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  • 1.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Adsorption of large hydrocarbons on coinage metals: a van der Waals density functional study2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 13, p. 2851-2858Article in journal (Refereed)
    Abstract [en]

    The adsorption of organic molecules onto the close-packed facets of coinage metals is studied, and how accurately adsorption heights can be described by using recent advances of the van der Waals density functional (vdWDF), with optPBE/vdWDF, optB86b/vdWDF, vdWDF2, and rev/vdWDF2 functionals is illustrated. The adsorption of two prototypical aromatic hydrocarbons is investigated, and the calculated adsorption heights are compared to experimental literature values from normal incident X-ray standing wave absorption and a state-of-the-art semi-empirical method. It is shown that both the optB86b/vdWDF and rev/vdWDF2 functionals describe adsorption heights with an accuracy of 0.1 Å, compared to experimental values, and are concluded as reliable methods of choice for related systems.

  • 2.
    Blaudeck, Thomas
    et al.
    Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
    Zenkevich, Eduard I
    Technical University of Chemnitz.
    Abdel-Mottaleb, Mohamed
    Technical University of Chemnitz.
    Szwaykowska, Klementyna
    Technical University of Chemnitz.
    Kowerko, Danny
    Technical University of Chemnitz.
    Cichos, Frank
    Technical University of Chemnitz.
    von Borczyskowski, Christian
    Technical University of Chemnitz.
    Formation Principles and Ligand Dynamics of Nanoassemblies of CdSe Quantum Dots and Functionalised Dye Molecules2012In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 13, no 4, p. 959-972Article in journal (Refereed)
    Abstract [en]

    Functional dye molecules, such as porphyrins, attached to CdSe quantum dots (QDs) through anchoring meso-pyridyl substituents, form quasi-stable nanoassemblies. This fact results in photoluminescence (PL) quenching of the QDs both due to Forster resonance energy transfer (FRET) and the formation of non-radiative surface states under conditions of quantum confinement (non-FRET). The formation process is in competition with the ligand dynamics. At least two timescales are found for the formation of the assemblies: 1) one faster than 60 s attributed to saturation of empty attachment sites and 2) one slower than 600 s, which is attributed to a reorganisation of the tri-n-octylphosphine oxide (TOPO) ligand shell. Finally, this process results in almost complete exchange of the TOPO shell by porphyrin dye molecules. Following a SternVolmer analysis, we established a microscopic description of PL quenching and assembly formation. Based on this formalism, we determined the equilibrium constant for assembly formation between QDs and the pyridyl-functionalised dye molecules to be K approximate to 10(5)-10(7) M-1, which is several orders of magnitude larger than that of the TOPO ligands. Our results give additional insights into the non-FRET PL quenching processes involved and show that the QD surface is inhomogeneous with respect to the involved attachment and detachment processes. In comparison with other methods, such as NMR spectroscopy, the advantage of our approach is that ligand dynamics can be investigated at extremely low ratios of dye molecules to QDs.

  • 3.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Steric Effects Govern the Photoactivation of Phytochromes2016In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 17, no 7, p. 954-957Article in journal (Refereed)
    Abstract [en]

    Phytochromes constitute a superfamily of photoreceptor proteins existing in two forms that absorb red (Pr) and far-red (Pfr) light. Although it is well-known that the conversion of Pr into Pfr (the biologically active form) is triggered by a ZE photoisomerization of the linear tetrapyrrole chromophore, direct evidence is scarce as to why this reaction always occurs at the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics calculations based on a high-resolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions render photoisomerizations at the AB and BC bridges much less probable than photoisomerization at the CD bridge.

  • 4.
    Gedefaw, Desta
    et al.
    Univ South Pacific, Fiji; Flinders Univ S Australia, Australia.
    Hedstrom, Svante
    Stockholm Univ, Sweden; Lund Univ, Sweden.
    Xia, Yuxin
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Persson, Petter
    Lund Univ, Sweden.
    Andersson, Mats R.
    Flinders Univ S Australia, Australia.
    Design, Synthesis and Computational Study of Fluorinated Quinoxaline-Oligothiophene-based Conjugated Polymers with Broad Spectral Coverage2018In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 19, no 24, p. 3393-3400Article in journal (Refereed)
    Abstract [en]

    Donor-acceptor (D-A) copolymers typically show two absorption peaks in the visible region, flanking a valley region of limited absorptivity. One strategy for more panchromatic light harvesting is to incorporate side-groups orthogonal to the polymer backbone, which enable 2D pi conjugation and can give rise to additional absorption peaks. Here we design and synthesize two D-A polymers which both carry a fluorinated quinoxaline acceptor unit, but while P1 includes a benzodithiophene donor moiety with thiophene side-groups (2D-BDT), the P2 polymer lacks 2D conjugation in its simpler pentathiophene donor segment. The P1 polymer consequently shows an atypical absorption profile with more panchromatic absorption with no apparent valley in the spectrum. In order to understand the structure-electronic relations, the optical and electrochemical properties were predicted using a previously developed computational approach. The predicted optical properties show very good agreement with the experimental results. Solar cells made from P1 show a short-circuit current more than twice as large as P2, attributed to its enhanced spectral coverage. However, poor fill factors limit the preliminary power conversion efficiencies to 3.3 % for P1 and 1.0 % for P2 as blended with PCBM[70] in a 1 : 1.5 (w/w) ratio.

