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  • 51. Hermida-Ramón, Jose Manuel
    et al.
    Karlström, Gunnar
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Analysis of the relative stability of cis-urocanic acid in condensed phase: The use of Langevin dipoles2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 28, p. 7115-7120Article in journal (Refereed)
    Abstract [en]

    A series of ab initio calculations employing a modified Langevin dipoles method to model neutral, cationic, and anionic cis-urocanic acid in human skin is presented. A comparison between the stability of the conformers in gas phase and in a condensed phase is performed. In particular, the energy barrier and transition state of the isomerization reaction of the anionic forms of cis-urocanic acid have been characterized. The modifications of the Langevin dipoles method, a procedure to obtain the required model parameters, and model verifications are presented. The latter include computing the water solvation energy and the free energy of the water dissociation.

  • 52.
    Herschend, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Baudin, Micael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Influence of Substrate Dynamics on CO-MgO(001) Bonding: Using Molecular Dynamics Snapshots in Quantum-Chemical Calculations2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 11, p. 5473-5479Article in journal (Refereed)
    Abstract [en]

    Combined molecular dynamics (MD) and quantum mechanics (QM) calculations have been performed for CO adsorbed on MgO(001) at 50 K. The changes in the adsorption energy caused by the surface dynamics have been analyzed, and a clear correlation was found between the dynamic variation of the adsorption energy and the electrostatic field above the adsorption site. By separating the electrostatic contributions arising from the local structure at the adsorption site from those originating from the rest of the slab, a linear expression of these contributions could be fitted which closely reproduces the dynamic changes in the adsorption energy. Using this simple linear expression, the distribution of adsorption energies for CO above the Mg2+ sites on the MgO(001) surface at 50, 80, and 150 K have been predicted.

  • 53. Hewitt, Dominic
    et al.
    Marklund, Erik
    Scott, David J
    Robinson, Carol V
    Borysik, Antoni J
    A hydrodynamic comparison of solution and gas phase proteins and their complexes.2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 29Article in journal (Refereed)
    Abstract [en]

    The extent to which protein structures are preserved on transfer from solution to gas phase is a central question for native mass spectrometry. Here we compare the collision cross sections (Ω) of a wide range of different proteins and protein complexes (15-500 kDa) with their corresponding Stokes radii (RS). Using these methods, we find that Ω and RS are well correlated, implying overall preservation of protein structure in the gas phase. Accounting for protein hydration, a scaling term is required to bring Ω and RS into parity. Interestingly, the magnitude of this scaling term agrees almost entirely with the drag factor proposed by Millikan. RS were then compared with various different predicted values of Ω taken from their atomic coordinates. We find that many of the approaches used to obtained Ω from atomic coordinates miscalculate the physical sizes of the proteins in solution by as much as 20%. Rescaling of Ω estimated from atomic coordinates may therefore seem appropriate as a general method to bring theoretical values in line with those observed in solution.

  • 54.
    Jidheden, Claes
    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.
    Single Microgels in Core-Shell Equilibrium: A Novel Method for Limited Volume Studies2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 37, p. 10030-10042Article in journal (Refereed)
    Abstract [en]

    The interactions of cationic surfactant dodecyl-trimethylammonium bromide and cationic protein cytochrome c with anionic polyacrylate microgels have been investigated in microscopic liquid droplets by means of a micropipette technique at ionic strength 0.01 M and pH 8. Experiments on single microgels in solutions of limited amounts of the surfactant provide the first evidence of microgels in a stable biphasic core shell state with the surfactant partitioned to the shell. Under the same conditions, the protein is found to distribute uniformly in the microgels. Quantitative data in the form of swelling and binding isotherms are presented and compared with literature data for macrogels and with predictions of a recent gel theory. Theory is found to be in semiquantitative agreement with the experiments. The importance of polyion-mediated attractions between the protein molecules is analyzed theoretically and proposed to explain the continuous but highly cooperative binding isotherms.

  • 55.
    Johannissen, Linus O.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Irebo, Tania
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Sjödin, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Johansson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    The Kinetic Effect of Internal Hydrogen Bonds on Proton-Coupled Electron Transfer from Phenols: A Theoretical Analysis with Modeling of Experimental Data2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 50, p. 16214-16225Article in journal (Refereed)
    Abstract [en]

    Proton-coupled electron transfer (PCET) was studied in two biomimetic covalently linked Ru(bpy)3−tyrosine complexes with the phenolic proton hydrogen-bonded to an internal carboxylate group. The phenolic group is either a salicylic acid (o-hydroxybenzoic acid, SA) or an o-hydroxyphenyl-acetic acid (PA), where the former gives a resonance-assisted hydrogen bond. Transient absorption data allowed direct determination of the rate constant for these intramolecular, bidirectional, and concerted PCET (CEP) reactions, as a function of temperature and H/D isotope. We found, unexpectedly, that the hydrogen bond in SA is in fact weaker than the hydrogen bond in the complex with PA, which forced us to reassess an earlier hypothesis that the proton coupling term for CEP with SA is increased by a stronger hydrogen bond. Consequently, the kinetic data was modeled numerically using a quantum mechanical rate expression. Sufficient experimentally determined observables were available to give robust and well-determined parameter values. This analysis, coupled with DFT/B3LYP and MP2 calculations and MD simulations, gave a detailed insight into the parameters that control the CEP reactions, and the effect of internal hydrogen bonds. We observed that a model with a static proton-tunneling distance is unable to describe the reaction correctly, requiring unrealistic values for the equilibrium proton-tunneling distances. Instead, when promoting vibrations that modulate the proton donor−acceptor distance were included, satisfactory fits to the experimental data were obtained, with parameter values that agree with DFT calculations and MD simulations. According to these results, it is in fact the weaker hydrogen bond of SA which increases the proton coupling. The inner reorganization energy of the phenolic groups is a significant factor contributing to the CEP barriers, but this is reduced by the hydrogen bonds to 0.35 and 0.50 eV for the two complexes. The promoting vibrations increase the rate of CEP by over 2 orders of magnitude, and dramatically reduce the kinetic isotope effect from ca. 40 for the static case to a modest value of 2−3.

  • 56.
    Johansson, Christian
    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.
    Malmsten, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Mechanism of lysozyme uptake in poly(acrylic acid) microgels2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 18, p. 6183-6193Article in journal (Refereed)
    Abstract [en]

    The uptake of lysozyme by oppositely charged poly(acrylic acid)  microgels was investigated by micromanipulator-assisted light microscopy and confocal microscopy. Lysozyme was observed to distribute nonuniformly within the microgels, forming a core-shell structure with   considerably higher lysozyme concentration in the shell than in the core. The core-shell formation can be divided into two periods. During the first of these, the shell is formed during rapid microgel deswelling, and with no lysozyme diffusing into the microgel core. This   is followed by a second period, during which microgel deswelling is negligible and lysozyme diffuses into the microgel core. Thus, the shell which is initially formed as a result of fast lysozyme transport to the gel network and fast protein-microgel interactions is able to   carry a mechanical load and prevents deswelling during the latter core diffusion period. These two distinct regimes of lysozyme loading were also successfully described theoretically, demonstrating the importance of lysozyme cluster formation for the observed phenomena.

  • 57.
    Johansson, Erik M. J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics I.
    Hedlund, M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics I.
    Siegbahn, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics I.
    Rensmo, Håkan
    Electronic and Molecular Surface Structure of Ru(tcterpy)(NCS)3 and Ru(dcbpy)2(NCS)2 Adsorbed from Solution onto Nanostructured TiO2: A Photoelectron Spectroscopy Study2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 47, p. 22256-22263Article in journal (Refereed)
    Abstract [en]

    The element specificity of photoelectron spectroscopy (PES) has been used to compare the electronic and molecular structure of the dyes Ru(tcterpy)(NCS)3 (BD) and Ru(dcbpy)2(NCS)2adsorbed from solution onto nanostructured TiO2. Ru(dcbpy)2(NCS)2 was investigated in its acid (N3) and in its 2-fold deprotonated form (N719) having tetrabutylammonium (TBA+) as counterions. A comparison of the O1s spectra for the dyes indicates that the interactions through the carboxylate groups with the TiO2 surface are very similar for the dyes. However, we observe that some of the dye molecules also interact through the NCS groups when adsorbed at the TiO2 surface. Comparing the N719 and the N3 molecule, the fraction of NCS groups interacting through the sulfur atoms is smaller for N719 than for N3. We also note that the counterion TBA+ is coadsorbed with the N719 and BD molecules although the amount was smaller than expected from the molecular formulas. Comparing the valence levels for the dyes adsorbed on TiO2, the position of the highest occupied electronic energy level is similar for N3 and N719, while that for BD is lower by 0.25 eV relative to that of the other complexes.

