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  • 1.
    Abramavicius, V.
    et al.
    Vilnius University, Lithuania; Centre Phys Science and Technology, Lithuania.
    Pranculis, V.
    Centre Phys Science and Technology, Lithuania.
    Melianas, Armantas
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Gulbinas, V.
    Centre Phys Science and Technology, Lithuania.
    Abramavicius, D.
    Vilnius University, Lithuania.
    Role of coherence and delocalization in photo-induced electron transfer at organic interfaces2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, no 32914Article in journal (Refereed)
    Abstract [en]

    Photo-induced charge transfer at molecular heterojunctions has gained particular interest due to the development of organic solar cells (OSC) based on blends of electron donating and accepting materials. While charge transfer between donor and acceptor molecules can be described by Marcus theory, additional carrier delocalization and coherent propagation might play the dominant role. Here, we describe ultrafast charge separation at the interface of a conjugated polymer and an aggregate of the fullerene derivative PCBM using the stochastic Schrodinger equation (SSE) and reveal the complex time evolution of electron transfer, mediated by electronic coherence and delocalization. By fitting the model to ultrafast charge separation experiments, we estimate the extent of electron delocalization and establish the transition from coherent electron propagation to incoherent hopping. Our results indicate that even a relatively weak coupling between PCBM molecules is sufficient to facilitate electron delocalization and efficient charge separation at organic interfaces.

  • 2.
    Adam, Stefan
    et al.
    Leibniz Institute Polymerforsch eV, Germany; Technical University of Dresden, Germany.
    Koenig, Meike
    Leibniz Institute Polymerforsch eV, Germany; Technical University of Dresden, Germany; Karlsruhe Institute Technology, Germany.
    Rodenhausen, Keith Brian
    University of Nebraska, NE 68588 USA; Biolin Science Inc, NJ 07652 USA.
    Eichhorn, Klaus-Jochen
    Leibniz Institute Polymerforsch eV, Germany.
    Oertel, Ulrich
    Leibniz Institute Polymerforsch eV, Germany.
    Schubert, Mathias
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering. Leibniz Institute Polymerforsch eV, Germany; University of Nebraska, NE 68588 USA; University of Nebraska, NE 68588 USA.
    Stamm, Manfred
    Leibniz Institute Polymerforsch eV, Germany; Technical University of Dresden, Germany.
    Uhlmann, Petra
    Leibniz Institute Polymerforsch eV, Germany; University of Nebraska, NE 68588 USA.
    Quartz crystal microbalance with coupled Spectroscopic Ellipsometry-study of temperature-responsive polymer brush systems2017In: Applied Surface Science, ISSN 0169-4332, E-ISSN 1873-5584, Vol. 421, p. 843-851Article in journal (Refereed)
    Abstract [en]

    Using a combined setup of quartz crystal microbalance with dissipation monitoring together with spectroscopic ellipsometry, the thermo-responsive behavior of two different brush systems (poly(N-isopropyl acrylamide) and poly(2-oxazoline)s) was investigated and compared to the behavior of the free polymer in solution. Poly(2-oxazoline)s with three different hydrophilicities were prepared by changing the content of a hydrophilic comonomer. While both polymer types exhibit a sharp, discontinuous thermal transition in solution, in the brush state the transition gets broader in the case of poly(N-isopropyl acrylamide) and is transformed into a continuous transition for poly(2-oxazoline)s. The position of the transition in solution is influenced by the degree of hydrophilicity of the poly(2-oxazoline). The difference in areal mass detected by quartz crystal microbalance and by spectroscopic ellipsometry, has been attributed to the chain segment density profile of the polymer brushes. Applying this density profile information, for poly(N-isopropyl acrylamide) two different swelling stages could be identified, while for poly(2-oxazoline) the transition between a parabolic and more step-wise profile is found continuous. The different swelling characteristics were attributed to the different miscibility behavior types, with the brush state acting similar to a crosslinked system. (C) 2017 Elsevier B.V. All rights reserved.

  • 3.
    Aleckovic, Ehlimana
    et al.
    Linköping University, Department of Physics, Chemistry and Biology.
    Andersson, Linnea
    Linköping University, Department of Physics, Chemistry and Biology.
    Chamoun, Sherley
    Linköping University, Department of Physics, Chemistry and Biology.
    Einarsson, Ellen
    Linköping University, Department of Physics, Chemistry and Biology.
    Ekstedt, Ebba
    Linköping University, Department of Physics, Chemistry and Biology.
    Eriksen, Emma
    Linköping University, Department of Physics, Chemistry and Biology.
    Madan-Andersson, Maria
    Linköping University, Department of Physics, Chemistry and Biology.
    Method Development for Determining the Stability of Heat Stable Proteins Combined with Biophysical Characterization of Human Calmodulin and the Disease Associated Variant D130G2016Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Calmodulin is a highly conserved calcium ion binding protein expressed in all eukaryotic species. The 149 amino acid residues in the primary structure are organized in seven α helices with the highly flexible central α helix connecting the two non-cooperative domains of calmodulin. Each domain contains two EF-hand motifs to which calcium ions bind in a cooperative manner, hence the binding of four calcium ions saturate one calmodulin molecule. In the cardiovascular area calmodulin is involved in the activation of cardiac muscle contraction, and mutations that arise in the genetic sequence of the protein often have severe consequences. One such consequential mutation that can arise brings about the replacement of the highly conserved aspartic acid with glycine at position 130 in the amino acid sequence. In this research, the thermal and chemical stability within the C domain of the D130G variant of human calmodulin was investigated using a new method only requiring circular dichroism spectroscopic measurements. Affinity studies within the C domain of the D130G variant of human calmodulin were performed using fluorescence spectroscopy, and the ligands chosen for this purpose were trifluoperazine and p- HTMI. All analytical experiments were performed with the C domain of wild type human calmodulin as a reference. From the new method, it was concluded that the C domain of the D130G variant of human calmodulin has a slightly decreased stability in terms of Tm and Cm values compared to the C domain of wild type human calmodulin. The affinity analyses indicated that neither trifluoperazine nor p-HTMI discriminates between the C domain of the D130G variant of human calmodulin and the C domain of wild type human calmodulin in terms of dissociation constants. The pivotal outcome from this research is that the new method is applicable for determination of the stability parameters Tm and Cm of heat stable proteins. 

  • 4.
    Aronsson, Christopher
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Tunable and modular assembly of polypeptides and polypeptide-hybrid biomaterials2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biomaterials are materials that are specifically designed to be in contact with biological systems and have for a long time been used in medicine. Examples of biomaterials range from sophisticated prostheses used for replacing outworn body parts to ordinary contact lenses. Currently it is possible to create biomaterials that can e.g. specifically interact with cells or respond to certain stimuli. Peptides, the shorter version of proteins, are excellent molecules for fabrication of such biomaterials. By following and developing design rules it is possible to obtain peptides that can self-assemble into well-defined nanostructures and biomaterials.

    The aim of this thesis is to create ”smart” and tunable biomaterials by molecular self-assembly using dimerizing –helical polypeptides. Two different, but structurally related, polypeptide-systems have been used in this thesis. The EKIV-polypeptide system was developed in this thesis and consists of four 28-residue polypeptides that can be mixed-and-matched to self-assemble into four different coiled coil heterodimers. The dissociation constant of the different heterodimers range from μM to < nM. Due to the large difference in affinities, the polypeptides are prone to thermodynamic social self-sorting. The JR-polypeptide system, on the other hand, consists of several 42-residue de novo designed helix-loop-helix polypeptides that can dimerize into four-helix bundles. In this work, primarily the glutamic acid-rich polypeptide JR2E has been explored as a component in supramolecular materials. Dimerization was induced by exposing the polypeptide to either Zn2+, acidic conditions or the complementary polypeptide JR2K.

    By conjugating JR2E to hyaluronic acid and the EKIV-polypeptides to star-shaped poly(ethylene glycol), respectively, highly tunable hydrogels that can be self-assembled in a modular fashion have been created. In addition, self-assembly of spherical superstructures has been investigated and were obtained by linking two thiol-modified JR2E polypeptides via a disulfide bridge in the loop region. ŒThe thesis also demonstrates that the polypeptides and the polypeptide-hybrids can be used for encapsulation and release of molecules and nanoparticles. In addition, some of the hydrogels have been explored for 3D cell culture. By using supramolecular interactions combined with bio-orthogonal covalent crosslinking reactions, hydrogels were obtained that enabled facile encapsulation of cells that retained high viability.

    The results of the work presented in this thesis show that dimerizing α–helical polypeptides can be used to create modular biomaterials with properties that can be tuned by specific molecular interactions. The modularity and the tunable properties of these smart biomaterials are conceptually very interesting andmake them useful in many emerging biomedical applications, such as 3D cell culture, cell therapy, and drug delivery

    .

    List of papers
    1. Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties
    Open this publication in new window or tab >>Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties
    Show others...
    2015 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, no 14063Article in journal (Refereed) Published
    Abstract [en]

    Coiled coils with defined assembly properties and dissociation constants are highly attractive components in synthetic biology and for fabrication of peptide-based hybrid nanomaterials and nanostructures. Complex assemblies based on multiple different peptides typically require orthogonal peptides obtained by negative design. Negative design does not necessarily exclude formation of undesired species and may eventually compromise the stability of the desired coiled coils. This work describe a set of four promiscuous 28-residue de novo designed peptides that heterodimerize and fold into parallel coiled coils. The peptides are non-orthogonal and can form four different heterodimers albeit with large differences in affinities. The peptides display dissociation constants for dimerization spanning from the micromolar to the picomolar range. The significant differences in affinities for dimerization make the peptides prone to thermodynamic social self-sorting as shown by thermal unfolding and fluorescence experiments, and confirmed by simulations. The peptides self-sort with high fidelity to form the two coiled coils with the highest and lowest affinities for heterodimerization. The possibility to exploit self-sorting of mutually complementary peptides could hence be a viable approach to guide the assembly of higher order architectures and a powerful strategy for fabrication of dynamic and tuneable nanostructured materials.

    Place, publisher, year, edition, pages
    NATURE PUBLISHING GROUP, 2015
    National Category
    Physical Sciences Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:liu:diva-121739 (URN)10.1038/srep14063 (DOI)000361177400001 ()26370878 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council (VR); Swedish Foundation for Strategic Research (SSF)

    Available from: 2015-10-06 Created: 2015-10-05 Last updated: 2017-12-01
    2. Tailoring Supramolecular Peptide-Poly(ethylene glycol) Hydrogels by Coiled Coil Self-Assembly and Self-Sorting
    Open this publication in new window or tab >>Tailoring Supramolecular Peptide-Poly(ethylene glycol) Hydrogels by Coiled Coil Self-Assembly and Self-Sorting
    2016 (English)In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 17, no 6, p. 2260-2267Article in journal (Refereed) Published
    Abstract [en]

    Physical hydrogels are extensively used in a wide range of biomedical applications. However, different applications require hydrogels with different mechanical and structural properties. Tailoring these properties demands exquisite control over the supramolecular peptides with different affinities for dimerization. Four different mechanical properties of hydrogels using de novo designed coiled coil interactions involved. Here we show that it is possible to control the nonorthogonal peptides, designed to fold into four different coiled coil heterodimers with dissociation constants spanning from mu M to pM, were conjugated to star-shaped 4-arm poly(ethylene glycol) (PEG). The different PEG-coiled coil conjugates self-assemble as a result of peptide heterodimerization. Different combinations of PEG peptide conjugates assemble into PEG peptide networks and hydrogels with distinctly different thermal stabilities, supramolecular, and rheological properties, reflecting the peptide dimer affinities. We also demonstrate that it is possible to rationally modulate the self-assembly process by means of thermodynamic self-sorting by sequential additions of nonpegylated peptides. The specific interactions involved in peptide dimerization thus provides means for programmable and reversible self-assembly of hydrogels with precise control over rheological properties, which can significantly facilitate optimization of their overall performance and adaption to different processing requirements and applications.

