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• 1.
Eindhoven University of Technology, Netherlands.
Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands.
Hybrid zinc oxide conjugated polymer bulk heterojunction solar cells2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 19, p. 9505-9516Article in journal (Refereed)

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

• 2.
Uppsala University, Sweden.
University of Siena, Italy.
Relative 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)

The conversion of the plant photoreceptor phytochrome from an inactive (Pr) to an active form (Pfr) is accomplished by a red-light induced Z $\rightarrow$ 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.

• 3.
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics . Linköping University, The Institute of Technology.
Universidade Federal do Rio de Janeiro. Universidade Federal do Rio de Janeiro. Universidade Federal do Rio de Janeiro. Universidade Federal do Rio de Janeiro. Australian National University . Australian National University . Australian National University .
Anion-Specific Partitioning in Two-Phase Finite Volume Systems: Possible Implications for Mechanisms of Ion Pumps.2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 23, p. 8124-8127Article in journal (Refereed)

In two-phase finite volume systems of electroneutral phospholipids, the electrolyte concentration is different in the two phases. The partitioning is highly anion-specific, a phenomenon not accounted for by classical electrolyte theories. It is explained if ionic dispersion forces that lead to specific ion binding are taken into account. The mechanism provides a contribution to active ion pumps not previously considered.

• 4.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics .
Research School of Physical Sciences and Engineering Australian National University Canberra. Research School of Physical Sciences and Engineering Australian National University.
Ion Specific Surface Forces between Membrane Surfaces2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, p. 9645-9649Article in journal (Refereed)
• 5.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics .
University of Florence. University of Florence. University of Florence. Australian National University.
Why pH titration in protein solutions follows a Hofmeister series2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 14, p. 7563-7566Article in journal (Refereed)

Measurements of pH in single-phase cytochrome c suspensions are reported. The pH, as determined by a glass electrode, has a fixed value. With the addition of salt, the supposedly fixed pH changes strongly. The pH depends on salt type and concentration and follows a Hofmeister series. A theoretical interpretation is given that provides insights into such Hofmeister effects. These occur generally in protein solutions. While classical electrostatic models provide partial understanding of such trends in protein solutions, they fail to explain the observed ion specificity. Such models neglect electrodynamic fluctuation (dispersion) forces acting between ions and proteins. We use a Poisson-Boltzmann cell model that takes these ionic dispersion potentials between ions and proteins into account. The observed ion specificity can then be accounted for. Proteins act as buffers that display similar salt-dependent pH trends not previously explained.

• 6.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics .
Res. Sch. of Phys. Sci./Engineering, Australian National University, Canberra, 0200, Australia, Inst. of Phys./Theoretical Chemistry, University of Regensburg, D-93040 Regensburg, Germany.
Contributions from dispersion and born self-free energies to the solvation energies of salt solutions2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 33, p. 12593-12595Article in journal (Refereed)

That the Born theory provides an accurate means of calculating solvation energies of ions in water has been demonstrated by Rashin and Honig (Rashin, A. A., Honig, B. J. Phys. Chem. 1985, 89, 5588). They could fit the experimental solvation energies of a number of salts nicely by a simple increase of 7% in the expected radii of all ions. However, as we demonstrate herein, there is an important previously ignored contribution due to the ionic dispersion self-free energy. The ionic parameters necessary to estimate the different contributions to solvation energy are the ionic radii, the ionic polarizabilities, and the ionization potentials. Whereas the polarizabilities and ionization potentials of a number of salts have recently been derived ab initio (in both vacuum and water), the appropriate choices of radii are less well-known. We pursue two different approaches to assign the ionic radii. In the first approach, we find that an increase of all expected radii by 23% gives reasonable agreement between theory and experiment (to within 6%). In the second approach, we increased the expected radii of six ions separately (10-30%) to obtain a best fit for the nine salts investigated. In this second approach, the deviations between theory and experiment were less than 0.1%. The essential point is that a proper theory must include contributions from both electrostatic (Born) and electrodynamic (dispersion) self-free energies.

• 7.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics .
Universidade Federal do Rio de Janeiro. Australian National University. University of California and Lawrence Berkeley National Lab..
Effect of Salt Identity on the Phase Diagram for a Globular Protein in Aqueous Electrolyte Solution2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, p. 24757-24760Article in journal (Refereed)
• 8.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics .
Escola de Química, Universidade Federal do Rio de Janeiro, Brazil. Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284. Research School of Physical Sciences and Engineering, Australian National University, Canberra 0200, Australia.
Specific ion effects in solutions of globular proteins: Comparison between analytical models and simulation2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 51, p. 24489-24494Article in journal (Refereed)

Monte Carlo simulations have been performed for ion distributions outside a single globular macroion and for a pair of macroions, in different salt solutions. The model that we use includes both electrostatic and van der Waals interactions between ions and between ions and macroions. Simulation results are compared with the predictions of the Ornstein-Zernike equation with the hypernetted chain closure approximation and the nonlinear Poisson-Boltzmann equation, both augmented by pertinent van der Waals terms. Ion distributions from analytical approximations are generally very close to the simulation results. This demonstrates that properties that are related to ion distributions in the double layer outside a single interface can to a good approximation be obtained from the Poisson-Boltzmann equation. We also present simulation and integral equation results for the mean force between two globular macroions (with properties corresponding to those of hen-egg-white lysozyme protein at pH 4.3) in different salt solutions. The mean force and potential of mean force between the macroions become more attractive upon increasing the polarizability of the counterions (anions), in qualitative agreement with experiments. We finally show that the deduced second virial coefficients agree quite well with experimental results. © 2005 American Chemical Society.

• 9.
University of Mons Mat Nova, Belgium .
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology. CNRS, France . University of Paris 11, France . University of Lyon 1, France . University of Paris 06, France . University of Paris 06, France . University of Mons Mat Nova, Belgium . University of Paris 06, France .
Conformational Plasticity of Hydrogen Bonded Bis-urea Supramolecular Polymers2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 17, p. 5379-5386Article in journal (Refereed)

We report a detailed structural investigation of supramolecular polymers formed by hydrogen bonded self assembly of bis-urea monomers The careful exploration of the energy landscape by molecular mechanics/molecular dynamics (MM/MD) simulations has allowed us to identify three distinct self assembled structures of similar stabilities. These structures have been compared to X-ray crystal data. We observe that a slight change in the molecular structure can favor a particular structure over the others. Detailed analysis shows that hydrogen bonds stabilize all three structures to a similar extent Therefore, it is the interactions among the lateral substituents, and with the filament environment, that are the decisive factors in the competition between the possible self-assembled structures. This study constitutes a clear reminder that the conformation of a supramolecular polymer is a sensitive function of the molecular structure and may significantly differ from the solid-state conformation of a model compound.