  • 58.
    Johansson, Erik M J
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology.
    Hedlund, Maria
    Uppsala University, Disciplinary Domain of Science and Technology.
    Siegbahn, Hans
    Uppsala University, Disciplinary Domain of Science and Technology.
    Rensmo, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology.
    Electronic and molecular surface structure of Ru(tcterpy)(NCS)(3) and Ru(dcbpy)(2)(NCS)(2) adsorbed from solution onto nanostructured TiO2: A photoelectron spectroscopy study2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 47, p. 22256-22263Article in journal (Refereed)
    Abstract [en]

    The element specificity of photoelectron spectroscopy (PES) has been used to compare the electronic and molecular structure of the dyes Ru(tcterpy)(NCS)(3) (BD) and Ru(dcbpY)(2)(NCS)(2) adsorbed from solution onto nanostructured TiO2. Ru(dcbpy)(2)(NCS)(2) was investigated in its acid (N3) and in its 2-fold deprotonated form (N719) having tetrabutylammonium (TBA(+)) as counterions. A comparison of the O1s spectra for the dyes indicates that the interactions through the carboxylate groups with the TiO2 surface are very similar for the dyes. However, we observe that some of the dye molecules also interact through the NCS groups when adsorbed at the TiO2 surface. Comparing the N719 and the N3 molecule, the fraction of NCS groups interacting through the sulfur atoms is smaller for N719 than for N3. We also note that the counterion TBA(+) is coadsorbed with the N719 and BD molecules although the amount was smaller than expected from the molecular formulas. Comparing the valence levels for the dyes adsorbed on TiO2, the position of the highest occupied electronic energy level is similar for N3 and N719, while that for BD is lower by 0.25 eV relative to that of the other complexes.

  • 59. Karlsson, Bjorn C. G.
    et al.
    Olsson, Gustaf D.
    Friedman, Ran
    Rosengren, Annika M.
    Henschel, Henning
    Nicholls, Ian A.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    How Warfarin's Structural Diversity Influences Its Phospholipid Bilayer Membrane Permeation2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 8, p. 2384-2395Article in journal (Refereed)
    Abstract [en]

    The role of the structural diversity of the widely used anticoagulant drug warfarin on its distribution in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer membranes was investigated using a series of both restrained (umbrella sampling) and unrestrained molecular dynamics simulations. Data collected from unrestrained simulations revealed favorable positions for neutral isomers of warfarin, the open side chain form (OCO), and the cyclic hemiketal (CCO), along the bilayer normal close to the polar headgroup region and even in the relatively distant nonpolar lipid tails. The deprotonated open side chain form (DCO) was found to have lower affinity for the DOPC bilayer membrane relative to the neutral forms, with only a small fraction interacting with the membrane, typically within the polar headgroup region. The conformation of OCO inside the lipid bilayer was found to be stabilized by intramolecular hydrogen bonding thereby mimicking the structure of CCO. Differences in free energies, for positions of OCO and CCO inside the bilayer membrane, as compared to positions in the aqueous phase, were -97 and -146 kJ.mol(-1). Kinetic analysis based on the computed free energy barriers reveal that warfarin will diffuse through the membranes within hours, in agreement with experimental results on warfarin's accumulation in the plasma, thus suggesting a passive diffusion mechanism. We propose that this membrane transport may be an isomerization-driven process where warfarin adapts to the various local molecular environments encountered under its journey through the membrane. Collectively, these results improve our understanding of the influence of warfarin's structural diversity on the drug's distribution and bioavailability, which in turn may provide insights for developing new formulations of this important pharmaceutical to better address its narrow therapeutic window.

  • 60.
    Karo, Jaanus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Aabloo, Alvo
    Thomas, John O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Brandell, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Molecular Dynamics Modeling of Proton Transport in Nation and Hylton Nanostructures2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 18, p. 6056-6064Article in journal (Refereed)
    Abstract [en]

    Classical molecular dynamics modeling studies at 363 K are reported of the local atomic-level and macroscopic nanostructures of two well-known perfluorosulfonic acid proton exchange polymer membrane materials: Nation and Hyflon. The influence of the different side-chain lengths in the two polymers on local structure is relatively small: Hyflon exhibits slightly greater sulfonate-group clustering, while Nation has more isolated side chains with a higher degree of hydration around the SO3- side-chain ends. This results in shorter mean residence times for water molecules around the end groups in Nation. Hyflon also displays a lower degree of phase separation than Nafion. The velocities of the water molecules and hydronium ions are seen to increase steadily from the polymer backbone/water interface toward the center of the water channels. Because of its shorter side chains, the number of hydronium ions is similar to 50% higher at the center of the water channels in Hyflon, and their velocities are similar to 10% higher. The water and H3O+ diffusion coefficients are therefore higher in the shorter side-chain Hyflon system: 6.5 x 10(-6) cm(2)/s and 25.2 x 10(-6) cm(2)/s, respectively; the corresponding values for Nation are 6.1 x 10(-6) cm(2)/s and 21.3 x 10(-6) cm(2)/s, respectively. These calculated values compare well with experiment: 4 x 10(-6) cm(2)/s for vehicular H3O+ diffusion.

  • 61. Kashtanov, S
    et al.
    Zhuang, G R V
    Augustsson, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics II.
    Nordgren, Joseph
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics II.
    Luo, Yi
    Ross, P N
    Guo, J H
    Structural conformation in a poly(ethylene oxide) film determined by X-ray emission spectroscopy2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 40, p. 11658-11661Article in journal (Refereed)
    Abstract [en]

    The electronic structure of pol(ethylene oxide) (PEO) in a thin (<1 μ) film sample was experimentally probed by X-ray emission spectroscopy. Both nonresonant and resonant X-ray emission spectra were simulated by using density functional theory (DFT) applied to four different models representing different conformations in the polymer. Calculated spectra were compared with experimental results for the PEO film. It was found that the best fit was obtained with the polymer conformation in PEO electrolytes from which the salt (LiMF6, M = P, As, or Sb) had been removed. This conformation is different from the crystalline bulk polymer and implies that film casting, commonly used to form electrolytes for Li polymer batteries, induces the same conformation in the polymer not depending upon the presence of salt.

  • 62.
    Kubin, Markus
    et al.
    Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ekimova, Maria
    Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Kern, Jan
    Lawrence Berkeley National Laboratory, Berkeley, United States.
    Yachandra, Vittal K.
    Lawrence Berkeley National Laboratory, Berkeley, United States.
    Yano, Junko
    Lawrence Berkeley National Laboratory, Berkeley, United States.
    Nibbering, Erik T. J.
    Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Wernet, Philippe
    Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.
    Cr L-Edge X-ray Absorption Spectroscopy of CrIII(acac)3 in Solution with Measured and Calculated Absolute Absorption Cross Sections2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 29, p. 7375-7384Article in journal (Refereed)
    Abstract [en]

    X-ray absorption spectroscopy at the L-edge of 3d transition metals is widely used for probing the valence electronic structure at the metal site via 2p–3d transitions. Assessing the information contained in L-edge absorption spectra requires systematic comparison of experiment and theory. We here investigate the Cr L-edge absorption spectrum of high-spin chromium acetylacetonate CrIII(acac)3 in solution. Using a transmission flatjet enables determining absolute absorption cross sections and spectra free from X-ray-induced sample damage. We address the challenges of measuring Cr L absorption edges spectrally close to the O K absorption edge of the solvent. We critically assess how experimental absorption cross sections can be used to extract information on the electronic structure of the studied system by comparing our results of this CrIII (3d3) complex to our previous work on L-edge absorption cross sections of MnIII(acac)3 (3d4) and MnII(acac)2 (3d5). Considering our experimental uncertainties, the most insightful experimental observable for this d3(CrIII)–d4(MnIII)–d5(MnII) series is the L-edge branching ratio, and we discuss it in comparison to semiempirical multiplet theory and ab initio restricted active space calculations. We further discuss and analyze trends in integrated absorption cross sections and correlate the spectral shapes with the local electronic structure at the metal sites.