    Place, publisher, year, edition, pages
    AMER CHEMICAL SOC, 2016
    National Category
    Polymer Chemistry
    Identifiers
    urn:nbn:se:liu:diva-130135 (URN)10.1021/acs.biomac.6b00528 (DOI)000377924800038 ()27219681 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council [621-2011-4319]; Swedish Foundation for Strategic Research [ICA10-0002]; Linkoping University; Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University (Faculty Grant SFO-Mat-LiU) [2009 00971]

    Available from: 2016-07-12 Created: 2016-07-11 Last updated: 2017-11-28
    3. Zinc-Triggered Hierarchical Self-Assembly of Fibrous Helix-Loop-Helix Peptide Superstructures for Controlled Encapsulation and Release
    Open this publication in new window or tab >>Zinc-Triggered Hierarchical Self-Assembly of Fibrous Helix-Loop-Helix Peptide Superstructures for Controlled Encapsulation and Release
    2016 (English)In: Macromolecules, ISSN 0024-9297, E-ISSN 1520-5835, Vol. 49, no 18, p. 6997-7003Article in journal (Refereed) Published
    Abstract [en]

    We demonstrate a novel route for hierarchical self-assembly of sub-micrometer-sized peptide superstructures that respond to subtle changes in Zn2+ concentration. The self-assembly process is triggered by a specific folding-dependent coordination of Zn2+ by a de novo designed nonlinear helix-loop-helix peptide, resulting in a propagating fiber formation and formation of spherical superstructures. The superstructures further form larger assemblies that can be completely disassembled upon removal of Zn2+ or degradation of the nonlinear peptide. This flexible and reversible assembly strategy of the superstructures enables facile encapsulation of nanoparticles and drugs that can be released by means of different stimuli.

    Place, publisher, year, edition, pages
    AMER CHEMICAL SOC, 2016
    National Category
    Polymer Chemistry
    Identifiers
    urn:nbn:se:liu:diva-132215 (URN)10.1021/acs.macromol.6b01724 (DOI)000384399100030 ()
    Note

    Funding Agencies|Swedish Research Council [621-2011-4319]; Swedish Foundation for Strategic Research [ICA10-0002]; Linkoping University; Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University [2009 00971]

    Available from: 2016-10-26 Created: 2016-10-21 Last updated: 2017-11-29
  • 5.
    Arrigan, Damien
    et al.
    NMRC, University College, Cork, Ireland.
    Ghita, Mihaela
    University of Salford, UK.
    Beni, Valerio
    NMRC, University College, Cork, Ireland.
    Selective voltammetric detection of dopamine in the presence ofascorbate2004In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, no 6, p. 732-733Article in journal (Refereed)
    Abstract [en]

    The selective detection of dopamine in the presence of ascorbateis demonstrated based on the voltammetry of dopamine transferacross the interface between two immiscible electrolyte solutions(ITIES) facilitated by an organic-phase ionophore; ascorbatetransfer does not occur, leading to highly selectivedetection of dopamine in the presence of excess ascorbate.

  • 6.
    Ashaduzzaman, Md
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering. University of Dhaka, Bangladesh.
    Anto Antony, Aswathi
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Murugan, N. Arul
    Royal Institute Technology, Sweden.
    Deshpande, Swapneel R.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Turner, Anthony
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Tiwari, Ashutosh
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering. Tekidag AB, UCS, S-58330 Linkoping, Sweden.
    Studies on an on/off-switchable immunosensor for troponin T2015In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 73, p. 100-107Article in journal (Refereed)
    Abstract [en]

    Regeneration is a key goal in the design of immunosensors. In this study, we report the temperature-regulated interaction of N-isopropylacrylamide (PNIPAAm) functionalised cardiac troponin T (cTnT) with anti-cTnT. Covalently bonded PNIPAAm on an anti-cTnT bioelectrode showed on/off-switchability, regeneration capacity and temperature triggered sensitivity for cTnT. Above the lower critical solution temperature (LCST), PNIPAAm provides a liphophilic microenvironment with specific volume reduction at the bioelectrode surface, making available binding space for cTnT, and facilitating analyte recognition. Computational studies provide details about the structural changes occurring at the electrode above and below the LCST. Furthermore, free energies associated with the binding of cTnT with PNIPAAm at 25 (Delta G(coil)=-6.0 Kcal/mole) and 37 degrees C (Delta G(globular)=-41.0 kcal/mole) were calculated to elucidate the interaction and stability of the antigen-antibody complex. The responsiveness of such assemblies opens the way for miniaturised, smart immuno-technologies with built-in programmable interactions of antigen-antibody upon receiving stimuli.

  • 7.
    Ashaduzzaman, Md.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering. UCS, Institute Adv Mat, Teknikringen 4A,Mjardevi Science Pk, SE-58330 Linkoping, Sweden.
    Deshpande, Swapneel R.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering. UCS, Institute Adv Mat, Teknikringen 4A,Mjardevi Science Pk, SE-58330 Linkoping, Sweden.
    Arul Murugan, N.
    Royal Institute Technology, Sweden.
    Kumar Mishra, Yogendra
    University of Kiel, Germany.
    Turner, Anthony
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Tiwari, Ashutosh
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. UCS, Institute Adv Mat, Teknikringen 4A,Mjardevi Science Pk, SE-58330 Linkoping, Sweden; Vinoba Bhave Research Institute, India.
    On/off-switchable LSPR nano-immunoassay for troponin-T2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 44027Article in journal (Refereed)
    Abstract [en]

    Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature.

  • 8.
    Atakan, Aylin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Nanostructured Materials. Linköping University, Faculty of Science & Engineering.
    Erdtman, Edvin
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Mäkie, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Nanostructured Materials. Linköping University, Faculty of Science & Engineering.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Odén, Magnus
    Linköping University, Department of Physics, Chemistry and Biology, Nanostructured Materials. Linköping University, Faculty of Science & Engineering.
    Time evolution of the CO2 hydrogenation to fuels over Cu-Zr-SBA-15 catalysts2018In: Journal of Catalysis, ISSN 0021-9517, E-ISSN 1090-2694, Vol. 362, p. 55-64Article in journal (Refereed)
    Abstract [en]

    Time evolution of catalytic CO2 hydrogenation to methanol and dimethyl ether (DME) has been investigated in a high-temperature high-pressure reaction chamber where products accumulate over time. The employed catalysts are based on a nano-assembly composed of Cu nanoparticles infiltrated into a Zr doped SiOx mesoporous framework (SBA-15): Cu-Zr-SBA-15. The CO2 conversion was recorded as a function of time by gas chromatography-mass spectrometry (GC-MS) and the molecular activity on the catalyst’s surface was examined by diffuse reflectance in-situ Fourier transform infrared spectroscopy (DRIFTS). The experimental results showed that after 14 days a CO2 conversion of 25% to methanol and DME was reached when a DME selective catalyst was used which was also illustrated by thermodynamic equilibrium calculations. With higher Zr content in the catalyst, greater selectivity for methanol and a total 9.5% conversion to methanol and DME was observed, yielding also CO as an additional product. The time evolution profiles indicated that DME is formed directly from methoxy groups in this reaction system. Both DME and methanol selective systems show the thermodynamically highest possible conversion.

  • 9.
    Augusto Berrocal, Jose
    et al.
    Eindhoven University of Technology, Netherlands.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering. University of Limoges, France.
    Garcia-Iglesias, Miguel
    Eindhoven University of Technology, Netherlands.
    Gosens, Ronald P. J.
    Eindhoven University of Technology, Netherlands.
    Meijer, E. W.
    Eindhoven University of Technology, Netherlands.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Palmans, Anja R. A.
    Eindhoven University of Technology, Netherlands.
    Consequences of conformational flexibility in hydrogen-bond-driven self-assembly processes2016In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 52, no 72, p. 10870-10873Article in journal (Refereed)
    Abstract [en]

    We report the synthesis and self-assembly of chiral, conformationally flexible C-3-symmetrical trisamides. A strong Cotton effect is observed for the supramolecular polymers in linear alkanes but not in cyclic alkanes. MD simulations suggest 2:1 conformations of the amides within the aggregates in both types of solvents, but a chiral bias in only linear alkanes.

  • 10.
    Bantikassegn, W.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, Faculty of Science & Engineering.
    Dannetun, Per
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, Faculty of Science & Engineering.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, Faculty of Science & Engineering.
    Salaneck, William R.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Absence of Schottky barrier formation in junctions of Al and polypyrrole-polyelectrolyte polymer complexes1993In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 224, no 2, p. 232-236Article in journal (Refereed)
    Abstract [en]

    Thin films of conducting polypyrrole doped with large polymeric anions of polystyrene-sulphonate are electrochemically prepared to study the metal/polymer junctions. Aluminium and gold contacts are vacuum deposited to form metal/polymer/gold sandwich structures for current-voltage characterization. Photoelectron spectroscopy, using UV and X-ray photons, is carried out to investigate the possible causes of current limitation in the Al/PPy(PSS) junction.

  • 11.
    Bantikassegn, W.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Dannetun, Per
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Salaneck, William R.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Proceedings of the International Conference on Science and Technology of Synthetic Metals Electronic properties of polypyrrole (polystyrene-sulphonate)/metal junctions1993In: Synthetic metals, ISSN 0379-6779, E-ISSN 1879-3290, Vol. 55, no 1, p. 36-42Article in journal (Refereed)
    Abstract [en]

    The nature of polymer/metal interfaces is decisive for the operation of polymer based electronic devices. At such interfaces charge transport may be affected by barrier formation, or by formation of insulating interfaces of various types. We have prepared thin films of conducting polypyrrole doped with large polymeric anions of polystyrenesulphonate for studies in metal/polymer junctions. Aluminium and gold contacts are vacuum deposited to form metal/polymer/gold sandwich structures. The current-voltage characteristics show that the interface between polypyrrole and gold is ohmic with no current limitation. However, the aluminium/polypyrrole interface forms highly resistive and nonohmic contacts. Photoelectron spectroscopy using UV and X-ray photons reveals a decrease of the work function upon Al deposition, reactions between Al and the sulphonate anions, and immediate oxidation of the aluminium upon exposure to oxygen. These observations corroborate the interpretation that the current limitation found at Al/polypyrrole junctions is due to formation of insulating aluminium oxide, not excluding reactions between the metal and dopant. It is also pointed out that interfaces between reactive metals and polymers are prone to such oxide interface formation, considering the high diffusivity of oxygen in many polymers.

  • 12.
    Beek, WJE
    et al.
    Eindhoven University of Technology, Netherlands.
    Wienk, MM
    Eindhoven University of Technology, Netherlands.
    Kemerink, Martijn
    Eindhoven University of Technology, Netherlands.
    Yang, XN
    Eindhoven University of Technology, Netherlands.
    Janssen, RAJ
    Eindhoven University of Technology, Netherlands.
    Hybrid zinc oxide conjugated polymer bulk heterojunction solar cells2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 19, p. 9505-9516Article in journal (Refereed)
    Abstract [en]

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

  • 13.
    Bengtsson, Katarina
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, Faculty of Science & Engineering.
    Additive manufacturing methods and materials for electrokinetic systems2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Fabrication of miniaturized devices is usually time-consuming, costly, and the materials commonly used limit the structures that are possible to create. The techniques most often used to make microsystems involve multiple steps, where each step takes considerable time, and if only a few systems are to be made, the price per device becomes excessive. This thesis describes how a simple syringebased 3D-printer, in combination with an appropriate choice of materials, can reduce the delay between design and prototype and simplify fabrication of microsystems. This thesis suggest two types of materials that we propose be used in combination with 3D-printing to further develop microsystems for biology and biochemistry.

