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

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

  • 2.
    Akhtar, Sultan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Experimental Physics.
    Strömberg, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Zardán Gómez de la Torre, Teresa
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Russell, Camilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Gunnarsson, Klas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Svedlindh, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Leifer, Klaus
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Experimental Physics.
    Real-Space Transmission Electron Microscopy Investigations of Attachment of Functionalized Magnetic Nanoparticles to DNA-Coils Acting as a Biosensor2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 41, p. 13255-13262Article in journal (Refereed)
    Abstract [en]

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

  • 3.
    Ali, Ehesan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Oppeneer, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Datta, Sambhu N.
    Influence of Solute-Solvent Hydrogen Bonding on Intramolecular Magnetic Exchange Interaction in Aminoxyl Diradicals: A QM/MM Broken-Symmetry DFT Study2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 16, p. 5545-5548Article in journal (Refereed)
    Abstract [en]

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

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

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

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

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

  • 6.
    Almgren, Mats
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Garamus, Vasil
    Asakawa, Tsuyoshi
    Jiang, Nan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Contrast Variation SANS Investigation of Composition Distributions in Mixed Surfactant Micelles2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 25, p. 7133-7141Article in journal (Refereed)
    Abstract [en]

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

  • 7.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Probst, Michael
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Molecular Dynamics simulation of Fe2+(aq) and Fe3+(aq)2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 1, p. 496-502Article in journal (Refereed)
    Abstract [en]

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

  • 8.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Zelin, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Probst, Michael
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Car-Parrinello Molecular Dynamics simulation of Fe3+(aq)2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 29, p. 14235-14242Article in journal (Refereed)
    Abstract [en]

    The optimized geometry and energetic properties of Fe(D2O)n3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell···second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.

  • 9.
    Andersson, M
    et al.
    Chalmers University of Technology.
    Österlund, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Ljungstrom, S
    Chalmers University of Technology.
    Palmqvist, A E C
    Chalmers University of Technology.
    Preparation of nanosize anatase and rutile TiO2 by hydrothermal treatment of microemulsions and their activity for photocatalytic wet oxidation of phenol2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 41, p. 10674-10679Article in journal (Refereed)
    Abstract [en]

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

  • 10.
    Andersson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Hansson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Phase Behavior of Salt-Free Polyelectrolyte Gel-Surfactant Systems2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 24, p. 6064-6080Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 12.
    Azuma, Tomoyuki
    et al.
    Univ Tokyo, Dept Bioengn, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1138656, Japan..
    Teramura, Yuji
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology. Univ Tokyo, Dept Bioengn, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1138656, Japan.
    Hoshi, Toru
    Nihon Univ, Dept Mat & Appl Chem, Coll Sci & Technol, Tokyo 1018308, Japan..
    Takai, Madoka
    Univ Tokyo, Dept Bioengn, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1138656, Japan..
    Enhancement of Cell Adhesion on a Phosphorylcholine-Based Surface through the Interaction with DNA Mediated by Ca2+ Ions2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 48, p. 12272-12278Article in journal (Refereed)
    Abstract [en]

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

  • 13.
    Bashardanesh, Zahedeh
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 33, p. 8018-8027Article in journal (Refereed)
    Abstract [en]

    In the context of studies of proteins under crowding conditions, it was found that there is a tendency of simulated proteins to coagulate in a seemingly unphysical manner. This points to an imbalance in the protein-protein or protein-water interactions. One way to resolve this is to strengthen the protein-water Lennard-Jones interactions. However, it has also been suggested that dispersion interactions may have been systematically overestimated in force fields due to parameterization with a short cutoff. Here, we test this proposition by performing simulations of liquids and of proteins in solution with systematically reduced C-6 (dispersion constant in a 12-6 Lennard-Jones potential) and evaluate the properties. We find that simulations of liquids with either a dispersion correction or explicit long-range Lennard-Jones interactions need little or no correction to the dispersion constant to reproduce the experimental density. For simulations of proteins, a significant reduction in the dispersion constant is needed to reduce the coagulation, however. Because the protein- and liquid force fields share atom types, at least to some extent, another solution for the coagulation problem may be needed, either through including explicit polarization or through strengthening protein-water interactions.

  • 14.
    Bauer, Christophe
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Boschloo, Gerrit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Mukhtar, Emad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Interfacial Elevtron-Transfer Dynamics in Ru(tcterpy)(NCS)3-Sensiitized TiO2 Nanocrystalline Solar Cells2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, p. 12693-12704Article in journal (Refereed)
    Abstract [en]

    The anchoring of the ruthenium dye {(C4H9)4N}[Ru(Htcterpy)(NCS)3] (with tcterpy = 4,4‘,4‘‘-tricarboxy-2,2‘:6‘,2‘‘-terpyridine), the so-called black dye, onto nanocrystalline TiO2 films has been characterized by UV−vis and FT-IR spectroscopies. FT-IR spectroscopy data suggest that dye molecules are bound to the surface by a bidentate binuclear coordination mode. The interfacial electron-transfer (ET) dynamics has been investigated by femtosecond pump−probe transient absorption spectroscopy and nanosecond laser flash photolysis. The electron-injection process from the dye excited state into the TiO2 conduction band is biexponential with a fast component (200 ± 50 fs) and a slow component (20 ps). These two components can be attributed to the electron injection from the initially formed and the relaxed dye excited states, respectively. Nanosecond kinetic data suggest the existence of two distinguishable regimes (I and II) for the rates of reactions between injected electrons and oxidized dye molecules or oxidized redox species (D+ or I2•-). The frontier between these two regimes is defined by the number of injected electrons per particle (Ne), which was determined to be about 1. The present kinetic study was undertaken within regime I (Ne > 1). Under these conditions, the back-electron-transfer kinetics is comparable to that in systems with other ruthenium complexes adsorbed onto TiO2. The reduction of oxidized dye molecules by iodide results in the formation of I2•- on a very fast time scale (<20 ns). Within regime I, the decay of I2•- occurs in 100 ns via reaction with injected electrons (I2•- + e- → 2I-). In regime II (Ne ≤ 1), which corresponds to the normal operating conditions of dye-sensitized solar cells, the decay of I2•- is very slow and likely occurs via the dismutation reaction (2I2•-→ I- + I3-). Our results predict that, under high light intensity (Ne > 1), the quantum efficiency losses in dye-sensitized solar cells will be important because of the dramatic acceleration of the reaction between I2•- and injected electrons. Mechanisms for the ET reactions involving injected electrons are proposed. The relevance of the present kinetic studies for dye-sensitized nanocrystalline solar cells is discussed.

