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  • 1.
    Ahrén, Maria
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Selegård, Linnéa
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Söderlind, Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Nanostructured Materials. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Kauczor, Joanna
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Käll, Per-Olov
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry. Linköping University, The Institute of Technology.
    Uvdal, Kajsa
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    A simple polyol-free synthesis route to Gd2O3 nanoparticles for MRI applications: an experimental and theoretical study2012In: Journal of nanoparticle research, ISSN 1388-0764, E-ISSN 1572-896X, Vol. 14, no 8Article in journal (Refereed)
    Abstract [en]

    Chelated gadolinium ions, e. g., GdDTPA, are today used clinically as contrast agents for magnetic resonance imaging (MRI). An attractive alternative contrast agent is composed of gadolinium oxide nanoparticles as they have shown to provide enhanced contrast and, in principle, more straightforward molecular capping possibilities. In this study, we report a new, simple, and polyol-free way of synthesizing 4-5-nm-sized Gd2O3 nanoparticles at room temperature, with high stability and water solubility. The nanoparticles induce high-proton relaxivity compared to Gd-DTPA showing r(1) and r(2) values almost as high as those for free Gd3+ ions in water. The Gd2O3 nanoparticles are capped with acetate and carbonate groups, as shown with infrared spectroscopy, near-edge X-ray absorption spectroscopy, X-ray photoelectron spectroscopy and combined thermogravimetric and mass spectroscopy analysis. Interpretation of infrared spectroscopy data is corroborated by extensive quantum chemical calculations. This nanomaterial is easily prepared and has promising properties to function as a core in a future contrast agent for MRI.

  • 2.
    Ahrén, Maria
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Söderlind, Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Nanostructured Materials. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Nordblad, Per
    Division of Solid State Physics, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Uvdal, Kajsa
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    One-step synthesis of sub 5 nm sized manganese oxide based nanoparticles2013Manuscript (preprint) (Other academic)
    Abstract [en]

    Sub 5 nm sized manganese oxide nanoparticles; MnOx (1 ≤ x ≤ 2), were synthesized via a short time room temperature synthesis route. The nanoparticles are crystalline, spherically shaped and in the size range of 2-4 nm as shown by transmission electron microscopy studies. Selected area electron diffraction patterns were collected and their appearance indicated that the nanoparticle cores are composed of MnO. Also, co-existence of the (II) and (III) oxidation states at the nanoparticle surface was verified by results achieved from infrared spectroscopy and X-ray photoelectron spectroscopy. These measurements also supported presence of a minor amount of acetate groups as well as a negligible fraction of carbonate groups at the nanoparticle surfaces. The interpretation of the IR spectra was confirmed by quantum chemical calculations using the high spin manganese nanoparticle Mn12O12(OAc)16(H2O)4, as a model system for the MnOx nanoparticle surface. Bulk MnO and Mn2O3 are known to be antiferromagnetic. The magnetic properties are however somewhat dependent of the crystallite size and changes when scaling down to the nanoregion. The MnOx (1 ≤ x ≤ 2) nanoparticles investigated in this work show a superparamagnetic behavior with a blocking temperature of approximately 12 K proven by means of SQUID measurements. The relaxivities of the nanoparticles and the Mn(OAc)2 precursors were studied with a bench top NMR analyzer verifying nanoparticle r1 and r2 of 0.5 and 6 mMs-1 respectively. The r1 relaxivity is lower than what is earlier reported for Gd based contrast agent, but improvements are expected by further surface modification, due to increased rotational time and higher water dispersability.

  • 3.
    Bouchet, Aude
    et al.
    University of Bordeaux 1.
    Brotin, Thierry
    Ecole Normale Super Lyon.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Cavagnat, Dominique
    University of Bordeaux 1.
    Buffeteau, Thierry
    University of Bordeaux 1.
    Influence of the Chemical Structure of Water-Soluble Cryptophanes on Their Overall Chiroptical and Binding Properties2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 19, p. 7816-7825Article in journal (Refereed)
    Abstract [en]

    The synthesis and the chiroptical properties of the two enantiomers of the hexacarboxylic acid cryptophane-A derivative, 1, are described in this article. The chiroptical and binding properties of 1 toward achiral and chiral guests have been investigated in water under basic conditions by polarimetry, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and (1)H NMR spectroscopy. These experiments reveal that the (1)H NMR spectra of 1 are very sensitive to the nature of the guest trapped in its cavity whereas ECD and VCD spectra remain unchanged. We also show that the two enantiomers of 1 are able to distinguish between the two enantiomers of a series of small chiral epoxides. The enantiodiscrimination increases with the size of the chiral guest whereas the corresponding binding constants decrease. In contrast to what was observed for other water-soluble cryptophanes, the molecular recognition process is found independent of the nature of the counterions surrounding host 1, shedding light on the importance of the chemical structure of cryptophanes on their binding and chiroptical properties.

  • 4.
    Brede, Jens
    et al.
    University of Hamburg.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Kuck, Stefan
    University of Hamburg.
    Schwoebel, Joerg
    University of Hamburg.
    Scarfato, Alessandro
    University of Hamburg.
    Chang, Shih-Hsin
    University of Hamburg.
    Hoffmann, Germar
    University of Hamburg.
    Wiesendanger, Roland
    University of Hamburg.
    Lensen, Roy
    Radboud University Nijmegen.
    Kouwer, Paul H J
    Radboud University Nijmegen.
    Hoogboom, Johan
    Radboud University Nijmegen.
    Rowan, Alan E
    Radboud University Nijmegen.
    Broering, Martin
    University of Marburg.
    Funk, Markus
    University of Marburg.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Zerbetto, Francesco
    University of Bologna.
    Lazzaroni, Roberto
    University of Mons.
    Dynamics of molecular self-ordering in tetraphenyl porphyrin monolayers on metallic substrates2009In: NANOTECHNOLOGY, ISSN 0957-4484, Vol. 20, no 27, p. 275602-Article in journal (Refereed)
    Abstract [en]

    A molecular model system of tetraphenyl porphyrins (TPP) adsorbed on metallic substrates is systematically investigated within a joint scanning tunnelling microscopy/molecular modelling approach. The molecular conformation of TPP molecules, their adsorption on a gold surface and the growth of highly ordered TPP islands are modelled with a combination of density functional theory and dynamic force field methods. The results indicate a subtle interplay between different contributions. The molecule-substrate interaction causes a bending of the porphyrin core which also determines the relative orientations of phenyl legs attached to the core. A major consequence of this is a characteristic (and energetically most favourable) arrangement of molecules within self-assembled molecular clusters; the phenyl legs of adjacent molecules are not aligned parallel to each other (often denoted as pi-pi stacking) but perpendicularly in a T-shaped arrangement. The results of the simulations are fully consistent with the scanning tunnelling microscopy observations, in terms of the symmetries of individual molecules, orientation and relative alignment of molecules in the self-assembled clusters.

  • 5.
    Brede, Jens
    et al.
    University of Hamburg.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Lensen, Roy
    Radboud University.
    Rowan, Alan E
    Radboud University.
    Funk, Markus
    University of Marburg.
    Broering, Martin
    University of Marburg.
    Hoffmann, Germar
    University of Marburg.
    Wiesendanger , Roland
    University of Marburg.
    Adsorption and conformation of porphyrins on metallic surfaces2009In: JOURNAL OF VACUUM SCIENCE and TECHNOLOGY B, ISSN 1071-1023 , Vol. 27, no 2, p. 799-804Article in journal (Refereed)
    Abstract [en]

    Tetraphenyl porphyrins (TPP) belong to a highly interesting class of molecules with a large variety of electronic, magnetic, and structural properties. So far, local investigations by scanning probe techniques were primarily focused on larger agglomerates of TPP molecules. Here, experimental results of the observation and manipulation of isolated molecules adsorbed on cold metal substrates by means of low temperature scanning tunneling microscopy are presented. Depending on the surface geometry, i.e., Cu(111) VS, Cu(100) three distinct deformations of the molecular structure are identified reflecting the interaction of the phenyl periphery with the substrate. In a second step, controlled manipulation in terms of deformation of the porphyrin core, ligand dissociation, and lateral displacement of the phenyl periphery are demonstrated.