    Analytical applications in biology and biochemistry often contain electrodes, such as in gel electrophoresis. Faradaic (electrochemical) reactions have to occur at the metal electrodes to allow electron-to-ion transduction through an electrolyte-based system to drive a current when a potential is applied to the electrodes in an electrolyte-based system. These electrochemical reactions at the electrodes, such as water electrolysis, are usually problematic when miniaturizing devices and analytical systems. An alternative to metal electrodes can be electrochemicallyactive conducting polymers, e.g. poly(3,4-ethylenedioxythiophene) (PEDOT), which can be used to reduce electrolysis when driving a current through water-based systems. Paper 1 describes gel electrophoresis where the platinum electrodes were replaced with the conductive polymer PEDOT, without affecting the separation.

    Manufacturing and prototyping of microsystems can be simplified by using 3Dprinting in combination with a sacrificial material. A sacrificial template material can further simplify bottom-up manufacturing of more complicated forms such as protruding and overhanging structures. We showed in paper 2 that polyethylene glycol (PEG), in combination with a carbonate-based plasticizer, functions well as a 3D-printable sacrificial template material. PEG2000 with between 20 wt% and 30 wt% ethylene carbonate or propylene carbonate has properties advantageous for 3D-printing, such as shear-thinning rheology, mechanical and chemical stability, and easy dissolution in water.

    List of papers
    1. Conducting Polymer Electrodes for Gel Electrophoresis
    Open this publication in new window or tab >>Conducting Polymer Electrodes for Gel Electrophoresis
    2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 2, p. 0089416-Article in journal (Refereed) Published
    Abstract [en]

    In nearly all cases, electrophoresis in gels is driven via the electrolysis of water at the electrodes, where the process consumes water and produces electrochemical by-products. We have previously demonstrated that p-conjugated polymers such as poly(3,4-ethylenedioxythiophene) (PEDOT) can be placed between traditional metal electrodes and an electrolyte to mitigate electrolysis in liquid (capillary electroosmosis/electrophoresis) systems. In this report, we extend our previous result to gel electrophoresis, and show that electrodes containing PEDOT can be used with a commercial polyacrylamide gel electrophoresis system with minimal impact to the resulting gel image or the ionic transport measured during a separation.

    Place, publisher, year, edition, pages
    Public Library of Science, 2014
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-105901 (URN)10.1371/journal.pone.0089416 (DOI)000331711900141 ()
    Available from: 2014-04-14 Created: 2014-04-12 Last updated: 2017-12-05Bibliographically approved
    2. Plasticized polyethylene glycol as sacrificial support and template material for syringe-based 3D-printing
    Open this publication in new window or tab >>Plasticized polyethylene glycol as sacrificial support and template material for syringe-based 3D-printing
    2015 (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Syringe-based 3D-printing is a powerful additive manufacturing method for fabricating short runs (small volumes) of components from multiple materials with a wide range of viscosities. However, objects that are hollow or not in complete contact with the printer’s stage are difficult to fabricate. Using a sacrificial template as a supporting layer enables bottom-up construction of complex structures. Template materials based on polyethylene glycol (PEG) plasticized with organic carbonates to tune their rheological (shear-thinning) and thermal (crystallization) properties have been evaluated, including results from rheometry, differential scanning calorimetry, dissolution rate, chemical compatibility with  polydimethylsiloxane (PDMS), and general functionality in a syringe-based 3D-printer. A family of such blends yields material that is easily printed, is stable over time, is soluble in water, and can support other materials and larger structures without collapsing. These mixtures are proposed for use with other extrudable or mouldable materials to enable 3D-printed devices with complex unsupported geometries.

    Keywords
    3D-Printing, polyethylene glycol, organic carbonates, sacrificial template, extrusion
    National Category
    Physical Sciences Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-121250 (URN)
    Available from: 2015-09-10 Created: 2015-09-10 Last updated: 2015-09-10Bibliographically approved
  • 14.
    Bengtsson, Katarina
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, The Institute of Technology.
    Mindemark, Jonas
    Department of Chemistry – Ångström Laboratory, Uppsala University, Uppsala, Sweden.
    Brandell, Daniel
    Department of Chemistry – Ångström Laboratory, Uppsala University, Uppsala, Sweden.
    Robinson, Nathaniel D
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, The Institute of Technology.
    Plasticized polyethylene glycol as sacrificial support and template material for syringe-based 3D-printing2015Manuscript (preprint) (Other academic)
    Abstract [en]

    Syringe-based 3D-printing is a powerful additive manufacturing method for fabricating short runs (small volumes) of components from multiple materials with a wide range of viscosities. However, objects that are hollow or not in complete contact with the printer’s stage are difficult to fabricate. Using a sacrificial template as a supporting layer enables bottom-up construction of complex structures. Template materials based on polyethylene glycol (PEG) plasticized with organic carbonates to tune their rheological (shear-thinning) and thermal (crystallization) properties have been evaluated, including results from rheometry, differential scanning calorimetry, dissolution rate, chemical compatibility with  polydimethylsiloxane (PDMS), and general functionality in a syringe-based 3D-printer. A family of such blends yields material that is easily printed, is stable over time, is soluble in water, and can support other materials and larger structures without collapsing. These mixtures are proposed for use with other extrudable or mouldable materials to enable 3D-printed devices with complex unsupported geometries.

  • 15.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Formation mechanisms of covalent nanostructures from density functional theory2016In: Proceedings of International Workshop on On-Surface Synthesis, Cham: Springer, 2016, p. 269-287Conference paper (Refereed)
    Abstract [en]

    In this chapter, it is demonstrated how electronic structure calculations, with focus on density functional theory, can be used to gain insight about on-surface reactions. I first give a brief introduction to how density functional theory can be used to study reactions. The focus is then shifted to two different types of on-surface reactions, highlighting the theoretical work that has been performed to gain detailed atomistic insight into them. First, the state of the art of the theory behind on-surface Ullmann coupling is described. In this reaction, molecular building blocks dehalogenate, which enables them to covalently couple. The most crucial reaction parameters are identified—the diffusion and coupling barriers of surface-supported radicals—and the potential for theory to optimize these is discussed. We then concentrate on the homo-coupling between terminal alkynes, a rudimentarily different process where molecules initially couple before undergoing a dehydrogenation step. The theory of the mechanism behind this coupling strategy is less developed than that of the on-surface Ullmann coupling, where fundamental questions remain to be unraveled. For example, by the subtle change of substrate from Ag to Au, the on-surface alkyne chemistry is completely altered from the homo-coupling to a cyclodehydrogenation reaction for the same molecular building block, of which origin remains unknown. The main objective of the chapter is to give an impression of what kind of information theory can obtain about reaction on surface, as well as to motivate and inspire for future theoretical studies, which will be needed to turn on-surface synthesis into a more predictive discipline.

  • 16.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Reaction mechanisms for on-surface synthesis of covalent nanostructures2016In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 28, no 8, p. 083002-Article, review/survey (Refereed)
    Abstract [en]

    In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms.

  • 17.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Linköping University.
    Thermodynamics of an Electrocyclic Ring-Closure Reaction on Au(111)2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 38, p. 21716-21721Article in journal (Refereed)
    Abstract [en]

    We have computationally studied the effects of temperature on the reaction pathway of an electrocyclic ring-closure reaction on the Au(111) surface, particularly focusing on thermodynamic aspects of the reaction. The electrocyclic ring closure is accompanied by a series of dehydrogenation steps, and while it is found that temperature, in terms of vibrational entropy and enthalpy, has a reducing effect on most energy barriers, it does not alter the qualitative appreciation of the reaction kinetics. However, it is found that the way the abstracted hydrogen atoms are treated is crucial for the thermodynamics of the reaction. The overall reaction is highly endothermic but becomes thermodynamically favorable due to the entropy gain of the hydrogen byproducts, which desorb associatively from the surface as H2. The study provides new outlooks for the theoretical treatment of reactions related to on-surface synthesis, anticipated to be instructive for future studies.

  • 18.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hanke, Felix
    Accelrys, 334 Science Park, Cambridge, CB4 0WN, United Kingdom.
    Towards Design Rules for Covalent Nanostructures on Metal Surfaces2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 4, p. 928-934Article in journal (Refereed)
    Abstract [en]

    The covalent molecular assembly on metal surfaces is explored, outlining the different types of applicable reactions. Density functional calculations for on-surface reactions are shown to yield valuable insights into specific reaction mechanisms and trends across the periodic table. Finally, it is shown how design rules could be derived for nanostructures on metal surfaces.

  • 19.
    Björk, Jonas
    et al.
    University of Liverpool, UK.
    Hanke, Felix
    University of Liverpool, UK.
    Palma, Carlos-Andres
    University de Strasbourg, France.
    Samorì, Paolo
    University de Strasbourg, France.
    Cecchini, Marco
    University de Strasbourg, France.
    Persson, Mats
    University of Liverpool, UK.
    Adsorption of Aromatic and Anti-Aromatic Systems on Graphene through π−π Stacking2010In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 1, p. 3407-3412Article in journal (Refereed)
    Abstract [en]

    The adsorption of neutral (poly)-aromatic, antiaromatic, and more generally π-conjugated systems on graphene is studied as a prototypical case of π-π stacking. To account for dispersive interactions, we compare the recent van der Waals density functional (vdw-DF) with three semiempirical corrections to density functional theory and two empirical force fields. The adsorption energies of the molecules binding to graphene predicted by the vdw-DFwere found to be in excellent agreement with temperature desorption experiments reported in litera- ture,whereas the results of theremaining functionals andforce fields only preserve the correct trends. The comparison of the dispersive versus electrostatic contribu- tions to the total binding energies in the aromatic and antiaromatic systems suggests that π-π interactions can be regarded as being prevalently dispersive in nature at large separations, whereas close to the equilibrium bonding distance, it is a complex interplay between dispersive and electrostatic Coulombic interactions. Moreover our results surprisingly indicate that the magnitude of π-π interactions normalized both per number of total atoms and carbon atoms increases signifi- cantly with the relative number of hydrogen atoms in the studied systems.

  • 20.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hanke, Felix
    Surface Science Research Centre, University of Liverpool, UK.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Mechanisms of halogen-based covalent self-assembly on metal surfaces2013In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, no 15, p. 5768-5775Article in journal (Refereed)
    Abstract [en]

    We computationally study the reaction mechanisms of halogen-based covalent self-assembly, a major route for synthesizing molecular nanostructures and nanographenes on surfaces. Focusing on biphenyl as a small model system, we describe the dehalogenation, recombination, and diffusion processes. The kinetics of the different processes are also investigated, in particular how diffusion and coupling barriers affect recombination rates. Trends across the periodic table are derived from three commonly used close-packed (111) surfaces (Cu, Ag, and Au) and two halogens (Br and I). We show that the halogen atoms can poison the surface, thus hindering long-range ordering of the self-assembled structures. Finally, we present core-level shifts of the relevant carbon and halogen atoms, to provide reference data for reliably detecting self-assembly without the need for atomic-resolution scanning tunneling microscopy.

  • 21.
    Björk, Jonas
    et al.
    University of Liverpool, UK.
    Matena, Manfred
    University of Basel, Switzerland.
    Dyer, Matthew S.
    University of Liverpool, UK.
    Enache, Mihaela
    University of Basel, Switzerland.
    Lobo-Checa, Jorge
    University of Basel, Switzerland.
    Gade, Lutz H.
    University of Heidelberg, Germany.
    Jung, Thomas A.
    Paul-Scherrer-Institute, Villigen, Switzerland.
    Stöhr, Meike
    University of Basel, Switzerland.
    Persson, Mats
    University of Liverpool, UK.
    STM fingerprint of molecule-adatom interactions in a self-assembled metal-organic surface coordination network on Cu(111)2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, p. 8815-8821Article in journal (Refereed)
    Abstract [en]

    A novel approach of identifying metal atoms within a metal-organic surface coordination network using scanning tunnelling microscopy (STM) is presented. The Cu adatoms coordinated in the porous surface network of 1,3,8,10-tetraazaperopyrene (TAPP) molecules on a Cu(111) surface give rise to a characteristic electronic resonance in STM experiments. Using density functional theory calculations, we provide strong evidence that this resonance is a fingerprint of the interaction between the molecules and the Cu adatoms. We also show that the bonding of the Cu adatoms to the organic exodentate ligands is characterised by both the mixing of the nitrogen lone-pair orbitals of TAPP with states on the Cu adatoms and the partial filling of the lowest unoccupied molecular orbital (LUMO) of the TAPP molecule. Furthermore, the key interactions determining the surface unit cell of the network are discussed.