  • 15.
    Bergkvist, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Surface Biotechnology.
    Carlsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Surface Biotechnology.
    Oscarsson, Sven
    A method for studying protein orientation with atomic force microscopy using relative protein volumes2001In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 105, no 10, p. 2062-2069Article in journal (Refereed)
    Abstract [en]

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

  • 16.
    Berraud-Pache, Romain
    et al.
    Univ Paris Est, Lab Modelisat & Simulat Multi Echelle, MSME, UMR CNRS 8208,UPEM, 5 Bd Descartes, F-77454 Marne La Vallee, France.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Navizet, Isabelle
    Univ Paris Est, Lab Modelisat & Simulat Multi Echelle, MSME, UMR CNRS 8208,UPEM, 5 Bd Descartes, F-77454 Marne La Vallee, France.
    QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 20, p. 5173-5182Article in journal (Refereed)
    Abstract [en]

    The bioluminescence emission from fireflies is an astounding tool to mark and view cells. However, the bioluminescent mechanism is not completely deciphered, limiting the comprehension of key processes. We use a theoretical approach to study for the first time the arrival of a dioxygen molecule inside the fireflies protein and one path of the formation of the dioxetanone ring, the high-energy intermediate precursor of the bioluminescence. To describe this reaction step, a joint approach combining classical molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations is used. The formation of the dioxetanone ring has been studied for both singlet and triplet states with the help of MS-CASPT2 calculations. We also emphasize the role played by the proteinic environment in the formation of the dioxetanone ring. The results obtained shed some light on an important reaction step and give new insights concerning the bioluminescence in fireflies.

  • 17. Bombelli, Francesca Baldelli
    et al.
    Berti, Debora
    Almgren, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Karlsson, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Baglioni, Piero
    Light scattering and cryo-transmission electron microscopy investigation of the self-assembling behavior of di-C12P-nucleosides in solution2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 35, p. 17627-17637Article in journal (Refereed)
    Abstract [en]

    Aggregates formed from freshly prepared and annealed samples of dilauroyl-phosphatidyl-adenosine, dilauroyl-phosphatidyl-uridine, and their 1: 1 mixture have been investigated by dynamic light scattering, cryo-transmission electron microscopy (cryo-TEM) observations, and circular dichroism. The two surfactants differ only for the nucleoside at the phospholipid polar headgroup and self-assemble in solution to form supramolecular structures that behave dissimilarly. The uridine derivative forms long wormlike aggregates that are invariant with the aging of the solution, while the wormlike aggregate of the adenosine derivative undergoes, as the sample ages, a subsequent self-assembling process forming giant helicoidal aggregates that coexist with the smaller wormlike aggregates. Dynamic light scattering and cryo-TEM show that the large helicoidal structures are formed at the expense of the small wormlike micelles. The 1: 1 mixture behaves as the adenosine derivative and evolves to form giant superstructures for all the lipid concentrations investigated. Circular dichroism measurements suggest that the formation of the supramolecular helicoidal structure might not be driven by a purely chiral effect, but rather stacking and hydrogen bonding, present at the phospholipid headgroups of the self-assembled nucleosides, contribute to the final supramolecular structure.

  • 18. Bondesson, Laban
    et al.
    Rudberg, Elias
    Luo, Yi
    Salek, Pawel
    A linear scaling study of solvent-solute interaction energy of drug molecules in aqua solution2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 34, p. 10320-10328Article in journal (Refereed)
  • 19. Bonhommeau, S.
    et al.
    Ottosson, Niklas
    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.
    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.
    Aziz, E.
    Solvent Effect of Alcohols at the L-edge of Iron in Solution: X-ray Absorption and Multiplet Calculations2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 40, p. 12571-12574Article in journal (Refereed)
  • 20.
    Borg, O. Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Durbeej, Bo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Relative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational StudyRelative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational Study2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 39, p. 11554-11565Article in journal (Refereed)
    Abstract [en]

    The conversion of the plant photoreceptor phytochrome from an inactive (Pr) to an active form (Pfr) is accomplished by a red-light induced Z→ E photoisomerization of its phytochromobilin chromophore. In recent years, the question whether the photoactivation involves a change in chromophore protonation state has been the subject of many experimental studies. Here, we have used quantum chemical methods to calculate relative ground and excited-state pKa values of the different pyrrole moieties of phytochromobilin in a protein-like environment. Assuming (based on experimental data) a Pr ZaZsZa chromophore and considering isomerizations at C15 and C5, it is found that moieties B and C are the strongest acids both in the ground state and in the bright first singlet excited state, which is rationalized in simple geometric and electronic terms. It is also shown that neither light absorption nor isomerization increases the acidity of phytochromobilin relative to the reference Pr state with all pyrrolenic nitrogens protonated. Hence, provided that the subset of chromophore geometries under investigation is biologically relevant, there appears to be no intrinsic driving force for a proton-transfer event. In a series of benchmark calculations, the performance of ab initio and time-dependent density functional theory methods for excited-state studies of phytochromobilin is evaluated in light of available experimental data.

  • 21.
    Borgström, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Blart, Errol
    Boschloo, Gerrit
    Mukhtar, Emad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Hagfeldt, Anders
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Odobel, Fabrice
    Sensitized Hole Injection of Phosphorus Porphyrin into NiO: Toward New Photovoltaic Devices2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 48, p. 22928-22934Article in journal (Refereed)
    Abstract [en]

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

  • 22.
    Boschloo, Gerrit
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Activation Energy of Electron Transport in Dye-Sensitized TiO2 Solar Cells2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 24, p. 12093-12098Article in journal (Refereed)
    Abstract [en]

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

  • 23.
    Brohede, Ulrika
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Bramer, Tobias
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Edsman, Katarina
    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.
    Electrodynamic Investigations of Ion Transport and Structural Properties in Drug-Containing Gels: Dielectric Spectroscopy and Transient Current Measurements on Catanionic Carbopol Systems2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 32, p. 15250-15255Article in journal (Refereed)
    Abstract [en]

    The aim of this study is to show the potential of using electrodynamic methods as characterization tools in the controlled drug release process, on complex drug release systems. The two formulations under study were a Carbopol gel containing diphenhydramine and an identical gel also containing the surfactant sodium dodecyl sulfate which forms catanionic vesicles with the diphenhydramine. The average diffusion coefficients were calculated from both the dielectric spectroscopy and the transient current measurements. Comparing the herein-obtained diffusion coefficients with those obtained in another study using a traditional USP technique for the same system, the values are virtually the same. The two electrodynamic methods proved to be potentially valuable tools for obtaining information about the concentration and the motion of the drug molecules inside the gel. The transient current measurements are particularly interesting in this case, as the method gives information not only on an average level, but also of the different charged moieties separately. Interestingly, it seems that the methods also are applicable for obtaining information about the mesh size in the gel.