• 10. Danilczuk, M.
Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland, Faculty of Chemistry, Department of Biochemistry and Biotechnology, Rzeszów University of Technology, 6 Powstancow Warszawy Ave., 35-959, Rzeszów, Poland. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics . Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland.
EPR and DFT study on the stabilization of radiation-generated methyl radicals in dehydrated Na-A zeolite2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 48, p. 24492-24497Article in journal (Refereed)

Electron paramagnetic resonance (EPR) spectroscopy was applied to study paramagnetic species stabilized in Na-A zeolite exposed to gaseous methane and ?-irradiated at 77 K. Two types of EPR spectra were recorded during thermal annealing of zeolite up to room temperature. Owing to the results for the zeolite exposed to 13CH4 the multiplet observed at 110 K was assigned to a ?CH3?Na+ complex. After decay of the multiplet, the isotropic quartet of methyl radical was recorded in the temperature range of 170-280 K. On the basis of the EPR parameters it is postulated that ?CH3 radicals in this temperature region are able to freely rotate inside the zeolite cage. The structures of the ?CH3?Na+ adsorption complex and respective hyperfine coupling constants were calculated by applying DFT quantum chemical methods. Two different models were applied to represent the zeolite framework: the 6T structure of one six-membered ring and the 3T cluster. The hyperfine coupling constants calculated for the ?CH3?Na+ adsorption complex for both applied models show very good agreement with those obtained experimentally. © 2006 American Chemical Society.

• 11.
University of Arizona.
Wysocki Jr., R.J., Department of Chemistry, University of Arizona, Tucson, AZ 85721. Department of Chemistry, University of Arizona, Tucson, AZ 85721. Department of Chemistry, University of Arizona, Tucson, AZ 85721.
Potential-modulated, attenuated total reflectance spectroscopy of poly(3,4-ethylenedioxythiophene) and poly(3,4-ethylenedioxythiophene methanol) copolymer films on indium-tin oxide2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 10, p. 4900-4907Article in journal (Refereed)

We report the first application of a potential-modulated spectroelectrochemical ATR (PM-ATR) instrument utilizing multiple internal reflections at an optically transparent electrode to study the charge-transfer kinetics and electrochromic response of adsorbed films. A sinusoidally modulated potential waveform was applied to an indium-tin oxide (ITO) electrode while simultaneously monitoring the optical reflectivity of thin (2-6 equivalent monolayers) copolymer films of poly(3,4-ethylenedioxythiophene) (PEDOT) and poly(3,4ethylenedioxythiophene methanol) (PEDTM), previously characterized in our laboratory.1 At high modulation frequencies the measured response of the polymer film is selective toward the fastest electrochromic processes in the film, presumably those occurring within the first adsorbed monolayer. Quantitative determination of the electrochromic switching rate, derived from the frequency response of the attenuated reflectivity, shows a linear decrease in the rate, from 11 × 103 s-1 to × 103 s -1, with increasing proportions of PEDTM in the copolymer, suggesting that interactions between the methanol substituent on EDTM and the ITO surface slow the switching process by limiting the rate of conformational change in the polymer film. © 2006 American Chemical Society.

• 12.
Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology.
Hydrogen Bond Interaction between Self-Assembled Monolayers and Adsorbed Water Molecules and Its Implications for Cluster Formation1995In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 99, no 39, p. 14198-14200Article in journal (Refereed)

Infrared spectroscopy is used to investigate the adsorption of D2O onto self-assembled monolayers of methyl 16-mercaptohexadecanoate on gold. The D2O molecules are shown to interact with the carbonyl oxygens of the monolayer, forming hydrogen bonds and causing a structural rearrangement of the CO2CH3 terminal group. The number of hydrogen bonds decreases as the amorphous-like, essentially flat (two-dimensional) ice overlayer that forms at 100 K changes into polycrystalline-like ice upon annealing at 140 K. This decrease is a consequence of the formation of three-dimensional ice clusters, which leaves a large fraction of the monolayer surface bare.

• 13.
Eindhoven University of Technology, Netherlands.
Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands. Katholieke University of Leuven, Belgium. Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands.
Polar Switching in Trialkylbenzene-1,3,5-tricarboxamides2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 13, p. 3928-3937Article in journal (Refereed)

The hydrogen-bonded hexagonal columnar LC (Col(hd)) phases formed by benzene-1,3,5-tricarboxamide (BTA) derivatives can be aligned uniformly by an electric field and display switching behavior with a high remnant polarization. The polar switching in three symmetrically substituted BTAs with alkyl chains varying in length between 6 and 18 carbon atoms (C6, C10, and C18) was investigated by electro-optical switching experiments, dielectric relaxation spectroscopy (DRS), and solid-state NMR The goal was to characterize ferroelectric properties of BTA-based columnar LCs, which display a macroscopic axial dipole moment due to the head-to-tail stacking of hydrogen-bonded amides. The Col(hd) phase of all three BTAs can be aligned uniformly by a dc field similar to 30 V/mu m. Moreover, C10 and C18 display extrinsic polar switching characterized by a remnant polarization and coercive field of 1-2 mu C/cm(2) and 20-30 V/mu m, respectively. In the absence of an external field, the polarization is lost in 1-1000 s, depending on device details and temperature. DRS revealed a columnar glass transition in the low-temperature region of the LC phase related to collective vibrations in the hydrogen-bonded columns that freeze out below 41-54 degrees C. At higher temperatures, a relaxation process is present originating from the collective reorientation of amide groups along the column axis (inversion of the macrodipole). Matching activation energies suggest that the molecular mechanism underlying the polar switching and the R-processes is identical. These results illustrate that LC phases based on BTAs offer the unique possibility to integrate polarization with other functionalities in a single nanostructured material.