  • 6.
    Brocorens, Patrick
    et al.
    University of Mons Mat Nova, Belgium .
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Guyard-Duhayon, Carine
    CNRS, France .
    Guillot, Regis
    University of Paris 11, France .
    Andrioletti, Bruno
    University of Lyon 1, France .
    Suhr, Dominique
    University of Paris 06, France .
    Isare, Benjamin
    University of Paris 06, France .
    Lazzaroni, Roberto
    University of Mons Mat Nova, Belgium .
    Bouteiller, Laurent
    University of Paris 06, France .
    Conformational Plasticity of Hydrogen Bonded Bis-urea Supramolecular Polymers2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 17, p. 5379-5386Article in journal (Refereed)
    Abstract [en]

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

  • 7.
    Christodoulou, C.
    et al.
    Humboldt University, Germany .
    Giannakopoulos, A.
    University of Mons, Belgium .
    Nardi, M.V.
    Humboldt University, Germany .
    Ligorio, G.
    Humboldt University, Germany .
    Oehzelt, M.
    Humboldt University, Germany Helmholtz Zentrum Berlin Mat and Energie GmbH, Germany .
    Chen, L.
    University of Mons, Belgium .
    Pasquali, L.
    University of Modena and Reggio Emilia, Italy IOM CNR, Italy University of Johannesburg, South Africa .
    Timpel, M.
    Humboldt University, Germany .
    Giglia, A.
    IOM CNR, Italy .
    Nannarone, S.
    University of Modena and Reggio Emilia, Italy IOM CNR, Italy .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Parvez, K.
    Max Planck Institute Polymer Research, Germany .
    Muellen, K.
    Max Planck Institute Polymer Research, Germany .
    Beljonne, D.
    University of Mons, Belgium .
    Koch, N.
    Humboldt University, Germany Helmholtz Zentrum Berlin Mat and Energie GmbH, Germany .
    Tuning the Work Function of Graphene-on-Quartz with a High Weight Molecular Acceptor2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 9, p. 4784-4790Article in journal (Refereed)
    Abstract [en]

    Ultraviolet and X-ray photoelectron spectroscopies in combination with density functional theory (DFT) calculations were used to study the change in the work function (Phi) of graphene, supported by quartz, as induced by adsorption of hexaazatriphenylene-hexacarbonitrile (HATCN). Near edge X-ray absorption fine structure spectroscopy (NEXAFS) and DFT modeling show that a molecular-density-dependent reorientation of HATCN from a planar to a vertically inclined adsorption geometry occurs upon increasing surface coverage. This, in conjunction with the orientation-dependent magnitude of the interface dipole, allows one to explain the evolution of graphene (Phi) from 4.5 eV up to 5.7 eV, rendering the molecularly modified graphene-on-quartz a highly suitable hole injection electrode.

  • 8.
    Di Meo, Florent
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Pedersen, Morten
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, The Institute of Technology. University of Southern Denmark, Denmark.
    Rubio-Magnieto, Jenifer
    University of Mons UMONS, Belgium.
    Surin, Mathieu
    University of Mons UMONS, Belgium.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology. University of Mons UMONS, Belgium.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental Theoretical Case Study of the AT Homo-Oligonucleotide2015In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 3, p. 355-359Article in journal (Refereed)
    Abstract [en]

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment.

  • 9.
    Elie, Margaux
    et al.
    Normandie University, France.
    Sguerra, Fabien
    CEA, France.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Weber, Michael D.
    University of Erlangen Nurnberg, Germany.
    Marion, Ronan
    Normandie University, France.
    Grimault, Adele
    Normandie University, France.
    Lohier, Jean-Francois
    Normandie University, France.
    Stallivieri, Aurelie
    Normandie University, France.
    Brosseau, Arnaud
    Paris Saclay University, France; Paris Saclay University, France.
    Pansu, Robert B.
    Paris Saclay University, France; Paris Saclay University, France.
    Renaud, Jean-Luc
    Normandie University, France.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Hamel, Matthieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering. CEA, France.
    Costa, Ruben D.
    University of Erlangen Nurnberg, Germany.
    Gaillard, Sylvain
    Normandie University, France.
    Designing NHC-Copper(I) Dipyridylamine Complexes for Blue Light-Emitting Electrochemical Cells2016In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 8, no 23, p. 14678-14691Article in journal (Refereed)
    Abstract [en]

    This study presents the influence of various substituents on the photophysical features of heteroleptic copper(I) complexes bearing both N-heterocyclic carbene (NHC) and dipyridylamine (dpa = dipyridylamine skeleton corresponding to ligand L1) ligands. The luminescent properties have been compared to our recently reported archetypal blue emitting [Cu(IPr)(dpa)][PF6] complex. The choice of the substituents on both ligands has been guided to explore the effect of the electron donor/acceptor and "push-pull" on the emission wavelengths and photoluminescence quantum yields. A selection of the best candidates in terms of their photophysical features were applied for developing the first blue light emitting electrochemical cells (LECs) based on copper(I) complexes. The device analysis suggests that the main concern is the moderate redox stability of the complexes under high applied driving currents, leading to devices with moderate stabilities pointing to a proof-of-concept for further development. Nevertheless, under low applied driving currents the blue emission is stable, showing performance levels competitive to those reported for blue LECs baged on iridium(III) complexes. Overall, this work provides valuable guidelines to tackle the design of enhanced NHC copper complexes for lighting applications in the near future.

  • 10.
    Fuchs, Franz
    et al.
    CEA INAC SPrAM UMR5819 CEA CNRS UJF, France.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    de Vet, Christiaan
    CEA INAC SPrAM UMR5819 CEA CNRS UJF, France.
    Leclere, Philippe
    University of Mons, Belgium.
    Demadrille, Renaud
    CEA INAC SPrAM UMR5819 CEA CNRS UJF, France.
    Grevin, Benjamin
    CEA INAC SPrAM UMR5819 CEA CNRS UJF, France.
    On the Photo-Induced Charge-Carrier Generation within Monolayers of Self-Assembled Organic Donor-Acceptor Dyads2014In: Advanced Materials, ISSN 0935-9648, E-ISSN 1521-4095, Vol. 26, no 37, p. 6416-6422Article in journal (Refereed)
    Abstract [en]

    n/a

  • 11.
    Giannicchi, Ilaria
    et al.
    University of Roma La Sapienza, Italy University of Roma La Sapienza, Italy .
    Jouvelet, Benjamin
    University of Paris 06, France CNRS, France .
    Isare, Benjamin
    University of Paris 06, France CNRS, France .
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Dalla Cort, Antonella
    University of Roma La Sapienza, Italy University of Roma La Sapienza, Italy .
    Bouteiller, Laurent
    University of Paris 06, France CNRS, France .
    Orthohalogen substituents dramatically enhance hydrogen bonding of aromatic ureas in solution2014In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 50, no 5, p. 611-613Article in journal (Refereed)
    Abstract [en]

    The phenylurea moiety is a ubiquitous synthon in supramolecular chemistry. Here we report that the introduction of chlorine or bromine atoms in the ortho positions to the urea unit is a simple and very efficient way to improve its intermolecular hydrogen bond (HB) donor character. This effect was demonstrated in solution both in the context of self-association of bis-ureas and hydrogen bonding of mono-ureas to strong HB acceptors.