  • 24.
    Bysell, Helena
    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.
    Effect of charge density on the interaction between cationic peptides and oppositely charged microgels2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 21, p. 7207-7215Article in journal (Refereed)
    Abstract [en]

    The effect of charge density on the interaction between cationic peptides and oppositely charged poly(acrylic acid-co-acrylamide) microgels was investigated together with effects of charge localization and interplay between electrostatic and hydrophobic interactions. The microgel charge content was controlled by varying acrylic acid/acrylamide ratios (25/75-100/0 mol %) in the microgel synthesis, whereas peptide charge density was controlled by using monodisperse peptides containing alanine and lysine in a series of repeated patterns (25-50 mol % lysine). Results show that peptide uptake in the microgels is largely determined by microgel charge density, whereas peptide-induced microgel deswelling kinetics is influenced by peptide charge density to a higher degree. Furthermore, electrolyte-induced peptide detachment is highly influenced by both microgel and peptide charge density. Thus, at high charge contrast, peptides could not be detached from the microgels, whereas reducing the charge density of either peptide or microgel promoted electrolyte-induced peptide release. The localization of charges in the peptide sequence also plays a significant role as the interaction strength increased for peptides where all charged groups are located at the end of the sequence, as opposed to homogenously distributed throughout the peptide. Such an asymmetrically charged peptide thus displayed higher uptake, faster deswelling response, and lower release degrees than its homogeneously charged analogue in microgels with high charge content, while these differences were absent for lower microgel charge densities. Hydrophobic substitutions (alanine → leucine) in the peptide chain at fixed charge content increased peptide binding strength and eliminated peptide detachment at high ionic strength. Theoretical modeling of the effect of peptide and microgel charge density on peptide-induced microgel deswelling gave good agreement with experimental results.

  • 25.
    Bysell, Helena
    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.
    Schmidtchen, Artur
    Section of Dermatology and Venerology, Department of Clinical Sciences, Lund University.
    Malmsten, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Effect of hydrophobicity on the interaction between antimicrobial peptides and poly(acrylic acid) microgels2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 3, p. 1307-1313Article in journal (Refereed)
    Abstract [en]

    The influence of peptide hydrophobicity on the interaction between antimicrobial peptides and poly(acrylic, acid) microgels wits studied by end-tagging the kininogen-derived antimicrobial peptide GKHKNKGKKNGKHNGWK (GKH17) and its truncated variant KNKGKKNGKH (KNK10) with oligotryptophan groups of different lengths. Microgel deswelling and reswelling in response to peptide binding and release was studied by micromanipulator-assisted light- and fluorescence microscopy, peptide uptake in microgels was determined from solution depletion measurements, and peptide oligomerization was monitored by fluorescence spectroscopy. Results showed that oligomerizition/aggregation of the hydrophobically end-tagged peptides is either absent or characterized by exposure of the tryptophan residues to the aqueous ambient, the latter suggesting small aggregation numbers. In addition, peptide uptake and affinity to the poly(acrylic acid) microgels increase with the number of trypthophan residues in the hydrophobic end tag, whereas peptide-induced microgel deswelling kinetics did not display this tag-length dependence to the same extent. Instead, long end tags resulted in anomalous shell formation, opposing further peptide-induced network deswelling. Theoretical modeling suggested that the deswelling kinetics in response to peptide binding is largely controlled by stagnant layer diffusion, but also that for peptides with Sufficiently long hydrophobic tags, the shell constitutes an additional diffusion barrier, thus resulting in slower microgel deswelling. In addition, GKH17 and KNK10 peptides lacking the tryptophan end tags were Substantially released on reducing peptide-microgel electrostatic interactions through addition of salt, an effect more pronounced for the shorter KNK10 peptide, whereas the hydrophobically end-tagged peptides remained bound to the microgels also at high ionic strength.

  • 26.
    Carlsson, Daniel O.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Sjödin, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Nyholm, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    A Comparative Study of the Effects of Rinsing and Aging of Polypyrrole/Nanocellulose Composites on Their Electrochemical Properties2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 14, p. 3900-3910Article in journal (Refereed)
    Abstract [en]

    The effects of polymerization conditions, rinsing, and storage on composites composed of polypyrrole (PPy) and Cladophora nanocellulose in terms of purity, chemical composition, conductivity, and electroactivity were investigated using conductivity measurements, cyclic voltammetry, FTIR-ATR, XPS, and ICP-AES. A clear correlation between rinsing volume and PPy degradation was found using water- or NaCl-rinsing solutions as evidenced by conductivity and electroactivity losses. It was further found, through FTIR-ATR as well as XPS-measurements, that this degradation was caused by incorporation of hydroxyl groups in the PPy-layer. The extent of degradation correlated with a shift in the FTIR-ATR peak around 1300 cm(-1), showing that FTIR-ATR may be used as a quick diagnostic tool to evaluate the extent of degradation. By the use of acidic rinsing solution, this degradation effect was eliminated and resulted in superior samples in terms of both conductivity and electroactivity and also in a more efficient removal of reactants. Upon ambient storage, over a period of 200 days, a gradual decrease in conductivity was found for initially highly conductive samples. The electroactivity, on the other hand, was relatively unaffected by storage, showing that conductivity measurements alone are ineffective to determine the degree of polymer degradation if the water content is not controlled. Also, FTIR-ATR measurements indicated that the oxidation state did not change to any large extent upon storage and that only minor degradation of PPy occurred. The results presented herein thus offer valuable guidelines on how to develop simple and reliable postsynthesis treatments of conducting polymer paper composites with performance fulfilling requirements on stability, electroactivity, and purity in applications such as environmentally friendly energy storage devices and biomedical applications.

