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  • 1. Bouchet, Aude
    et al.
    Brotin, Thierry
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cavagnat, Dominique
    Buffeteaeu, Thierry
    Enantioselective Complexation of Chiral Propylene Oxide by an Enantiopure Water-Soluble Cryptophane2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 10, p. 4178-4181Article in journal (Refereed)
    Abstract [en]

    ECD and NMR experiments show that the complexation of propylene oxide (PrO) within the cavity of an enantiopure water-soluble cryptophane 1 in NaOH solution is enantioselective and that the (R)-PrO@PP-1 diastereomer is more stable than the (S)-PrO@PP-1 diastereomer with a free energy difference of 1.7 kJ/mol. This result has been confirmed to by molecular dynamics (MD) and ab initio calculations. The enantioselectivity is preserved in LiOH and KOH solutions even though the binding constants decrease, whereas PrO is not complexed in CsOH solution.

  • 2. Bouchet, Aude
    et al.
    Brotin, Thierry
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cavagnat, Dominique
    Buffeteau, Thierry
    Conformational Effects Induced by Guest Encapsulation in an Enantiopure Water-Soluble Cryptophane2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 5, p. 1372-1383Article in journal (Refereed)
    Abstract [en]

    A new water-soluble cryptophane 1 derivative (penta-hydroxyl cryptophane-A) has been synthesized from cryptophanol-A and the chiroptical properties of its two enantiomers M M-1 and P P-1 have been studied by polarimetry, electronic circular dichroism (ECD), and vibrational circular dichroism (VCD). Cryptophane 1 shows specific circular dichroism responses upon complexation that depend on the size of the guest and on the nature of the counterion (Li+, Na+, K+, Cs+) present in the solution. In LiOH and NaOH solutions, chiroptical changes induced by the encapsulation of guests and by the presence of cations in the vicinity of hosts can be interpreted from molecular dynamics (MD) and ab initio calculations by subtle conformational changes of the bridges. In KOH solution, the exchange dynamics is dependent on the size of the guest molecules, whereas in CsOH solution no encapsulation effect is observed whatever the size of the guest molecule. This last behavior comes from the fact that host 1 exhibits a very high affinity for cesium cations.

  • 3. Brotin, Thierry
    et al.
    Montserret, Roland
    Bouchet, Aude
    Cavagnat, Dominique
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Buffeteau, Thierry
    High Affinity of Water-Soluble Cryptophanes for Cesium Cations2012In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 77, no 2, p. 1198-1201Article in journal (Refereed)
    Abstract [en]

    Exceptionally high affinity for cesium cations was achieved in aqueous solution using two enantiopure cryptophanes. Complexation of cesium was evidenced by Cs-133 NMR spectroscopy and by electronic circular dichroism (ECD). Binding constants as high as 6 X 10(9) M-1 have been measured by isothermal titration calorimetry (ITC). Very strong complexation of rubidium cations (K similar to 10(6) M-1) has also been measured. Chiral hosts allowed the detection of the two cations at low concentrations (mu M) using ECD.

  • 4. Böhlin, J.
    et al.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Stafström, S.
    Effect of dynamic disorder on charge transport along a pentacene chain2011In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 83, no 8, p. 085209-Article in journal (Refereed)
    Abstract [en]

    The lattice equation of motion and a numerical solution of the time-dependent Schrodinger equation provide us with amicroscopic picture of charge transport in highly ordered molecular crystals. We have chosen the pentacene single crystal as a model system, and we study charge transport as a function of phonon-mode time-dependent fluctuations in the intermolecular electron transfer integral. For comparison, we include similar fluctuations also in the intramolecular potentials. The variance in these energy quantities is closely related to the temperature of the system. The pentacene system is shown to be very sensitive to fluctuation in the intermolecular transfer integral, revealing a transition from adiabatic to nonadiabatic polaron transport for increasing temperatures. The extension of the polaron at temperatures above 200 K is limited by the electron localization length rather than the interplay between the electron transfer integral and the electron-phonon coupling strength.