  • 63.
    Kulesza, Alexander
    et al.
    Univ Lyon, Lyon, France; CNRS, Paris, France.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    MacAleese, Luke
    Univ Lyon, Lyon, France; CNRS, Paris, France.
    Chirot, Fabien
    Université Lyon, Université Claude Bernard Lyon 1, Ens de Lyon, CNRS, Institut des Sciences Analytiques, Villeurbanne, France.
    Dugourd, Philippe
    Univ Lyon, Lyon, France; CNRS, Paris, France.
    Bringing Molecular Dynamics and Ion-Mobility Spectrometry Closer Together: Shape Correlations, Structure-Based Predictors, and Dissociation2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 35, p. 8317-8329Article in journal (Refereed)
    Abstract [en]

    Unfolding of proteins gives detailed information about their structure and energetics and can be probed as a response to a change of experimental conditions. Ion mobility coupled to native mass spectrometry is a gas-phase technique that can observe such unfolding in the gas phase by monitoring the collision cross section (CCS) after applying an activation, for example, by collisions (collision-induced unfolding, CIU). The structural assignments needed to interpret the experiments can profit from dedicated modeling strategies. While predictions of ion-mobility data for well-defined and structurally characterized systems is straightforward, systematic free-energy calculations or biased molecular dynamics simulations that employ IMS data are still limited. The methods with which CCS values are calculated so far do not allow for analytical gradients needed in biased molecular dynamics (MD), and further, explicit CCS calculations still can pose computational bottleneck—when integrated into MD-bioinformatics workflows. These limitations motivate one to revisit known correlations of the CCS with the aim to find computationally cheap and versatile but still at least semiquantitative descriptions of the CCS by pure structural descriptors. We have therefore investigated the correlation of CCS with the key structural parameter often used in computational unfolding studies—the gyration radius—for several small monomeric and dimeric proteins. We work out the challenges and caveats of the combinations of the configurational sampling method and the CCS-calculation algorithm. The correlations were found to be sensitive to the generation conditions and additionally to the system topology. To reduce the amount of fitting to be undertaken, we devise a simple structural model for the CCS that shares some commonalities with the hard-sphere model and the projection algorithm but is designed to take unfolding into account. With this model, we suggest a two-point interpolating function rather than fitting a large data set, at only little deterioration of the predictive power. We further proceed to a model with composition and structure dependence that builds only upon the gyration radius and the chemical formula to apply the found CCS scaling behavior—the scaled macroscopic sphere (sMS) predictor. We demonstrate its applicability to describe unfolding and also its transferability for a larger set of structures from the RSCPDB. As we have found for the dimeric systems, that shape correlations with one global descriptor qualitatively break down, we finally suggest a recipe to switch between global and fragment-based CCS prediction, that takes up the ideas of coarse-graining protein complexes. The presented models and approaches might provide a basis to boost the integration of structural modeling with multistage IMS experiments, especially in the field of large-scale bioinformatics or “on-the-fly” biasing of MD, where computational efficiency is critical.

  • 64.
    Kunnus, Kristjan
    et al.
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA..
    Zhang, Wenkai
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA.;Beijing Normal Univ, Dept Phys, Beijing 100875, Peoples R China..
    Delcey, Mickael G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pinjari, Rahul V.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Miedema, Piter S.
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Schreck, Simon
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Quevedo, Wilson
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Schröder, Henning
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Foehlisch, Alexander
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Gaffney, Kelly J.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA..
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Odelius, Michael
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Wernet, Philippe
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Viewing the Valence Electronic Structure of Ferric and Ferrous Hexacyanide in Solution from the Fe and Cyanide Perspectives2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 29, p. 7182-7194Article in journal (Refereed)
    Abstract [en]

    The valence-excited states of ferric and ferrous hexacyanide ions in aqueous solution were mapped by resonant inelastic X-ray scattering (RIXS) at the Fe L-2,L-3 and N K edges. Probing of both the central Fe and the ligand N atoms enabled identification of the metal-and ligand-centered excited states, as well as ligand-to-metal and metal-to-ligand charge-transfer excited states. Ab initio calculations utilizing the RASPT2 method were used to simulate the Fe L-2,L-3-edge RIXS spectra and enabled quantification of the covalencies of both occupied and empty orbitals of pi and sigma symmetry. We found that pi back-donation in the ferric complex is smaller than that in the ferrous complex. This is evidenced by the relative amounts of Fe 3d character in the nominally 2 pi CN- molecular orbital of 7% and 9% in ferric and ferrous hexacyanide, respectively. Utilizing the direct sensitivity of Fe L-3-edge RIXS to the Fe 3d character in the occupied molecular orbitals, we also found that the donation interactions are dominated by sigma bonding. The latter was found to be stronger in the ferric complex, with an Fe 3d contribution to the nominally 5 sigma CN- molecular orbitals of 29% compared to 20% in the ferrous complex. These results are consistent with the notion that a higher charge at the central metal atom increases donation and decreases back-donation.

  • 65.
    Landström, Lars
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Lu, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Physics.
    Heszler, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Size-Distribution and Emission Spectroscopy of W Nanoparticles Generated byLaser-Assisted CVD for Different WF6/H2/Ar Mixtures2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 42, p. 11615-11621Article in journal (Refereed)
    Abstract [en]

    Tungsten nanoparticles were produced by ArF excimer laser-assisted chemical vapor deposition fromWF6/H2/Ar gas mixtures. Subsequent pulses excited the gas-phase particles, allowing optical emissionspectroscopy to monitor the intensity of the emitted radiation and temperature of the laser-heated particles.A systematic study on size-distributions of the deposited particles, determined by electron microscopy, inconnection with emission spectroscopy and rate of deposition measurements is presented, with respect todifferent partial pressures of the reactants. The rates of deposition of W nanoparticle films were determinedby X-ray fluorescence spectroscopy. In addition, the intensity of the scattered 193 nm laser line was alsomonitored as the partial pressure of H2 was varied.

  • 66.
    Le Bras, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Mihranyan, Albert
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Characterization of dielectric properties of nanocellulose from wood and algae for electrical insulator applications2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 18, p. 5911-5917Article in journal (Refereed)
    Abstract [en]

    Cellulose is one of the oldest electrically insulating materials used in oil-filled high-power transformers and cables. However, reports on the dielectric properties of nanocellulose for electrical insulator applications are scarce. The aim of this study was to characterize the dielectric properties of two nanocellulose types from wood, viz., nanofibrillated cellulose (NFC), and algae, viz., Cladophora cellulose, for electrical insulator applications. The cellulose materials were characterized with X-ray diffraction, nitrogen gas and moisture sorption isotherms, helium pycnometry, mechanical testing, and dielectric spectroscopy at various relative humidities. The algae nanocellulose sample was more crystalline and had a lower moisture sorption capacity at low and moderate relative humidities, compared to NFC. On the other hand, it was much more porous, which resulted in lower strength and higher dielectric loss than for NFC. It is concluded that the solid-state properties of nanocellulose may have a substantial impact on the dielectric properties of electrical insulator applications.

  • 67.
    Liao, Qinghua
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Lüking, Malin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Krueger, Dennis M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. German Ctr Neurodegenerat Dis, Bioinformat Unit, Dept Epigenet & Syst Med Neurodegenerat Dis, Siebold Str 3A, D-37075 Gottingen, Germany.
    Deindl, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kasson, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition2019In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, no 17, p. 3576-3590Article in journal (Refereed)
    Abstract [en]

    Recent years have witnessed an explosion of interest in computational studies of DNA binding proteins, including both coarse grained and atomistic simulations of transcription factor-DNA recognition, to understand how these transcription factors recognize their binding sites on the DNA with such exquisite specificity. The present study performs microsecond time scale all-atom simulations of the dimeric form of the lactose repressor (Lad), both in the absence of any DNA and in the presence of both specific and nonspecific complexes, considering three different DNA sequences. We examine, specifically, the conformational differences between specific and nonspecific protein DNA interactions, as well as the behavior of the helix-turn-helix motif of Lad when interacting with the DNA. Our simulations suggest that stable Lad binding occurs primarily to bent A-form DNA, with a loss of Lad conformational entropy and optimization of correlated conformational equilibria across the protein. In addition, binding to the specific operator sequence involves a slightly larger number of stabilizing DNA protein hydrogen bonds (in comparison to nonspecific complexes), which may account for the experimentally observed specificity for this operator. In doing so, our simulations provide a detailed atomistic description of potential structural drivers for LacI selectivity.

  • 68.
    Lindgren, Torbjörn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Mwabora, Julius M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Avendaño, Esteban
    Fasta tillståndets fysik. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Jonsson, Jacob
    Hoel, Anders
    Granqvist, Claes-Göran
    Fasta tillståndets fysik. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Lindquist, Sten-Eric
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Photoelectrochemical and Optical Properties of Nitrogen Doped Titanium Dioxide Films Prepared by Reactive DC Magnetron Sputtering2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, p. 5709-5716Article in journal (Refereed)
  • 69.
    Lindgren, Torbjörn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Mwabora, Julius M.
    Avendaño, Esteban
    Jonsson, Jacob
    Hoel, Anders
    Granqvist, Claes-Göran
    Lindquist, Sten-Eric
    Photoelectrochemical Study of Nitrogen-Doped Titanium Dioxide for Water Oxidatin2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, p. 5709-5716Article in journal (Refereed)
  • 70.
    Lipfert, Jan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Quantum Chemistry.
    Llano, Jorge
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Eriksson, Leif A.
    Radiation Induced Damage in Serine Phosphate: Insights into a Mechanism for Direct DNA Strand Breakage2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 23, p. 8036-8042Article in journal (Refereed)
    Abstract [en]

    The radiation-induced decomposition mechanisms of l-O-serine phosphate and the properties of the resulting radicals are explored at the hybrid Hartree−Fock−density functional theory level B3LYP, incorporating a polarized continuum model (IEF-PCM). Three different radical products were identified in earlier experimental studies, formed through deamination (radical I), decarboxylation plus radical exchange (radical II), or dephosphorylation (radical III) reactions, respectively. The calculated hyperfine coupling constants of the resulting radicals agree well with experimental data. The computed energetics for the two competing mechanisms resulting from electron capture, radicals I and III, show that the deamination reaction is barrierless, whereas the dephosphorylation reaction requires an initial electronic redistribution and formation of a phosphoranyl radical with trigonal bipyramidal geometry. From this, the dephosphorylation reaction has to overcome a barrier of approximately 26 kcal/mol, which explains the predominance of radical I over radical III in the experimental measurements. For radical II, the initial decarboxylation step resulting from electron loss was explored and found to proceed without barriers. The results of the current study have implications for radiation-induced damage of amino acids. In addition, serine phosphate is a model of a DNA sugar−phosphate fragment, and thus we may obtain new insights into a possible mechanism for cleavage of the phosphate ester bond of the DNA backbone leading to strand break.