• 14.
Linköping University, Department of Science and Technology. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Molecular Dynamics Study of Morphology of Doped PEDOT: From Solution to Dry Phase2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 16, p. 4299-4307Article in journal (Refereed)

Morphology of the conducting polymer PEDOT:TOS (poly(3,4-ethylenedioxythiopherre) doped with molecular, tosylate) and its crystallization in aqueous solution, were Studied using atomistic molecular dynamics simulations. It was foirnd that (a) PEDOT comprises crystallite aggregates consisting of 3-6 pi-pi stacked chains. The crystallites are linked by interpenetrating pi-pi stacked chains such that percolative paths in the structure are formed. (b) The size of the crystallites.deperids on the water content, but the pi-pi stacking distance is practically independent of the chain length, charge,Concentration and water content. (c) TOS counterions are located either on the top of the,chains or on the side of the crystalliteS and their distribution depends on the charge concentration but is practically independent of the water content; (d) PEDOT depends On their length and water,content. 2 chains and crystallites exhibit bending that depends On their length and water content.

• 15.
Linköping University, Faculty of Health Sciences. Linköping University, Department of Medicine and Health Sciences, Radiation Physics .
Krakow, Polen. Linköping University, Faculty of Health Sciences. Linköping University, Department of Medicine and Health Sciences, Radiation Physics . Detroit, USA.
Visualizing the dose distribution and linear energy transfer by ID and 2D ESR imaging: A potassium dithionate dosimeter irradiated with C6+ and N7+ ions2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 29, p. 8437-8442Article in journal (Refereed)

We report the application of one- and two-dimensional (1D and 2D) spectral-spatial electron spin resonance imaging (ESRI) for visualizing the dose distribution and linear energy transfer (LET) in a potassium dithionate, K 2S2O6 (PDT), dosimeter irradiated with the heavy ions C6+ and N7+. The ESR spectrum in the irradiated PDT consists of a superposition of two isotropic signals assigned to two ·SO3- radicals, R1 and R2, with no hyperfine splittings and slightly different g values. The ID ESRI profiles clearly indicate the spatial penetration of the beams and the location of the sharp maximum dose, the "Bragg peak", detected for each beam. The depth penetrations are different: ≈2.3 mm for C6+ and ≈1.8 mm for N7+ beams, ±0.1 mm, beyond these limits, no radicals were detected. 2D spectral-spatial ESRI images reflect both the dose distribution and the spatial dependence of the relative intensities of radicals R1 and R2, an effect that is assigned to the depth variation of the LET. This study has demonstrated that ESRI is a promising new method for dose and LET determination. Of particular interest are applications in the field of radiotherapy with heavy ions, because in this case the Bragg peak is pronounced and the dose can be focused at specific depths while the surrounding areas are protected. © 2008 American Chemical Society.

• 16.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Mimicking the properties of antifreeze glycoproteins: synthesis and characterization of a model system for ice nucleation and antifreeze studies2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 33, p. 15849-15859Article in journal (Refereed)

Synthesis of β-D-Gal-(1 → 3)-β-D-GalNAc coupled to HOC2H4NHCOC15H30SH is described. This compound was coadsorbed at various proportions with C2H5OC2H4NHCOC15H30SH to form statistically mixed self-assembled monolayers (SAMs) on gold in an attempt to mimic the properties of the active domain in antifreeze glycoproteins (AFGPs). The monolayers were characterized by null ellipsometry, contact angle goniometry, X-ray photoelectron spectroscopy, and infrared reflection−absorption spectroscopy. The disaccharide compound adsorbed preferentially, and SAMs prepared at a solution molar ratio >0.3 displayed total wetting. The mixed SAMs showed well-organized alkyl chains up to a disaccharide surface fraction of 0.8. The amount of gauche conformers in the alkyls increased rapidly above this point, and the monolayers became disordered and less densely packed. Furthermore, the generated mixed SAMs were subjected to water vapor at constant relative humidity and the subsequent ice crystallization on a cooled substrate was monitored via an optical microscope. Interestingly, rapid crystallization occurred within a narrow range of temperatures on mixed SAMs with a high disaccharide content, surface fraction >0.3. The reported crystallization temperatures and the ice layer topography were compared with results obtained for a much simpler reference system composed of −OH/−CH3 terminated n-alkanethiols in order to account for changes in topography of the water/ice layer with surface energy. Although preliminary, the obtained results can be useful in the search for the molecular mechanism behind the antifreeze activity of AFGPs.

• 17.
Royal Institute Technology, Sweden .
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology. Royal Institute Technology, Sweden . Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology. Royal Institute Technology, Sweden .
Dark States in Ionic Oligothiophene Bioprobes-Evidence from Fluorescence Correlation Spectroscopy and Dynamic Light Scattering2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 22, p. 5924-5933Article in journal (Refereed)

Luminescent conjugated polyelectrolytes (LCPs) can upon interaction with biological macromolecules change their luminescent properties, and thereby serve as conformation- and interaction-sensitive biomolecular probes. However, to exploit this in a more quantitative manner, there is a need to better understand the photophysical processes involved. We report studies of the conjugated pentameric oligothiophene, derivative p-FTAA, which changes optical properties with different p-FTAA concentrations in aqueous buffers, and in a pH and oxygen saturation dependent manner. Using dynamic light scattering, luminescence spectroscopy and fluorescence correlation spectroscopy, we find evidence for a monomer dimer equilibrium, for the formation of large clusters of p-FTAA in aqueous environment, and can couple aggregation to changed emission properties of oligothiophenes. In addition, we observe the presence of at least two dark transient states, one presumably being a triplet state. Oxygen was found to statically quench the p-FTAA fluorescence but also to promote molecular fluorescence by quenching dark transient states of the p-FTAA molecules. Taken together, this study provides knowledge of fluorescence and photophysical features essential for applying p-FTAA and other oligothiophene derivatives for diagnostic purposes, including detection and staining of amyloid aggregates.

• 18.
Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry .
Quantum-chemical and force-field investigations of ice Ih: Computation of proton-ordered structures and prediction of their lattice energies2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 40, p. 15856-15864Article in journal (Refereed)

The different possible proton-ordered structures of ice Ih for an orthorombic unit cell with 8 water molecules were derived. The number of unique structures was found to be 16. The crystallographic coordinates of these are reported. The energetics of the different polymorphs were investigated by quantum-mechanical density-functional theory calculations and for comparison by molecular-mechanics analytical potential models. The polymorphs were found to be close in energy, i.e., within approximately 0.25 kcal/mol H2O, on the basis of the quantum-chemical DFT methods. At 277 K, the different energy levels are about evenly populated, but at a lower temperature, a transition to an ordered form is expected. This form was found to agree with the ice phase XI. The difference in lattice energies among the polymorphs was rationalized in terms of structural characteristics. The most important parameters to determine the lattice energies were found to be the distributions of water dimer H-bonded pair conformations, in an intricate manner.