  • 12.
    Grevin, Benjamin
    et al.
    University Grenoble 1, CNRS, INAC CEA Grenoble, Lab Elect Mol Organ and Hybride,UMR5819 SPrAM, F-38054 Grenoble 9, France .
    Demadrille, Renaud
    University Grenoble 1, CNRS, INAC CEA Grenoble, Lab Elect Mol Organ and Hybride,UMR5819 SPrAM, F-38054 Grenoble 9, France .
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Lazzaroni, Roberto
    University Mons, Serv Chim Mat Nouveaux, B-7000 Mons, Belgium .
    Leclere, Philippe
    University Mons, Serv Chim Mat Nouveaux, B-7000 Mons, Belgium .
    Probing the Local Conformation within pi-Conjugated One-dimensional Supramolecular Stacks using Frequency Modulation Atomic Force Microscopy2009In: ADVANCED MATERIALS, ISSN 0935-9648, Vol. 21, no 41, p. 4124-Article in journal (Refereed)
    Abstract [en]

    Frequency-modulation atomic force microscopy is used to investigate the local conformation within 1D stacks obtained by the self-assembly of pi-conjugated molecules from solution. The structural parameters extracted from the experimental data can be interpreted in terms of local molecular conformation, by comparison with models obtained by molecular mechanics and dynamics simulations.

  • 13.
    Hayton, James
    et al.
    CEA.
    Lincker, Frederic
    CEA.
    Demadrille, Renaud
    CEA.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Brun, Mickael
    CEA.
    Grevin, Benjamin
    CEA.
    Pi-Conjugated Molecular Nanowire Stacks Investigated by Frequency-Modulation Atomic Force Microscopy in the qPlus Configuration2009In: APPLIED PHYSICS EXPRESS, ISSN 1882-0778, Vol. 2, no 9, p. 091501-Article in journal (Refereed)
    Abstract [en]

    Self-assembled pi-conjugated nanowire stacks were imaged using a tuning-fork probe mounted in the qPlus configuration in frequency modulation mode under ultrahigh vacuum. High resolution topographic and dissipation images demonstrate the applicability of such probes to soft conjugated materials, with sub-molecular resolution achieved perpendicular to the stacking axis. A new insight is gained from the damping contrast into the local mechanical properties of edge-on pi-conjugated stacks.

  • 14.
    Isare, B.
    et al.
    CNRS.
    Linares, Mathieu
    CNRS.
    Lazzaroni, R.
    CNRS.
    Bouteiller, L.
    CNRS.
    Engineering the cavity of self-assembled dynamic nanotubes2009In: Journal of Physical Chemistry B, ISSN 1520-6106, Vol. 113, no 11, p. 3360-3364Article in journal (Refereed)
    Abstract [en]

    By analogy with hydrogen-bonded molecular capsules, self-assembled nanotubes are of interest because they can temporarily isolate guest molecules from the solution. We show here that the stability of a particular bis-urea based dynamic self-assembled nanotube is related to the possibility for solvent molecules to fit inside the tubular cavity. The diameter of the cavity can be finely tuned by introducing a modified monomer in controlled amount.

  • 15.
    Jakobsson, Mattias
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Linares, Mathieu
    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.
    Monte Carlo simulations of charge transport in organic systems with true off-diagonal disorder2012In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, no 11Article in journal (Refereed)
    Abstract [en]

    In this work, a novel method to model off-diagonal disorder in organic materials has been developed. The off-diagonal disorder is taken directly from the geometry of the system, which includes both a distance and an orientational dependence on the constituent molecules, and does not rely on a parametric random distribution. To study this method, a system is generated by running molecular dynamics simulations on phenylene-vinylene oligomers packed into boxes. The impact of the model is then investigated by means of Monte Carlo simulations of the charge transport in these boxes and a comparison is made to the commonly used model of off-diagonal disorder, where only the distance dependence is properly accounted for. It is shown that this new model has a significant impact on the charge transport, while still being compliant with previously published and confirmed results.

  • 16.
    Linares, Mathieu
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Hultell (Andersson), Magnus
    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.
    The effect of lattice dynamics on electron localization in poly-(para-phenylene vinylene)2009In: Synthetic metals, ISSN 0379-6779, E-ISSN 1879-3290, Vol. 159, no 21-22, p. 2219-2221Article in journal (Refereed)
    Abstract [en]

    The lattice dynamics in poly-(para-phenylenevinylene) and its effect on the electron localization properties have been investigated. The simulations were performed using a hybrid quantum mechanical/molecular dynamics approach including the Pariser–Parr–Pople Hamiltonian. It is found that the dynamic disorder that exists at room temperature induces electron localization. The most important lattice modes in the context of localization are the torsional modes of the phenylene rings, that are shown to couple strongly to the electronic system. Since these modes occur at low frequencies, they will also have a strong impact on intra-chain charge transport.

  • 17.
    Linares, Mathieu
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Humbel, Stephane
    Aix Marseille University.
    Braida , Benoit
    University of Paris.
    The Nature of Resonance in Allyl Ions and Radical2008In: JOURNAL OF PHYSICAL CHEMISTRY A, ISSN 1089-5639 , Vol. 112, no 50, p. 13249-13255Article in journal (Refereed)
    Abstract [en]

    A recent valence bond scheme based on Lewis structures, the valence bond BOND (VBB) method (BOND: Breathing Orbitals Naturally Delocalized) method (Linares, M.; Braida, B.; Humbel, S. J. Phys. Chem. A 2006, 110, 2505-2509), is applied to explore the nature of resonance in allyl systems. Whereas allyl radical is correctly described by the resonance between the two traditional Lewis structures, a third "long-bonded" structure, which apparently creates a pi bond between the two distant carbon atoms, appears to plays an important role in allyl ions description. The similar vertical resonance energy (VRE) for both allyl ions is rather moderate (similar to 37 kcal/mol) in the two-structure description but is significantly enhanced when the long-bonded structure is included into the VBB wave function (by up to 20 kcal/mol). The allyl radical is much less resonant and is correctly described by the traditional two-structure picture. The development of VBB Lewis structures into "pure" valence bond determinants enlightens the role of the third structure in the description of allyl ions. The existence of a long bond between the two distant carbon atoms is clearly ruled out. Charge equilibration effect is shown to be a minor factor. The third structure is finally attributed to one- and three-electron bonding character revealed in the g systems of the cation and anion, respectively. This makes these systems two surprising examples of odd electron bonding within a singlet state. Last, the two-structure description of allyl radical is improved by addition of missing ionic structures.

  • 18.
    Linares, Mathieu
    et al.
    Université de Mons-Hainaut.
    Minoia, A.
    Université de Mons-Hainaut.
    Brocorens, P.
    Université de Mons-Hainaut.
    Beljonne, D.
    Université de Mons-Hainaut.
    Lazzaroni, R.
    Université de Mons-Hainaut.
    Expression of chirality in molecular layers at surfaces: Insights from modelling2009In: Chemical Society Reviews, ISSN 0306-0012, Vol. 38, no 3, p. 806-816Article in journal (Refereed)
    Abstract [en]

    This tutorial review illustrates how modelling can be used to understand the structure and properties of chiral surfaces formed by adsorption of molecular layers. The two major theoretical approaches for such modelling (Density Functional Theory and classical force-field methods) are briefly described and compared. A few examples of their use are given, focussing on: (i) the expression of chirality at the local and global scale in layers of chiral molecules, (ii) the appearance of chirality in layers of achiral molecules on achiral surfaces, and (iii) the molecular organisation in layers formed from racemic mixtures.

  • 19.
    Linares, Mathieu
    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.
    Norman , Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Effects of pi-stacking interactions on the near carbon K-edge x-ray absorption fine structure: A theoretical study of the ethylene pentamer and the phthalocyanine dimer2009In: JOURNAL OF CHEMICAL PHYSICS, ISSN 0021-9606 , Vol. 130, no 10, p. 104305-Article in journal (Refereed)
    Abstract [en]

    X-ray absorption spectra have been determined for ethylene and free base phthalocyanine at the carbon K-edge with use of the complex polarization propagator method combined with Kohn-Sham density functional theory and the Coulomb attenuated method B3LYP exchange-correlation functional. Apart from isolated molecules, the study includes pi-stacked systems of the phthalocyanine dimer and the ethylene dimer, trimer, tetramer, and pentamer. For ethylene, pi-stacking involves a reduction in transition energy of the valence pi(*)-band by some 70 meV and large spectral changes (regarding also shape and intensity) of the Rydberg bands. For phthalocyanine, there are large spectral changes in the entire valence pi(*)-part of the spectrum.