  • 27.
    Carlsson, Jens
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Absolute hydration entropies of alkali metal ions from molecular dynamics simulations2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 30, p. 10255-10260Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations in combination with the free energy   perturbation technique are used in this work to calculate absolute ion   hydration entropies. The hydration entropies for five alkali metal ions   are estimated from van't Hoff plots using hydration free energies   calculated at eight different temperatures. Considering that the   ion-water potentials were parametrized only on absolute hydration free   energies and ionic radii, the absolute hydration entropies agree very   well with experimental data. Simulation lengths of about 3 ns at each   temperature were required to achieve an uncertainty below 1 kcal/mol   for the entropic contribution to the hydration free energy (-T Delta   S-hyd). The uncertainties for the calculated entropies are typically   four times larger than for the free energies. The possibility to use   approximate approaches to calculate hydration entropies is also   investigated. The entropy of creating the uncharged van der Waals spheres in water correlates well with the solvent accessible surface area of the ions. The Born continuum model and the linear response   approximation cannot be used to predict the entropy of charging the van   der Waals spheres in water without introducing temperature dependent empirical parameters.

  • 28.
    Carravetta, Vincenzo
    et al.
    CNR, IPCF, Inst Chem & Phys Proc, Via G Moruzzi 1, I-56124 Pisa, Italy.
    de Abreu Gomes, Anderson Herbert
    Univ Estadual Campinas, Inst Phys Gleb Wataghin, Dept Appl Phys, BR-13083859 Campinas, SP, Brazil;LNLS, BR-13084971 Campinas, SP, Brazil.
    Monti, Susanna
    CNR, ICCOM, Inst Chem Organometall Cpds, Via G Moruzzi 1, I-56124 Pisa, Italy.
    Mocellin, Alexandra
    Brasilia Univ, Inst Phys, Box 4455, BR-70910970 Brasilia, DF, Brazil.
    Marinho, Ricardo R. T.
    Brasilia Univ, Inst Phys, Box 4455, BR-70910970 Brasilia, DF, Brazil;Univ Fed Bahia, Inst Phys, BR-40170115 Salvador, BA, Brazil.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. KTH Royal Inst Technol, Theoret Chem & Biol, Sch Chem Biotechnol & Hlth, SE-10044 Stockholm, Sweden.
    de Brito, Arnaldo Naves
    Univ Estadual Campinas, Inst Phys Gleb Wataghin, Dept Appl Phys, BR-13083859 Campinas, SP, Brazil.
    pH-dependent X-ray Photoelectron Chemical Shifts and Surface Distribution of Cysteine in Aqueous Solution2019In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, no 17, p. 3776-3785Article in journal (Refereed)
    Abstract [en]

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

  • 29. Chen, Shufeng
    et al.
    Navizet, Isabelle
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Liu, Yajun
    Ferre, Nicolas
    Hybrid QM/MM Simulations of the Obelin Bioluminescence and Fluorescence Reveal an Unexpected Light Emitter2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 11, p. 2896-2903Article in journal (Refereed)
    Abstract [en]

    Obelia longissima, a tiny hydrozoan living in temperate and cold seas, features the Obelin photoprotein, which emits blue light. The Obelin bioluminescence and the Ca2+-discharged Obelin fluorescence spectra show multimodal characteristics that are currently interpreted by the concomitant participation of several light emitters. Up to now, the coelenteramide luminophore is thought to exist in different protonation states, one of them engaged in an ion-pair with the nearby residue, His22. Using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, we demonstrate that such an ion-pair cannot exist as a stable light emitter. However, when His22 electric neutrality is maintained by means of another proton transfer, the phenolate state of coelenteramide exhibits emission properties in agreement with experiment. Finally, an alternative nonradiative decay pathway, involving the formation of a diradical excited state, is postulated for the first time.

  • 30.
    Clulow, Andrew J.
    et al.
    Monash Inst Pharmaceut Sci, Drug Delivery Disposit & Dynam, 381 Royal Parade, Parkville, Vic 3052, Australia..
    Parrow, Albin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Hawley, Adrian
    ANSTO, Australian Synchrotron, 800 Blackburn Rd, Clayton, Vic 3168, Australia..
    Khan, Jamal
    Monash Inst Pharmaceut Sci, Drug Delivery Disposit & Dynam, 381 Royal Parade, Parkville, Vic 3052, Australia..
    Pham, Anna C.
    Monash Inst Pharmaceut Sci, Drug Delivery Disposit & Dynam, 381 Royal Parade, Parkville, Vic 3052, Australia..
    Larsson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Bergström, Christel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Boyd, Ben J.
    Monash Inst Pharmaceut Sci, Drug Delivery Disposit & Dynam, 381 Royal Parade, Parkville, Vic 3052, Australia..
    Characterization of Solubilizing Nanoaggregates Present in Different Versions of Simulated Intestinal Fluid2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 48, p. 10869-10881Article in journal (Refereed)
    Abstract [en]

    The absorption of hydrophobic drugs and nutrients from the intestine is principally determined by the amount that can be dissolved by the endogenous fluids present in the gut. Human intestinal fluids (HIFs) comprise a complex mixture of bile salts, phospholipids, steroids and glycerides that vary in composition in the fed and fasted state and between subjects. A number of simulated intestinal fluid (SIF) compositions have been developed to mimic fasted and fed state intestinal conditions and allow the in vitro determination of drug solubility as a proxy for the maximum dissolved concentration it is possible to reach. In particular these solvents are used during the development of lipophilic and poorly water-soluble drugs but questions remain around the differences that may arise from the source and methods of preparation of these fluids. In this work, a range of SIFs were studied using small angle X-ray scattering (SAXS), cryogenic -transmission electron microscopy (cryo-TEM) and molecular dynamics (MD) simulations in order to analyze their structures. In-house prepared SIFs based on sodium taurodeoxycholate (NaTDC) and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) formed oblate ellipsoidal micelles irrespective of lipid concentration and preparation conditions. In contrast, commercially available SIFs based on sodium taurocholate and lecithin formed prolate ellipsoidal micelles in the fed state and vesicles in the fasted state. These structural variations are the likely reason for the dramatic differences sometimes observed in the solubility enhancements for hydrophobic drugs, nutrients and digestion products when using different SIFs. However, the structural homogeneity of the NaTDC/DOPC micelles makes them ideal candidates for standardizing SIF formulations as the structures of the solubilizing nanoaggregates therein are not sensitive to the preparation method.