• 19.
Technical University of Eindhoven, Netherlands.
Technical University of Eindhoven, Netherlands. Technical University of Eindhoven, Netherlands. Technical University of Eindhoven, Netherlands. Technical University of Eindhoven, Netherlands. Technical University of Eindhoven, Netherlands. Technical University of Eindhoven, Netherlands. Technical University of Eindhoven, Netherlands.
The optimal structure-conductivity relation in epoxy-phthalocyanine nanocomposites2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 46, p. 23115-23122Article in journal (Refereed)

Phthalcon-11 (aquocyanophthalocyaninatocobalt (III)) forms semiconducting nanocrystals that can be dispersed in epoxy coatings to obtain a semiconducting material with a low percolation threshold. We investigated the structure-conductivity relation in this composite and the deviation from its optimal realization by combining two techniques. The real parts of the electrical conductivity of a Phthalcon-11/ epoxy coating and of Phthalcon-11 powder were measured by dielectric spectroscopy as a function of frequency and temperature. Conducting atomic force microscopy (C-AFM) was applied to quantify the conductivity through the coating locally along the surface. This combination gives an excellent tool to visualize the particle network. We found that a large fraction of the crystals is organized in conducting channels of fractal building blocks. In this picture, a low percolation threshold automatically leads to a conductivity that is much lower than that of the filler. Since the structure-conductivity relation for the found network is almost optimal, a drastic increase in the conductivity of the coating cannot be achieved by changing the particle network, but only by using a filler with a higher conductivity level.

• 20.
Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. R&D Materials, Chemistry Department, AGFA-Gevaert NV, Mortsel, Belgium. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Phenyl-capped EDOT trimer: its chemical and electronic structure and its interface with aluminum2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 39, p. 10793-10800Article in journal (Refereed)

The chemical and electronic properties of a phenyl-capped 3,4-(ethylenedioxy)thiophene trimer (EDOT trimer) and its interface formation with aluminum have been studied. Thin EDOT trimer films were prepared on clean gold substrates through in-situ vapor deposition. Aluminum was deposited stepwise on top of the EDOT trimer, and the initial stages of interface formation were investigated by photoelectron spectroscopy. The organic/metal interface formed was not completely abrupt; some degree of diffusion of aluminum into the EDOT trimer film occurred. The aluminum atoms preferentially react with the α-position of the trimer (C−S carbon atoms) forming covalent bonds. The formation of these covalent bonds causes a break in the π-conjugation of the system due to the introduction of sp3 defects. The charge density also is somewhat redistributed within the oligomer as a whole, mainly affecting the neighboring atoms:  sulfur and β-position of the trimer (C=C−O carbon atoms). Once the C−S carbon sites are saturated, the aluminum instead reacts with the less favorable carbon atom of the ethylene bridge (C−O−C carbons). Worth noting is the decrease in work function from 5.2 eV for sputter cleaned gold to 4.1 eV upon deposition of the EDOT trimer. Our results have several implications for organic electronics. The sp3 defects introduced by the aluminum−EDOT contacting will influence the charge injection into the material across the EDOT trimer/aluminum interface negatively. The change in work function could potentially be used to modify gold contacts for electron injection into molecules with low electron affinity.

• 21.
Eindhoven University of Technology, Netherlands.
Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands.
Three-dimensional inhomogeneities in PEDOT : PSS films2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 49, p. 18820-18825Article in journal (Refereed)

Spin-cast PEDOT/PSS film are investigated using scanning probe-based spectroscopic techniques. The films are found to consist of relatively well-conducting islands that are embedded in a less conductive matrix. A scanning-tunneling microscope-based method is developed to obtain three-dimensional conductivity images with nanometer resolution. Order-of-magnitude variations in the film conductivity are observed in all spatial directions. In addition, charge transport in the normal direction depends on the injection spot and is found to be ohmic or space-charge-limited. We found that both the morphology and the conductivity of the top layer differ substantially from those in the bulk, which is attributed to an enhanced PSS content in the top layer.

• 22. Kuritka, I.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry .
Lithium intercalation of phenyl-capped aniline dimers: A study by photoelectron spectroscopy and quantum chemical calculations2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 38, p. 19023-19030Article in journal (Refereed)

Structural and electronic properties of pristine and lithium-intercalated, phenyl-capped aniline dimers as a model for the lithium-polyaniline system have been studied by photoelectron spectroscopy and quantum chemical calculations. It was found that the electronic structure of reduced and oxidized forms of oligoanilines is only weakly affected by isomerism. Upon intercalation, charge transfer from the Li-atoms is remarkable and highly localized at N-atomic sites, where configurations are energetically favored in which both N atoms of the dimers are bound to Li atoms. Conversion of nitrogen sites is different for the two forms of aniline dimers and incomplete up to high intercalation levels, indicating a pronounced role of solid-state effects in the formation of such compounds. © 2006 American Chemical Society.

• 23.
Eindhoven University of Technology, Netherlands.
Radboud University of Nijmegen, Netherlands. Eindhoven University of Technology, Netherlands. Radboud University of Nijmegen, Netherlands. Eindhoven University of Technology, Netherlands. Eindhoven University of Technology, Netherlands.
Intensive Chiroptical Properties of Chiral Polyfluorenes Associated with Fibril Formation2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 43, p. 14047-14051Article in journal (Refereed)

Thin films of chiral poly {9,9-bis[(3S)-3,7-dimethyloctyl]-2,7-fluorene} (1) were studied using circular dichroism (CD) spectroscopy. Films spin coated from chloroform solution, show CD with a degree of polarization g(abs) (= +4 x 10(-4) at 400 nm) that is independent of film thickness (50-290 nm). This implies that gabs is an intensive property of the material and related to the chiral organization of the molecules on a length scale less than 50 nm. Atomic force microscopy (AFM) on the films reveals fibrils. Addition of nonsolvent methanol to a solution of 1 in chloroform leads to fibril formation in solution and results in CD similar in band shape to that of the pristine spin coated films from chloroform solution and a g(abs) comparable in magnitude. Thus the chiral molecular arrangement leading to circular dichroism is part of the internal structure of these fibrils.