  • 20.
    Linares, Mathieu
    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.
    Rinkevicius, Zilvinas
    Royal Institute Technology.
    Agren, Hans
    Royal Institute Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Complex Polarization Propagator Approach in the Restricted Open-Shell, Self-Consistent Field Approximation: The Near K-Edge X-ray Absorption Fine Structure Spectra of Allyl and Copper Phthalocyanine2011In: JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, Vol. 115, no 18, p. 5096-5102Article in journal (Refereed)
    Abstract [en]

    A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order polarization propagator approach that makes it possible to directly calculate the X-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted X-ray spectra relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects. The method is applied to the calculation of the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine. Comparison is made between the spectra of the radicals and those of the corresponding cations and anions to assess the effect of the increase of electron charge in the frontier orbital. The method offers the possibility for unique assign-lent of symmetry-independent atoms. The overall excellent spectral agreement motivates the application of the method as a routine precise tool for analyzing X-ray absorption of large systems of technological interest.

  • 21.
    Marion, Ronan
    et al.
    University of Caen Basse Normandie, France.
    Sguerra, Fabien
    CEA, France.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Sauvageot, Elodie
    University of Caen Basse Normandie, France.
    Lohier, Jean-Francois
    University of Caen Basse Normandie, France.
    Daniellou, Richard
    University of Orleans, France.
    Renaud, Jean-Luc
    University of Caen Basse Normandie, France.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hamel, Matthieu
    CEA, France.
    Gaillard, Sylvain
    University of Caen Basse Normandie, France.
    NHC Copper(I) Complexes Bearing Dipyridylamine Ligands: Synthesis, Structural, and Photoluminescent Studies2014In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 53, no 17, p. 9181-9191Article in journal (Refereed)
    Abstract [en]

    We describe the synthesis of new cationic tricoordinated copper complexes bearing bidentate pyridine-type ligands and N-heterocyclic carbene as ancillary ligands. These cationic copper complexes were fully characterized by NMR, electrochemistry, X-ray analysis, and photophysical studies in different environments. Density functional theory calculations were also undertaken to rationalize the assignment of the electronic structure and the photophysical properties. These tricoordinated cationic copper complexes possess a stabilizing CH-pi interaction leading to high stability in both solid and liquid states. In addition, these copper complexes, bearing dipyridylamine ligands having a central nitrogen atom as potential anchoring point, exhibit very interesting luminescent properties that render them potential candidates for organic light-emitting diode applications.

  • 22.
    Nieto-Ortega, Belen
    et al.
    University of Malaga, Spain .
    Ramirez, Francisco J
    University of Malaga, Spain .
    Amabilino, David B
    CSIC, Spain .
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Beljonne, David
    University of Mons, Belgium .
    Lopez Navarrete, Juan T
    University of Malaga, Spain .
    Casado, Juan
    University of Malaga, Spain .
    Electronic and vibrational circular dichroism spectroscopies for the understanding of chiral organization in porphyrin aggregates2012In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 48, no 73, p. 9147-9149Article in journal (Refereed)
    Abstract [en]

    Dichroic optical spectroscopies and theoretical modelling have been used to describe the structure of aggregates of porphyrins in their gels in terms of: (i) the formation of helicoidal structures, (ii) the sign of the handedness, (iii) their extent and degree of structural order, and (iv) the annealing of the structural defects.

  • 23.
    Norman, Patrick
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    On the Interplay Between Chirality and Exciton Coupling: A DFT Calculation of the Circular Dichroism in pi-Stacked Ethylene2014In: Chirality, ISSN 0899-0042, E-ISSN 1520-636X, Vol. 26, no 9, p. 483-489Article in journal (Refereed)
    Abstract [en]

    The chirality of stacked weakly interacting p-systems was interpreted in terms of Frenkel exciton states and the formation of excitonic circular dichroism (CD) bands was monitored for ethylene stacks of varying sizes. Convergence of CD bands with respect to the system size was observed for stacks involving around 10 molecules. By means of rotation around the C-C double bond in ethylene, chirality was induced in the monomeric system and which was shown to dominate the spectral responses, even for polymer aggregates. In helical assemblies of chiral entities, there will always be a mix of excitonic and monomeric contributions to the CD signal and it is demonstrated that the complex polarization propagator approach in combination with Density Functional Theory is a suitable method to address this situation.

  • 24.
    Norman, Patrick
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Parello, Joseph
    Vanderbilt University, TN 37235 USA.
    Polavarapu, Prasad L.
    Vanderbilt University, TN 37235 USA.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 34, p. 21866-21879Article in journal (Refereed)
    Abstract [en]

    It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles. At the DFT/B3LYP level of theory, the ECD signal response is reduced by a factor of 6.7 in going from the B-DNA to the N-DNA form, and it is illustrated how more than 90% of the individual base-pair dimers contribute to this strong hypochromic effect. Of the several inter-base pair parameters, an increase in twist angles is identified as to strongly contribute to a reduced ellipticity. The present work provides first evidence that first-principles calculations can elucidate changes in DNA dichroism due to the supramolecular organization of the nucleoprotein particle and associates these changes with the local structural features of nucleosomal DNA.

  • 25.
    Oliveras-Gonzalez, Cristina
    et al.
    Institute Ciencia Mat Barcelona ICMAB CSIC, Spain.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Gonzalez-Campo, Arantzazu
    Institute Ciencia Mat Barcelona ICMAB CSIC, Spain.
    Beljonne, David
    University of Mons, Belgium.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Simon-Sorbed, Maite
    Institute Ciencia Mat Barcelona ICMAB CSIC, Spain.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Amabilino, David B.
    Institute Ciencia Mat Barcelona ICMAB CSIC, Spain; University of Nottingham, England.
    Bottom-Up Hierarchical Self-Assembly of Chiral Porphyrins through Coordination and Hydrogen Bonds2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 50, p. 15795-15808Article in journal (Refereed)
    Abstract [en]

    A series of chiral synthetic compounds is reported that shows intricate but specific hierarchical assembly because of varying positions of coordination and hydrogen bonds. The evolution of the aggregates (followed by absorption spectroscopy and temperature-dependent circular dichroism studies in solution) reveal the influence of the proportion of stereogenic centers in the side groups connected to the chromophore ring in their optical activity and the important role of pyridyl groups in the self-assembly of these chiral macrocycles. The optical activity spans 2 orders of magnitude depending on composition and constitution. Two of the aggregates show very high optical activity even though the isolated chromophores barely give a circular dichroism signal. Molecular modeling of the aggregates, starting from the pyridine zinc(II) porphyrin interaction and working up, and calculation of the circular dichroism signal confirm the origin of this optical activity as the chiral supramolecular organization of the molecules. The aggregates show a broad absorption range, between approximately 390 and 475 rim for the transitions associated with the Soret region alone, that spans wavelengths far more than the isolated chromophore. The supramolecular assemblies of the metalloporphyrins in solution were deposited onto highly oriented pyrolitic graphite in order to study their hierarchy in assembly by atomic force microscopy. Zero and one-dimensional aggregates were observed, and a clear dependence on deposition temperature was shown, indicating that the hierarchical assembly took place largely in solution. Moreover, scanning electron microscopy images of porphyrins and metalloporphyrins precipitated under out-of-equilibrium conditions showed the dependence of the number and position of chiral amide groups in the formation of a fibrillar nanomaterial. The combination of coordination and hydrogen bonding in the complicated assembly of these molecules where there is a clear hierarchy for zinc(II)-pyridyl interaction followed by hydrogen-bonding between amide groups, and then van der Waals interactions paves the way for the preparation of molecular materials with multiple chromophore environments.