  • 31. Corchado, José C.
    et al.
    Sánchez, M. Luz
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Martín, M. Elena
    Muñoz-Losa, Aurora
    Barata-Morgado, Rute
    Aguilar, Manuel A.
    Theoretical Study of Solvent Effects on the Ground and Low-Lying Excited Free Energy Surfaces of a Push–Pull Substituted Azobenzene2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 43, p. 12518-12530Article in journal (Refereed)
    Abstract [en]

    The ground and low-lying excited free energy surfaces of 4-amino-4'-cyano azobenzene, a molecule that has been proposed as building block for chiroptical switches, are studied in gas phase and a variety of solvents (benzene, chloroform, acetone, and water). Solvent effects on the absorption and emission spectra and on the cistrans thermal and photo isomerizations are analyzed using two levels of calculation: TD-DFT and CASPT2/CASSCF. The solvent effects are introduced using a polarizable continuum model and a QM/MM method, which permits one to highlight the role played by specific interactions. We found that, in gas phase and in agreement with the results found for other azobenzenes, the thermal cistrans isomerization follows a rotation-assisted inversion mechanism where the inversion angle must reach values close to 180 degrees but where the rotation angle can take almost any value. On the contrary, in polar solvents the mechanism is controlled by the rotation of the CN=NC angle. The change in the mechanism is mainly related to a better solvation of the nitrogen atoms of the azo group in the rotational transition state. The photoisomerization follows a rotational pathway both in gas phase and in polar and nonpolar solvents. The solvent introduces only small modifications in the n pi* free energy surface (S-1), but it has a larger effect on the pi pi* surface (S-2) that, in polar solvents, gets closer to S-1. In fact, the S-2 band of the absorption spectrum is red-shifted 0.27 eV for the trans isomer and 0.17 eV for the cis. In the emission spectrum the trend is similar: only S-2 is appreciably affected by the solvent, but in this case a blue shift is found.

  • 32. Deshpande, M D
    et al.
    Scheicher, Ralph H
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics IV.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics IV.
    Pandey, Ravindra
    Binding strength of sodium ions in cellulose for different water contents2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 30, p. 8985-8989Article in journal (Refereed)
    Abstract [en]

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

  • 33. Dourado, Daniel F A R
    et al.
    Fernandes, Pedro Alexandrino
    Mannervik, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Ramos, Maria João
    Glutathione Transferase A1-1: Catalytic Importance of Arginine 152010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 4, p. 1690-1697Article in journal (Refereed)
    Abstract [en]

    Glutathione transferases (GSTs) are fundamental enzymes of the cell detoxification system. They catalyze the nucleophilic attack Of glutathione (GSH) on electrophilic substrates to produce less toxic compounds. The resulting Substrate can then be recognized by ATP-dependent transmembrane PUMPS and consequently expelled from the cell. Despite all the existing studies on GSTs, many aspects of the catalytic events are still poorly understood. Recently, using as a model the GSTAI-1 enzyme, we proposed it GSH activation mechanism. Resorting to the density functional theory (DFT), we demonstrated that a water molecule could assist a proton transfer between (lie GSH thiol and (x-carboxylic groups. after all initial conformational rearrangement of GSH, as evidenced by potential of mean force calculations. In this work to elucidate the catalytic role of Arg 15, a strictly conserved active site residue in class alpha GSTs. we analyzed the activation energy barrier and Structural details associated with the GSTAI-1 Mutants R15A, R15R epsilon, eta-c (an Arg residue with the epsilon-eta-nitrogens Substituted by carbons), and R 15Rneutral (a neutral Arg residue due to the a addition of a hydride in the zeta-carbon. A similar mechanism to the one used in Our GSH activation proposal was implemented.

  • 34.
    Duarte, Fernanda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Bauer, Paul
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Barrozo, Alexandre
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Amrein, Beat Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Purg, Miha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Force Field Independent Metal Parameters Using a Nonbonded Dummy Model2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 16, p. 4351-4362Article in journal (Refereed)
    Abstract [en]

    The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase 1 as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers.

  • 35.
    Eriksson, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Edwards, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Agmo Hernández, Víctor
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Physicochemical Characterization of Phosphopeptide/Titanium Dioxide Interactions Employing the Quartz Crystal Microbalance Technique2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 7, p. 2019-2025Article in journal (Refereed)
    Abstract [en]

    The rapidly growing field of phosphoproteomics has led to a strong demand for procedures enabling fast and reliable isolation and enrichment of phosphorylated proteins and peptides. During the past decade, several novel phosphopeptide enrichment methods based on the affinity of phosphoryl groups for titanium dioxide (TiO2) have been developed and tested. The ultimate goal of obtaining comprehensive phosphoproteomes has, however, been found difficult to achieve and the obtained results often vary, dependent on the enrichment method and protocol used. In the present study, the physical chemistry of the phosphopeptide binding to TiO2 is investigated by means of measurements using a quartz crystal microbalance with dissipation monitoring (QCM-D). Special emphasis is put on the effect of the degree of phosphorylation of the phosphopeptide, the impact of the primary amino acid structure, and the role of electrostatic interactions. The results show that, in general, adsorption of phosphopeptides follows the Langmuir model and that the affinity for the TiO2 surface increases in a nonlinear fashion with increasing degree of phosphorylation. An exception was detected, however, where positive cooperativity between the peptides existed and the Langmuir model no longer applied. The source behind the cooperativity could be traced back to the primary amino acid structure and, more specifically, the presence of positively charged amino acids in positions that enable electrostatic interaction with phosphoryl groups on neighboring peptides. Regardless of the net peptide charge, the TiO2–phosphopeptide interaction was for all phosphopeptides investigated found to be mainly of electrostatic origin. This study highlights and explains some of the most common problems with the TiO2-based enrichment methods used today.