• 24.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
Bogolyubov Institute for Theoretical Physics Kiev, Ukraine. Division of Physics Luleå University of Technology, Luleå. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Molecular Orientation in Helical and All-Trans Oligo(ethylene glycol)-Terminated Assemblies on Gold: Results of ab Initio Modeling2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 34, p. 7788-7796Article in journal (Refereed)

The structural properties of self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-terminated and amide-containing alkanethiols (HS(CH2)15CONH(CH2CH2O) 6H and related molecules with shorter alkyl or OEG portions) on gold are addressed. Optimized geometry of the molecular constituents, characteristic vibration frequencies, and transition dipole moments are obtained using density-functional theory methods with gradient corrections. These data are used to simulate IR reflection-absorption (RA) spectra associated with different OEG conformations. It is shown that the positions and relative intensities of all characteristic peaks in the fingerprint region are accurately reproduced by the model spectra within a narrow range of the tilt and rotation angles of the alkyl plane, which turns out to be nearly the same for the helical and all-trans OEG conformations. In contrast, the tilt of the OEG axis changes considerably under conformational transition from helical to all-trans OEG. By means of ab initio modeling, we also clarify other details of the molecular structure and orientation, including lateral hydrogen bonding, the latter of which is readily possessed by the SAMs in focus. These results are crucial for understanding phase and folding characteristics of OEG SAMs and other complex molecular assemblies. They are also expected to contribute to an improved understanding of the interaction with water, ions, and ultimately biological macromolecules.

• 25.
Escola de Quimica Universidade Federal do Rio de Janeiro, Brazil.
Technische Universität München. Technische Universität München. Programa de Engenharia Qufmica Federal do Rio de Janeiro, Brazil. Escola de Quimica Universidade Federal do Rio de Janeiro. University of Tegensburg. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics .
Specific Ion Adsorption and Surface Forces in Colloid Science2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 6, p. 1580-1585Article in journal (Refereed)
• 26. LiU, Ya-Jun
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
Density functional theory study of NO adsorbed in A-zeolite2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 16, p. 7948-7951Article in journal (Refereed)

Density functional theory was employed to investigate the adsorption site and hyperfine interactions of nitric oxide adsorbed in Na-LTA (previous name NaA) zeolite. Three different cluster models of increasing complexity were used to represent the zeolite network: (1) a six-membered ring terminated by hydrogen atoms with one sodium ion above the ring, (2) as model 1 with the addition of three sodium ions located at the centers of three imagined four-membered rings adjacent to the six-membered ring, and (3) as model 2 with the addition of the three four-membered rings adjacent to the six-membered ring. Calculations on the largest system (model 3) showed very good agreement with measured electronic Zeeman interaction couplings, 14N hyperfine coupling tensors, and 23Na hyperfine and nuclear quadruple coupling tensors of the S = 1/2 Na+⋯N-O adsorption complex when the position of the sodium ion was relaxed. The optimized geometry of the complex agreed nicely with that estimated experimentally, except for the Na-N distance, where the present results indicate that the distance deduced from previous ENDOR experiments may be underestimated by as much as 0.5 Å. © 2005 American Chemical Society.

• 27.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
Raman and IR Spectra of Ice Ih and Ice XI with an Assessment of DFT Methods2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 42, p. 11043-11051Article in journal (Refereed)

IR and Raman spectroscopic technology can be directly used to identify the occurrence of ferroelectric ice XI in laboratory or extraterrestrial settings. The performance of 16 different DFT methods applied on the ice Ih, VIII, IX, and XI crystal phases is evaluated. Based on a selected DFT computational scheme, the IR and Raman spectra of ice Ih and XI are derived and compared. When the spectra, both IR and Raman, of ice Ih and ice XI are compared, the librational vibrations are found to be the most affected by the proton ordering. The spectroscopic fingerprint of ice XI can be used to distinguish ferroelectric ice XI from ice Ih in the universe. Furthermore, the existence of only one kind of H-bond in ice Ih is demonstrated from the overlapping subspectra for different types of H-bonded pair configurations in 16 isomers of ice Ih, which provides an illustration to the historic debate on whether one or two kinds of H-bonds existed in ice.

• 28.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
Department of Chemistry and Biochemistry, University of Detroit Mercy, 4001 West McNichols, Detroit, MI 48221. Department of Chemistry and Biochemistry, University of Detroit Mercy, 4001 West McNichols, Detroit, MI 48221, Institute of Nuclear Chemistry and Technology, Warsaw, Poland. Department of Chemistry and Biochemistry, University of Detroit Mercy, 4001 West McNichols, Detroit, MI 48221. Department of Chemistry and Biochemistry, University of Detroit Mercy, 4001 West McNichols, Detroit, MI 48221.
Determining the geometry and magnetic parameters of fluorinated radicals by simulation of powder ESR spectra and DFT calculations: The case of the radical RCF2CF2. in nafion perfluorinated ionomers2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 32, p. 9484-9491Article in journal (Refereed)

The ESR spectrum of the chain-end radical RCF2CF 2. detected in Nafion perfluorinated membranes exposed to the photo-Fenton reagent was accurately simulated by an automatic fitting procedure, using as input the hyperfine coupling tensors of the two F a and two Fß nuclei as well as the corresponding directions of the principal values from density functional theory (DFT) calculations. An accurate fit was obtained only for different orientations of the hyperfine coupling tensors for the two Fa nuclei, indicating a nonplanar structure about the Ca radical center. The fitted isotropic hyperfine splittings for the two Fß nuclei in the Nafion radical, 24.9 and 27.5 G, are significantly larger than those for the chain-end radical in Teflon (15 G), implying different radical conformations in the two systems. The excellent fit indicated that the geometry and electronic structure of free radicals can be obtained not only from single-crystal ESR spectroscopy, but also, in certain cases, from powder spectra, by combination with data from DFT calculations. The optimized structures obtained by DFT calculations for the CF3CF 2CF2CF2. or CF3OCF 2CF2. radicals as models provided additional support for the pyramidal structure determined from the spectral fit. Comparison and analysis of calculated and fitted values for the hyperfine splittings of the two Fß nuclei suggested that the radical detected by ESR in Nafion is ROCF2CF2., which originates from attack of oxygen radicals on the Nafion side chain. The combination of spectrum fitting and DFT is considered important in terms of understanding the hyperfine splittings from 19F nuclei and the different conformations of fluorinated chain-end-type radicals RCF2CF2. in different systems, and also for elucidating the mechanism of Nafion fragmentation when exposed to oxygen radicals in fuel cell conditions. © 2007 American Chemical Society.