  • 5.
    Cornelissen, Tim D.
    et al.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Urbanaviciute, Indre
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Kemerink, Martijn
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Kinetic Monte Carlo simulations of organic ferroelectrics2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 3, p. 1375-1383Article in journal (Refereed)
    Abstract [en]

    Ferroelectrics find broad applications, e.g. in non-volatile memories, but the switching kinetics in real, disordered, materials is still incompletely understood. Here, we develop an electrostatic model to study ferroelectric switching using 3D Monte Carlo simulations. We apply this model to the prototypical small molecular ferroelectric trialkylbenzene-1,3,5-tricarboxamide (BTA) and find good agreement between the Monte Carlo simulations, experiments, and molecular dynamics studies. Since the model lacks any explicit steric effects, we conclude that these are of minor importance. While the material is shown to have a frustrated antiferroelectric ground state, it behaves as a normal ferroelectric under practical conditions due to the large energy barrier for switching that prevents the material from reaching its ground state after poling. We find that field-driven polarization reversal and spontaneous depolarization have orders of magnitude different switching kinetics. For the former, which determines the coercive field and is relevant for data writing, nucleation occurs at the electrodes, whereas for the latter, which governs data retention, nucleation occurs at disorder-induced defects. As a result, by reducing the disorder in the system, the polarization retention time can be increased dramatically while the coercive field remains unchanged.

  • 6. Danila, Ion
    et al.
    Riobe, Francois
    Piron, Flavia
    Puigmarti-Luis, Josep
    Wallis, John D.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Beljonne, David
    Amabilino, David B.
    Avarvari, Narcis
    Hierarchical Chiral Expression from the Nano- to Mesoscale in Synthetic Supramolecular Helical Fibers of a Nonamphiphilic C(3)-Symmetrical pi-Functional Molecule2011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 21, p. 8344-8353Article in journal (Refereed)
    Abstract [en]

    The controlled preparation of chiral structures is a contemporary challenge for supramolecular science because of the interesting properties that can arise from the resulting materials, and here we show that a synthetic nonamphiphilic C(3) compound containing pi-functional tetrathiafulvalene units can form this kind of object. We describe the synthesis, characterization, and self-assembly properties in solution and in the solid state of the enantiopure materials. Circular dichroism (CD) measurements show optical activity resulting from the presence of twisted stacks of preferential helicity and also reveal the critical importance of fiber nucleation in their formation. Molecular mechanics (MM) and molecular dynamics (MD) simulations combined with CD theoretical calculations demonstrate that the (5) enantiomer provides the (M) helix, which is more stable than the (P) helix for this enantiomer. This relationship is for the first time established in this family of C(3) symmetric compounds. In addition, we show that introduction of the "wrong" enantiomer in a stack decreases the helical reversal barrier in a nonlinear manner, which very probably accounts for the absence of a "majority rules" effect. Mesoscopic chiral fibers, which show inverted helicity, i.e. (P) for the (S) enantiomer and (M) for the (R) one, have been obtained upon reprecipitation from dioxane and analyzed by optical and electronic microscopy. The fibers obtained with the racemic mixture present, as a remarkable feature, opposite homochiral domains within the same fiber, separated by points of helical reversal. Their formation can be explained through an "oscillating" crystallization mechanism. Although C(3) symmetric disk-shaped molecules containing a central benzene core substituted in the 1,3,5 positions with 3,3'-diamido-2,2'-bipyridine based wedges have shown peculiar self-assembly properties for amphiphilic derivatives, the present result shows the benefits of reducing the nonfunctional part of the molecule, in our case with short chiral isopentyl chains. The research reported herein represents an important step toward the preparation of functional mesostructures with controlled helical architectures.

  • 7. Elie, Margaux
    et al.
    Weber, Michael D.
    Di Meo, Florent
    Sguerra, Fabien
    Lohier, Jean-Francois
    Pansu, Robert B.
    Renaud, Jean-Luc
    Hamel, Matthieu
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Costa, Ruben D.
    Gaillard, Sylvain
    Role of the Bridging Group in Bis-Pyridyl Ligands: Enhancing Both the Photo- and Electroluminescent Features of Cationic (IPr) Cu-I Complexes2017In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 23, no 64, p. 16328-16337Article in journal (Refereed)
    Abstract [en]

    We report on the benefits of changing the bridging group X of bis-pyridyl ligands, that is, Py-X-Py where X is NH, CH2, C(CH3)(2), or PPh, on the photo-and electroluminescent properties of a new family of luminescent cationic H-heterocyclic carbene (NHC) copper(I) complexes. A joint experimental and theoretical study demonstrates that the bridging group affects the molecular conformation from a planar-like structure (X is NH and CH2) to a boat-like structure (X is C(CH3)(2) and PPh), leading to i) four-fold enhancement of the photoluminescence quantum yield (phi(em)) without affecting the thermally activated delayed fluorescence mechanism, and ii) one order of magnitude reduction of the ionic conductivity (sigma) of thin films. This leads to an overall enhancement of the device efficacy and luminance owing to the increased phi(em) and the use of low applied driving currents.