  • 36.
    Eriksson, Susanna K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Josefsson, Ida
    Ottosson, Niklas
    Ohrwall, Gunnar
    Bjorneholm, Olle
    Siegbahn, Hans
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Odelius, Michael
    Rensmo, Hakan
    Solvent Dependence of the Electronic Structure of I- and I-3(-)2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 11, p. 3164-3174Article in journal (Refereed)
    Abstract [en]

    We present synchrotron-based I4d photoelectron spectroscopy experiments of solutions from LiI and LiI3 in water, ethanol, and acetonitrile. The experimentally determined solvent-induced binding energy shifts (SIBES) for the monatomic I- anion are compared to predictions from simple Born theory, PCM calculations, as well as multiconfigurational quantum chemical spectral calculations from geometries obtained through molecular dynamics of solvated clusters. We show that the SIBES for I- explicitly depend on the details of the hydrogen bonding configurations of the solvent to the I- and that static continuum models such as the Born model cannot capture the trends in the SIBES observed both in experiments and in higher-level calculations. To extend the discussion to more complex polyatomic anions, we also performed experiments on I-3(-) and I-/I-3(-) mixtures in different solvents and the results are analyzed in the perspective of SIBES. The experimental SIBES values indicate that the solvation effects even for such similar anions as I- and I-3(-) can be rather different in nature.

  • 37.
    Farstad, M. H.
    et al.
    Norwegian Univ Sci & Technol, Dept Chem Engn, Trondheim.
    Ragazzon, Davide
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Strømsheim, M. D.
    Norwegian Univ Sci & Technol, Dept Chem Engn, Trondheim.
    Gustafson, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Sandell, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Borg, A.
    Norwegian Univ Sci & Technol, Dept Phys, Trondheim.
    Oxidation and Reduction of TiOx Thin Films on Pd(111) and Pd(100)2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 2, p. 688-694Article in journal (Refereed)
    Abstract [en]

    Thin films of TiOx on Pd(100) and Pd(111) have been investigated with respect to their properties after oxidation and reduction cycles. High-resolution photoemission spectroscopy (HRPES) and low energy electron diffraction (LEED) have been applied to characterize the thin film oxidation states and structure before and after oxidation and reduction under ultrahigh vacuum conditions. Fully oxidized TiO2 films were formed on both surfaces. These structures display Moiré patterns in LEED, in one dimension for Pd(100) and in two dimensions for Pd(111), and they have previously not been reported for TiO2/Pd. The oxidation process causes strong reduction in the interaction between the oxide thin film and the Pd substrate, most significantly for Pd(111). Reversible oxidation/reduction cycling of TiOx thin films on Pd(111) and Pd(100) was possible.

  • 38.
    Feliciano, Gustavo T.
    et al.
    Univ Estadual Paulista UNESP, Inst Quim, Dept Fis Quim, Araraquara.
    Sanz-Navarro, Carlos
    CSIC, Catalan Inst Nanosci & Nanotechnol ICN2, Campus UAB, Barcelona; Barcelona Inst Sci & Technol, Campus UAB, Barcelona.
    Coutinho-Neto, Mauricio Domingues
    Univ Fed ABC, Ctr Ciencias Nat & Humanas, Santo Andre.
    Ordejon, Pablo
    CSIC, Catalan Inst Nanosci & Nanotechnol ICN2, Campus UAB, Barcelona; Barcelona Inst Sci & Technol, Campus UAB, Barcelona .
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Rocha, Alexandre Reily
    Univ Estadual Paulista UNESP, Inst Fis Teor, Sao Paulo; MIT, Dept Chem Engn, Cambridge.
    Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 2, p. 485-492Article in journal (Refereed)
    Abstract [en]

    The effects of the environment in nanoscopic materials can play a crucial role in device design. Particularly in biosensors, where the system is usually embedded in a solution, water and ions have to be taken into consideration in atomistic simulations of electronic transport for a realistic description of the system. In this work, we present a methodology that combines quantum mechanics/molecular mechanics methods (QM/MM) with the nonequilibrium Green’s function framework to simulate the electronic transport properties of nanoscopic devices in the presence of solvents. As a case in point, we present further results for DNA translocation through a graphene nanopore. In particular, we take a closer look into general assumptions in a previous work. For this sake, we consider larger QM regions that include the first two solvation shells and investigate the effects of adding extra k-points to the NEGF calculations. The transverse conductance is then calculated in a prototype sequencing device in order to highlight the effects of the solvent.

  • 39. Fogarty, Heather A.
    et al.
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Michl, Josef
    Calculation of relative energies of permethylated oligosilane conformers in vapor and in alkane solution2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 50, p. 25485-25495Article in journal (Refereed)
    Abstract [en]

    The geometries of 35 conformers of Me(SiMe2) nMe (n= 4, 1; n = 5, 2; n = 6, 3; n = 7, 4) were optimized at the MP2/VTDZ level, and CCSD(T) single-point calculations were done at three MP2/VTDZ conformer geometries of 1. The relative ground-state energies of the conformers of 1-4 in the gas phase were obtained from the MP2/VTDZ electronic energy, zero- point vibrational energy, and thermal corrections at 0, 77, and 298 K. Relative energies in an alkane solvent at 77 and 298 K were obtained by the addition of solvation energies, obtained from the SM5.42R model. The calculated energies of 26 of the conformers (n = 4-6) have been least-squares fitted to a set of 15 additive increments associated with each Si-Si bond conformation and each pair of adjacent bond conformations, with mean deviations of 0.06-0.20 kcal/mol. An even better fit for the energies of 24 conformers (mean deviations, 0.01-0.09 kcal/mol) has been obtained with a larger set of 19 increments, which also contained contributions from selected combinations of conformations of three adjacent bonds. The utility of the additive increments for the prediction of relative conformer energies in the gas phase and in solution has been tested on the remaining nine conformers (n = 6, 7). With the improved increment set, the average deviation from the SM5.42R//MP2 results for solvated conformers at 298 K was 0.18 kcal/mol, and the maximum error was 0.98 kcal/mol.

  • 40.
    Gernandt, Jonas
    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.
    Hysteresis in the surfactant-induced volume transition of hydrogels2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 4, p. 1717-1725Article in journal (Refereed)
    Abstract [en]

    The discontinuous uptake and release of surfactants by hydrogels and the accompanying discontinuous volume transition is known to occur with a hysteresis. We have performed a theoretical analysis in order to find the mechanistic origin of this phenomenon. Using a mean-field model, we have quantitatively reproduced the experimental behavior by considering the cost of elastically deforming the gel material to allow phase coexistence. The major part of the hysteresis is due to the high phase coexistence cost of the swelling transition, since in this direction the coexistence cost depends not only on the elasticity of the network (being a weak force in comparison) but also on the entropy of the monovalent nonsurfactant electrolyte present in the system.