  • 26.
    Pop, Flavia
    et al.
    University of Angers, France.
    Melan, Caroline
    University of Angers, France.
    Danila, Ion
    University of Angers, France.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Beljonne, David
    University of Mons, Belgium.
    Amabilino, David B.
    Insitut Ciencia Mat Barcelona ICMAB CSIC, Spain.
    Avarvari, Narcis
    University of Angers, France.
    Hierarchical Self-Assembly of Supramolecular Helical Fibres from Amphiphilic C3-Symmetrical Functional Tris(tetrathiafulvalenes)2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 52, p. 17443-17453Article in journal (Refereed)
    Abstract [en]

    The preparation and self-assembly of the enantiomers of a series of C-3-symmetric compounds incorporating three tetrathiafulvalene (TTF) residues is reported. The chiral citronellyl and dihydrocitronellyl alkyl chains lead to helical one dimensional stacks in solution. Molecular mechanics and dynamics simulations combined with experimental and theoretical circular dichroism support the observed helicity in solution. These stacks self-assemble to give fibres that have morphologies that depend on the nature of the chiral alkyl group and the medium in which the compounds aggregate. An inversion of macroscopic helical morphology of the citronellyl compound is observed when compared to analogous 2-methylbutyl chains, which is presumably a result of the stereogenic centre being further away from the core of the molecule. This composition still allows both morphologies to be observed, whereas an achiral compound shows no helicity. The morphology of the fibres also depends on the flexibility at the chain ends of the amphiphilic components, as there is not such an apparently persistent helical morphology for the dihydrocitronellyl derivative as for that prepared from citronellyl chains.

  • 27.
    Qian, Deping
    et al.
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics.
    Liu, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
    Wang, Suhao
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
    Himmelberger, Scott
    Stanford University, CA 94305 USA.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Vagin, Mikhail
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
    Muller, Christian
    Chalmers, Sweden.
    Zaifei, Zaifei
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Fabiano, Simone
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
    Berggren, Magnus
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
    Salleo, Alberto
    Stanford University, CA 94305 USA.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Zou, Yingping
    Central S University, Peoples R China.
    Zhang, Fengling
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Modulating molecular aggregation by facile heteroatom substitution of diketopyrrolopyrrole based small molecules for efficient organic solar cells2015In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 3, no 48, p. 24349-24357Article in journal (Refereed)
    Abstract [en]

    In conjugated polymers and small molecules of organic solar cells, aggregation induced by intermolecular interactions governs the performance of photovoltaics. However, little attention has been paid to the connection between molecular structure and aggregation within solar cells based on soluble small molecules. Here we demonstrate modulation of intermolecular aggregation of two synthesized molecules through heteroatom substitution to develop an understanding of the role of aggregation in conjugated molecules. Molecule 1 (M1) based on 2-ethylhexyloxy-benzene substituted benzo[1,2-b:4,5-b]dithiophene (BDTP) and diketopyrrolopyrrole (DPP) displays strong aggregation in commonly used organic solvents, which is reduced in molecule 2 (M2) by facile oxygen atom substitution on the BDTP unit confirmed by absorption spectroscopy and optical microscopy, while it successfully maintains molecular planarity and favorable charge transport characteristics. Solar cells based on M2 exhibit more than double the photocurrent of devices based on M1 and yield a power conversion efficiency of 5.5%. A systematic investigation of molecular conformation, optoelectronic properties, molecular packing and crystallinity as well as film morphology reveals structure dependent aggregation responsible for the performance difference between the two conjugated molecules.

  • 28.
    Rinkevicius, Zilvinas
    et al.
    KTH Royal Institute Technology, Sweden.
    Sandberg, Jaime A. R.
    KTH Royal Institute Technology, Sweden.
    Li, Xin
    KTH Royal Institute Technology, Sweden.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Ågren, Hans
    KTH Royal Institute Technology, Sweden.
    Hybrid Complex Polarization Propagator/Molecular Mechanics Method for Heterogeneous Environments2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 6, p. 2661-2667Article in journal (Refereed)
    Abstract [en]

    We introduce a hybrid complex polarization propagator/molecular mechanics method for the calculation of near-resonant and resonant response properties of molecules in heterogeneous environments, which consist of a metallic surface, or nanoparticle, and a solvent. The applicability and performance of the method is demonstrated by computations of linear absorption spectra of p-nitroaniline physisorbed at a gold/dimethyl sulfoxide interface in the UV/vis and near carbon-K-edge regions of the spectrum. It is shown that the shift of absorption cross-section induced by the heterogeneous environment varies significantly depending on the nature,of the excited states encountered in the targeted frequency region as well as on the actual size of the resonant frequencies, and that the solvent component of the heterogeneous environment is responsible for the major part of the environmental shift, especially in the higher frequency range of the carbon K-edge region.

  • 29.
    Rubio-Magnieto, Jenifer
    et al.
    University of Mons UMONS, Belgium.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Lo, Mamadou
    University of Montpellier 2, France.
    Delcourt, Cecile
    University of Mons UMONS, Belgium.
    Clement, Sebastien
    University of Montpellier 2, France.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Richeter, Sebastien
    University of Montpellier 2, France.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology. University of Mons UMONS, Belgium.
    Surin, Mathieu
    University of Mons UMONS, Belgium.
    Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes2015In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 8, p. 2453-2463Article in journal (Refereed)
    Abstract [en]

    The molecular recognition of human telomeric G-quadruplexes by a novel cationic pi-extended Ni-II-porphyrin (Ni-II-TImidP4) is studied in aqueous solutions via (chir) optical spectroscopy, Fluorescence Resonance Energy Transfer (FRET) melting assay, and computational molecular modeling. The results are systematically compared with the recognition by a conventional meso-substituted Ni-II-porphyrin (Ni-II-TMPyP4), which allows us to pinpoint the differences in binding modes depending on the G-quadruplex topology. Importantly, FRET melting assays show the higher selectivity of Ni-II-TImidP4 towards human telomeric G4 than that of Ni-II-TMPyP4.

  • 30.
    Schall, Anna P.
    et al.
    Haverford Coll, PA 19041 USA.
    Iavicoli, Patrizia
    CSIC, Spain.
    John Qi, Zhengling
    University of Penn, PA 19104 USA.
    Menko, Julien
    Haverford Coll, PA 19041 USA.
    Lu, Ye
    University of Penn, PA 19104 USA.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    de Paula, Julio C.
    Lewis and Clark Coll, OR 97219 USA.
    Amabilino, David B.
    CSIC, Spain.
    Johnson, A. T.
    University of Penn, PA 19104 USA.
    Smith, Walter F.
    Haverford Coll, PA 19041 USA.
    Photoconductivity of Nanofilaments That are Self-Assembled from a Porphyrin with Long Alkyl-Chain Substituents2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 46, p. 26154-26163Article in journal (Refereed)
    Abstract [en]

    Photoelectronically active nanostructures that are Self-assembled from organic rnolecules hold the prortu se of tailored functionality.with simple and inexpensive production. Comparison of nanoWires assembled from related componnds can give important insightS into the details of self-assembly and the,conduction meehanisms. We report the photoconductivity of nanofibers that are self-assembled from a porphyrin With long alkyl substituents. In contrast to previously studied porphyrin nanowires, the photoconductivity increases as atthospheric O-2 is increased. This can be explained-using the same model aS used in the previous studies, by assuming a different, line-up of the bands of the nanofilaments. with the electrode Fermi level. However, this model does not explain our observation that-at O-2 concentrations above 1%, the conduction increases with continued- illunation; this may be due to photoactivation of shallow O-2 adsorption sites. The overall conduction level is low even at high O-2 Concentration, because the alkyl substituents form an insulating sheath around the rianofibers. Such inSulation could be valuable in applications where it would prevent cross-talk between signal S darried in different nanofilaments. Schottky barriers at the interface between- organic nanostructures and electrodes strongly affect conduction and photoconduction, and are strongly influenced by atmospheric gases such, as O-2.

  • 31.
    Shirani, Hamid
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Sigurdson, Christina J.
    University of Calif San Diego, CA 92093 USA.
    Lindgren, Mikael
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Nilsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    A Palette of Fluorescent Thiophene-Based Ligands for the Identification of Protein Aggregates2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 43, p. 15133-15137Article in journal (Refereed)
    Abstract [en]

    By replacing the central thiophene unit of an anionic pentameric oligothiophene with other heterocyclic moities, a palette of pentameric thiophene-based ligands with distinct fluorescent properties were synthesized. All ligands displayed superior selectivity towards recombinant amyloid fibrils as well as disease-associated protein aggregates in tissue sections.