  • 22.
    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.

  • 23.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Zhang, Yi-Qi
    Technische Universität München, Garching, Germany.
    Klappenberger, Florian
    Technische Universität München, Garching, Germany.
    Barth, Johannes V.
    Technische Universität München, Garching, Germany.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Unraveling the Mechanism of the Covalent Coupling Between Terminal Alkynes on a Noble Metal2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 6, p. 3181-3187Article in journal (Refereed)
    Abstract [en]

    The mechanism of the newly reported route for surface-assisted covalent coupling of terminal alkynes on Ag(111) is unraveled by density functional theory based transition state calculations. We illustrate that the reaction path is fundamentally different from the classical coupling schemes in wet chemistry. It is initiated by the covalent coupling between two molecules instead of single-molecule dehydrogenation. The silver substrate is found to play an important role stabilizing the intermediate species by chemical bonds, although it is hardly active electronically in the actual coupling step. The dimer intermediate is concluded to undergo two subsequent dehydrogenation processes expected to be rate-limiting according to the comparatively large barriers, which origin is discussed.

  • 24.
    Borga, Magnus
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Dahlqvist, Leinhard Olof
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV). Östergötlands Läns Landsting, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics.
    Lundberg, Peter
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV). Östergötlands Läns Landsting, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics.
    Improvement in Magnetic Resonance Imaging Relating to Correction of Chemical Shift Artifact and Intensity Inhomogeneity2011Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    Present invention discloses systems and methods for improvement of magnetic resonance images. Correction of a chemical shift artefact in an image acquired from a magnetic resonance imaging system is obtained by a system and a method involving iterative - compensation for the misregistration effect in an image domain. Correction of an intensity inhomogeneity in such images is obtained by a system and a method involving locating voxels corresponding to pure adipose tissue and estimating correction field from these points.

  • 25.
    Bounechada, Djamela
    et al.
    Chalmers Institute of Technology, Gothenburg.
    Darmastuti, Zhafira
    Linköping University, Department of Physics, Chemistry and Biology, Applied Sensor Science. Linköping University, The Institute of Technology.
    Ojamae, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Andersson, Mike
    Linköping University, Department of Physics, Chemistry and Biology, Applied Sensor Science. Linköping University, The Institute of Technology.
    Lloyd Spetz, Anita
    Linköping University, Department of Physics, Chemistry and Biology, Applied Sensor Science. Linköping University, The Institute of Technology.
    Skoglundh, Magnus
    Competence Centre for Catalysis / Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
    Carlsson, P-A
    Competence Centre for Catalysis / Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
    Vibrational analysis of SO2 on Pt / SiO2 systemManuscript (preprint) (Other academic)
    Abstract [en]

    In situ diffuse reflectance infrared Fourier transformed spectroscopy was used to study the interactions of SOx species with Pt/SiO2 between 200 and 400°C, and for SO2 concentrations between 10 and 50 ppm, which represents a concentration range where MISFET sensors exhibit good responses. In parallel, first-principles calculations have been carried out to support the experimental interpretations. It was found that sulfate species were formed on the silica surface, accompanied with removal/rearrangement of silanol groups upon exposure to SO2. Both experimental and theoretical calculations also suggest that the surface species were only formed after SO2 oxidation to SO3 on the metal surface. These evidences support the idea of SO2 oxidation to SO3 as the first step in the process of sulfate formation, followed by spillover of SO3 to the oxide, and finally the formation of sulfate species on the hydroxyl positions on the oxide. The results also indicate that the sulfate formation on silica depends both on the temperature and the SO2 concentration. Furthermore, hydrogen exposure was shown to be efficient for sulfur removal from the silica surface.

  • 26.
    Bronner, Christopher
    et al.
    Heidelberg Univ, Phys Chem Inst, D-69120 Heidelberg, Germany ; Free Univ Berlin, Fachbereich Phys, D-14195 Berlin, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Tegeder, Petra
    Heidelberg Univ, Phys Chem Inst, D-69120 Heidelberg, Germany ; Free Univ Berlin, Fachbereich Phys, D-14195 Berlin, Germany.
    Tracking and removing Br during the on-surface synthesis of a graphene nanoribbon2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 1, p. 486-493Article in journal (Refereed)
    Abstract [en]

    The fabrication of graphene nanoribbons (GNRs) requires a high degree of precision due to the sensitivity of the electronic structure on the edge shape. Using Br-substituted molecular precursors, this atomic precision can be achieved in a thermally induced two-step reaction following Br dissociation on a Au(111) surface. Using DFT, we find evidence that the Br atoms are bound to the intermediate polyanthrylene chains. We employ temperature-programmed desorption to demonstrate the associative desorption of HBr and molecular hydrogen during the final cyclodehydrogenation step of the reaction. Both processes are found to have similar activation barriers. Furthermore, we are able to remove Br atoms from the polyanthrylene chains by providing molecular hydrogen. The subsequent formation of GNR via a cyclodehydrogenation demonstrates that Br does not influence this part of the overall reaction.

  • 27.
    Bur, Christian
    Linköping University, Department of Physics, Chemistry and Biology, Applied Sensor Science. Linköping University, The Institute of Technology. Department of Physics and Mechatronics Engineering, Lab for Measurement Technology, Saarland University, Saarbrücken, Germany.
    Selectivity Enhancement of Gas Sensitive Field Effect Transistors by Dynamic Operation2015Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Gas sensitive field effect transistors based on silicon carbide, SiC-FETs, have been applied to various applications mainly in the area of exhaust and combustion monitoring. So far, these sensors have normally been operated at constant temperatures and adaptations to specific applications have been done by material and transducer platform optimization.

    In this thesis, the methodology of dynamic operation for selectivity enhancement is systematically developed for SiC-FETs. Temperature cycling, which is well known for metal oxide gas sensors, is transferred to SiC-FETs. Additionally, gate bias modulation is introduced increasing the performance further.

    The multi-dimensional sensor data are evaluated by use of pattern recognition mainly based on multivariate statistics. Different strategies for feature selection, crossvalidation, and classification methods are studied.

    After developing the methodology of dynamic operation, i.e., applying the virtual multi-sensor approach on SiC-FETs, the concept is validated by two different case studies under laboratory conditions: Discrimination of typical exhaust gases and quantification of nitrogen oxides in a varying background is presented. Additionally, discrimination and quantification of volatile organic compounds in the low parts-perbillion range for indoor air quality applications is demonstrated. The selectivity of SiC-FETs is enhanced further by combining temperature and gate bias cycled operation. Stability is increased by extended training.

  • 28.
    Burakovsky, L.
    et al.
    Los Alamos National Lab, NM 87545 USA.
    Cawkwell, M. J.
    Los Alamos National Lab, NM 87545 USA.
    Preston, D. L.
    Los Alamos National Lab, NM 87545 USA.
    Errandonea, D.
    University of Valencia, Spain.
    Simak, Sergey
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Recent ab initio phase diagram studies: Iridium2017In: JOINT AIRAPT-25TH and EHPRG-53RD INTERNATIONAL CONFERENCE ON HIGH PRESSURE SCIENCE AND TECHNOLOGY, 2015, IOP PUBLISHING LTD , 2017, Vol. 950, article id UNSP 042021Conference paper (Refereed)
    Abstract [en]

    The phase diagram of iridium is investigated using the Z methodology in conjunction with the VASP ab initio molecular dynamics package. The Z methodology is a novel technique for phase diagram studies which combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. We compare our results to the available experimental data on iridium. We offer explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.

  • 29.
    Bushnell, Eric A. C.
    et al.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Erdtman, Edvin
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Llano, Jorge
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    Örebro universitet, Akademin för naturvetenskap och teknik; School of Chemistry, National University of Ireland, Galway, Ireland.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 5, p. 822-834Article in journal (Refereed)
    Abstract [en]

    In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.

  • 30.
    Bäcklund, Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Preparation and Application of Functionalized Protein Fibrils2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many proteins have an innate ability to self-assemble into fibrous structures known as amyloid fibrils. From a material science perspective, fibrils have several interesting characteristics, including a high stability, a distinct shape and tunable surface properties. Such structures can be given additional properties through functionalization by other compounds such as fluorophores. Combination of fibrils with a function yielding compound can be achieved in several ways. Covalent bond attachment is specific, but cumbersome. External surface adhesion is nonspecific, but simple. However, in addition, internal non-covalent functionalization is possible. In this thesis, particular emphasis is put on internal functionalization of fibrils; by co-grinding fibril forming proteins with a hydrophobic molecule, a protein-hydrophobic compound molecule composite can be created that retains the proteins innate ability to form fibrils. Subsequently formed fibrils will thus have the structural properties of the protein fibril as well as the properties of the incorporated compound. The functionalization procedures used throughout this thesis are applicable for a wide range of chromophores commonly used for organic electronics and photonics. The methods developed and the prepared materials are useful for applications within optoelectronics as well as biomedicine.

    Regardless of the methodology of functionalization, using functionalized fibrils in a controlled fashion for material design requires an intimate understanding of the formation process and knowledge of the tools available to control not only the formation but also any subsequent macroscale assembly of fibrils. The development and application of such tools are described in several of the papers included in this thesis. With the required knowledge in hand, the possible influence of fibrils on the functionalizing agents, and vice versa, can be probed. The characteristic traits of the functionalized fibril can be customized and the resulting material can be organized and steered towards a specific shape and form. This thesis describes how control over the process of formation, functionalization and organization of functionalized fibrils can be utilized to influence the hierarchical assembly of fibrils – ranging from spherical structures to  spirals; the function – fluorescent or conducting; and macroscopic properties – optical birefringence and specific arrangement of functionalized fibrils in the solid state. In conclusion, the use of amyloid fibrils in material science has great potential. Herein is presented a possible route towards a fully bottom up approach ranging from the nanoscale to the macroscale.

    List of papers
    1. Controlling Amyloid Fibril Formation by Partial Stirring
    Open this publication in new window or tab >>Controlling Amyloid Fibril Formation by Partial Stirring
    2016 (English)In: Biopolymers, ISSN 0006-3525, E-ISSN 1097-0282, Vol. 105, no 5, p. 249-259Article in journal (Refereed) Published
    Abstract [en]

    Many proteins undergoes self-assembly into fibrillar structures known as amyloid fibrils. During the self-assembly process related structures, known as spherulites, can be formed. Herein we report a facile method where the balance between amyloid fibrils and spherulites can be controlled by stirring of the reaction mixture during the initial stages of the self-assembly process. Moreover, we report how this methodology can be used to prepare non-covalently functionalized amyloid fibrils. By stirring the reaction mixture continuously or for a limited time during the lag phase the fibril length, and hence the propensity to form liquid crystalline phases, can be influenced. This phenomena is utilized by preparing films consisting of aligned protein fibrils incorporating the laser dye Nile red. The resulting films display polarized Nile red fluorescence.