  • 41. Giussani, Angelo
    et al.
    Serrano-Andres, Luis
    Merchan, Manuela
    Roca-Sanjuan, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Garavelli, Marco
    Photoinduced Formation Mechanism of the Thymine-Thymine (6-4) Adduct2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 7, p. 1999-2004Article in journal (Refereed)
    Abstract [en]

    The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet 3(n pi*) state of thymine. This state, displaying an elongated C-4=O bond, triggers (6-4) dimer formation by reaction with the C-5=C-6 double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just one thymine, whose main decay channel (by radiationless repopulation of its ground state) is nonphotochemical, can rationalize the experimentally observed low quantum yield of formation for the thymine-thymine (6-4) adduct.

  • 42. Gobbo, Joao Paulo
    et al.
    Sauri, Vicenta
    Roca Sanjuán, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Serrano-Andres, Luis
    Merchan, Manuela
    Borin, Antonio Carlos
    On the Deactivation Mechanisms of Adenine-Thymine Base Pair2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 13, p. 4089-4097Article in journal (Refereed)
    Abstract [en]

    In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)] and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.

  • 43.
    Grime, John M A
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Khan, Malek O
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Decreased Osmotic Pressure via Interfacial Charge Clustering2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 31, p. 10049-10056Article in journal (Refereed)
    Abstract [en]

    Behaviors of a model interfacial system featuring the clustering of discrete, mobile wall charges and a counterion solution are investigated. The results demonstrate that even very small localized charge clusters produce significant effects for the osmotic pressure, effects that are not adequately represented in common colloidal models. We observe a pronounced decrease in osmotic pressure where a certain level of clustering is attained, with potentially significant implications for theories of colloidal stability and biochemical processes at microscopic length scales. The stable level of wall charge clustering, and thus the osmotic pressure, is found to be variable in the addition of an attractive potential, as measured via the excess free energy of clustering.

  • 44.
    Gråsjö, Johan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Andersson, Egil
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Forsberg, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Aziz, Emad F.
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Johansson, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Nordgren, Joseph
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Duda, Laurent
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Andersson, Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Hennies, Franz
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Soft X-Ray Physics.
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Hansson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Electronic structure of water molecules confined in a micelle lattice2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 24, p. 8201-8205Article in journal (Refereed)
    Abstract [en]

    Oxygen K absorption and emission spectra of water molecules confined in dodecyltrimethyl ammonium chloride micelle structures are presented. The local electronic structure of the water molecules is found to be dramatically different from the electronic structure of water molecules in the gas-phase as well as in liquid water. Hybridization with states of the ions in the surrounding ions is directly observed, and evidence for stabilization of the water molecules relative to molecules in bulk water is found.

  • 45.
    Gråsjö, Johan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Andersson, Egil
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Forsberg, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Duda, Laurent
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Henke, Ev
    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.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Surface and Interface Science.
    Andersson, Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Pietsch, Annette
    Hennies, Franz
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Jan-Erik, Rubensson
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Soft X-Ray Physics.
    Local Electronic Structure of Functional Groups in Glycine As Anion, Zwitterion, and Cation in Aqueous Solution2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 49, p. 16002-16006Article in journal (Refereed)
    Abstract [en]

    Nitrogen and oxygen K emission spectra of glycine in the form of  anions, zwitterions, and cations in aqueous solution are presented. It  is shown that protonation has a dramatic influence on the local   electronic structure and that the functional groups give a distinct  spectral fingerprint.

     

  • 46.
    Hagglund, C
    et al.
    Chalmers University of Technology.
    Kasemo, B
    Chalmers University of Technology.
    Österlund, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    In situ reactivity and FTIR study of the wet and dry photooxidation of propane on anatase TiO22005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 21, p. 10886-10895Article in journal (Refereed)
    Abstract [en]

    The photocatalytic oxidation (PCO) of trace amounts of propane (500 ppm) on nanocrystalline anatase TiO2 has been investigated in situ as a function of temperature (T = 318-473 K), humidity (C-H2O = 0-4%), and time by means of mass spectrometry and diffuse reflectance Fourier transform infrared spectroscopy (DRIFT). Propane adsorbs associatively on TiO2 at 318 K in dry air, while at 473 K small amounts of thermal dissociation products appear on the surface. In agreement with previous studies, propane is found primarily to be converted to acetone by reactions with photogenerated oxygen radicals. Various successive reaction paths exist, where the branching depends on the temperature and hydroxylation state of the surface. Under dry conditions at 318 K, acetone oxidation is initially kinetically hindered, while, above 400 K, acetone readily decomposes. The thermally assisted reaction channel leads to detrimental bonding of surface species and inhibition of the catalytic activity. It is manifested by a coloration of the sample and suggested to be coupled to surface reduction. Under humidified conditions, there is an optimum of the PCO in C-H2O and T space, which is estimated to correspond to an equilibrium coverage of one monolayer of H2O (or bilayer). The latter reaction condition also corresponds to sustained high propane conversion and is characterized by rapid establishment of steady state rates. The optimum PCO is discussed in terms of a balance between (i) sustaining enough of a photoactive water monolayer to avoid detrimental bonding of surface species, (ii) allowing reactants to adsorb and access bulk TiO2 photoexcitations, and at the same time (iii) maximizing the thermally assisted decomposition of intermediates.