  • 32.
    Sjoqvist, Jonas
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Platinum(II) and Phosphorus MM3 Force Field Parametrization for Chromophore Absorption Spectra at Room Temperature2010In: JOURNAL OF PHYSICAL CHEMISTRY A, ISSN 1089-5639, Vol. 114, no 14, p. 4981-4987Article in journal (Refereed)
    Abstract [en]

    Platinum(II) and phosphine MM3 force field parameters are derived from fits to the ground state potential energy surface at the level of Kohn-Sham density functional theory with employment of the B3LYP exchange-correlation functional. The parametrization includes bond stretch, angle bend, and torsional parameters for a planar platinum(II) center with phosphine and ethynyl ligands. The force field is used to study the dynamics of a fifth-generation dendrimer-coated platinum(II)organic compound in tetrahydrofurane solution at room temperature, and, based on a selection of conformations from the molecular dynamics simulation, the averaged linear absorption spectrum is determined with use of the CAM-B3LYP functional. The main absorption peak in the theoretical absorption spectrum is found at a transition wavelength of 325 nm with a full-width at half-maximum of 26 am clue to conformational broadening.

  • 33.
    Sjöqvist, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    González-Cano, Rafael C.
    University of Málaga, Spain.
    López Navarette, Juan T.
    University of Málaga, Spain.
    Casado, Juan
    University of Málaga, Spain.
    Ruiz Delgado, M. Carmen
    University of Málaga, Spain.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 45, p. 24841-24852Article in journal (Refereed)
    Abstract [en]

    Infrared (IR) absorption and vibrational Raman spectra of a family of branched oligothiophenes have been determined experimentally as well as theoretically. The molecular spectra have been compared to those of the linear analogues, with identification made of spectral features due to structural properties that are valued in organic solar cell applications. The theoretical spectra have been obtained through a newly developed method in which individual conformer spectra, calculated at the time-dependent DFT level in this work, are weighted by statistics extracted from classical molecular dynamics trajectories. The agreement with experiment for the resulting averaged spectra is at least as good as, and often better than, what is observed for Boltzmann-weighted spectra. As the weights are available before the costly step of spectrum calculation, the method has the additional advantage of enabling efficient approximations. For simulating the molecular dynamics of the studied α,β-linked thiophenes and 2-methylthiophenes, high quality parameters have been derived for the CHARMM force field. Furthermore, the temperature dependence of the IR and Raman spectra have been investigated, both experimentally and theoretically.

  • 34.
    Sjöqvist, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Lindgren, Mikael
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Molecular dynamics effects on luminescence properties of oligothiophene derivatives: a molecular mechanics-response theory study based on the CHARMM force field and density functional theory2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 39, p. 17532-17542Article in journal (Refereed)
    Abstract [en]

    CHARMM force field parameter values for a class of oligothiophene derivatives have been derived with reference to density functional theory/B3LYP potential energy surfaces. The force field parametrization of these luminescent conjugated polyelectrolytes includes the electronic ground state as well as the strongly light absorbing first excited state. In conjunction with quantum chemical response theory calculations of transition state properties, a molecular dynamical model of the Stokes shift is obtained. The theoretical model is benchmarked against experimental data recorded at room temperature which refer to sodium salts of p-HTAA and p-FTAA with distilled water as a solvent. For p-HTAA the theoretically predicted Stokes shift of 112 nm is in good agreement with the experimental result of 124 nm, given the approximations about exciton localization that were introduced to obtain a force field for the excited state.

  • 35.
    Sjöqvist, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Mikkelsen, Kurt V.
    University of Copenhagen, Denmark .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    QM/MM-MD Simulations of Conjugated Polyelectrolytes: A Study of Luminescent Conjugated Oligothiophenes for Use as Biophysical Probes2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 19, p. 3419-3428Article in journal (Refereed)
    Abstract [en]

    A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field description of the solvent in its electronic ground state well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (in) ii) spectral response calculations by means of the quantum mechanics/molecular mechanics QM/MM approach. A detailed analysis of the combined polarization effects of the ionic moiety and the polar water solvent is presented. At an increased computational cost of 30% compared to a calculation excluding the solvent, the error in the transition wavelength of the dominant absorption band is kept as small as 1 nm as compared to the high-quality benchmark result, based largely on a QM description of the solvent. At a reduced computational cost the error of the same quantity is kept as small as 6 nm, with the cost reduction being the result of an effective description of the effects of the solvent by means of replacing the carboxylate ions with neutral hydrogens. In absorption spectroscopy, the obtained best theoretical results are in excellent agreement with the experimental benchmark measurement, regarding excitation energies as well as band intensities and profiles. In fluorescence spectroscopy, the experimental spectrum shows a vibrational progression that is not addressed by theory, but the theoretical band position is in excellent agreement with experiment, with a highly accurate description of the Stokes shift as a result.

  • 36.
    Sjöqvist, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Maria, Jerôme
    Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.
    Simon, Rozalyn
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Nilsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Lindgren, Mikael
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.
    Toward a molecular understanding of the detection of amyloid proteins with flexible conjugated oligothiophenes2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 42, p. 9820-9827Article in journal (Refereed)
    Abstract [en]

    Molecular and electronic structures and optical absorption properties of oligothiophenes used for spectral assignment of amyloid deposits have been investigated for a family of probes known as luminescent conjugated oligothiophenes (LCOs). Theoretical absorption spectra have been determined using conformational averaging, combining classical molecular dynamics (MD) simulations with quantum mechanical/molecular mechanics (QM/MM) time-dependent density functional theory (TD-DFT) spectrum calculations. Theoretical absorption spectra are in excellent agreement with experiments, showing average errors below 5 nm for absorption maxima. To couple observed properties to molecular structures, a measure of planarity is defined, revealing a strong correlation between the transition wavelength of the first and dominating electronically excited state and dihedral rotations. It is shown that from this correlation, predictions can be made of the absorption properties of probes based only on information from MD trajectories. We show experimentally that red shifts observed in the excitation maxima of LCOs when bound to amyloid protein aggregates are also evident in absorption spectra. We predict that these red shifts are due to conformational restriction of the LCO in a protein binding pocket, causing a planarization of the conjugated backbone. On the basis of our studies of planarity, it is shown that such shifts are both possible and realistic.

  • 37.
    Spadafora, Evan J
    et al.
    CEA CNRS UJF.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Zaireen Nisa Yahya, Wan
    CEA CNRS UJF.
    Lincker, Frederic
    CEA CNRS UJF.
    Demadrille, Renaud
    CEA CNRS UJF.
    Grevin, Benjamin
    CEA CNRS UJF.
    Local contact potential difference of molecular self-assemblies investigated by Kelvin probe force microscopy2011In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 99, no 23, p. 233102-Article in journal (Refereed)
    Abstract [en]

    Self-assembled pi-conjugated oligomer nanowires have been investigated by frequency modulation atomic force microscopy and amplitude modulation Kelvin probe force microscopy under ultra high vacuum. The distance dependence of the contact potential difference (CPD) has been analyzed by combining high resolution imaging with distance-spectroscopy measurements. It is shown that the apparition of a damping contrast characterizes the onset of short range electrostatic (SRE) forces, which are responsible for the occurrence of local CPD (LCPD) modulations correlated with the molecular lattice. By working at the onset of the damping contrast, the tip-surface separation can be adjusted to minimize the contribution of SRE forces to the measured CPD. VC 2011 American Institute of Physics. [doi:10.1063/1.3662850]