    Place, publisher, year, edition, pages
    Wiley-Blackwell, 2016
    National Category
    Organic Chemistry Biomaterials Science
    Identifiers
    urn:nbn:se:liu:diva-121017 (URN)10.1002/bip.22803 (DOI)000371690100001 ()
    Note

    Funding agencies:  Swedish Government [2009-00971]; Knut and Alice Wallenberg foundation

    Vid tiden för disputation förelåg publikationen endast som manuskript

    Available from: 2015-09-02 Created: 2015-09-02 Last updated: 2017-12-04Bibliographically approved
    2. Amyloid fibrils as dispersing agents for oligothiophenes: control of photophysical properties through nanoscale templating and flow induced fibril alignment
    Open this publication in new window or tab >>Amyloid fibrils as dispersing agents for oligothiophenes: control of photophysical properties through nanoscale templating and flow induced fibril alignment
    Show others...
    2014 (English)In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 2, no 37, p. 7811-7822Article in journal (Refereed) Published
    Abstract [en]

    Herein we report that protein fibrils formed from aggregated proteins, so called amyloid fibrils, serve as an excellent dispersing agent for hydrophobic oligothiophenes such as alpha-sexithiophene (6T). Furthermore, the protein fibrils are capable of orienting 6T along the fibril long axis, as demonstrated by flow-aligned linear dichroism spectroscopy and polarized fluorescence microscopy. The materials are prepared by solid state mixing of 6T with a protein capable of self-assembly. This results in a water soluble composite material that upon heating in aqueous acid undergoes self-assembly into protein fibrils non-covalently functionalized with 6T, with a typical diameter of 5-10 nm and lengths in the micrometre range. The resulting aqueous fibril dispersions are a readily available source of oligothiophenes that can be processed from aqueous solvent, and we demonstrate the fabrication of macroscopic structures consisting of aligned 6T functionalized protein fibrils. Due to the fibril induced ordering of 6T these structures exhibit polarized light emission.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry, 2014
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-111311 (URN)10.1039/c4tc00692e (DOI)000341458000013 ()
    Note

    Funding Agencies|Swedish Research Council [20114324]; Swedish Strategic Research Foundation (SSF); Knut and Alice Wallenberg foundation through a Wallenberg Scholar grant; Chalmers Area of Advance in Nanoscience and Nanotechnology; Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University (Faculty Grant SFO-Mat-LiU) [2009-00971]

    Available from: 2014-10-14 Created: 2014-10-14 Last updated: 2017-12-05
    3. Development and Application of Methodology for Rapid Screening of Potential Amyloid Probes
    Open this publication in new window or tab >>Development and Application of Methodology for Rapid Screening of Potential Amyloid Probes
    2014 (English)In: ACS COMBINATORIAL SCIENCE, ISSN 2156-8952, Vol. 16, no 12, p. 721-729Article in journal (Refereed) Published
    Abstract [en]

    Herein, we demonstrate that it is possible to rapidly screen hydrophobic fluorescent aromatic molecules with regards to their properties as amyloid probes. By grinding the hydrophobic molecule with the amyloidogenic protein insulin, we obtained a water-soluble composite material. When this material is dissolved and exposed to conditions promoting amyloid formation, the protein aggregates into amyloid fibrils incorporating the hydrophobic molecule. As a result, changes in the fluorescence spectra of the hydrophobic molecule can be correlated to the formation of amyloid fibrils, and the suitability of the hydrophobic molecular skeleton as an amyloid probe can thus be assessed. As a result, we discovered two new amyloid probes, of which one is the well-known laser dye DCM. The grinding method can also be used for rapid preparation of novel composite materials between dyes and proteins, which can be used in materials science applications such as organic electronics and photonics.

    Place, publisher, year, edition, pages
    ACS Publications, 2014
    Keywords
    amyloid probes; rapid screening; fluorescent; aromatic molecules; laser dye DCM
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-113169 (URN)10.1021/co5001212 (DOI)000346114600009 ()25383488 (PubMedID)
    Note

    Funding Agencies|Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University [2009-00971]; Knut and Alice Wallenberg Foundation

    Available from: 2015-01-14 Created: 2015-01-12 Last updated: 2015-09-02
    4. Tuning the aqueous self-assembly process of insulin by a hydrophobic additive
    Open this publication in new window or tab >>Tuning the aqueous self-assembly process of insulin by a hydrophobic additive
    2015 (English)In: RSC ADVANCES, ISSN 2046-2069, Vol. 5, no 112, p. 92254-92262Article in journal (Refereed) Published
    Abstract [en]

    Biomolecular self-assembly is an efficient way of preparing soft-matter based materials. Herein we report a novel method, based on the use of insoluble additives in aqueous media, for influencing the self-assembly process. Due to their low solubility, the use of hydrophobic additives in aqueous media is problematic; however, by mixing the additive with the biomolecule in the solid state, prior to solvation, this problem can be circumvented. In the investigated self-assembly system, where bovine insulin self-assembles into spherical structures, the inclusion of the hydrophobic material α-sexithiophene (6T) results in significant changes in the self-assembly process. Under our reaction conditions, in the case of materials prepared from insulin-only the growth of spherulites typically stops at a diameter of 150μm. However, by adding 2 weight % of hydrophobic material, spherulite growth continues up to diameters in the mm-range. The spherulites incorporate 6T and are thus fluorescent. The method reported herein should be of interest to all scientists working in the field of self-assembly as the flexible materials preparation, based simply on co-grinding of commercially available materials, adds another option to influence the structure and properties of products formed by  self-assembly reactions.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry, 2015
    National Category
    Organic Chemistry Biomaterials Science
    Identifiers
    urn:nbn:se:liu:diva-121018 (URN)10.1039/c5ra16144d (DOI)000364032500040 ()
    Note

    Funding agencies: Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University (Faculty Grant SFO-Mat-LiU) [2009-00971]; Knut and Alice Wallenberg foundation

    Available from: 2015-09-02 Created: 2015-09-02 Last updated: 2015-12-03
    5. Convection Induced Air-Water Interface Assembly of Amyloid Fibrils
    Open this publication in new window or tab >>Convection Induced Air-Water Interface Assembly of Amyloid Fibrils
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    We report that hydrophobically modified amyloid fibrils form macroscopic films at the air-water interface. The hydrophobically modified fibrils are prepared in a two step process. First bovine insulin is ground with a hydrophobic compound. The resulting material is dissolved in acidic water and heated to induce assembly into fibrils incorporating the hydrophobic compounds. Upon dilution followed by asymmetric heating, resulting in convection flow, the fibrills form highly ordered films with thicknesses from 80 nm and up. The thickness of the film can be controlled by the fibril concentration and/or reaction time. The films contain anisotropic domains spanning several square centimeters. In addition, the films contains ordered assemblies of dyes that display emission of polarized light.

    National Category
    Organic Chemistry Biomaterials Science
    Identifiers
    urn:nbn:se:liu:diva-121019 (URN)
    Available from: 2015-09-02 Created: 2015-09-02 Last updated: 2015-09-02
    6. Protein nanowires with conductive properties
    Open this publication in new window or tab >>Protein nanowires with conductive properties
    Show others...
    2015 (English)In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 3, no 25, p. 6499-6504Article in journal (Refereed) Published
    Abstract [en]

    Herein we report on the investigation of self-assembled protein nanofibrils functionalized with metallic organic compounds. We have characterized the electronic behaviour of individual nanowires using conductive atomic force microscopy. In order to follow the self assembly process we have incorporated fluorescent molecules into the protein and used the energy transfer between the internalized dye and the metallic coating to probe the binding of the polyelectrolyte to the fibril.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry, 2015
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-120179 (URN)10.1039/c5tc00896d (DOI)000356529100010 ()
    Note

    Funding Agencies|Knut and Alice Wallenberg Foundation through a Wallenberg Scholar grant

    Available from: 2015-07-13 Created: 2015-07-13 Last updated: 2017-12-04
    7. PEDOT-S coated protein fibril microhelices
    Open this publication in new window or tab >>PEDOT-S coated protein fibril microhelices
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    We show here the preparation and characterization of micrometer sized conductive helices. We utilize protein fibrils as structural templates to create chiral helices with either right or left handed helicity. The helices are coated with the conductive polymer alkoxysulfonate poly(ethylenedioxythiophene) (PEDOT-S) to create micrometer sized conductive helices. The coating acts as a stabilizer for the template structure, facilitates the preparation of solid state films and shows significant conductivity. The helices have been investigated using Circular Dichroism (CD) and scanning electron microscopy (SEM) and the conductivity have been measured for solid state films.

    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:liu:diva-121020 (URN)
    Available from: 2015-09-02 Created: 2015-09-02 Last updated: 2015-09-02Bibliographically approved
  • 31.
    Börjesson, L.
    et al.
    Linköping University, Department of Neuroscience and Locomotion, Neurology. Linköping University, Faculty of Health Sciences.
    Stockhaus, J.
    Linköping University, Department of Neuroscience and Locomotion, Neurology. Linköping University, Faculty of Health Sciences.
    Gauffin, Helena
    Linköping University, Department of Neuroscience and Locomotion, Neurology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Local Health Care Services in Central Östergötland, Department of Neurology.
    Ragnehed, Mattias
    Linköping University, Department of Medicine and Care, Medical Radiology. Linköping University, Faculty of Health Sciences.
    Lundberg, Peter
    Linköping University, Department of Medicine and Care, Radiation Physics. Linköping University, Faculty of Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Söderfeldt, Birgitta
    Linköping University, Department of Neuroscience and Locomotion, Neurology. Linköping University, Faculty of Health Sciences.
    Comparison between fMRI and Wada test2004In: Epilepsia, ISSN 0013-9580, E-ISSN 1528-1167, Vol. 45, no Suppl. 3, p. 84-84Article in journal (Refereed)
    Abstract [en]

    Purpose: Language lateralisation in patients with epilepsy is more often atypical compared to a normal population. The Wada procedure for testing language and memory has some shortcomings; it is invasive and there is always a risk that the patient becomes too sedated, leading to difficulties in performing the tests. fMR1have shown promising results, showing good correlation to the Wadaprocedure concerning language-lateralisation. The aim of this studywas to investigate if fMRI could be used to determine which hemisphere was language dominant and compare the fMR1 results with the Wada-tests with a focus on patients with a complicated lateralisation.

    Method: 4 subjects were tested and they had a heterogeneous (I left handed, I ambidexter and 2 right handed) lateralisation and one had a severe dyslexia. A standard Wada procedure was used and compared with a fMRl investigation using a language paradigm.

    Results: The patients studied showed different language lateralisation patterns (2 left hemisphere and 2 bilateral). In two patients the two tests were fully concordant, in the others the fMRI showed a more bilateral pattern.

    Conclusion: fMR1 adds valuable information in the pre-surgical investigation for patients with a complex language lateralisation.

  • 32.
    Cheung, Kitt
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Lai, Kwok Kei
    Hong Kong Univ Sci and Technol, Peoples R China.
    Mak, Wing Cheung
    Linköping University, Department of Physics, Chemistry and Biology, Sensor and Actuator Systems. Linköping University, Faculty of Science & Engineering.
    Fabrication of Protein Microparticles and Microcapsules with Biomolecular Tools2018In: Zeitschrift fur physikalische Chemie (Munchen. 1991), ISSN 0942-9352, Vol. 232, no 5-6, p. 759-771Article in journal (Refereed)
    Abstract [en]

    Microparticles have attracted much attention for medical, analytical and biological applications. Calcium carbonate (CaCO3) templating method with the advantages of having narrow size distribution, controlled morphology and good biocompatibility that has been widely used for the synthesis of various protein-based microparticles. Despite CaCO3 template is biocompatible, most of the conventional methods to create stable protein microparticles are mainly driven by chemical crosslink reagents which may induce potential harmful effect and remains undesirable especially for biomedical or clinical applications. In this article, we demonstrate the fabrication of protein microparticles and microcapsules with an innovative method using biomolecular tools such as enzymes and affinity molecules to trigger the assembling of protein molecules within a porous CaCO3 template followed by a template removal step. We demonstrated the enzyme-assisted fabrication of collagen microparticles triggered by transglutaminase, as well as the affinity-assisted fabrication of BSA-biotin avidin microcapsules triggered by biotin-avidin affinity interaction, respectively. Based on the different protein assemble mechanisms, the collagen microparticles appeared as a solid-structured particles, while the BSA-biotin avidin microcapsules appeared as hollow-structured morphology. The fabrication procedures are simple and robust that allows producing protein microparticles or microcapsules under mild conditions at physiological pH and temperature. In addition, the microparticle morphologies, protein compositions and the assemble mechanisms were studied. Our technology provides a facile approach to design and fabricate protein microparticles and microcapsules that are useful in the area of biomaterials, pharmaceuticals and analytical chemistry.