  • 71.
    Llano, Jorge
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Eriksson, Leif A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Quantum Chemistry.
    Mechanism of Hydroxyl Radical Addition to Imidazole and Subsequent Water Elimination1999In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 103, no 26, p. 5598-5607Article in journal (Refereed)
    Abstract [en]

    The addition reaction of the hydroxyl radical to imidazole and subsequent elimination of water to form the 1-dehydroimidazolyl radical is investigated using MP2 and B3LYP methods, including large basis sets and SCI-PCM modeling of solvent effects. It is found that the barrier to addition of the hydroxyl radical at the 5-position is energetically favored over addition to the 2- or 4-positions by 2−3 kcal/mol at the SCI-PCM/MP2/6-311G(2df,p)//MP2/6-31G(d,p) level, whereas the corresponding B3LYP calculations yield a barrier-free addition at the 5-position. The lower barrier and NBO analysis explain the experimentally observed specificity for the 5-hydroxylation of imidazole and histidine, albeit the 2-adduct is about 4 kcal/mol more stable than the 5-adduct. The NBO energetic analysis shows that the exoanomeric effect stabilizes the transition state at the 5-position about 0.3 kcal/mol more than that at the 2-position. Moreover, the π-interaction between the attacking nonbonding spin orbital of the hydroxyl radical and the π-cloud of imidazole is the least for the transition state at the 5-position, favoring the σC5-O bond formation. The 5-hydroxyimidazolyl radical undergoes a slow elimination of water (the added OH group and the hydrogen at the N1 position) to yield the 1-dehydroimidazolyl radical. The base-catalyzed dehydration profile was modeled in two steps at the B3LYP/6-311G(2df,p)//6-31G(d,p) level. The PES for the dehydration reaction seems rather flat. The first step is a barrier-free loss of the proton at N1 induced by the hydroxide ion to yield the 1-dehydro-5-hydroxyimidazolyl radical anion. In the second step, the hydroxide ion is regenerated from the intermediate to yield the final product with a barrier of 2.7 kcal/mol. The calculated hyperfine structures in the presence of the continuum solvent model for the 5-hydroxyimidazolyl and 1-dehydroimidazolyl radicals are in close agreement with the experimental ones recorded in aqueous solution.

  • 72. Lo Nostro, Pierandrea
    et al.
    Murgia, Sergio
    Lagi, Marco
    Fratini, Emiliano
    Karlsson, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Almgren, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Monduzzi, Maura
    Ninham, Barry W.
    Baglioni, Piero
    Interconnected Networks: Structural and Dynamic Characterization of Aqueous Dispersions of Dioctanoylphosphatidylcholine2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 40, p. 12625-12634Article in journal (Refereed)
    Abstract [en]

    Aqueous dispersions of the phospholipid dioctanoylphosphatidylcholine (diC8PC) phase-separate below a cloud-point temperature, depending on lipid concentration. The lower phase is viscous and rich in lipid. The structure and dynamics of this system were explored via cryo-transmission electron microscopy (cryo-TEM), small-angle X-ray scattering (SAXS), and NMR. The lower phase comprises a highly interconnected tridimensional network of wormlike micelles. A molecular mechanism for the phase separation is suggested.

  • 73.
    Lundberg, Marcus
    et al.
    Fukui Institute for Fundamental Chemistry, Kyoto University.
    Morokuma, Keiji
    Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan, Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 .
    Protein environment facilitates O-2 binding in non-heme iron enzyme: An insight from ONIOM calculations on isopenicillin N synthase (IPNS)2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 31, p. 9380-9389Article in journal (Refereed)
    Abstract [en]

    Binding of dioxygen to a non-heme enzyme has been modeled using the ONIOM combined quantum mechanical/molecular mechanical (QM/MM) method. For the present system, isopenicillin N synthase (IPNS), binding of dioxygen is stabilized by 8-10 kcal/mol for a QM:MM (B3LYP:Amber) protein model compared to a quantum mechanical model of the active site only. In the protein system, the free energy change of O-2 binding is close to zero. Two major factors consistently stabilize O-2 binding. The first effect, evaluated at the QM level, originates from a change in coordination geometry of the iron center. The active-site model artificially favors the deoxy state (O-2 not bound) because it allows too-large rearrangements of the five-coordinate iron site. This error is corrected when the protein is included. The corresponding effect on binding energies is 3-6 kcal/mol, depending on the coordination mode of O-2 (side-on or end-on). The second major factor that stabilizes O-2 binding is van der Waals interactions between dioxygen and the surrounding enzyme. These interactions, 3-4 kcal/mol at the MM level, are neglected in models that include only the active site. Polarization of the active site by surrounding amino acids does not have a significant effect on the binding energy in the present system.

  • 74.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm University, AlbaNoVa University Center.
    Siegbahn, Per E. M.
    Optimized spin crossings and transition states for short-range electron transfer in transition metal dimers2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 20, p. 10513-10520Article in journal (Refereed)
    Abstract [en]

    Electron-transfer reactions in eight mixed-valence manganese dimers are studied using B3LYP. One of the dimers is a model of the active site of manganese catalase, while another represents a basic building block of the oxygen-evolving complex in photosystem II. The adiabatic reactions are characterized by fully optimized transition states where the single imaginary frequency represents the electron-transfer coordinate. When there is antiferromagnetic coupling between different high-spin centers, electron transfer must be accompanied by a spin transition. Spin transitions are characterized by minimum-energy crossing points between spin surfaces. Three reaction mechanisms have been investigated. First, a single-step reaction where spin flip is concerted with electron transfer. Second, an initial transition to a center with intermediate spin that can be followed by electron transfer. Third, an initial transition to a ferromagnetic state from which the electron can be transferred adiabatically. The complexes prefer the third route with rate-determining barriers ranging from 5.7 kcal/mol to 17.2 kcal/mol for different complexes. The origins of these differences are discussed in terms of oxidation states and ligand environments. Many DFT functionals overestimate charge-transfer interactions, but for the present complexes, the error should be limited because of short Mn-Mn distances.

  • 75.
    Lundqvist, Maria J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Nilsing, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Åkermark, Björn
    Persson, Petter
    Spacer and anchor effects on the electronic coupling in Ruthenium-bis-terpyridine dye-sensitized TiO2 nanocrystals studied by DFT2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 41, p. 20513-20525Article in journal (Refereed)
    Abstract [en]

    Structural and electronic properties of TiO2 nanoparticles sensitized with a set of Ru(II)(tpy)2 based dyes have been investigated using density functional theory (DFT) calculations combined with time-dependent (TD) DFT calculations. The effects of carboxylic and phosphonic acid anchor groups, as well as a phenylene spacer group, on the optical properties of the dyes and the electronic interactions in the dye-sensitized TiO2 nanoparticles have been investigated. Inclusion of explicit counterions in the modeling shows that the description of the environment is important in order to obtain a realistic interfacial energy level alignment. A comparison of calculated electronic coupling strengths suggests that both the nature of the anchor group and the inclusion of the phenylene spacer group are capable of significantly influencing electron-transfer rates across the dye-metal oxide interface.

  • 76.
    Ma, Huan
    et al.
    Department of Chemistry, North Carolina State University, Chemical Department , Zhejiang University.
    Thompson, Matthew K
    Department of Chemistry, North Carolina State University,.
    Gaff, John
    Department of Chemistry, North Carolina State University,.
    Franzen, Stefan
    Department of Chemistry, North Carolina State University,.
    Kinetic analysis of a naturally occurring bioremediation enzyme: dehaloperoxidase-hemoglobin from Amphitrite ornata2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 43, p. 13823-13829Article in journal (Refereed)
    Abstract [en]

    The temperature dependence of the rate constant for substrate oxidation by the dehaloperoxidase-hemoglobin (DHP) of Amphitrite ornata has been measured from 278 to 308 K. The rate constant is observed to increase over this range by approximately a factor of 2 for each 10 °C temperature increment. An analysis of the initial rates using a phenomenological approach that expresses the peroxidase ping-pong mechanism in the form of the Michaelis-Menten equation leads to an interpretation of the effects in terms of the fundamental rate constants. The analysis of kinetic data considers a combination of diffusion rate constants for substrate and H(2)O(2), elementary steps involving activation and heterolysis of the O-O bond of H(2)O(2), and two electron transfers from the substrate to the iron. To complete the analysis from the perspective of turnover of substrate into product, density function theory (DFT) calculations were used to address the fate of phenoxy radical intermediates. The analysis suggests a dominant role for diffusion in the kinetics of DHP.