  • 8.
    Holmgaard List, Nanna
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Knoops, Jeremie
    Rubio-Magnieto, Jenifer
    Ide, Julien
    Beljonne, David
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Surin, Mathieu
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 42, p. 14947-14953Article in journal (Refereed)
    Abstract [en]

    Induced circular dichroism (ICD) of DNA-binding ligands is well known to be strongly influenced by the specific mode of binding, but the relative importance of the possible mechanisms has remained undetermined. With a combination of molecular dynamics simulations, CD response calculations, and experiments on an AT-sequence, we show that the ICD of minor-groove-bound 4',6-diamidino-2-phenylindole (DAPI) originates from an intricate interplay between the chiral imprint of DNA, off-resonant excitonic coupling to nucleobases, charge-transfer, and resonant excitonic coupling between DAPIs. The significant contributions from charge-transfer and the chiral imprint to the ICD demonstrate the inadequacy of a standard Frenkel exciton theory of the DAPI-DNA interactions.

  • 9. Iavicoli, P.
    et al.
    Xu, H.
    Feldborg, L. N.
    Linares, Mathieu
    Linköping University, Sweden .
    Paradinas, M.
    Stafström, S.
    Ocal, C.
    Nieto-Ortega, B.
    Casado, J.
    Navarrete, J. T. L.
    Lazzaroni, R.
    De Feyter, S.
    Amabilino, D. B.
    Tuning the supramolecular chirality of one-and two-dimensional aggregates with the number of stereogenic centers in the component porphyrins2010In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 132, no 27, p. 9350-9362Article in journal (Refereed)
    Abstract [en]

    A synthetic strategy was developed for the preparation of porphyrins containing between one and four stereogenic centers, such that their molecular weights vary only as a result of methyl groups which give the chiral forms. The low-dimensional nanoscale aggregates of these compounds Reveal the profound effects of this varying molecular chirality on their supramolecular structure and optical activity. The number of stereogenic centers influences significantly the self-assembly and chiral structure of the aggregates of porphyrin molecules described here. A scanning tunneling microscopy study of monolayers on graphite shows that the degree of structural chirality with respect to the surface increases almost linearly with the number of stereogenic centers, and only one handedness is formed in the monolayers, whereas the achiral compound forms a mixture of mirror-image domains at the surface. In solution, four hydrogen bonds induce the formation of an H-aggregate, and circular dichroism measurements and theoretical studies indicate that the compounds self-assemble into helical structures. Both the chirality and stability of the aggregates depend critically on the number of stereocenters. The chiral porphyrin derivatives gelate methylcyclohexane at concentrations dependent on the number and position of chiral groups at the periphery of the aromatic core, reflecting the different aggregation forces of the molecules in solution. Increasing the number of stereogenic centers requires more material to immobilize the solvent, in all likelihood because of the greater solubility of the porphyrins. The vibrational circular dichroism spectra of the gels show that all compounds have a chiral environment around the amide bonds, confirming the helical model proposed by calculations. The morphologies of the xerogels (studied by scanning electron microscopy and scanning force microscopy) are similar, although more fibrous features are present in the molecules with fewer stereogenic centers. Importantly, the presence of only one stereogenic center, bearing a methyl group as the desymmetrizing ligand, in a molecule of considerable molecular weight is enough to induce singlehanded chirality in both the one-and two-dimensional supramolecular self-assembled structures.