• 29.
Bogolyubov Institute for Theoretical Physics, Kiev, Ukraine.
Division of Physics, Luleå University of Technology, S-971 87 Luleå, Sweden. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
First-principle DFT and MP2 modeling of infrared reflection - Absorption spectra of oriented helical ethylene glycol oligomers2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 27, p. 13221-13227Article in journal (Refereed)

First-principle modeling is used to obtain a comprehensive understanding of infrared reflection absorption (RA) spectra of helical oligo(ethylene glycol) (OEG) containing self-assembled monolayers (SAMs). Highly ordered SAMs of methyl-terminated 1-thiaoligo(ethylene glycols) [HS(CH2CH 2O)nCH3, n = 5, 6] on gold recently became accessible for systematic infrared analyses [Vanderah et al., Langmuir, 2003, 19, 3752]. We utilized the quoted experimental data to validate the first-principle modeling of infrared RA spectra of HS-(CH2CH 2O)5,6CH3 obtained by (i) DFT methods with gradient corrections (using different basis sets, including 6-311++G* *) and (ii) HF method followed by a Møller-Plesset (MP2) correlation energy correction. In focus are fundamental modes in the fingerprint and CH-stretching regions. The frequencies and relative intensities in the calculated spectra for a single molecule are unambiguously identified with the bands observed in the experimental RA spectra of the corresponding SAMs. In addition to confirming our earlier assignment of the dominating peak in the CH-stretching region to CH2 asymmetric stretching vibrations, all other spectral features observed in that region have received an interpretation consistent (but not in all cases coinciding) with previous investigations. The obtained results provide an improved understanding of the orientation and conformation of the molecular building blocks within OEG-containing assemblies, which, in our opinion, is crucial for being able to predict the folding and phase characteristics and interaction of OEG-SAMs with water and proteins. © 2005 American Chemical Society.

• 30.
Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology.
Structural investigation of 3,4-dihydroxyphenylalanine-terminated propanethiol assembled on gold2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 48, p. 13396-13402Article in journal (Refereed)

3,4-Dihydroxyphenylalanine-terminated propanethiol (DOPA-PT), an amino acid DOPA linked to 3-mercaptopropionic acid through an amide bond, is adsorbed and self-assembled to polycrystalline gold surfaces. The structure of the adsorbates was characterized by means of X-ray photoelectron spectroscopy (XPS), infrared reflection−absorption spectroscopy (IRAS), and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). Strong molecular binding of a DOPA derivative on gold surfaces through the sulfur atom was attained. Angle-dependent XPS results showed that the aromatic ring is oriented away from the gold surface. Both IRAS and NEXAFS results showed parallel orientation of the C=O bond of the amide moiety relative to the gold surface. Hydrogen bonding between amide moieties is achieved, and it seemed to provide additional orientation stabilization. Deduced orientation of the amide moiety on the short alkyl chain (or the peptide plane) is assumed to give the average orientation of the main molecular axis. The main molecular axis is estimated to have an average tilt angle of approximately 37° relative to the gold surface normal based on NEXAFS results. The aromatic ring exhibits a preferred orientation with an average tilt angle of about 64°. The experimental results showed that DOPA-thiol with amide linkage is able to self-assemble and form a layered structured film consisting of a layer of alkane chains with a gauche conformation beneath an oriented layer of DOPA.

• 31.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Structure of tert-butyl carbamate-terminated thiol chemisorbed to gold2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 33, p. 16040-16046Article in journal (Refereed)

Monolayers of tert-butyl carbamate-terminated thiol were formed by adsorption of the molecules onto polycrystalline gold substrate. The adsorbates were studied using techniques as X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and infrared reflection−absorption spectroscopy (IRAS). The results provide the electronic structure, composition, characteristic fingerprint, and orientation of the molecular adsorbate. XPS verified that the thiolate group is chemically bonded to the gold surface and that a complete chemisorption of the molecule occurs. Elemental depth profiling by varying the excitation energy in XPS supports the angle-dependent XPS results. Both techniques showed that the tert-butyl group is oriented away from the gold surface. A nearly parallel orientation of the carbonyl group relative to the gold surface is deduced from the IRAS results. The main molecular axis is estimated to have an average tilt angle of about 38° relative to the gold surface normal on the basis of the NEXAFS results. Cyclic voltammetry indicates a less blocking capability of the adsorbates. Overall, the molecules are oriented in an upright manner with indications of presence of pinholes and/or defects possibly due to steric hindrance of the bulky tert-butyl group. This molecular system is envisioned to be of use for surface-based organic synthesis on gold substrates.

• 32.
Rhein Westfal TH Aachen.
Rhein Westfal TH Aachen. Uppsala University.
Thin film growth related adsorption study of Al and O ions on an alpha-Al2O3 surface2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 50, p. 19320-19324Article in journal (Refereed)

The surface reactivity of alpha-Al2O3 (0001) has been investigated theoretically using density functional theory. The adsorption process of Al+, Al2+, Al3+, and O+ were studied to identify possible preferential adsorption sites during thin film growth. Differences in near surface atomic displacements (e.g., adsorption-induced surface reconstructions), energies, and bonding character have been evaluated. The adsorption energies for the metallic ions showed a strong dependence on both initial charge and adsorption site. The O+ ions showed no site dependence, but adsorption energies similar to those calculated for Al+. The results indicate that the adsorption of O+ and Al3+ may favor the formation of an amorphous structure, which is consistent with experimental observations. The results are of fundamental importance for the understanding of thin film microstructure evolution.

• 33. Rotomskis, R
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
Hierarchical structure of TPPS4 J-aggregates on substrate revealed by atomic force microscopy2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 9, p. 2833-2838Article in journal (Refereed)

The spatial structure of the J-aggregates of meso-tetra(4-sulfonatophenyl)porphine (TPPS4) formed in acidic aqueous solutions and coated on silicon substrates was analyzed by means of atomic force microscopy (AFM). The AFM experiments indicate the presence of the stripelike J-aggregate structures on the surface. The size of the individual stripes ranged from 4.5 x 40 x 200 to 4.5 x 40 x 1000 nm(3) (height x width x length). The length of the stripelike structures varied, whereas stripe width and thickness remained unchanged. The stripes stacked into larger domains, "fibers", containing typically 2-20 stripes aligned parallel with a longitudinal shift with respect to each other. The size of individual stripes remained the same when interacting side-by-side in fibers. At lower magnification it is clearly seen that fibers form a network-like structure. The J-aggregates assemble into large (up to several millimeters) bushlike structures. It takes several weeks to form such structures in acidic aqueous solutions. On the basis of our experimental findings, it is also suggested that the stripes consist of rings that form nanotube-like TPPS4 J-aggregates, which are flattened as a result of attractive interactions with the substrate.