  • 77.
    Mahrov, Boriss
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Boschloo, Gerrit
    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.
    Siegbahn, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Rensmo, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Photoelectron spectroscopy studies of Ru(dcbpyH(2))(2)(NCS)(2)/CuI and Ru(dcbpyH(2))(2)(NCS)(2)/CuSCN interfaces for solar cell applications2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 31, p. 11604-11610Article in journal (Refereed)
    Abstract [en]

    In this work, the electronic structure of the wide band gap hole conductors Cut and CuSCN in contact with an organic dye (Ru(dcbpyH(2))(2)(NCS)(2), cis-bis(4,4'-dicarboxy-2,2-bipyridine)bis(isothiocyanato)ruthenium(II)) were investigated by means of photoelectron spectroscopy. The experiments show specific interaction between the NCS groups of the dye molecules and the Cut and CuSCN surfaces. For Cut there are strong indications that the dye molecules interact with Cut through both NCS ligands. Also, one of the carboxylic groups is affected by the surface adsorption on the CuI substrate. For the CuSCN surface the results indicate that about half of the molecules interact with the surface through both NCS ligands, that about half of the molecules interact with the surface through one NCS ligand, and that there is no specific interaction with the carboxylic groups. The measurements also reveal changes in the electronic structure of the dye molecule when adsorbed onto the substrates. In particular, changes in the upper valence electronic structure, important for the function of this material combination in a solar cell device, are discussed.

  • 78.
    Marinho, Ricardo R. T.
    et al.
    Univ Fed Bahia, Inst Phys, BR-40170115 Salvador, BA, Brazil..
    Walz, Marie-Madeleine
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Ekholm, Victor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ohrwall, Gunnar
    Lund Univ, MAX Lab 4, POB 118, SE-22100 Lund, Sweden..
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    de Brito, Arnaldo Naves
    Univ Estadual Campinas, Inst Phys Gleb Wataghin, BR-13083859 Campinas, SP, Brazil..
    Ethanol Solvation in Water Studied on a Molecular Scale by Photoelectron Spectroscopy2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 33, p. 7916-7923Article in journal (Refereed)
    Abstract [en]

    Because of the amphiphilic properties of alcohols, hydrophobic hydration is important in the alcohol water system. In the present paper we employ X-ray photoelectron spectroscopy (XPS) to investigate the bulk and surface molecular structure of ethanol water mixtures from 0.2 to 95 mol %. The observed XPS binding energy splitting between the methyl C is and hydroxymethyl C is groups (BES_[CH3-CH2OH]) as a function of the ethanol molar percentage can be divided into different regions: one below 35 mol % with higher values (about 1.53 eV) and one starting at 60 mol % up to 95 mol % with 1.49 eV as an average value. The chemical shifts agree with previous quantum mechanics/molecular mechanics (QM/MM) calculations [Loytynoja, T.; et al. J. Phys. Chem. B 2014, 118, 13217]. According to these calculations, the BES_[CH3-CH2OH] is related to the number of hydrogen bonds between the ethanol and the surrounding molecules. As the ethanol concentration increases, the average number of hydrogen bonds decreases from 2.5 for water-rich mixtures to 2 for pure ethanol. We give an interpretation for this behavior based on how the hydrogen bonds are distributed according to the mixing ratio. Since our experimental data are surface sensitive, we propose that this effect may also be manifested at the interface. From the ratio between the XPS C is core lines intensities we infer that below 20 mol % the ethanol molecules have their hydroxyl groups more hydrated and possibly facing the solution's bulk. Between 0.1 and 14 mol %, we show the formation of an ethanol monolayer at approximately 2 mol %. Several parameters are derived for the surface region at monolayer coverage.

  • 79.
    Markle, Todd F.
    et al.
    Univ Washington, Dept Chem, Seattle, WA 98195 USA..
    Tenderholt, Adam L.
    Univ Washington, Dept Chem, Seattle, WA 98195 USA..
    Mayer, James M.
    Univ Washington, Dept Chem, Seattle, WA 98195 USA..
    Probing Quantum and Dynamic Effects in Concerted Proton-Electron Transfer Reactions of Phenol-Base Compounds2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 1, p. 571-584Article in journal (Refereed)
    Abstract [en]

    The oxidation of three phenols, which contain an intramolecular hydrogen bond to a pendent pyridine or amine group, has been shown, in a previous experimental study, to undergo concerted proton electron transfer (CPET). In this reaction, the electron is transferred to an outer-sphere oxidant, and the proton is transferred from the oxygen to nitrogen atom. In the present study, this reaction is studied computationally using a version of Hammes-Schiffer's multistate continuum theory where CPET is formulated as a transmission frequency between neutral and cation vibrational-electronic states. The neutral and cation proton vibrational wave functions are computed from one-dimensional potential energy surfaces (PESs) for the transferring proton in a fixed heavy atom framework The overlap integrals for these neutral/cation wave functions, considering several initial (i.e., neutral) and final (i.e., cation) vibrational states, are used to evaluate the relative rates of oxidation. The analysis is extended to heavy atom configurations with various proton donor acceptor (i.e., O-N) distances to assess the importance of heavy atom "gating". Such changes in d(ON) dramatically affect the nature of the proton PESs and wave functions. Surprisingly, the most reactive configurations have similar donor acceptor distances despite the large (similar to 0.2 angstrom) differences in the optimized structures. These theoretical results qualitatively reproduce the experimental faster reactivity of the reaction of the pyridyl derivative 1 versus the CH(2)-pyridyl 2, but the computed factor of 5 is smaller than the experimental 10(2). The amine derivative is calculated to react similarly to 1, which does not agree with the experiments, likely due to some of the simplifying assumptions made in applying the theory. The computed kinetic isotope effects (KIEs) and their temperature dependence are in agreement with experimental results.

  • 80.
    Markle, Todd F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Yale Univ, Dept Chem, 225 Prospect St,POB 208107, New Haven, CT 06520 USA..
    Zhang, Ming-Tian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Tsinghua Univ, Dept Chem, Beijing 100084, Peoples R China..
    Santoni, Marie-Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Univ Messina, Dipartimento Sci Chim, Via F Stagno dAlcontres 31, Messina, Italy..
    Johannissen, Linus O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Univ Manchester, Sch Chem Engn & Analyt Sci, Manchester M13 9PL, Lancs, England..
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Proton-Coupled Electron Transfer in a Series of Ruthenium-Linked Tyrosines with Internal Bases: Evaluation of a Tunneling Model for Experimental Temperature-Dependent Kinetics2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 35, p. 9308-9321Article in journal (Refereed)
    Abstract [en]

    Photoinitiated proton-coupled electron transfer (PCET) kinetics has been investigated in a series of four modified tyrosines linked to a ruthenium photosensitizer in acetonitrile, with each tyrosine bearing an internal hydrogen bond to a covalently linked pyridine or benzimidazole base. After correcting for differences in driving force, it is found that the intrinsic PCET rate constant still varies by 2 orders of magnitude. The differences in rates, as well as the magnitude of the kinetic isotope effect (KIE = k(H)/k(D)), both generally correlate with DFT calculated proton donor-acceptor distances. An Arrhenius analysis of temperature dependent data shows that the difference in reactivity arises primarily from differences in activation energies. We use this kinetic data to evaluate a commonly employed theoretical model for proton tunneling which includes a harmonic distribution of proton donor-acceptor distances due to vibrational motions of the molecule: Applying this model to the experimental data yields the conclusion that donor-acceptor compression is more facile in the Compounds with shorter PT distance; however, this is contrary to independent calculations for the same compounds. This discrepancy is likely because the assumption in the model of Morse-shaped proton potential energy surfaces is inappropriate for (strongly) hydrogen-bonded systems. These results question the general applicability of this, model. The results also suggest that a correlation of rate vs proton tunneling distance for the series of compounds is complicated by a concomitant variation of other relevant parameters.