  • 38.
    Stochkel, Kristian
    et al.
    Aarhus University, Denmark .
    Nygaard Hansen, Christian
    Aarhus University, Denmark .
    Houmoller, Jorgen
    Aarhus University, Denmark .
    Munksgaard Nielsen, Lisbeth
    Aarhus University, Denmark .
    Anggara, Kelvin
    Aarhus University, Denmark .
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Nogueira, Fernando
    University of Coimbra, Portugal .
    Maltsev, Oleg V.
    Technical University of Munich, Germany .
    Hintermann, Lukas
    Technical University of Munich, Germany .
    Brondsted Nielsen, Steen
    Aarhus University, Denmark .
    Naumov, Pance
    New York University of Abu Dhabi, U Arab Emirates .
    Milne, Bruce F.
    University of Coimbra, Portugal .
    On the Influence of Water on the Electronic Structure of Firefly Oxyluciferin Anions from Absorption Spectroscopy of Bare and Monohydrated Ions in Vacuo2013In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, no 17, p. 6485-6493Article in journal (Refereed)
    Abstract [en]

    A complete understanding of the physics underlying the varied colors of firefly bioluminescence remains elusive because it is difficult to disentangle different enzyme-lumophore interactions. Experiments on isolated ions are useful to establish a proper reference when there are no microenvironmental perturbations. Here, we use action spectroscopy to compare the absorption by the firefly oxyluciferin lumophore isolated in vacuo and complexed with a single water molecule. While the process relevant to bioluminescence within the luciferase cavity is light emission, the absorption data presented here provide a unique insight into how the electronic states of oxyluciferin are altered by microenvironmental perturbations. For the bare ion we observe broad absorption with a maximum at 548 +/- 10 nm, and addition of a water molecule is found to blue-shift the absorption by approximately 50 nm (0.23 eV). Test calculations at various levels of theory uniformly predict a blue-shift in absorption caused by a single water molecule, but are only qualitatively in agreement with experiment highlighting limitations in what can be expected from methods commonly used in studies on oxyluciferin. Combined molecular dynamics simulations and time-dependent density functional theory calculations closely reproduce the broad experimental peaks and also indicate that the preferred binding site for the water molecule is the phenolate oxygen of the anion. Predicting the effects of microenvironmental interactions on the electronic structure of the oxyluciferin anion with high accuracy is a nontrivial task for theory, and our experimental results therefore serve as important benchmarks for future calculations.

  • 39.
    Trouillas, Patrick
    et al.
    University of Limoges, France; Palacky University, Czech Republic.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Gierschner, Johannes
    Madrid Institute Adv Studies IMDEA Nanosci, Spain.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Carlos Sancho-Garcia, Juan
    University of Alicante, Spain.
    Otyepka, Michal
    Palacky University, Czech Republic.
    Optical properties of wine pigments: theoretical guidelines with new methodological perspectives2015In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 71, no 20, p. 3079-3088Article in journal (Refereed)
    Abstract [en]

    Wine pigmentation results from the complex chemistry of anthocyanins. Their flavylium cation form is stabilized either by chemical transformation occurring during wine aging (e.g., pyranoanthocyanin formation), or by the formation of non-covalent complexes with (phenolic) copigments. Molecular modeling (quantum mechanics and molecular dynamics) is more and more adapted to understand wine chemistry and pigmentation. The constant developments of theoretical methodologies might get non-specialists easily lost. This manuscript is a review of the theoretical studies dedicated to the field of wine pigments, showing conformational analysis, energetics of the various forms, pigment/copigment (non-)covalent association, and charge transfer excited states. QM/MM calculations are newly performed here, which improve solvent description. The conclusion is a comprehensive guideline for an accurate prediction of light absorption by wine pigments and all related supramolecular processes.

  • 40.
    Vahlberg, Cecilia
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Uvdal, Kajsa
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Phenylboronic ester- and Phenylboronic acid-terminated alkanethiols on Gold SurfacesManuscript (preprint) (Other academic)
    Abstract [en]

    In this work, it is shown that well-organized monolayer of phenylboronic ester-terminated thiol (BOR-Capped) on gold surfaces can be prepared. Our results also show that the BORCapped molecular system can be cleaved directly on the surface, resulting in an unprotected BOR-Uncapped monolayer with the boronic acid functional groups available for dopamine coordination. The monolayers of BOR-Capped and BOR-Uncapped were characterized using infrared spectroscopy, near edge X-ray absorption fine structure spectroscopy, X-ray photoelectron spectroscopy, ellipsometry and contact angle goniometry. The X-ray photoelectron spectroscopy results showed that both BOR-Capped and BOR-Uncapped are chemically linked to the gold substrate. According to the infrared spectroscopy results, the main component of the C=O vibrational mode present in the amide moiety is perpendicular oriented relative to the gold surface normal for the BOR-Capped molecular system. The near edge X-ray absorption fine structure spectroscopy resonance peak located at approximately 285 eV, assigned to π* transitions, was used to estimate the average tilt angle of the vector parallel to the π* orbitals of the aromatic ring relative to the gold surface normal. The average tilt angle is estimated to be approximately 63º for BOR-Capped monolayer on gold surfaces. The aromatic ring of the BOR-Uncapped molecule has a more tilted orientation compared to BOR-Capped. The experimental infrared spectroscopy and near edge X-ray absorption fine structure spectroscopy results were supported with theoretical modeling including calculations of vibrational modes and of excitation processes.

  • 41.
    Vahlberg, Cecilia
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Uvdal, Kajsa
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Phenylboronic Ester- and Phenylboronic Acid-Terminated Alkanethiols on Gold Surfaces2012In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 116, no 1, p. 796-806Article in journal (Refereed)
    Abstract [en]

    In this work, it is shown that a well-organized monolayer of phenylboronic ester-terminated thiol (BOR-capped) on gold surfaces can be prepared. Our results also show that the BOR-capped molecular system can be cleaved directly on the surface, resulting in an unprotected BOR-uncapped monolayer with the boronic acid functional groups available for coordination to diol molecules in the ambient media. The monolayers of BOR-capped and BOR-uncapped were characterized using infrared spectroscopy, near edge X-ray absorption fine structure spectroscopy, X-ray photoelectron spectroscopy, ellipsometry, and contact angle goniometry. The X-ray photoelectron spectroscopy results showed that both BOR-capped and BOR-uncapped are chemically linked to the gold substrate. According to the infrared spectroscopy results, the main component of the CO vibrational mode present in the amide moiety is perpendicular oriented relative to the gold surface normal for the BOR-capped molecular system. The near edge X-ray absorption fine structure spectroscopy resonance peak located at approximately 285 eV, assigned to pi(1)* transitions, was used to estimate the average tilt angle of the vector parallel to the pi* orbitals of the aromatic ring relative to the gold surface normal. The average tilt angle is estimated to be approximately 63 degrees for the BOR-capped monolayer on gold surfaces. The aromatic ring of the BOR-uncapped molecule has a more tilted orientation compared to the BOR-capped one. The experimental infrared spectroscopy and near edge X-ray absorption fine structure spectroscopy results were supported with theoretical modeling including calculations of vibrational modes and of excitation processes.

  • 42.
    Vahlberg, Cecilia
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Villaume, Sebastien
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Uvdal, Kajsa
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, The Institute of Technology.
    Noradrenaline and a Thiol Analogue on Gold Surfaces: An Infrared Reflection-Absorption Spectroscopy, X-ray Photoelectron Spectroscopy, and Near-Edge X-ray Absorption Fine Structure Spectroscopy Study2011In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 115, no 1, p. 165-175Article in journal (Refereed)
    Abstract [en]

    Self-assembled monolayers and multilayers of a noradrenaline analogue (Nor-Pt) on gold substrates as well as multilayers of noradrenaline have been investigated by means of the molecular orientation, the molecule surface interaction, the molecular composition and the functional group availability for further biointeraction processes, using X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. A chemical shift (1.7 eV) of the S 2p peak to lower binding energies is observed, in the XPS spectrum, indicating that the Nor-Pt molecules are chemisorbed onto the gold substrate. The IR results show that Nor-Pt adsorbate has the C=O stretching vibration modes parallel oriented relative to the gold substrate. The average tilt angle of the aromatic ring relative to the gold surface normal is determined to be approximately 51 degrees, based on the NEXAFS measurements on Nor-Pt monolayers. The experimental results and assignments are supported with theoretical studies where we use the building block principle in the spectral analysis and compare with the measurements of noradrenaline and Nor-Pt. The theoretical calculations are shown to be useful; for angle dependence NEXAFS studies as resonances with fully pi* or sigma* character are preferred for correct analysis.