  • 10.
    König, Carolin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Skanberg, Robin
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Hotz, Ingrid
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Ynnerman, Anders
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Norman, P.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations2018In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, no 24, p. 3030-3033Article in journal (Refereed)
    Abstract [en]

    A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol(-1) due to the interactions between the anionic carboxyl groups of the probe and the cationic epsilon-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

  • 11.
    Linares, Mathieu
    et al.
    University of Mons, Belgium .
    Beljonne, D.
    Cornil, J.
    Lancaster, K.
    Brédas, J. -L
    Verlaak, S.
    Mityashin, A.
    Heremans, P.
    Fuchs, A.
    Lennartz, C.
    Idé, J.
    Méreau, R.
    Aurel, P.
    Ducasse, L.
    Castet, F.
    On the interface dipole at the pentacene-fullerene heterojunction: A theoretical study2010In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 7, p. 3215-3224Article in journal (Refereed)
    Abstract [en]

    The electronic structure at organic/organic interfaces plays a key role, among others, in defining the quantum efficiency of organics-based photovoltaic cells. Here, we perform quantum-chemical and microelectrostatic calculations on molecular aggregates of various sizes and shapes to characterize the interfacial dipole moment at pentacene/C60 heterojunctions. The results show that the interfacial dipole mostly originates in polarization effects due to the asymmetry in the multipolar expansion of the electronic density distribution between the interacting molecules, rather than in a charge transfer from donor to acceptor. The local dipole is found to fluctuate in sign and magnitude over the interface and appears as a sensitive probe of the relative arrangements of the pentacene and C60 molecules (and of the resulting local electrical fields sensed by the molecular units).

  • 12.
    Linares, Mathieu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Stafström, Sven
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    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, E-ISSN 1520-5207, 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.

  • 13.
    Linares, Mathieu
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sun, Haofan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. East China Univ Sci & Technol, Shanghai Key Lab Funct Mat Chem, Dept Chem & Mol Engn, Shanghai 200237, Peoples R China.
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Andreasson, Joakim
    Chalmers Univ Technol, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Norman, P.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 7, p. 3637-3643Article in journal (Refereed)
    Abstract [en]

    DNA binding modes of the stereoisomeric rotamers of two dithenylethene derivatives (DTE1 and DTE2) representing candidate molecular photoswitches of great promise for photopharmacology and nanotechnology have been identified and characterized in terms of their binding energies and electronic circular dichroism (CD) responses. In the open form, two binding modes are identified namely minor-groove binding of the lowest-energy conformer with an anti-parallel arrangement of methyl groups and major-groove double-intercalation of the P-enantiomers of an intermediate-state rotamer. Only the latter binding mode is found to be enantiomerically selective and expected to have an overall negative linear dichroism (LD) as observed in the experiment for DTE1 (Angew. Chem., Int. Ed., 2013, 52, 4393). In the closed form, the most favorable binding mode is found to be minor groove binding. Also this binding mode is found to be enantiomerically selective and for DTE1, it is the M-enantiomer that binds the strongest, showing a positive theoretical signature CD band in the long wavelength region with origin in pyridinium ligands. The theoretical CD spectrum is found to be in good agreement with the experimental one, which provides an indirect evidence for a correct identification of the binding mode in the closed form.

  • 14.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Hugosson, Håkan W.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics. 5)Department of Physics and Astronomy, Materials Theory Division, Uppsala University.
    Temperature dependence of band gaps and conformational disorder in PEDOT and its selenium and tellurium derivatives: density functional calculations2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690Article in journal (Refereed)
    Abstract [en]

    The conducting polymer poly(3,4-ethylenedioxythiophene), or PEDOT, is an attractive material for flexibleelectronics. We present combined molecular dynamics and quantum chemical calculations, based on den-sity functional theory, of EDOT oligomers and isoelectronic selenium and tellurium derivatives (EDOS andEDOTe) to address the effect of temperature on the geometrical and electronic properties of these systems.With finite size scaling, we also extrapolate our results to the infinite polymers, i.e. PEDOT, PEDOS and PEDOTe. Our computations indicate that the most favourable oligomer conformations at finite temperature are conformations around the flat trans-conformation and a non-flat conformation around 45 from the cis-conformation. Also, the dihedral stiffness increases with the atomic number of the heteroatom. We find excellent agreement with experimentally measured gaps for PEDOT and PEDOS. For PEDOT, the gap does not increase with temperature where as this is the case for its derivatives. The conformational disorder as well as the choice of basis set both significantly affect the calculated gaps.