  • 81.
    Mattsson, Andreas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Leideborg, M
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Larsson, K
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Westin, G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Österlund, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Adsorption and solar light decomposition of acetone on anatase TiO2 and niobium doped TiO2 thin films2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 3, p. 1210-1220Article in journal (Refereed)
    Abstract [en]

    Adsorption and solar light decomposition of acetone was studied on nanostructured anatase TiO2 and Nb-doped TiO2 films made by sol-gel methods (10 and 20 mol % NbO2.5). A detailed characterization of the film materials show that films contain only nanoparticles with the anatase modification with pentavalent Nb oxide dissolved into the anatase structure, which is interpreted as formation of substituted Nb=O clusters in the anatase lattice. The Nb-doped films displayed a slight yellow color and an enhanced the visible light absorption with a red-shift of the optical absorption edge from 394 nm for the pure TiO2 film to 411 nm for 20 mol % NbO2.5. In-situ Fourier transform infrared (FTIR) transmission spectroscopy shows that acetone adsorbs associatively with eta(1)-coordination to the surface cations on all films. On Nb-doped TiO2 films, the carbonyl bonding to the surface is stabilized, which is evidenced by a lowering of the v(C=O) frequency by about 20 cm(-1) to 1672 cm(-1). Upon solar light illumination acetone is readily decomposed on TiO2, and stable surface coordinated intermediates are formed. The decomposition rate is an order of magnitude smaller on the Nb-doped films despite an enhanced visible light absorption in these materials. The quantum yield is determined to be 0.053, 0.004 and 0.002 for the pure, 10% Nb:TiO2, and 20%Nb:TiO2, respectively. Using an interplay between FTIR and DFT calculations we show that the key surface intermediates are bidentate bridged formate and carbonate, and H-bonded bicarbonate, respectively, whose concentration on the surface can be correlated with their heats of formation and bond strength to coordinatively unsaturated surface Ti and Nb atoms at the surface. The oxidation rate of these intermediates is substantially slower than the initial acetone decomposition rate, and limits the total oxidation rate at t > 7 min on TiO2, while no decrease of the rate is observed on the Nb-doped films. The rate of degradation of key surface intermediates is different on pure TiO2 and Nb-doped TiO2, but cannot explain the overall lower total oxidation rate for the Nb-doped films. Instead the inferior photocatalytic activity in Nb-doped TiO2 is attributed to an enhanced electronhole pair recombination rate due to Nb=O cluster and cation vacancy formation.

  • 82.
    Maximoff, Sergey N.
    et al.
    Loyola Univ, Dept Chem & Biochem, 1032 W Sheridan Rd, Chicago, IL 60660 USA..
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Florian, Jan
    Loyola Univ, Dept Chem & Biochem, 1032 W Sheridan Rd, Chicago, IL 60660 USA..
    DNA Polymerase lambda Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 33, p. 7813-7822Article in journal (Refereed)
    Abstract [en]

    Human DNA polymerise lambda is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase 2, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an . unexpected Watson Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thyMine in the DNA or guanine in the deoxyguanosine triphosphate analogue may Spend, a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the,polymerase lambda mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, We investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson-Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis.

  • 83. Meyer, F.
    et al.
    Blum, M.
    Benkert, A.
    Hauschild, D.
    Nagarajan, S.
    Wilks, R. G.
    Andersson, Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Yang, W.
    Zharnikov, M.
    Baer, M.
    Heske, C.
    Reinert, F.
    Weinhardt, L.
    "Building Block Picture" of the Electronic Structure of Aqueous Cysteine Derived from Resonant Inelastic Soft X-ray Scattering2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 46, p. 13142-13150Article in journal (Refereed)
    Abstract [en]

    The electronic structure of the amino acid l-cysteine in an aqueous environment was studied using resonant inelastic soft X-ray scattering (RIXS) in a 2D map representation and analyzed in the framework of a building block approach. The element selectivity of RIXS allows a local investigation of the electronic structure of the three functional groups of cysteine, namely, the carboxyl, amino, and thiol groups, by measuring at the O K, N K, and S L-2,L-3 edges, respectively. Variation of the pH value allows an investigation of molecules with protonated and deprotonated functional groups, which can then be compared with simple reference molecules that represent the isolated functional groups. We find that such building blocks can provide an excellent description of X-ray emission spectroscopy (XES) and RIXS spectra, but only if all nearest-neighbor atoms are included. This finding is analogous to the building block principle commonly used in X-ray absorption spectroscopy. The building blocks show a distinct spectral character (fingerprint) and allow a comprehensive interpretation of the cysteine spectra. This simple approach opens the path to investigate the electronic structure of more complex biological molecules in aqueous solutions using XES and RIXS.

  • 84.
    Mihranyan, Albert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Nyholm, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Garcia Bennett, Alfonso E.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    A Novel High Specific Surface Area Conducting Paper Material Composed of Polypyrrole and Cladophora Cellulose2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 39, p. 12249-12255Article in journal (Refereed)
    Abstract [en]

    We present a novel conducting polypyrrole-based composite material, obtained by polymerization of pyrrole in the presence of iron(III) chloride on a cellulose substrate derived from the environmentally polluting Cladophora sp. algae. The material, which was doped with chloride ions, was molded into paper sheets and characterized using scanning and transmission electron microscopy, N2 gas adsorption analysis, cyclic voltammetry, chronoamperometry and conductivity measurements at varying relative humidities. The specific surface area of the composite was found to be 57 m2/g and the fibrous structure of the Cladophora cellulose remained intact even after a 50 nm thick layer of polypyrrole had been coated on the cellulose fibers. The composite could be repeatedly used for electrochemically controlled extraction and desorption of chloride and an ion exchanging capacity of 370 C per g of composite was obtained as a result of the high surface area of the cellulose substrate. The influence of the oxidation and reduction potentials on the chloride ion exchange capacity and the nucleation of delocalized positive charges, forming conductive paths in the polypyrrole film, was also investigated. The creation of conductive paths during oxidation followed an effective medium rather than a percolative behavior, indicating that some conduction paths survive the polymer reduction steps. The present high surface area material should be well-suited for use in, e.g., electrochemically controlled ion exchange or separation devices, as well as sensors based on the fact that the material is compact, light, mechanically stable, and moldable into paper sheets.

  • 85.
    Mocellin, Alexandra
    et al.
    Brasilia Univ UnB, Inst Phys, Box 4455, BR-70910970 Brasilia, DF, Brazil..
    de Abreu Gomes, Anderson Herbert
    Univ Estadual Campinas, UNICAMP, Dept Appl Phys, Inst Phys Gleb Wataghin, BR-13083859 Campinas, SP, Brazil..
    Araujo, Oscar Cardoso
    Brasilia Univ UnB, Inst Phys, Box 4455, BR-70910970 Brasilia, DF, Brazil..
    de Brito, Arnaldo Naves
    Univ Estadual Campinas, UNICAMP, Dept Appl Phys, Inst Phys Gleb Wataghin, BR-13083859 Campinas, SP, Brazil..
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Surface Propensity of Atmospherically Relevant Amino Acids Studied by XPS2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 16, p. 4220-4225Article in journal (Refereed)
    Abstract [en]

    Amino acids constitute an important fraction of the water-soluble organic nitrogen (WSON) compounds in aerosols and are involved in many processes in the atmosphere. In this-Work, we applied X-ray photoelectron spectroscopy (XPS) to study aqueous solutions of four amino acids, glycine, alanine, Valirie) and methionine, in their zwitterionic forms. We found that amino acids with hydrophilic side chains and smaller size, GLY and ALA, tend to stay in the bulk of the liquid, while the hydrophobic and bigger amino acids, VAL and MET, are found to concentrate more on the surface. We found experimental evidence that the amino acids have preferential orientation relative to the surface, with the hydrophobic side chain being closer to the surface than the hydrophilic carboxylate group. The observed amino acid surface propensity has implications in atmospheric science as the surface interactions play a central role in cloud droplet formation, and they should be considered in climate models.

  • 86.
    Morandeira, Ana
    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.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Photoinduced Ultrafast Dynamics of Coumarin 343 Sensitized p-Type-Nanostructured NiO Films2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 41, p. 19403-19410Article in journal (Refereed)
    Abstract [en]

    Photoinduced electron transfer from the valence band of nanocrystalline NiO, a p-type semiconductor, to an excited bound dye, coumarin 343, and the subsequent recombination have been measured by femtosecond transient absorbance spectroscopy probing with white light. It was found that both processes are nonexponential. The photoinduced electron transfer from the semiconductor to the excited bound dye has an ultrafast component (similar to 200 fs), which is comparable to the time constants measured for photoinduced electron injection in C343-TiO2 colloid solutions. The process is very efficient and constitutes the main path of deactivation of the excited dye. Back electron transfer is also remarkably fast, with the main part of the recombination process happening with a time constant of similar to 20 ps. Dye-sensitized nanostructured p-type semiconductors are attractive materials due to their potential use as photocathodes in dye-sensitized solar cells and solid electrolytes in solid-state dye-sensitized solar cells. To our knowledge, this is the first time that the photoinduced electron-transfer kinetics of a sensitized p-type semiconductor has been studied.

