intermolecular interactions. This finding may shed light on glycan glycan interactions and glycan recognition by proteins.

  • 38. Bauer, C.
    et al.
    Boschloo, Gerrit
    Mukhtar, E.
    Hagfeldt, A.
    Interfacial electron-transfer dynamics in Ru(tcterpy)(NCS)(3)-sensitized TiO2 nanocrystalline solar cells2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 49, p. 12693-12704Article in journal (Refereed)
    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.

  • 39.
    Bauer, Christophe
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Boschloo, Gerrit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Mukhtar, Emad
    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.
    Interfacial Elevtron-Transfer Dynamics in Ru(tcterpy)(NCS)3-Sensiitized TiO2 Nanocrystalline Solar Cells2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, p. 12693-12704Article in journal (Refereed)
    Abstract [en]

    The anchoring of the ruthenium dye {(C4H9)4N}[Ru(Htcterpy)(NCS)3] (with tcterpy = 4,4‘,4‘‘-tricarboxy-2,2‘: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 I2•-). 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 (Ne > 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 I2•- on a very fast time scale (<20 ns). Within regime I, the decay of I2•- occurs in 100 ns via reaction with injected electrons (I2•- + e- → 2I-). In regime II (Ne ≤ 1), which corresponds to the normal operating conditions of dye-sensitized solar cells, the decay of I2•- is very slow and likely occurs via the dismutation reaction (2I2•-→ I- + I3-). Our results predict that, under high light intensity (Ne > 1), the quantum efficiency losses in dye-sensitized solar cells will be important because of the dramatic acceleration of the reaction between I2•- 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.

  • 40. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    Bartkowiak, Wojciech
    Agren, Hans
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Elucidating the Mechanism of Zn2+ Sensing by a Bipyridine Probe Based on Two-Photon Absorption2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 34, p. 9067-9075Article in journal (Refereed)
    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.

  • 41. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Elucidating the Mechanism of Zn2+ Sensing by a Bipyridine Probe Based on Two-Photon Absorption2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 34, p. 9067-9075Article in journal (Refereed)
    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.

  • 42.
    Beek, WJE
    et al.
    Eindhoven University of Technology, Netherlands.
    Wienk, MM
    Eindhoven University of Technology, Netherlands.
    Kemerink, Martijn
    Eindhoven University of Technology, Netherlands.
    Yang, XN
    Eindhoven University of Technology, Netherlands.
    Janssen, RAJ
    Eindhoven University of Technology, Netherlands.
    Hybrid zinc oxide conjugated polymer bulk heterojunction solar cells2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 19, p. 9505-9516Article in journal (Refereed)
    Abstract [en]

    Bulk heterojunction photovoltaic devices based on blends of a conjugated polymer poly [2-methoxy-5-(3,7-dimethyloctyloxy)-1,4-phenylenevinylene] (MDMO-PPV) as electron donor and crystalline ZnO nanoparticles (nc-ZnO) as electron acceptor have been studied. Composite nc-ZnO:MDMO-PPV films were cast from a common solvent mixture. Time-resolved pump-probe spectroscopy revealed that a photoinduced electron transfer from MDMO-PPV to nc-ZnO occurs in these blends on a sub-picosecond time scale and produces a long-lived (milliseconds) charge-separated state. The photovoltaic effect in devices, made by sandwiching the active nc-ZnO:MDMO-PPV layer between charge-selective electrodes, has been studied as a function of the ZnO concentration and the thickness of the layer. We also investigated changing the degree and type of mixing of the two components through the use of a surfactant for ZnO and by altering the size and shape of the nc-ZnO particles. Optimized devices have an estimated AM1.5 performance of 1.6% with incident photon to current conversion efficiencies up to 50%. Photoluminescence spectroscopy, atomic force microscopy, and transmission electron microscopy have been used to gain insight in the morphology of these blends.

  • 43.
    Bengtsson, Jenny
    et al.
    RISE - Research Institutes of Sweden, Swerea, Swerea IVF.
    Olsson, Carina
    RISE - Research Institutes of Sweden, Swerea, Swerea IVF.
    Hedlund, Artur
    RISE - Research Institutes of Sweden, Swerea, Swerea IVF.
    Köhnke, Tobias
    RISE - Research Institutes of Sweden, Swerea, Swerea IVF.
    Bialik, Erik
    Molecules in Motion, Sweden.
    Understanding the Inhibiting Effect of Small-Molecule Hydrogen Bond Donors on the Solubility of Cellulose in Tetrabutylammonium Acetate/DMSO2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 50, p. 11241-11248Article in journal (Refereed)
    Abstract [en]