  • 33.
    Cirera, Borja
    et al.
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain.
    Giménez-Agulló, Nelson
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Martínez-Peña, Francisco
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Martin-Jimenez, Alberto
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Rodriguez-Fernandez, Jonathan
    Departamento de F´ısica de la Materia Condensada, Universidad Auto´noma de Madrid, c/Francisco Toma´s y Valiente.
    Pizarro, Ana M.
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Otero, Roberto
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco, 28049 Madrid, Spain,Universidad Auto´noma de Madrid, c/Francisco Toma´s y Valiente.
    Gallego, José M.
    Instituto de Ciencia de Materiales de Madrid, c/ Sor Juana Ine´s de la Cruz 3, Cantoblanco,Madrid, Spain..
    Ballester, Pablo
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain/Catalan Institutionfor Research and Advanced Studies, Passeig Lluis Companys 23, Barcelona, Spain..
    Galan-Mascaros, José R.
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain/Catalan Institutionfor Research and Advanced Studies, Passeig Lluis Companys 23, Barcelona, Spain..
    Ecija, David
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco, Madrid, Spain.
    Thermal selectivity of intermolecular versus intramolecular reactions on surfaces2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, no 11002Article in journal (Refereed)
    Abstract [en]

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

  • 34.
    Crispin, Xavier
    et al.
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
    Kalinin, Sergei V.
    Oak Ridge National Lab, TN 37831 USA.
    Semiconducting Polymers: Probing the solid-liquid interface2017In: Nature Materials, ISSN 1476-1122, E-ISSN 1476-4660, Vol. 16, no 7, p. 704-705Article in journal (Refereed)
    Abstract [en]

    Exploring the minute mechanical deformations induced by electrical bias at the interface with electrolytes allows the identification of local crystallinity and distinguishing adsorption and intercalation of ions in electroactive polymers.

  • 35.
    Danielsson, Örjan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Li, Xun
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Janzén, Erik
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Pedersen, Henrik
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Forsberg, Urban
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    A model for carbon incorporation from trimethyl gallium in chemical vapor deposition of gallium nitride2016In: Journal of Materials Chemistry, ISSN 0959-9428, E-ISSN 1364-5501, Vol. 4, no 4, p. 863-871Article in journal (Refereed)
    Abstract [en]

    Gallium nitride (GaN) semiconductor material can become semi-insulating when doping with carbon. Semi-insulating buffer layers are utilized to prevent leakage currents in GaN high power devices. Carbon is inherently present during chemical vapor deposition (CVD) of GaN from the use of trimethyl gallium (TMGa) as precursor. TMGa decomposes in the gas phase, releasing its methyl groups, which could act as carbon source for doping. It is previously known that the carbon doping levels can be controlled by tuning the CVD process parameters, such as temperature, pressure and precursor flow rates. However, the mechanism for carbon incorporation from TMGa is not yet understood. In this paper, a model for predicting carbon incorporation from TMGa in GaN layers grown by CVD is proposed. The model is based on ab initio quantum chemical calculations of molecular adsorption and reaction energies. Using Computational Fluid Dynamics, with a chemical kinetic model for decomposition of the precursors and reactions in the gas phase, to calculate gas phase compositions at realistic process conditions, together with the proposed model, we obtain good correlations with measurements, for both carbon doping concentrations and growth rates, when varying the inlet NH3/TMGa ratio. When varying temperature (800 – 1050°C), the model overpredicts carbon doping concentrations at the lower temperatures, but predicts growth rates well, and the agreement with measured carbon doping concentrations is good above 1000°C.

  • 36.
    Danielsson, Örjan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Sukkaew, Pitsiri
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry. Linköping University, The Institute of Technology.
    Kordina, Olof
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Janzén, Erik
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Shortcomings of CVD modeling of SiC today2013In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 132, no 11, p. 1398-Article in journal (Refereed)
    Abstract [en]

    The active, epitaxial layers of silicon carbide (SiC) devices are grown by chemical vapor deposition (CVD), at temperatures above 1,600 °C, using silane and light hydrocarbons as precursors, diluted in hydrogen. A better understanding of the epitaxial growth process of SiC by CVD is crucial to improve CVD tools and optimize growth conditions. Through computational fluid dynamic (CFD) simulations, the process may be studied in great detail, giving insight to both flow characteristics, temperature gradients and distributions, and gas mixture composition and species concentrations throughout the whole CVD reactor. In this paper, some of the important parts where improvements are very much needed for accurate CFD simulations of the SiC CVD process to be accomplished are pointed out. First, the thermochemical properties of 30 species that are thought to be part of the gas-phase chemistry in the SiC CVD process are calculated by means of quantum-chemical computations based on ab initio theory and density functional theory. It is shown that completely different results are obtained in the CFD simulations, depending on which data are used for some molecules, and that this may lead to erroneous conclusions of the importance of certain species. Second, three different models for the gas-phase chemistry are compared, using three different hydrocarbon precursors. It is shown that the predicted gas-phase composition varies largely, depending on which model is used. Third, the surface reactions leading to the actual deposition are discussed. We suggest that hydrocarbon molecules in fact have a much higher surface reactivity with the SiC surface than previously accepted values.

  • 37.
    Dannetun, Per
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Boman, Magnus
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Salaneck, William R.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Lazzaroni, R.
    Service de Chimie des Matériaux Nouveaux, Département des Matériaux et Procédés, Université de Mons‐Hainaut, Belgium.
    Fredriksson, C.
    Service de Chimie des Matériaux Nouveaux, Département des Matériaux et Procédés, Université de Mons‐Hainaut, Belgium.
    Brédas, J. L.
    Service de Chimie des Matériaux Nouveaux, Département des Matériaux et Procédés, Université de Mons‐Hainaut, Belgium.
    Zamboni, R.
    Istituto di Spettroscopia Molecolare, CNR, Bologna, Italy.
    Taliani, C.
    Istituto di Spettroscopia Molecolare, CNR, Bologna, Italy.
    The chemical and electronic structure of the interface between aluminum and polythiophene semiconductors1993In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 99, no 1, p. 664-672Article in journal (Refereed)
    Abstract [en]

    We have investigated the chemical nature and the electronic structure of the interface between a low work function metal,aluminum, and a conjugated polymersemiconductor, polythiophene. We have studied the initial stages of the interface formation by depositing the metal onto the surface of a polymer film. Charge transfer processes between the metal and the polymer are analyzed using core‐level x‐ray photoelectron spectroscopy (XPS); the evolution upon metallization of the valence electronic levels directly related to the polymerelectronic structure is followed with ultraviolet photoelectron spectroscopy (UPS). With these techniques, we investigate the deposition of aluminum on two polythiophene systems (i) the alkyl‐substituted poly‐3‐octylthiophene and (ii) the α‐sexithiophene oligomer. The experimental data are compared to the results of a recent quantum chemical study on model systems consisting of thiophene oligomers (up to sexithiophene) interacting with a few Al atoms. The interaction of polythiophene with Al atoms is found to modify dramatically the structure of the conjugated backbone, as strong carbon–aluminum bonds are formed in the α positions of the thiophene rings. A large charge transfer takes place from the Al atoms to the polymer chain, and the upper π levels of the polymer are strongly affected. The metallization is contrasted to the doping of conjugated polymers with alkali metals

  • 38.
    Dannetun, Per
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Lögdlund, Michael
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Fahlman, Mats
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Boman, Magnus
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Salaneck, William R.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Lazzaroni, R.
    Service de Chimie des Matériaux Nouveaux, Université de Mons-Hainaut, Mons Belgium.
    Fredriksson, C.
    Service de Chimie des Matériaux Nouveaux, Université de Mons-Hainaut, Mons Belgium.
    Brédas, J. L.
    Service de Chimie des Matériaux Nouveaux, Université de Mons-Hainaut, Mons Belgium.
    Graham, S.
    Cavendish Laboratory, University of Cambridge, Cambridge, UK.
    Friend, R. H.
    Cavendish Laboratory, University of Cambridge, Cambridge, UK.
    Holmes, A. B.
    University Chemical Laboratory, Lensfield road, Cambridge, UK.
    Zamboni, R.
    Instituto di Spettroscopia Molecolare, Bologna, Italy.
    Taliani, C.
    Instituto di Spettroscopia Molecolare, Bologna, Italy.
    Proceedings of the International Conference on Science and Technology of Synthetic Metals The chemical and electronic structure of the interface between aluminum and conjugated polymers or molecules1993In: Synthetic metals, ISSN 0379-6779, E-ISSN 1879-3290, Vol. 55, no 1, p. 212-217Article in journal (Refereed)
    Abstract [en]

    The interaction between aluminum and α-ω-diphenyltetradecaheptaenee (DP7), α-sexithienyl (6T), and poly(p-phenylenevinylene) (PPV), respectively have been studied using both X-ray Photoelectron Spectroscopy (XPS) and Ultraviolet Photoelectron Spectroscopy (UPS). The UPS valence band spectra, are interpreted with the help of quantum chemical calculations based upon Modified Neglect of Diatomic Overlap (MNDO), Valence Effective Hamitonian (VEH) and ab initio Hartree-Fock methods. DP7 is a model molecule for polyacetylene, while 6T is a model molecule (an oligomer) of polythiophene. The results indicate that aluminum reacts strongly with the surfaces of all of the materials studied. The π-electronic structure of each material was strongly modified. Furthermore, aluminum reacts preferentially with the polyene partof DP7, with the vinylene part of PPV, and with the α-carbons of the thiophene nits of 6T.

  • 39.
    Darmastuti, Zhafira
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Applied Sensor Science. Linköping University, The Institute of Technology.
    Bounechada, Djamela
    Competence Centre for Catalysis / Dept. of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
    Carlsson, P-A
    Competence Centre for Catalysis / Dept. of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
    Lindqvist, N.
    Alstom Power AB, Växjö, Sweden.
    Andersson, Mike
    Linköping University, Department of Physics, Chemistry and Biology, Applied Sensor Science. Linköping University, The Institute of Technology.
    Skoglundh, Magnus
    Competence Centre for Catalysis / Dept. of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
    Carlsson, P-A
    Competence Centre for Catalysis /Dept. of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
    Lloyd Spetz, Anita
    Linköping University, Department of Physics, Chemistry and Biology, Applied Sensor Science. Linköping University, The Institute of Technology.
    Ojamae, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Detection mechanism studies of SO2 on Pt / SiO2 systemManuscript (preprint) (Other academic)
    Abstract [en]

    Experiment was performed with Pt-gate SiC-FET sensors to study the detection mechanism of the sensors. The sensing measurement showed that oxygen influenced the response quite strongly. The sensor response became larger in the presence of oxygen. Experiment with mass spectroscopy indicated the formation of SO3 during the sensing measurement. Further experiment with DRIFT spectroscopy showed the formation of sulfate species on the oxide surface, accompanied by the disappearance of the silanol groups. An explanatory model was built based on quantum-chemical calculations. The results strengthened the experimental results by showing that it was more energetically favorable for SO2 to oxidize into SO3 before being adsorbed on the oxide surface. It was also observed that the overall adsorption reaction was exothermic, the activation energy for the SO2 oxidation was 48,75 kJ/mol, and the rate limiting step was the desorption of SO3 from the Pt surface.