  • 87.
    Mwabora, Julius M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Lindgren, Torbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Avendaño, Esteban
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Jaramillo, Thomas F.
    Lu, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Lindquist, Sten-Eric
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Granqvist, Claes-Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Structure, Composition and Morphology of Photoelectrochemically Active TiO2-xNx Thin Films Deposited by Reactive DC Magnetron Sputtering2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 52, p. 20193-20198Article in journal (Refereed)
    Abstract [en]

    Films of nitrogen-doped TiO2 were made by reactive DC magnetron sputtering in a mixture of argon, oxygen, and nitrogen. The nitrogen gas ratio Φ was varied in the 0 < Φ < 0.025 range during the depositions, resulting in TiO2-xNx films with 0 ≤ x ≤ 0.022 as determined by X-ray photoelectron spectroscopy. Structural and morphological properties of the films were investigated by X-ray diffraction, atomic force microscopy, and scanning and transmission electron microscopy. Films prepared without nitrogen had a rutile structure, while the nitrogen-doped films were either rutile or anatase depending on Φ being below or above ∼0.007. Deposition rate, effective grain size, root-mean-square roughness, morphology, and optical absorption were also found to depend on Φ. The films were photoelectrochemically active, as reported in an earlier papers of ours [J. Phys. Chem. B 2003, 107, 5709-5716 and J. Phys. Chem. B 2004, 108, 5995-6003].

  • 88.
    Nilsson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Frenning, Göran
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Gråsjö, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Alderborn, Göran
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Conductivity percolation in loosely compacted microcrystalline cellulose: An in situ study by dielectric spectroscopy during densification2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 41, p. 20502-20506Article in journal (Refereed)
    Abstract [en]

    The present study aims at contributing to a complete understanding of the water-induced ionic charge transport in cellulose. The behavior of this transport in loosely compacted microcrystalline cellulose (MCC) powder was investigated as a function of density utilizing a new type of measurement setup, allowing for dielectric spectroscopy measurement in situ during compaction. The ionic conductivity in MCC was found to increase with increasing density until a leveling-out was observed for densities above similar to 0.7 g/cm(3). Further, it was shown that the ionic conductivity vs density followed a percolation type behavior signifying the percolation of conductive paths in a 3D conducting network. The density percolation threshold was found to be between similar to 0.2 and 0.4 g/cm(3), depending strongly on the cellulose moisture content. The observed percolation behavior was attributed to the forming of interparticulate bonds in the MCC and the percolation threshold dependence on moisture was linked to the moisture dependence of particle rearrangement and plastic deformation in MCC during compaction. The obtained results add to the understanding of the density-dependent water-induced ionic transport in cellulose showing that, at given moisture content, the two major parameters determining the magnitude of the conductivity are the connectedness of the interparticluate bonds and the connectedness of pores with a diameter in the 5-20 nm size range. At densities between similar to 0.7 and 1.2 g/cm(3) both the bond and the pore networks have percolated, facilitating charge transport through the MCC compact.

  • 89.
    Nilsson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Mihranyan, Albert
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Valizadeh, Sima
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Mesopore structure of microcrystalline cellulose tablets characterized by nitrogen adsorption and SEM: The influence on water-induced ionic conduction2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 32, p. 15776-15781Article in journal (Refereed)
    Abstract [en]

    Tablets of microcrystalline cellulose were formed at different compaction pressures and physical properties, such as pore size distribution, surface area, and pore surface fractality, were extracted from N-2 adsorption isotherms. These properties were compared to previously published data on the water-induced ionic conductivity of the tablets. The conduction process was shown to follow a percolation model with a percolation exponent of 2 and a porosity percolation threshold of similar to 0.1. The critical pore diameter for facilitated charge transport was shown to be in the 5-20 nm range. When the network of pores with a diameter in this interval is reduced to the point where it no longer forms a continuous passageway throughout the compact, the conduction process is dominated by charge transport on the surfaces of individual microfibrils mainly situated in the bulk of fibril aggregates. A fractal analysis of nitrogen adsorption isotherms showed that the dominant interface forces during adsorption is attributed to surface tensions between the gas and the adsorbed liquid phase. The extracted fractal dimension of the analyzed pore surfaces remained unaffected by the densification process at low compaction pressures (< similar to 200 MPa). At increased densification, however, pore-surface structures smaller than similar to 100 nm become smoother as the fractal dimension decreases from similar to 2.5 at high porosities to similar to 2.3 for the densest tablets under study.

  • 90.
    Nilsson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Electrodynamic investigations of conduction processes in humid microcrystalline cellulose tablets2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 12, p. 5450-5455Article in journal (Refereed)
    Abstract [en]

    The conduction mechanism in microcrystalline cellulose (MCC) tablets at varying relative humidity (RH) has been investigated by using the techniques of low frequency dielectric spectroscopy and transient current analysis at room temperature. The dependence on RH on the measured conductivity and charge carrier density indicates that a high-power-law-exponent percolation process of cations being conducted on water molecules occupying available 6-OH units on the cellulose chains is the dominating dc conduction mechanism at RH below 3 wt % of moisture content. The experimentally observed decrease in charge carrier mobility with increasing moisture content shows that protons and H3O+ ions that are being blocked at empty 6-OH sites also contribute to the charge transport process in cellulose at low moisture contents.

  • 91.
    Nilsson, Peter
    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.
    Deswelling Kinetics of Polyacrylate Gels in Solutions of Cetyltrimethylammonium Bromide2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 33, p. 9770-9778Article in journal (Refereed)
    Abstract [en]

    The deswelling kinetics of single sodium polyacrylate gel beads (radius 40−160 μm) in aqueous solutions of cetyltrimethylammonium bromide under conditions of forced convection are investigated using micromanipulator assisted light microscopy. The purpose of the study is to further evaluate a previously published model (J. Phys. Chem. B 2003, 107, 9203) using a higher homolog surfactant. For gels with expected fast deswelling (small gel size/low surfactant concentration) and/or in low electrolyte concentration, the model is found to correctly predict the deswelling characteristics of the gel beads. However, for some gels with expected slow deswelling, especially in high electrolyte concentration (10 mM NaBr), the model widely underestimates the required deswelling time. The reason for this is argued to be the longer time frame and high bromide concentration allowing the formation of a denser, more ordered structure in the surface phase, which resists the deformation and reorganization of material necessary for deswelling. Unexpectedly long lag times before the start of deswelling are also found for gels in low surfactant concentration, indicating that a relatively high surfactant concentration in the gel, greatly exceeding the critical aggregation concentration, is needed to start formation of a collapsed surface phase. This critical surfactant concentration is found to be dependent on initial gel radius, as small gels require a relatively higher concentration to initiate collapse.

  • 92.
    Nilsson, Peter
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Unga, Johan
    Hansson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Effect of Salt and Surfactant Concentration on the Structure of Polyacrylate Gel/Surfactant Complexes2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 37, p. 10959-10964Article in journal (Refereed)
    Abstract [en]

    Small-angle X-ray scattering was used to elucidate the structure of crosslinked polyacrylate gel/dodecyltrimethylammonium bromide complexes equilibrated in solutions of varying concentrations of surfactant and sodium bromide (NaBr). Samples were swollen with no ordering (micelle free), or they were collapsed with either several distinct peaks (cubic Pm3n) or one broad correlation peak (disordered micellar). The main factor determining the structure of the collapsed complexes was found to be the NaBr concentration, with the cubic structure existing up to 150 mM NaBr and above which only the disordered micellar structure was found. Increasing the salt concentration decreases the polyion mediated attractive forces holding the micelles together causing swelling of the gel. At sufficiently high salt concentration the micelle−micelle distance in the gel becomes too large for the cubic structure to be retained, and it melts into a disordered micellar structure. As most samples were above the critical micelle concentration, the bulk of the surfactant was in the form of micelles in the solution and the surfactant concentration thereby had only a minor influence on the structure. However, in the region around 150 mM NaBr, increasing the surfactant concentration, at constant NaBr concentration, was found to change the structure from disordered micellar to ordered cubic and back to disordered again.

  • 93. Nour-Mohhamadi, Farahnaz
    et al.
    Nguyen, Sau Doan
    Boschloo, Gerrit
    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.
    Lund, Torben
    Determination of the Light-Induced Degradation Rate of the Solar Cell Sensitizer N719 on TiO2 Nanocrystalline Particles2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 47, p. 22413-22419Article in journal (Refereed)
    Abstract [en]

    The oxidative degradation rate, k(deg), of the solar cell dye (Bu4N+)(2)[Ru(dcbpyH)(2)(NCS)(2)](2-), referred to as N719 or [RuL2(NCS)(2)], was obtained by applying a simple model system. Colloidal solutions of N719-dyed TiO2 particles in acetonitrile were irradiated with 532-nm monochromatic light, and the sum of the quantum yields for the oxidative degradation products [RuL2(CN)(2)], [RuL2(NCS)(CN)(2)], and [RuL2(NCS)(ACN)], Phi(deg) was obtained at eight different light intensities in the range of 0.1-16.30 mW/cm(2) by LC-UV-MS. The Phi(deg) values decreased from 3.3 x 10(-3) to 2.0 x 10(-4) in the applied intensity range. By using the relation k(deg) = Phi(deg)k(back) and back electron-transfer reaction rates, k(back), obtained with photoinduced absorption spectroscopy, it was possible to calculate an average value for the oxidative degradation rate of N719 dye attached to TiO2 particles, k(deg) = 4.0 x 10(-2) s(-1). The stability of N719 dye during solar cell operation was discussed based on this number, and on values of the electron-transfer rate between [(RuL2)-L-(III)(NCS)(2)] and iodide ion that are available in the literature.