    Certain ionic liquids are powerful cellulose solvents, but tend to be less effective when small-molecule hydrogen bond donors are present. This is generally attributed to competition with cellulose for hydrogen bonding opportunities to the anion of the ionic liquid. We show that the solubility of cellulose in dimethyl sulfoxide solutions of tetrabutylammonium acetate is less strongly affected by water than by ethanol on a molar basis, contrary to what can be expected based on hydrogen bond stoichiometry. Molecular dynamics simulations indicate that the higher tolerance to water is due to water-cellulose interactions that improves solvation of cellulose and, thereby, marginally favors dissolution. Through Kirkwood-Buff theory we show that water, but not ethanol, improves the solvent quality of DMSO and partly compensates for the loss of acetate-cellulose hydrogen bonds.

  • 44. Bergenstråhle, M.
    et al.
    Wohlert, J.
    Larsson, Per Tomas
    RISE, STFI-Packforsk.
    Mazeau, K.
    Berglund, L. A.
    Dynamics of cellulose - Water interfaces: NMR spin - Lattice relaxation times calculated from atomistic computer simulations2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Journal of Physical Chemistry B, Vol. 112, no 9, p. 2590-2595Article in journal (Refereed)
    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 I β-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 (110). 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.

  • 45.
    Bergenstråhle, Malin
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Berglund, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Mazeau, Karim
    CERMAV-CNRS .
    Thermal Response in Crystalline Iβ Cellulose: A Molecular Dynamics Study2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 30, p. 9138-9145Article in journal (Refereed)
    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.

  • 46.
    Bergenstråhle, Malin
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Wohlert, Jakob
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Larsson, Per Tomas
    STFI-PACKFORSK AB.
    Mazeau, Karim
    CERMAV-CNRS.
    Berglund, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Dynamics of Cellulose-Water Interfaces: NMR Spin-Lattice Relaxation Times Calculated from Atomistic Computer Simulations2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 9, p. 2590-2595Article in journal (Refereed)
    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.

  • 47.
    Bergkvist, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Surface Biotechnology.
    Carlsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Surface Biotechnology.
    Oscarsson, Sven
    A method for studying protein orientation with atomic force microscopy using relative protein volumes2001In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 105, no 10, p. 2062-2069Article in journal (Refereed)
    Abstract [en]

    A method for studying protein orientation is described, in which the relative volumes of single proteins and single molecule complexes are measured using atomic force microscopy (AFM). Site-specific ligands are used as “probes” to bind to surface adsorbed proteins. The quantity of formed complexes gives an estimate of the amount of protein oriented in such a way as to allow ligand binding. The volume distribution for single proteins adsorbed to a surface was calculated and fitted to a Gaussian function. This volume distribution was used to localize the same proteins on surfaces with protein−ligand complexes, thus rendering it possible to find the amount of complex formed. Two model systems were used: one with two different mouse monoclonal antibodies of IgG1 type (mAb's against human serum transferrin, hST) adsorbed on silicon surfaces, and one with hST adsorbed to unmodified mica and aminated mica. The adsorbed proteins were allowed to react with a site-specific ligand, which binds to a defined region of the adsorbed protein (hST in the case of adsorbed mAb and lectin in the case of adsorbed hST). A great difference in ligand binding was found between the two antibodies adsorbed to the same type of surface as well as between hST adsorbed to different surfaces. This differance can be attributed to different orientation of the proteins on the surface. The general approach of this method suggests that it can be used for almost any site-specific molecule, either for surface orientation studies or studies where single molecule interactions need to be investigated.

  • 48.
    Bergström, L. M.
    et al.
    Department of Pharmacy, Pharmaceutical Physical Chemistry, Uppsala University.
    Bastardo Zambrano, Luis Alejandro
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    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 surfactant2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 25, p. 12387-12393Article in journal (Refereed)
    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.

  • 49.
    Bergström, Lars Magnus
    et al.
    KTH, Superseded Departments, Chemistry.
    Kjellin, Mikael
    KTH, Superseded Departments, Chemistry.
    Claesson, Per M.
    KTH, Superseded Departments, Chemistry.
    Grillo, I.
    Small-angle neutron scattering study of mixtures of cationic polyelectrolyte and anionic surfactant: Effect of polyelectrolyte charge density2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 6, p. 1874-1881Article in journal (Refereed)
    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.

  • 50.
    Bergström, Lars Magnus
    et al.
    KTH, Superseded Departments, Chemistry.
    Kjellin, U. R. M.
    Claesson, Per M
    KTH, Superseded Departments, Chemistry.
    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 surfactant2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 44, p. 11412-11419Article in journal (Refereed)
    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.

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