  • 5.
    Greczynski, Grzegorz
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Hultman, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    C1s Peak of Adventitious Carbon Aligns to the Vacuum Level: Dire Consequences for Materials Bonding Assignment by Photoelectron Spectroscopy2017In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 18, no 12, p. 1507-1512Article in journal (Refereed)
    Abstract [en]

    The C1s signal from ubiquitous carbon contamination on samples forming during air exposure, so called adventitious carbon (AdC) layers, is the most common binding energy (BE) reference in X-ray photoelectron spectroscopy studies. We demonstrate here, by using a series of transition-metal nitride films with different AdC coverage, that the BE of the C1s peak E-B(F) varies by as much as 1.44 eV. This is a factor of 10 more than the typical resolvable difference between two chemical states of the same element, which makes BE referencing against the C1s peak highly unreliable. Surprisingly, we find that C1s shifts correlate to changes in sample work function phi(SA), such that the sum E-B(F) + phi(SA) is constant at 289.50 +/- 0.15 eV, irrespective of materials system and air exposure time, indicating vacuum level alignment. This discovery allows for significantly better accuracy of chemical state determination than offered by the conventional methods. Our findings are not specific to nitrides and likely apply to all systems in which charge transfer at the AdC/substrate interface is negligible.

  • 6.
    Li, Feng
    et al.
    Wageningen University.
    Palaniswamy, Ganesan
    Wageningen University.
    de Jong, Menno R.
    Biomade Technol Fdn.
    Åslund, Andreas
    Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry . Linköping University, The Institute of Technology.
    Konradsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry . Linköping University, The Institute of Technology.
    Marcelis, Antonius T. M.
    Wageningen University.
    Sudholter, Ernst J. R.
    Delft University of Technology.
    Cohen Stuart, Martien A.
    Wageningen University.
    Leermakers, Frans A. M.
    Wageningen University.
    Nanowires Formed by the Co-Assembly of a Negatively Charged Low-Molecular Weight Gelator and a Zwitterionic Polythiophene2010In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 11, no 9, p. 1956-1960Article in journal (Refereed)
    Abstract [en]

    Conjugated organic nanowires have been prepared by co-assembling a carboxylate containing low-molecular weight gelator (LMWG) and an amino acid substituted polythiophene derivative (PTT). Upon introducing the zwitterionic polyelectrolyte PTT to a basic molecular solution of the organogelator, the negative charges on the LMWG are compensated by the positive charges of the PTT. As a result, nanowires form through co-assembly. These nanowires are visualized by both transmission electron microscopy (TEM) and atomic force microscopy (AFM). Depending on the concentration and ratio of the components these nanowires can be micrometers long. These measurements further suggest that the aggregates adopt a helical conformation. The morphology of these nanowires are studied with fluorescent confocal laser scanning microscopy (CLSM). The interactions between LMWG and PTT are characterized by steady-state and time-resolved fluorescence spectroscopy studies. The steady-state spectra indicate that the backbone of the PTT adopts a more planar and more aggregated conformation when interacting with LMWG. The time-resolved fluorescence decay studies confirm this interpretation.

  • 7.
    Oruganti, Baswanth
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Wang, Jun
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Computational Insight to Improve the Thermal Isomerisation Performance of Overcrowded Alkene-Based Molecular Motors through Structural Redesign2016In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 17, no 21, p. 3399-3408Article in journal (Refereed)
    Abstract [en]

    Synthetic overcrowded alkene-based molecular motors achieve 360° unidirectional rotary motion of one motor half (rotator) relative to the other (stator) through sequential photochemical and thermal isomerisation steps. In order to facilitate and expand the use of these motors for various applications, it is important to investigate ways to increase the rates and efficiencies of the reactions governing the rotary motion. Here, we use computational methods to explore whether the thermal isomerisation performance of some of the fastest available motors of this type can be further improved by reducing the sizes of the motor halves. Presenting three new redesigned motors that combine an indanylidene rotator with a cyclohexadiene, pyran or thiopyran stator, we first use multiconfigurational quantum chemical methods to verify that the photoisomerisations of these motors sustain unidirectional rotary motion. Then, by performing density functional calculations, we identify both stepwise and concerted mechanisms for the thermal isomerisations of the motors and show that the rate-determining free-energy barriers of these processes are up to 25 kJ mol−1 smaller than those of the original motors. Furthermore, the thermal isomerisations of the redesigned motors proceed in fewer steps. Altogether, the results suggest that the redesigned motors are useful templates for improving the thermal isomerisation performance of existing overcrowded alkene-based motors.