  • 94.
    Nyqvist, Ida
    et al.
    Stockholm Univ, Dept Biochem & Biophys, SE-10691 Stockholm, Sweden.
    Andersson, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Dogan, Jakob
    Stockholm Univ, Dept Biochem & Biophys, SE-10691 Stockholm, Sweden.
    Role of Conformational Entropy in Molecular Recognition by TAZ1 of CBP2019In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, no 13, p. 2882-2888Article in journal (Refereed)
    Abstract [en]

    The globular transcriptional adapter zinc binding 1 (TAZ1) domain of CREB binding protein participates in protein-protein interactions that are involved in transcriptional regulation. TAZ1 binds numerous targets, of which many are intrinsically disordered proteins that undergo a disorder-to-order transition to various degrees. One such target is the disordered transactivation domain of transcription factor RelA (TAD-RelA), which with its interaction with TAZ1 is involved in transcriptional regulation of genes in NF-kappa B signaling. We have here performed nuclear magnetic resonance backbone and side-chain relaxation studies to investigate the influence of RelA-TA2 (residues 425-490 in TAD-RelA) binding on the subnanosecond internal motions of TAZ1. We find a considerable dynamic response on both the backbone and side-chain levels, which corresponds to a conformational entropy change that contributes significantly to the binding energetics. We further show that the microscopic origins of the dynamic response of TAZ1 vary depending on the target. This study demonstrates that folded protein domains that are able to interact with various targets are not dynamically passive but can have a significant role in the motional response upon target association.

  • 95.
    Nyström, Gustav
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Mihranyan, Albert
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Razaq, Aamir
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Lindström, Tom
    Nyholm, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Strømme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    A Nanocellulose Polypyrrole Composite Based on Microfibrillated Cellulose from Wood2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 12, p. 4178-4182Article in journal (Refereed)
    Abstract [en]

    It is demonstrated that it is possible to coat the individual fibers of wood-based nanocellulose with polypyrrole using in situ chemical polymerization to obtain an electrically conducting continuous high-surface-area composite. The experimental results indicate that the high surface area of the water dispersed material, to a large extent, is maintained upon normal drying without the use of any solvent exchange. Thus, the employed chemical polymerization of polypyrrole on the microfibrillated cellulose (MFC) nanofibers in the hydrogel gives rise to a composite, the structure of which—unlike that of uncoated MFC paper—does not collapse upon drying. The dry composite has a surface area of 90 m2/g and a conductivity of 1.5 S/cm, is electrochemically active, and exhibits an ion-exchange capacity for chloride ions of 289 C/g corresponding to a specific capacity of 80 mAh/g. The straightforwardness of the fabrication of the present nanocellulose composites should significantly facilitate industrial manufacturing of highly porous, electroactive conductive paper materials for applications including ion-exchange and paper-based energy storage devices.

  • 96. Ohrwall, Gunnar
    et al.
    Prisle, Nonne L.
    Ottosson, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Werner, Josephina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Ekholm, Victor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Walz, Marie-Madeleine
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Acid-Base Speciation of Carboxylate Ions in the Surface Region of Aqueous Solutions in the Presence of Ammonium and Aminium Ions2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 10, p. 4033-4040Article in journal (Refereed)
    Abstract [en]

    The acid base speciation of surface-active carboxylate ions in the surface region of aqueous solutions was studied with synchrotron-radiation-based photoelectron spectroscopy. The protonated form was found at an extraordinarily large fraction compared to that expected from the bulk pH. When adding salts containing the weak acid NH4+ to the solution, the fraction of the acidic form at the surface increases, and to a Much greatet extent than expected from the bulk pH of the solution. We show that ammonium ions also are overrepresented in the surface region, and propose that the interaction between the surface-active anionic carboxylates and cationic ammonium ions creates a carboxylateammonium bilayer close to the surface, which increases the probability of the protonation of the carboxylae ions. By comparing the situation when a salt of the less volatile amine diethanolatnine is used, We also show that the observed evaporation of ammonia that occurs after such an event only affects the equilibrium marginally.

  • 97.
    Olson, Carol L.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Ballard, Ian
    Charge accumulation and polarization in titanium dioxide electrodes2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 37, p. 18286-18290Article in journal (Refereed)
    Abstract [en]

    Nanocrystalline TiO2 electrodes were studied spectroelectrochemically by observing the simultaneous relaxation of the current and absorbance after applying a voltage step. The absorbance behaved differently in two time regimes: (1) ionic polarization in the oxide electrode, in which charged ions, such as Ti3+ sites and/or interstitial Ti4+ sites, move in response to the applied electric field, and ( 2) the diffusion of Li+ ions into the TiO2. These two behaviors were analyzed with equivalent circuit models. Li+ ions reduce the resistance of the TiO2 by similar to 90%, increase the capacitance by similar to 350%, and decrease the inductance by similar to 30%. Voltage cycling produces a buildup of intercalated Li+ ions, lessening the electrode's response to the potential step, and causing it to become a more efficient inductor. The potential distribution in the nanoparticles is described by using a dielectric model in which roughly half the applied potential is dropped across the interface with a Li+-ion-ontaining electrolyte.

  • 98.
    Ottosson, Niklas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Surface and Interface Science.
    Aziz, E.
    Bergersen, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Surface and Interface Science.
    Pokapanich, Wandared
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Surface and Interface Science.
    Öhrwall, Gunnar
    Svensson, Svante
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Surface and Interface Science.
    Eberhardt, W.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Surface and Interface Science.
    Electronic rearrangement upon the hydrolyzation of aqueous formaldehyde studied by core-electron spectroscopies2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 51, p. 16642-16646Article in journal (Refereed)
    Abstract [en]

    We have combined near edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoelectron spectroscopy (XPS) to study the electronic rearrangement associated with the hydrolyzation of formaldehyde to methanediol in aqueous solution. The spectra are   contrasted against those of aqueous formamide and urea, which are structurally similar but do not undergo hydrolysis in solution. We have recently demonstrated that the hydrolyzation of formaldehyde is manifested in the oxygen Is NEXAFS spectrum by the disappearance of the oxygen 1s -> pi* absorption line. This is a characteristic signature   that the C=O double bond has been broken. In the present study we extend our investigation to include carbon Is NEXAFS and XPS spectra of the three solutions. The carbon NEXAFS spectra show the C 1s -> pi* absorption line for each solute except for formaldehyde. Moreover, the   carbon Is photoelectron spectra exhibit a single peak for each solute. These observations point to a near complete hydrolyzation of formaldehyde, whereas formamide and urea remain intact in the solution. The analysis is further supported by density functional theory (DFT) calculations, showing a C Is chemical shift of approximately 1.0 eV between hydrolyzed and nonhydrolyzed forms, which would give   distinguishable features in the photoemission spectrum, if coexisting forms were present in the solutions.

  • 99.
    Ottosson, Niklas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Romanova, Anastasia O.
    Söderström, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Öhrwall, Gunnar
    Fedorov, Maxim V.
    Molecular Sinkers: X-ray Photoemission and Atomistic Simulations of Benzoic Acid and Benzoate at the Aqueous Solution/Vapor Interface2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 43, p. 13017-13023Article in journal (Refereed)
    Abstract [en]

    In this work we, for the first time, provide a detailed microscopic picture of the behavior of benzoic acid at the aqueous solution/vapor interface in its neutral as well as in its dissociated form (benzoate). This is achieved through a combination of highly surface-sensitive X-ray photoelectron spectroscopy experiments and fully atomistic molecular simulations. We show that drastic changes occur in the interface behavior of the neutral acid upon release of the proton. The benzoic acid molecules are found to be strongly adsorbed in the interface layer with the planes of the aromatic rings oriented almost parallel to the water surface. In contrast, in the benzoate form the carboxylate group shows a sinker-like behavior while the aromatic ring acts as a buoy, oriented nearly perpendicular to the surface. Furthermore, a significant fraction of the molecular ions move from the interface layer into the bulk of the solution. We rationalize these findings in terms of the very different hydration properties of benzoic acid's carboxylic group in the two charge states. The molecule has an amphiphilic nature and the deprotonation thus changes the hydrophobic/hydrophilic balance between the nonpolar aromatic and the polar carboxylic parts of the molecule. That, consequently, leads to a pronounced reorientation of the molecule at the interface.

  • 100.
    Papadakis, Raffaello
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Preferential Solvation of a Highly Medium Responsive Pentacyanoferrate(II) Complex in Binary Solvent Mixtures: Understanding the Role of Dielectric Enrichment and the Specificity of Solute-Solvent Interactions2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 35, p. 9422-9433Article in journal (Refereed)
    Abstract [en]

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

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