  • 43.
    Vahlberg, Cecilia
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Skoglund, Caroline
    Linköping University, Department of Medical and Health Sciences, Pharmacology. Linköping University, Faculty of Health Sciences.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Uvdal, Jahsa
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    The Structure of Benzenesulfonamide-Terminated Thiol on Gold Surfaces and the Interaction with Carbonic AnhydraseManuscript (preprint) (Other academic)
    Abstract [en]

    A well-structured and robust biomolecular monolayer based upon a benzenesulfonamideterminated alkane thiol, to be used as a model system for molecular recognition processes, was prepared. The benzenesulfonamide-terminated thiol adsorbed onto gold substrates was characterized using X-ray photoelectron spectroscopy, near edge X-ray absorption fine structure spectroscopy, infrared-reflection absorption spectroscopy and ellipsometry. The results showed that the benzenesulfonamide-terminated alkane thiol forms a wellorganized molecular layer on the gold substrates. The orientation of the aromatic ring relative to the gold surface was investigated by means of the angle defined as the normal to the aromatic ring relative to the normal to the gold surface. It was shown that the average tilt angle is approximately 62º. In a second step, the  benzenesulfonamideterminated thiol monolayer was exposed to carbonic anhydrase, which is an enzyme and a therapeutic target. Benzenesulfonamides are used in biomedical applications as inhibitors for carbonic anhydrase. Our purpose in this study was to investigate the recognition capability of the benzenesulfonamide when designed as a thiol monolayer. The interaction between the benzenesulfonamide-terminated monolayer and carbonic anhydrase was studied using ellipsometry and surface plasmon resonance. The results show that the benzenesulfonamide-terminated thiol adsorbed onto the gold substrates is able to bind carbonic anhydrase. The results also indicate that the interaction is specific.

  • 44.
    Verlaak, Stijn
    et al.
    IMEC VZW, B-3001 Louvain, Belgium.
    Beljonne, David
    Univ Mons, B-7000 Mons, Belgium.
    Cheyns, David
    IMEC VZW, B-3001 Louvain, Belgium.
    Rolin, Cedric
    IMEC VZW, B-3001 Louvain, Belgium.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Castet, Frederic
    Univ Bordeaux 1, Inst Mol Sci, F-33405 Talence, France.
    Cornil, Jerome
    Univ Mons, B-7000 Mons, Belgium.
    Heremans, Paul
    IMEC VZW, B-3001 Louvain, Belgium.
    Electronic Structure and Geminate Pair Energetics at Organic-Organic Interfaces: The Case of Pentacene/C-60 Heterojunctions2009In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 19, no 23, p. 3809-3814Article in journal (Refereed)
    Abstract [en]

    Organic semiconductors are characterized by localized states whose energies are predominantly determined by electrostatic interactions with their immediate molecular environment. As a result, the details of the energy landscape at heterojunctions between different organic semiconductors cannot simply be deduced from those of the individual semiconductors, and they have so far remained largely unexplored. Here, microelectrostatic computations are performed to clarify the nature of the electronic structure and geminate pair energetics at the pentacene/C-60 interface, as archetype for an interface between a donor molecule and a fullerene electron acceptor. The size and orientation of the molecular quadrupole moments, determined by material choice, crystal orientation, and thermodynamic growth parameters of the semiconductors, dominate the interface energetics. Not only do quadrupoles produce direct electrostatic interactions with charge carriers, but, in addition, the discontinuity of the quadrupole field at the interface induces permanent interface dipoles. That discontinuity is particularly striking for an interface with C-60 molecules, which by virtue of their symmetry possess no quadrupole. Consequently, at a pentacene/C-60 interface, both the vacuum-level shift and geminate pair dissociation critically depend on the orientation of the pentacene pi-system relative to the adjacent C-60.

  • 45.
    Volpi, Riccardo
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Kottravel, Sathish
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Norby, Morten Sten
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Denmark.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Effect of Polarization on the Mobility of C60: A Kinetic Monte-Carlo Study2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 2, p. 812-824Article in journal (Refereed)
    Abstract [en]

    We present a study of mobility field and temperature dependence for C60 with Kinetic Monte-Carlo simulations. We propose a new scheme to take into account polarization effects in organic materials through atomic induced dipoles on nearby molecules. This leads to an energy correction for the single site energies and to an external reorganization happening after each hopping. The inclusion of polarization allows us to obtain a good agreement with experiments for both mobility field and temperature dependence.

  • 46.
    Volpi, Riccardo
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Nassau, Racine
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Charge-transfer state dynamics at C60-anthracene interfaces: a kinetic Monte Carlo approach2015Manuscript (preprint) (Other academic)
    Abstract [en]

    The morphology of organic interfaces plays an important role in charge-transfer (CT) state splitting, and therefore has a significant impact on the efficiency of organic solar cells. In this article, we use our kinetic Monte Carlo (KMC) method on molecular dynamics-simulated anthracene-C60 interfaces to study the relation between interface morphology and CT state splitting. These KMC simulations were performed at a range of applied electric fields, and with the fields applied at a range of angles to the interface. The results show that depending on the relative orientation of the anthracene and C60 molecules, CT state splitting shows different behavior with respect to both applied field strength and applied field angle. Different orientations may be better suited for different applications. The inclusion of polarization in our model is shown to  increase CT state splitting for both orientations studied.

  • 47.
    Volpi, Riccardo
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Transition fields in organic materials: From percolation to inverted Marcus regime. A consistent Monte Carlo simulation in disordered PPV2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 142, no 9, p. 094503-Article in journal (Refereed)
    Abstract [en]

    In this article, we analyze the electric field dependence of the hole mobility in disordered poly (p-phenylene vinylene). The charge carrier mobility is obtained from Monte Carlo simulations. Depending on the field strength three regions can be identified: the percolation region, the correlation region, and the inverted region. Each region is characterized by a different conduction mechanism and thus a different functional dependence of the mobility on the electric field. Earlier studies have highlighted that Poole-Frenkel law, which appears in the correlation region, is based on the type of correlation caused by randomly distributed electric dipoles. This behavior is thus observed in a limited range of field strengths, and by studying a broader range of electric fields, a more fundamental understanding of the transport mechanism is obtained. We identify the electric fields determining the transitions between the different conduction mechanisms in the material and we explain their physical origin. In principle, this allows us to characterize the mobility field dependence for any organic material. Additionally, we study the charge carrier trapping mechanisms due to diagonal and off-diagonal disorder, respectively. (C) 2015 AIP Publishing LLC.

  • 48.
    Vonau, F
    et al.
    University Haute Alsace.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Isare, B
    University of Paris.
    Aubel, D
    University Haute Alsace.
    Habar, M
    University Haute Alsace.
    Bouteiller, L
    University Paris.
    Reiter, G
    University of Freiburg.
    Geskin, V
    University Mons Hainaut Mat Nova.
    Zerbetto, F
    Dipartimento Chim G Ciamician.
    Lazzaroni, R
    University Mons Hainaut Mat Nova.
    Simon , L
    University Haute Alsace.
    Branched Substituents Generate Improved Supramolecular Ordering in Physisorbed Molecular Assemblies2009In: JOURNAL OF PHYSICAL CHEMISTRY C, ISSN 1932-7447 , Vol. 113, no 12, p. 4955-4959Article in journal (Refereed)
    Abstract [en]

    We present an experimental study supported by molecular simulations of the influence of the shape of alkyl side groups on the interactions and self-organization of supramolecular assemblies, built from bis-ureasubstituted toluene molecules deposited on Au(111) surfaces. In particular, we demonstrate the crucial importance of the presence of branched alkyl groups (i.e., ethylhexyl) that allow two adjacent supramolecular polymers to arrange closer to each other, leading to the formation of molecular "zippers". Thus, steric constraints at the level of individual molecules can generate improved Ordering between neighboring supramolecular polymers interacting with a planar substrate.

1 - 48 of 48
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