• 34.
Sánchez-Carrera, R.S., School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400. Da Silva Filho, D.A., School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry . Brédas, J.-L., School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400.
Vibronic coupling in the ground and excited states of oligoacene cations2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 38, p. 18904-18911Article in journal (Refereed)

The vibrational coupling in the ground and excited states of positively charged naphthalene, anthracene, tetracene, and pentacene molecules is studied on the basis of a joint experimental and theoretical study of ionization spectra using high-resolution gas-phase photoelectron spectroscopy and first-principles correlated quantum-mechanical calculations. Our theoretical and experimental results reveal that, while the main contribution to relaxation energy in the ground state of oligoacene systems comes from high-energy vibrations, the excited-state relaxation energies show a significant redistribution toward lower-frequency vibrations. A direct correlation is found between the nature of the vibronic interaction and the pattern of the electronic state structure. © 2006 American Chemical Society.

• 35. Sancho-Garcia, JC
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry .
Joint theoretical and experimental characterization of the structural and electronic properties of poly(dioctylfluorene-alt-N-butylphenyl diphenylamine)2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 18, p. 5594-5599Article in journal (Refereed)

Fluorene-based copolymers are currently attracting considerable interest for use in a wide range of optoelectronic devices. Here, we present the results of a joint quantum-chemical and experimental characterization of the structural, electronic, and optical properties of an alternating fluorene-triphenylamine copolymer. We compare the results from this study with those from similar studies of polyfluorene. Although calculations are performed for the gas phase and experiments are performed on the solid state, the results from the two methodologies are in good agreement: the relevant electronic levels, HOMO and LUMO, of polyfluorene are found to be destabilized by incorporation of triphenylamine units in the conjugated backbone, whereas the optical properties of polyfluorene chains are largely unperturbed by the presence of triphenylamine.

• 36.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
pH Dependence of γ-Aminobutyric Acid Iontronic Transport2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 30, p. 7284-7289Article in journal (Refereed)

The organic electronic ion pump (OEIP) has been developed as an “iontronic” tool for delivery of biological signaling compounds. OEIPs rely on electrophoretically “pumping” charged compounds, either at neutral or shifted pH, through an ion-selective channel. Significant shifts in pH lead to an abundance of H+ or OH–, which are delivered along with the intended substance. While this method has been used to transport various neurotransmitters, the role of pH has not been explored. Here we present an investigation of the role of pH on OEIP transport efficiency using the neurotransmitter γ-aminobutyric acid (GABA) as the model cationic delivery substance. GABA transport is evaluated at various pHs using electrical and chemical characterization and compared to molecular dynamics simulations, all of which agree that pH 3 is ideal for GABA transport. These results demonstrate a useful method for optimizing transport of other substances and thus broadening OEIP applications.

The full text will be freely available from 2018-07-25 12:32
• 37.
University of Siena, Italy .
Uppsala University, Sweden.
Excited-state modeling of the astaxanthin dimer predicts a minor contribution from exciton coupling to the bathochromic shift in crustacyanin2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 15, p. 5311-5317Article in journal (Refereed)

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

• 38.
Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Hungary, Budapest.
Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Hungary, Budapest. Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös Loránd University, H-1518 Budapest, Hungary. Dipartimento di Scienze Farmaceutiche and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy. Dipartimento di Scienze Farmaceutiche and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy. Dipartimento di Scienze Farmaceutiche and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy. Department of Chemistry, University of Namur (FUNDP), Rue de Bruxelles 61, 5000 Namur, Belgium. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology. Surface Science Research Centre, University of Liverpool, UK. Surface Science Research Centre, University of Liverpool, UK.
Melting of Hydrogen Bonds in Uracil Derivatives Probed by Infrared Spectroscopy and ab Initio Molecular Dynamics2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 15, p. 4626-4633Article in journal (Refereed)

The thermal response of hydrogen bonds is a crucial aspect in the self-assembly of molecular nanostructures. To gain a detailed understanding of their response, we investigated infrared spectra of monomers and hydrogen-bonded dimers of two uracil-derivative molecules, supported by density functional theory calculations. Matrix isolation spectra of monomers, temperature dependence in the solid state, and ab initio molecular dynamics calculations give a comprehensive picture about the dimer structure and dynamics of such systems as well as a proper assignment of hydrogen-bond affected bands. The evolution of the hydrogen bond melting is followed by calculating the C═O···H–N distance distributions at different temperatures. The result of this calculation yields excellent agreement with the H-bond melting temperature observed by experiment.

• 39.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Metal ion interaction with phosphorylated tyrosine analogue monolayers on gold2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 46, p. 23410-23416Article in journal (Refereed)

Phosphorylated tyrosine analogue molecules (pTyr-PT) were assembled onto gold substrates, and the resulting monolayers were used for metal ion interaction studies. The monolayers were characterized by X-ray photoelectron spectroscopy (XPS), infrared reflection−absorption spectroscopy (IRAS), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS), both prior to and after exposure to metal ions. XPS verified the elemental composition of the molecular adsorbate and the presence of metal ions coordinated to the phosphate groups. Both the angle-dependent XPS and IRAS results were consistent with the change in the structural orientation of the pTyr-PT monolayer upon exposure to metal ions. The differential capacitance of the monolayers upon coordination of the metal ions was evaluated using EIS. These metal ions were found to significantly change the capacitance of the pTyr-PT monolayers in contrast to the nonphosphorylated tyrosine analogue (TPT). CV results showed reduced electrochemical blocking capabilities of the phosphorylated analogue monolayer when exposed to metal ions, supporting the change in the structure of the monolayer observed by XPS and IRAS. The largest change in the structure and interfacial capacitance was observed for aluminum ions, compared to calcium, magnesium, and chromium ions. This type of monolayer shows an excellent capability to coordinate metal ions and has a high potential for use as sensing layers in biochip applications to monitor the presence of metal ions.