  • 47.
    Hans, Andreas
    et al.
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Ozga, Christian
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Seidel, Robert
    Helmholtz Zentrum Berlin Mat & Energie, Methods Mat Dev, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Schmidt, Philipp
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Ueltzhoeffer, Timo
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Holzapfel, Xaver
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Wenzel, Philip
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Reiss, Philipp
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Pohl, Marvin N.
    Helmholtz Zentrum Berlin Mat & Energie, Methods Mat Dev, Albert Einstein Str 15, D-12489 Berlin, Germany.;Free Univ Berlin, Dept Phys, Arnimallee 14, D-14195 Berlin, Germany.;Max Planck Gesell, Fritz Haber Inst, Faradayweg 4-6, D-14195 Berlin, Germany..
    Unger, Isaak
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Aziz, Emad F.
    Helmholtz Zentrum Berlin Mat & Energie, Methods Mat Dev, Albert Einstein Str 15, D-12489 Berlin, Germany.;Free Univ Berlin, Dept Phys, Arnimallee 14, D-14195 Berlin, Germany.;Monash Univ, Sch Chem, Clayton Campus, Clayton, Vic 3800, Australia..
    Ehresmann, Arno
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Slavicek, Petr
    Univ Chem & Technol Prague, Dept Phys Chem, Tech 5, Prague 16628, Czech Republic..
    Winter, Bernd
    Helmholtz Zentrum Berlin Mat & Energie, Methods Mat Dev, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Knie, Andre
    Univ Kassel, Heinrich Plett Str 40, D-34132 Kassel, Germany.;Ctr Interdisciplinary Nanostruct Sci & Technol CI, Heinrich Plett Str 40, D-34132 Kassel, Germany..
    Optical Fluorescence Detected from X-ray Irradiated Liquid Water2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 10, p. 2326-2330Article in journal (Refereed)
    Abstract [en]

    Despite its importance, the structure and dynamics of liquid water are still poorly understood in many apsects. Here, we report on the observation of optical fluorescence upon soft X-ray irradiation of liquid water. Detection of spectrally resolved fluorescence was achieved by a combination of the liquid microjet technique and fluorescence spectroscopy. We observe a genuine liquid-phase fluorescence manifested by a broad emission band in the 170-340 nm (4-7 eV) photon wavelength range. In addition, another narrower emission near 300 nm can be assigned to the fluorescence of OH (A state) in the gas phase, the emitting species being formed by Auger electrons escaping from liquid water. We argue that the newly observed broad-band emission of liquid water is relevant in search of extraterrestrial life, and we also envision the observed electron-ejection mechanism to find application for exploring solutes at liquid vapor interfaces.

  • 48.
    Hansson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Surfactant self-assembly in oppositely charged polymer networks. Theory2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 39, p. 12903-12915Article in journal (Refereed)
    Abstract [en]

    The interaction of ionic surfactants with polyion networks of opposite charge in an aqueous environment is analyzed theoretically by applying a recent theory of surfactant ion-polyion complex salts (J. Colloid. Int. Sci. 2009, 332, 183). The theory takes into account attractive and repulsive polyion-mediated interactions between the micelles, the deformation of the polymer network, the mixing of micelles, polyion chains, and simple ions with water, and the hydrophobic free energy at the micelle surface. The theory is used to calculate binding isotherms, swelling isotherms, surfactant aggregation numbers, compositions of complexes,and phase structure under various conditions. Factors controlling the gel volume transition and conditions for core/shell phase coexistence are investigated in detail, as well as the influence of salt. In particular, the interplay between electrostatic and elastic interactions is highlighted. Results from theory are compared with experimental data reported in the literature. The agreement is found to be semiquantitative or qualitative. The theory explains both the discrete volume transition observed in systems where the surfactant is in excess over the polyion and the core/shell phase coexistence in systems where the polyion is in excess.

  • 49.
    Hansson, Per
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Bysell, Helena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Månsson, Ronja
    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.
    Peptide-Microgel Interactions in the Strong Coupling Regime2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 35, p. 10964-10975Article in journal (Refereed)
    Abstract [en]

    The interaction between lightly cross-linked poly(acrylic acid) microgels and oppositely charged peptides was investigated as a function of peptide length, charge density, pH, and salt concentration, with emphasis on the strong coupling regime at high charge contrast. By micromanipulator-assisted light microscopy, the equilibrium volume response of single microgel particles upon oligolysine and oligo(lysine/alanine) absorption could be monitored in a controlled fashion. Results show that microgel deswelling, caused by peptide binding and network neutralization, increases with peptide length (3 < 5 < 10) and charge density (30% < 50% < 100%). Furthermore, oligomer-induced microgel deswelling was more pronounced at pH 5 than at pH 8, reflecting the lower network charge density in the former case (pK(a) for the isolated acrylic acid approximate to 4.7). In order to describe these highly coupled systems, a model was developed, in which counterion/peptide-mediated electrostatic attraction between the network chains is described using an exponential force law, and the network elasticity by the inverse Langevin theory. The model was used to calculate the composition of microgels in contact with reservoir solutions of peptides and simple electrolytes. At high electrostatic coupling, the calculated swelling curves were found to display first-order phase transition behavior. The model was demonstrated to capture pH- and electrolyte-dependent microgel swelling, as well as effects of peptide length and charge density on microgel deswelling. The analysis demonstrated that the peptide charge (length), rather than the peptide charge density, determines microgel deswelling. Furthermore, a transition between continuous and discrete network collapse was identified, consistent with experimental results in the present investigations, as well as with results from the literature on microgel deswelling caused by multivalent cations.

  • 50.
    Hellberg, D
    et al.
    Universität Greifswald.
    Scholz, Fritz
    Universität Greifswald.
    Schubert, F
    Lovric, M
    Omanovic, D
    Agmo Hernandez, Victor
    Thede, R
    Kinetics of liposome adhesion on a mercury electrode2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, p. 14715-14726Article in journal (Refereed)
    Abstract [en]

    The adhesion of liposomes on a mercury electrode leads to capacitive signals due to the formation of islands of lecithin monolayers. Integration of the current-time transients gives charge-time transients that can be fitted by the empirical equation Q(t) = Q(0) + Q(1)(1 - exp(-t/tau(1))) + Q(2)(1 - exp(-t/tau(2))), where the first term on the right side is caused by the docking of the liposome on the mercury surface, the second term is caused by the opening of the liposome, and the third term is caused by the spreading of the lecithin island on the mercury surface. The temperature dependence of the two time constants tau(1) and tau(2) and the temperature dependence of the overall adhesion rate allow determination of the activation energies of the opening, the spreading, and the overall adhesion process both for gel-phase 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and for liquid-crystalline-phase DMPC liposomes. In all cases, the spreading is the rate-determining process. Negative apparent activation energies for the spreading and overall adhesion process of liquid-crystalline-phase DMPC liposomes can be explained by taking into account the weak adsorption equilibria of the intact liposomes and the opened but not yet spread liposomes. A formal kinetic analysis of the reaction scheme supports the empirical equation used for fitting the charge-time transients. The developed kinetic model of liposome adhesion on mercury is similar to kinetic models published earlier to describe the fusion of liposomes. The new approach can be used to probe the stability of liposome membranes.

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