  • 40.
    D'Ercole, A
    et al.
    Unita INFM Torino, I-10125 Turin, Italy.
    Giamello, E
    Unita INFM Torino, I-10125 Turin, Italy.
    Pisani, C
    Unita INFM Torino, I-10125 Turin, Italy.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Embedded-cluster study of hydrogen interaction with an oxygen vacancy at the magnesium oxide surface1999In: JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1089-5647, Vol. 103, no 19, p. 3872-3876Article in journal (Refereed)
    Abstract [en]

    An embedded-cluster Hartree−Fock approximation is adopted for simulating the formation of Fs(H) color centers at the (001) surface of magnesium oxide. This process is assumed to take place in two steps at an isolated surface anion vacancy:  first, a hydrogen molecule is adsorbed dissociatively at the defect; second, following UV irradiation, a neutral hydrogen atom is removed and an electron remains trapped at the vacancy with a hydroxyl group nearby. According to the present calculations, the activation energy for the dissociation is appreciable (about 25 kcal/mol) and the products (a proton bound to a low-coordinated oxygen and a hydride ion above the vacancy) are considerably less stable than the reactants. The excitation of the adsorbed species owing to the UV irradiation is simulated by considering a singlet−triplet transition of the hydride−vacancy complex, which then dissociates into an H atom and a trapped lone electron. The electronic structure and the EPR parameters of the resulting paramagnetic state are explored. The theoretical results agree in many respects with the experimental data as concerns one of the forms of heterolitically dissociated hydrogen which are found at the defective MgO surface. However, from the viewpoint of the energetics, this model is untenable because that species is known to form irreversibly at room temperature with low activation energy.

  • 41.
    dos Santos, Renato B.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. University of Federal Bahia, Brazil.
    de Brito Mota, F.
    University of Federal Bahia, Brazil.
    Rivelino, R.
    University of Federal Bahia, Brazil.
    Kakanakova-Gueorguie, Anelia
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Gueorguiev, Gueorgui Kustov
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Van der Waals stacks of few-layer h-AlN with graphene: an ab initio study of structural, interaction and electronic properties2016In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 27, no 14, p. 145601-Article in journal (Refereed)
    Abstract [en]

    Graphite-like hexagonal AlN (h-AlN) multilayers have been experimentally manifested and theoretically modeled. The development of any functional electronics applications of h-AlN would most certainly require its integration with other layered materials, particularly graphene. Here, by employing vdW-corrected density functional theory calculations, we investigate structure, interaction energy, and electronic properties of van der Waals stacking sequences of few-layer h-AlN with graphene. We find that the presence of a template such as graphene induces enough interlayer charge separation in h-AlN, favoring a graphite-like stacking formation. We also find that the interface dipole, calculated per unit cell of the stacks, tends to increase with the number of stacked layers of h-AlN and graphene.

  • 42.
    Dudman, N. P. B.
    et al.
    Department of Medicine, University of New South Wales, Prince Henry Hospital, Uttle Bay, UK.
    Wilcken, D. E.
    Department of Medicine, University of New South Wales, Prince Henry Hospital, Uttle Bay, UK.
    Wang, J.
    Department of Medicine, University of New South Wales, Prince Henry Hospital, Uttle Bay, UK.
    Lynch, J. F.
    Department of Medicine, University of New South Wales, Prince Henry Hospital, Uttle Bay, UK.
    Macey, D.
    Department of Medicine, University of New South Wales, Prince Henry Hospital, Uttle Bay, UK.
    Lundberg, Peter
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV). Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics. Department of Biochemistry, University of Sydney, Sydney (P.L.), Australia.
    Disordered methionine/homocysteine metabolism in premature vascular disease. Its occurrence, cofactor therapy, and enzymology1993In: Arteriosclerosis, Thrombosis and Vascular Biology, ISSN 1079-5642, E-ISSN 1524-4636, Vol. 13, no 9, p. 1253-1260Article in journal (Refereed)
    Abstract [en]

    Mild homocysteinemia occurs surprisingly often in patients with premature vascular disease. We studied the possible enzymatic sources of this mild hyperhomocysteinemia and the control of homocysteine levels in plasma by treatment of patients with the cofactors and cosubstrates of homocysteine catabolism. We assessed homocysteine metabolism in 131 patients who had premature disease in their coronary, peripheral, or cerebrovascular circulation by using a standard oral methionine-load test. Impaired homocysteine metabolism occurred in 28 patients. We assayed levels of the primary enzymes of homocysteine catabolism in cultured skin fibroblast extracts from 15 of these 28 patients. The patients' cystathionine beta-synthase levels (3.68 +/- 2.52 nmol/h per milligram of cell protein, mean +/- SD) were markedly depressed compared with those from 31 healthy adult control subjects (7.61 +/- 4.49, P < .001). The patients' levels of 5-methyltetrahydrofolate: homocysteine methyltransferase were normal. While betaine: homocysteine methyltransferase was not expressed in skin fibroblasts, 24-hour urinary betaine and N,N-dimethylglycine measurements were consistent with normal or enhanced remethylation of homocysteine by betaine: homocysteine methyltransferase in the 13 patients tested. When treated daily with choline and betaine, pyridoxine, or folic acid, there was a normalization of the postmethionine plasma homocysteine level in 16 of 19 patients. Our results indicate that mild homocysteinemia in premature vascular disease may be caused by either a folate deficiency or deficiencies in cystathionine beta-synthase activity. It does not necessarily involve deficiencies of either 5-methyltetrahydrofolate:homocysteine methyltransferase or betaine:homocysteine methyltransferase. Effective treatment regimens are also defined.

  • 43.
    Ederth, Thomas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Nygren, Patrik
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Pettitt, M. E.
    University of Birmingham.
    Oumlstblom, M.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Du, Chun-Xia
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Broo, Klas
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Callow, M. E.
    University of Birmingham.
    Callow, J.
    University of Birmingham.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Anomalous settlement behavior of Ulva linza zoospores on cationic oligopeptide surfaces2008In: Biofouling (Print), ISSN 0892-7014, E-ISSN 1029-2454, Vol. 24, no 4, p. 303-312Article in journal (Refereed)
    Abstract [en]

    Identification of settlement cues for marine fouling organisms opens up new strategies and methods for biofouling prevention, and enables the development of more effective antifouling materials. To this end, the settlement behaviour of zoospores of the green alga Ulva linza onto cationic oligopeptide self-assembled monolayers (SAMs) has been investigated. The spores interact strongly with lysine- and arginine-rich SAMs, and their settlement appears to be stimulated by these surfaces. Of particular interest is an arginine-rich oligopeptide, which is effective in attracting spores to the surface, but in a way which leaves a large fraction of the settled spores attached to the surface in an anomalous fashion. These 'pseudo-settled' spores are relatively easily detached from the surface and do not undergo the full range of cellular responses associated with normal commitment to settlement. This is a hitherto undocumented mode of settlement, and surface dilution of the arginine-rich peptide with a neutral triglycine peptide demonstrates that both normal and anomalous settlement is proportional to the surface density of the arginine-rich peptide. The settlement experiments are complemented with physical studies of the oligopeptide SAMs, before and after extended immersion in artificial seawater, using infrared spectroscopy, null ellipsometry and contact angle measurements.

  • 44.
    Ektarawong, Annop
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Alling, Björn
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Max Planck Inst Eisenforsch GmbH, Germany.
    Stability of SnSe1-xSx solid solutions revealed by first-principles cluster expansion2018In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 30, no 29, article id 29LT01Article in journal (Refereed)
    Abstract [en]

    The configurational thermodynamics of a pseudo-binary alloy SnSe1-xSx in the Pnma phase is studied using first-principles cluster-expansion method in combination with canonical Monte Carlo simulations. We find that, despite the alloy having a tendency toward a phase decomposition into SnSe and SnS at 0 K, the two constituent binaries readily mix with each other to form random SnSe1-xSx solid solutions even at a temperature below room temperature. The obtained isostructural phase diagram of SnSe1-xSx reveals that the alloy is thermodynamically stable as a single-phase random solid solution over a whole composition range above 200 K. These findings provide a fundamental understanding on the alloying behavior of SnSe1-xSx and bring clarity to the debated clustering tendency in this alloy system.

  • 45.
    Elhag, Sami
    et al.
    Linköping University, Department of Science and Technology.
    Ibupoto, Zafar Hussain
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, The Institute of Technology.
    Khranovskyy, Volodymyr
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Willander, Magnus
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
    Nour, Omer
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
    Habit-modifying additives and their morphological consequences on photoluminescence and glucose sensing properties of ZnO nanostructures, grown via aqueous chemical synthesis2015In: Vacuum, ISSN 0042-207X, E-ISSN 1879-2715, Vol. 116, p. 21-26Article in journal (Refereed)
    Abstract [en]

    Generally, the anisotropic shape of inorganic nano-crystal can be influenced by one or more of different parameters i.e. kinetic energy barrier, temperature, time, and the nature of the capping molecules. Here, different surfactants acting as capping molecules were used to assist the aqueous chemical growth of zinc oxide (ZnO) nanostructures on Au coated glass substrates. The morphology, crystal quality and the photoluminescence (PL) properties of the ZnO nanostructures were investigated. The PL properties of the prepared ZnO nanostructures at room temperature showed a dominant UV luminescence peak, while the "green yellow" emissions were essentially suppressed. Moreover, the ZnO nanostructures were investigated for the development of a glucose biosensor. An adsorbed molecule has direct contribution on the glucose oxidase/ZnO/Au sensing properties. We show that the performance of a ZnO-based biosensor can be improved by tailoring the properties of the ZnO biomolecule interface through engineering of the morphology, effective surface area, and adsorption capability.

  • 46.
    Elofsson, Viktor
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Nanoscale engineering. Linköping University, Faculty of Science & Engineering.
    Almyras, Georgios
    Linköping University, Department of Physics, Chemistry and Biology, Nanoscale engineering. Linköping University, Faculty of Science & Engineering.
    Lü, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Nanoscale engineering. Linköping University, Faculty of Science & Engineering.
    Garbrecht, Magnus
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Boyd, Robert
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics. Linköping University, Faculty of Science & Engineering.
    Sarakinos, Kostas
    Linköping University, Department of Physics, Chemistry and Biology, Nanoscale engineering. Linköping University, Faculty of Science & Engineering.
    Structure formation in Ag-X (X = Au, Cu) alloys synthesized far-from-equilibrium2018In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 123, no 16Article in journal (Refereed)
    Abstract [en]

    We employ sub-monolayer, pulsed Ag and Au vapor fluxes, along with deterministic growth simulations, and nanoscale probes to study structure formation in miscible Ag-Au films synthesized under far-from-equilibrium conditions. Our results show that nanoscale atomic arrangement is primarily determined by roughness build up at the film growth front, whereby larger roughness leads to increased intermixing between Ag and Au. These findings suggest a different structure formation pathway as compared to the immiscible Ag-Cu system for which the present study, in combination with previously published data, reveals that no significant roughness is developed, and the local atomic structure is predominantly determined by the tendency of Ag and Cu to phase-separate.

  • 47.
    Erdtman, Edvin
    Örebro universitet, Akademin för naturvetenskap och teknik.
    5-Aminolevulinic acid and derivatives thereof: properties, lipid permeability and enzymatic reactions2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    5-aminolevulinic acid (5-ALA) and derivatives thereof are widely usedprodrugs in treatment of pre-malignant skin diseases of the cancer treatmentmethod photodynamic therapy (PDT). The target molecule in 5-ALAPDTis protoporphyrin IX (PpIX), which is synthesized endogenously from5-ALA via the heme pathway in the cell. This thesis is focused on 5-ALA,which is studied in different perspectives and with a variety of computationalmethods. The structural and energetic properties of 5-ALA, itsmethyl-, ethyl- and hexyl esters, four different 5-ALA enols, and hydrated5-ALA have been investigated using Quantum Mechanical (QM) first principlesdensity functional theory (DFT) calculations. 5-ALA is found to bemore stable than its isomers and the hydrolysations of the esters are morespontaneous for longer 5-ALA ester chains than shorter. The keto-enoltautomerization mechanism of 5-ALA has been studied, and a self-catalysismechanism has been proposed to be the most probable. Molecular Dynamics(MD) simulations of a lipid bilayer have been performed to study themembrane permeability of 5-ALA and its esters. The methyl ester of 5-ALAwas found to have the highest permeability constant (PMe-5-ALA = 52.8 cm/s).The mechanism of the two heme pathway enzymes; Porphobilinogen synthase(PBGS) and Uroporphyrinogen III decarboxylase (UROD), have beenstudied by DFT calculations and QM/MM methodology. The rate-limitingstep is found to have a barrier of 19.4 kcal/mol for PBGS and 13.7kcal/mol for the first decarboxylation step in UROD. Generally, the resultsare in good agreement with experimental results available to date.