• 40.
Competence Center for Catalysis Chalmers University.
Competence Center for Catalysis Chalmers University. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Applied Physics . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Applied Physics . Competence Center for Catalysis Chalmers University.
Vibrational analysis of H2 and D2 adsorption on Pt/SiO22005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, p. 9581-9588Article in journal (Refereed)
• 41.
Department of Physics, University of Uppsala, Box 530, S-751 21 Uppsala, Sweden.
Department of Physics, University of Uppsala, Box 530, S-751 21 Uppsala, Sweden. Department of Physics, University of Uppsala, Box 530, S-751 21 Uppsala, Sweden. Department of Physical Chemistry, University of Uppsala, Box 532, S-751 21 Uppsala, Sweden. Department of Physical Chemistry, University of Uppsala, Box 532, S-751 21 Uppsala. Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry . Department of Quantum Chemistry, University of Uppsala, Box 518, S-751 21 Uppsala, Sweden.
PES Studies of Ru(dcbpyH2)2(NCS)2 Adsorption on Nanostructured ZnO for Solar Cell Applications2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 39, p. 10102-10107Article in journal (Refereed)

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

• 42.
Department of Polymer Technology, Royal Institute of Technology, Stockholm, Sweden.
Physics Department, Chalmers University of Technology, Göteborg, Sweden. Department of Polymer Technology, Royal Institute of Technology, Stockholm, Sweden. Department of Polymer Technology, Royal Institute of Technology, Stockholm, Sweden. Department of Polymer Technology, Royal Institute of Technology, Stockholm, Sweden. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Health Sciences. National Defence Research Establishment, Linköping, Sweden.
Improved thermal stability of pyroelectric polymers by crosslinking of ferroelectric liquid crystals2001In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 105, no 42, p. 10223-10227Article in journal (Refereed)

Monofunctional ferroelectric liquid crystalline monomers and a blend of monofunctional/bifunctional ferroelectric liquid crystalline monomers were photopolymerized, yielding a side-chain liquid crystalline polymer and a cross-linked polymer, respectively. The cross-linked polymer exhibited higher thermal stability than the side-chain liquid crystalline polymer and was pyroelectric up to 170 °C, whereas the side-chain liquid crystalline polymer lost most of its pyroelectricity at 38 °C. It is shown by electrooptic and birefringence measurements that cross-linking in the unwound SmC* phase prevented the reoccurrence of the helical superstructure.

• 43.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
Structure and desorption energetics of ultrathin D2O ice overlay ers on serine- And serinephosphate-terminated self-assembled monolayers2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 4, p. 1695-1700Article in journal (Refereed)

This paper reports on the structure and desorption dynamics of thin D 2O ice overlayers (0.2-10 monolayers) deposited on serine- and serinephosphate- (with H+, Na+, Ca2+ counterions) terminated self-assembled monolayers (SAMs). The D2O ice overlayers are deposited on the SAMs at ~85 K in ultrahigh vacuum and characterized with infrared reflection absorption spectroscopy (IRAS). Reflection absorption (RA) spectra obtained at sub-monolayer D2O coverage reveal that surface modes, e.g. free dangling OD stretch, dominate on the serine SAM surface, whereas vibrational modes characteristic for bulk ice are more prominent on the serinephosphate SAMs. Temperature programmed desorption mass spectrometry (TPD-MS) and TPD-IRAS are subsequently used to investigate the energetics and the structural transitions occurring in the ice overlayer during temperature ramping. D2O ice (~2.5 monolayers) on the serine SAMs undergoes a gradual change from an amorphous- to a crystalline-like phase upon increasing the substrate temperature. This transition is not as pronounced on the serine phosphate SAM most likely because of reduced mobility due to strong pinning to the surface. We show also that the energy of desorption for a sub-monolayer of D2O ice on serinephosphate SAM surfaces with a Na+ and Ca2+ counterions is equally high or even exceeds previously reported values for analogous high-energy SAMs. © 2006 American Chemical Society.

• 44.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Department of Chemistry, Center for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208. Department of Chemistry, Center for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208.
On the structure and desorption dynamics of DNA bases adsorbed on gold: A temperature-programmed study2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 31, p. 15150-15160Article in journal (Refereed)

The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption spectroscopy (TPD-IRAS) and temperature-programmed desorption-mass spectroscopy (TPD-MS). It is shown that the pyrimidines, adenine and guanine, adsorb to gold in a complex manner and that both adhesive (adenine) and cohesive (guanine) interactions contribute the apparent binding energies to the substrate surface. Adenine displays at least two adsorption sites, including a high-energy site (210°C, ~136 kj/mol), wherein the molecule coordinates to the gold substrate via the NH2 group in an sp3-like, strongly perturbed, nonplanar configuration. The purines, cytosine and thymine, display a less complicated adsorption/desorption behavior. The desorption energy for cytosine (160°C, ~122 kJ/mol) is similar to those obtained for adenine and guanine, but desorption occurs from a single site of dispersed, nonaggregated cytosine. Thymine desorbs also from a single site but at a significantly lower energy (100°C, ~104 kJ/mol). Infrared data reveal that the monolayer architectures discussed herein are structurally very different from those observed for the bases in the bulk crystalline state. It is also evident that both pyrimidines and purines adsorb on gold with the plane of the molecule in a nonparallel orientation with respect to the substrate surface. The results of this work are discussed in the context of improving the understanding of the design of capturing oligonucleotides or DNA strands for bioanalytical applications, in particular, for gold nanoparticle-based assays. © 2005 American Chemical Society.

• 45.
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Department of Chemistry and Materials Science, Pennsylvania State University, University Park, PA 16802. Department of Chemistry and Materials Science, Pennsylvania State University, University Park, PA 16802.
Ice nucleation and phase behavior on oligo(ethylene glycol) and hydroxyl self-assembled monolayers: Simulations and experiments2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 4, p. 1830-1836Article in journal (Refereed)

The nucleation and phase behavior of ultrathin D2O-ice overlayers have been studied on oligo(ethylene glycol) (OEG)-terminated and hydroxyl self-assembled monolayers (SAMs) at low temperatures in ultrahigh vacuum. Infrared reflection-absorption spectroscopy (IRAS) is used to characterize the ice overlayers, the SAMs, and the interactions occurring between the ice and the SAM surfaces. Spectral simulations, based on optical models in conjunction with Maxwell Garnett effective medium theory, point out the importance of including voids in the modeling of the ice structures, with void fractions reaching 60% in some overlayers. The kinetics of the phase transition from amorphous-like to crystalline-like ice upon isothermal annealing at 140 K is found to depend on the conformational state of the supporting OEG SAM surface. The rate is fast on the helical OEG SAMs and slow on the corresponding all-trans SAMs. This difference in kinetics is most likely due to a pronounced D2O interpenetration and binding to the all-trans segments of the ethylene glycol portion of the SAM. No such penetration and binding was observed on the helical OEG SAM. © 2006 American Chemical Society.

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