  • 8.
    Palermo, V.
    et al.
    Istituto Per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale Delle Ricerche, via Gobetti 101, 40129 Bologna, Italy.
    Palma, M.
    Istituto Per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale Delle Ricerche, via Gobetti 101, 40129 Bologna, Italy, Nanochemistry Laboratory, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université Louis Pasteur, 8, allée Gaspard Monge, 67083 Strasbourg, France.
    Tomovic, Z.
    Tomovic, Ž., Max-Planck Institute for Polymer Research, Ackermannweg 10, 55124 Mainz, Germany.
    Watson, M.D.
    Max-Planck Institute for Polymer Research, Ackermannweg 10, 55124 Mainz, Germany, Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, United States.
    Friedlein, Rainer
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry .
    Mullen, K.
    Müllen, K., Max-Planck Institute for Polymer Research, Ackermannweg 10, 55124 Mainz, Germany.
    Samori, P.
    Samorì, P., Istituto Per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale Delle Ricerche, via Gobetti 101, 40129 Bologna, Italy, Nanochemistry Laboratory, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université Louis Pasteur, 8, allée Gaspard Monge, 67083 Strasbourg, France.
    Influence of molecular order on the local work function of nanographene architectures: A Kelvin-probe force microscopy study2005In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 6, no 11, p. 2371-2375Article in journal (Refereed)
    Abstract [en]

    We report a Kelvin-probe force microscopy (KPFM) investigation on the structural and electronic properties of different submicronscale supramolecular architectures of a synthetic nanographene, including extended layers, percolated networks and broken patterm grown from solutions at surfaces. This study made it possible to determine the local work function (WF) of the different p-conjugated nanostructures adsorbed on mica with a resolution below 10 nm and 0.05 eV. It revealed that the WF strongly depends on the local molecular order at the surface, in particular on the delocalization of electrons in the p-states, on the molecular orientation at surfaces, on the molecular packing density, on the presence of defects in the film and on the different conformations of the aliphatic peripheral chains that might cover the conjugated core. These results were confirmed by comparing the KPFM-estimated local WF of layers supported on mica, where the molecules are preferentially packed edge-on on the substrate, with the ultraviolet photoelectron spectroscopy microscopically measured WF of layers adsorbed on graphite, where the molecules should tend to assemble face-on at the surface. It appears that local WF studies are of paramount importance for understanding the electronic properties of active organic nanostructures, being therefore fundamental for the building of high-performance organic electronic devices, including field-effect transistors, light-emitting diodes and solar cells. © 2005 Wiley-VCH Verlag GmbH & Co. KGaA.

  • 9.
    Zhang, Jun
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Wang, Jun
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Sandberg, Alexander
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Wu, Xiongyu
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Nyström, Sofie
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    LeVine, Harry III
    Sanders-Brown Center on Aging, University of Kentucky, KY 40536-0230, Lexington, USA..
    Konradsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Hammarström, Per
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Lindgren, Mikael
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. Department of Physics, Norwegian University of Science and Technology, 7491, Trondheim, Norway..
    Intramolecular Proton and Charge Transfer of Pyrene-based trans-Stilbene Salicylic Acids Applied to Detection of Aggregated Proteins.2018In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 19, no 22, p. 3001-3009Article in journal (Refereed)
    Abstract [en]

    Two analogues to the fluorescent amyloid probe 2,5-bis(4'-hydroxy-3'-carboxy-styryl)benzene (X-34) were synthesized based on the trans-stilbene pyrene scaffold (Py1SA and Py2SA). The compounds show strikingly different emission spectra when bound to preformed Aβ1-42 fibrils. This remarkable emission difference is retained when bound to amyloid fibrils of four distinct proteins, suggesting a common binding configuration for each molecule. Density functional theory calculations show that Py1SA is twisted, while Py2SA is more planar. Still, an analysis of the highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs) of the two compounds indicates that the degree of electronic coupling between the pyrene and salicylic acid (SA) moieties is larger in Py1SA than in Py2SA. Excited state intramolecular proton transfer (ESIPT) coupled-charge transfer (ICT) was observed for the anionic form in polar solvents. We conclude that ICT properties of trans-stilbene derivatives can be utilized for amyloid probe design with large changes in emission spectra and decay times from analogous chemical structures depending on the detailed physical nature of the binding site.less thanbr /greater than (© 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim.)

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