    List of papers
    1. Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives
    Open this publication in new window or tab >>Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives
    2007 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 434, no 1-3, p. 101-106Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. The addition of extracorporeal 5ALA and its alkyl ester derivatives are in current clinical use in photodynamical diagnostics and photodynamic therapy of tumors and skin disorders. In the current study density functional theory calculations are performed on 5ALA and its methyl, ethyl, and hexyl esters, in order to explore the basic chemical properties of these species. It is concluded that even in aqueous media the zwitterionic form of 5ALA is less stable than the non-zwitterionic one, that the local environment (lipid vs water) affects the energetics of reaction considerably, and that the hexyl species is most prone to hydrolysis of the three alkyl ester derivatives.

    Place, publisher, year, edition, pages
    Amsterdam: North-Holland Publishing Co, 2007
    Keywords
    5-aminolevulinic acid, 5ALA, B3LYP, DFT, Protonation states, Alkyl esters
    National Category
    Theoretical Chemistry Physical Chemistry
    Research subject
    Biochemistry; Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150073 (URN)10.1016/j.cplett.2006.11.084 (DOI)000243820100020 ()2-s2.0-33846018089 (Scopus ID)
    Available from: 2007-06-25 Created: 2018-08-09 Last updated: 2018-08-09
    2. Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism
    Open this publication in new window or tab >>Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism
    2008 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 18, p. 4367-4374Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.

    Place, publisher, year, edition, pages
    Washington DC: American Chemical Society, 2008
    Keywords
    Aminolevulinic Acid/*chemistry, Carboxylic Acids/chemistry, Catalysis, Isomerism, Protons, Quantum Theory, Thermodynamics, Water/chemistry
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Physical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150074 (URN)10.1021/jp7118197 (DOI)000255486400026 ()18416542 (PubMedID)2-s2.0-43949116597 (Scopus ID)
    Available from: 2008-10-13 Created: 2018-08-09 Last updated: 2018-08-09
    3. Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
    Open this publication in new window or tab >>Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
    2008 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 463, no 1-3, p. 178-182Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.

    Place, publisher, year, edition, pages
    Amsterdam: North-Holland Publishing Co, 2008
    Keywords
    Molecular-dynamics simulations, photodynamic therapy, adenocarcinoma cells, beta transporters, hydrated DPPC, derivates, permeation, protoporphyrin, transition, membranes
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Medicinal Chemistry Physical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150071 (URN)10.1016/j.cplett.2008.08.021 (DOI)000259150400035 ()2-s2.0-51349091343 (Scopus ID)
    Available from: 2008-10-13 Created: 2018-08-09 Last updated: 2018-08-09
    4. Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase
    Open this publication in new window or tab >>Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase
    2011 (English)In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2-3, p. 479-489Article in journal (Refereed) Published
    Abstract [en]

    Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

    Place, publisher, year, edition, pages
    Amsterdam: Elsevier, 2011
    Keywords
    Schiff base, 5-Aminolevulinic acid, Porphobilinogen synthase, Density functional theory, Catalysis
    National Category
    Natural Sciences Physical Chemistry Physical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150070 (URN)10.1016/j.comptc.2010.11.015 (DOI)000288834500036 ()2-s2.0-80054879916 (Scopus ID)
    Available from: 2011-01-14 Created: 2018-08-09 Last updated: 2018-08-09
    5. Computational insights into the mechanism of porphobilinogen synthase
    Open this publication in new window or tab >>Computational insights into the mechanism of porphobilinogen synthase
    2010 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 50, p. 16860-16870Article in journal (Refereed) Published
    Abstract [en]

    Porphobilinogen synthase (PBGS) is a key enzyme in heme biosynthesis that catalyzes the formation of porphobilinogen (PBG) from two 5-aminolevulinic acid (5-ALA) molecules via formation of intersubstrateC-N and C-C bonds. The active site consists of several invariant residues, including two lysyl residues (Lys210 and Lys263; yeast numbering) that bind the two substrate moieties as Schiff bases. Based on experimental studies, various reaction mechanisms have been proposed for this enzyme that generally can be classified according to whether the intersubstrate C-C or C-N bond is formed first. However, the detailed catalytic mechanism of PBGS remains unclear. In the present study, we have employed density functional theory methods in combination with chemical models of the two key lysyl residues and two substrate moieties in order to investigate various proposed reaction steps and gain insight into the mechanism of PBGS. Importantly, it is found that mechanisms in which the intersubstrate C-N bond is formed first have a ratelimiting barrier (17.5 kcal/mol) that is lower than those in which the intersubstrate C-C bond is formed first (22.8 kcal/mol).

    Place, publisher, year, edition, pages
    Washington: American Chemical Society (ACS), 2010
    National Category
    Natural Sciences Physical Chemistry Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150069 (URN)10.1021/jp103590d (DOI)000285236700023 ()21090799 (PubMedID)2-s2.0-78650384685 (Scopus ID)
    Available from: 2011-01-14 Created: 2018-08-09 Last updated: 2018-08-09
    6. The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
    Open this publication in new window or tab >>The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
    Show others...
    2011 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 5, p. 822-834Article in journal (Refereed) Published
    Abstract [en]

    In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.

    Place, publisher, year, edition, pages
    New York: John Wiley & Sons, 2011
    Keywords
    uroporphyrinogen decarboxylase III, uroporphyrinogen III, porphyrin biosynthesis, quantum mechanics/molecular mechanics and density functional theory
    National Category
    Natural Sciences Physical Chemistry Physical Chemistry Theoretical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150066 (URN)10.1002/jcc.21661 (DOI)000288400600007 ()20941734 (PubMedID)2-s2.0-79951968121 (Scopus ID)
    Available from: 2011-01-14 Created: 2018-08-09 Last updated: 2018-08-09
  • 48.
    Erdtman, Edvin
    Department of Natural Sciences, Örebro Life Science Center and Modelling and Simulation Center, Örebro University, Örebro, Sweden.
    A theoretical study of 5-Aminolevulinic acid and its esters: properties and lipid permeability2008Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    5-aminolevulinic acid (5ALA) is a widely used prodrug in Photodynamic therapy (PDT). The target molecule in 5ALA-PDT is Protoporphyrin IX (PpIX), which is synthesized endogenously via the heme pathway in the cell. In this thesis; the structural and energetic properties of 5ALA, its methyl-, ethyl- and hexyl esters, four different 5ALA enols, and hydrated 5ALA have been investigated using Quantum Mechanical (QM) first principles calculations. The vacuum proton affinity (PA) of 5ALA is found to be in good agreement with other similar compounds. The keto-enol tautomerization mechanism of 5ALA has been studied, and a self-catalysis mechanism has been proposed to be the most probable. Molecular Dynamics (MD) simulations of a lipid bilayer have been performed to study the membrane permeability of 5ALA and its esters. In the simulations the molecules were inserted in the middle of the membrane, equilibrated, and then simulated in 20 ns. It has been found that there are some differences in penetration between the molecules studied. The methyl ester of 5ALA is diverging from the others by having its barrier not in the middle of the membrane, as the others have.

    List of papers
    1. Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives
    Open this publication in new window or tab >>Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives
    2007 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 434, no 1-3, p. 101-106Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. The addition of extracorporeal 5ALA and its alkyl ester derivatives are in current clinical use in photodynamical diagnostics and photodynamic therapy of tumors and skin disorders. In the current study density functional theory calculations are performed on 5ALA and its methyl, ethyl, and hexyl esters, in order to explore the basic chemical properties of these species. It is concluded that even in aqueous media the zwitterionic form of 5ALA is less stable than the non-zwitterionic one, that the local environment (lipid vs water) affects the energetics of reaction considerably, and that the hexyl species is most prone to hydrolysis of the three alkyl ester derivatives.

    Place, publisher, year, edition, pages
    Amsterdam: North-Holland Publishing Co, 2007
    Keywords
    5-aminolevulinic acid, 5ALA, B3LYP, DFT, Protonation states, Alkyl esters
    National Category
    Theoretical Chemistry Physical Chemistry
    Research subject
    Biochemistry; Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150073 (URN)10.1016/j.cplett.2006.11.084 (DOI)000243820100020 ()2-s2.0-33846018089 (Scopus ID)
    Available from: 2007-06-25 Created: 2018-08-09 Last updated: 2018-08-09
    2. Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism
    Open this publication in new window or tab >>Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism
    2008 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 18, p. 4367-4374Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.

    Place, publisher, year, edition, pages
    Washington DC: American Chemical Society, 2008
    Keywords
    Aminolevulinic Acid/*chemistry, Carboxylic Acids/chemistry, Catalysis, Isomerism, Protons, Quantum Theory, Thermodynamics, Water/chemistry
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Physical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150074 (URN)10.1021/jp7118197 (DOI)000255486400026 ()18416542 (PubMedID)2-s2.0-43949116597 (Scopus ID)
    Available from: 2008-10-13 Created: 2018-08-09 Last updated: 2018-08-09
    3. Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
    Open this publication in new window or tab >>Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
    2008 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 463, no 1-3, p. 178-182Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.

    Place, publisher, year, edition, pages
    Amsterdam: North-Holland Publishing Co, 2008
    Keywords
    Molecular-dynamics simulations, photodynamic therapy, adenocarcinoma cells, beta transporters, hydrated DPPC, derivates, permeation, protoporphyrin, transition, membranes
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Medicinal Chemistry Physical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150071 (URN)10.1016/j.cplett.2008.08.021 (DOI)000259150400035 ()2-s2.0-51349091343 (Scopus ID)
    Available from: 2008-10-13 Created: 2018-08-09 Last updated: 2018-08-09
  • 49.
    Erdtman, Edvin
    et al.
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Bushnell, Eric A. C.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    School of Chemistry, National University Ireland (NUI) Galway, Galway, Ireland.
    Computational insights into the mechanism of porphobilinogen synthase2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 50, p. 16860-16870Article in journal (Refereed)
    Abstract [en]

    Porphobilinogen synthase (PBGS) is a key enzyme in heme biosynthesis that catalyzes the formation of porphobilinogen (PBG) from two 5-aminolevulinic acid (5-ALA) molecules via formation of intersubstrateC-N and C-C bonds. The active site consists of several invariant residues, including two lysyl residues (Lys210 and Lys263; yeast numbering) that bind the two substrate moieties as Schiff bases. Based on experimental studies, various reaction mechanisms have been proposed for this enzyme that generally can be classified according to whether the intersubstrate C-C or C-N bond is formed first. However, the detailed catalytic mechanism of PBGS remains unclear. In the present study, we have employed density functional theory methods in combination with chemical models of the two key lysyl residues and two substrate moieties in order to investigate various proposed reaction steps and gain insight into the mechanism of PBGS. Importantly, it is found that mechanisms in which the intersubstrate C-N bond is formed first have a ratelimiting barrier (17.5 kcal/mol) that is lower than those in which the intersubstrate C-C bond is formed first (22.8 kcal/mol).

  • 50.
    Erdtman, Edvin
    et al.
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Bushnell, Eric A. C.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    School of Chemistry, National University of Ireland (NUI Galway), Galway, Ireland.
    Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase2011In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2-3, p. 479-489Article in journal (Refereed)
    Abstract [en]

    Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

1234 1 - 50 of 166
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