  • 15.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University,.
    Optical properties of Naphthobischalcogenadiazoles from density functional perspectiveManuscript (preprint) (Other academic)
    Abstract [en]

    In the present work the density functional calculations of two naphthobischalcogenadiazole (NXz) oligomers are shown. The oxygen- and sulphur-containing NXz trimers were optimized in a form of a neutral oligomer and a radical cation in order to investigate structural changes resulting from the polaron formation. The influence of polaron on band gaps is determined and supported with densities of states analysis together with absorption spectra. This manuscript used B3LYP and ωB97XD functionals in combination with 6-31+G(d) basis set.

  • 16.
    Mirsakiyeva, Amina
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University,.
    Polaron formation and optical absorption in PEDOT and its selenium and tellurium derivatives: density functional calculationsManuscript (preprint) (Other academic)
    Abstract [en]

    We present a density functional theory (DFT) study on polaron formation and optical properties of PEDOT and its selenium and tellurium derivatives. Comparing a number of combinations of basis set and approximations to the exchange-correlation functional, we find that the ωB97XD functional is an overall good choice giving well-localized polarons and optical spectra in good agreement with experiment. This functional has the correct long-range  asymptotic behavior, and also includes some short-range Hartree-Fock exchange. Despite the  long-range Hartree-Fock exchange part present in this functional, the spin contamination remains relatively limited and it also stably produces results that are virtually independent of the basis set used.

  • 17.
    Rolland, Nicolas
    et al.
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Franco-Gonzalez, Juan Felipe
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Volpi, Riccardo
    Linkoping Univ, Dept Phys Chem & Biol IFM, SE-58183 Linkoping 3, Sweden.;RIST, Machine Learning & Optimizat Grp, Cluj Napoca, Romania..
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Zozoulenko, Igor, V
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Understanding morphology-mobility dependence in PEDOT:Tos2018In: Physical Review Materials, ISSN 2475-9953, Vol. 2, no 4, article id 045605Article in journal (Refereed)
    Abstract [en]

    The potential of conjugated polymers to compete with inorganic materials in the field of semiconductor is conditional on fine-tuning of the charge carriers mobility. The latter is closely related to the material morphology, and various studies have shown that the bottleneck for charge transport is the connectivity between well-ordered crystallites, with a high degree of pi-pi stacking, dispersed into a disordered matrix. However, at this time there is a lack of theoretical descriptions accounting for this link between morphology and mobility, hindering the development of systematic material designs. Here we propose a computational model to predict charge carriers mobility in conducting polymer PEDOT depending on the physicochemical properties of the system. We start by calculating the morphology using molecular dynamics simulations. Based on the calculated morphology we perform quantum mechanical calculation of the transfer integrals between states in polymer chains and calculate corresponding hopping rates using the Miller-Abrahams formalism. We then construct a transport resistive network, calculate the mobility using a mean-field approach, and analyze the calculated mobility in terms of transfer integrals distributions and percolation thresholds. Our results provide theoretical support for the recent study [Noriega et al., Nat Mater 12, 1038 (2013)] explaining why the mobility in polymers rapidly increases as the chain length is increased and then saturates for sufficiently long chains. Our study also provides the answer to the long-standing question whether the enhancement of the crystallinity is the key to designing high-mobility polymers. We demonstrate, that it is the effective pi-pi stacking, not the long-range order that is essential for the material design for the enhanced electrical performance. This generic model can compare the mobility of a polymer thin film with different solvent contents, solvent additives, dopant species or polymer characteristics, providing a general framework to design new high mobility conjugated polymer materials.

  • 18.
    Rubio-Magnieto, Jenifer
    et al.
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium.;Univ Jaume 1, Dept Quim Inorgan & Organ, Bioinspired Supramol Chem & Mat Grp, Avda Sos Baynat S-N, E-12071 Castellon de La Plana, Spain..
    Kajouj, Sofia
    Univ Libre Bruxelles, Chim Organ & Photochim CP160 08, 50 Ave FD Roosevelt, B-1050 Brussels, Belgium..
    Di Meo, Florent
    Univ Limoges, Sch Pharm, INSERM, U1248,IPPRITT, 2 Rue Dr Marcland, F-87025 Limoges, France..
    Fossepre, Mathieu
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium..
    Trouillas, Patrick
    Univ Limoges, Sch Pharm, INSERM, U1248,IPPRITT, 2 Rue Dr Marcland, F-87025 Limoges, France.;Palacky Univ, Fac Sci, RCPTM, Slechtitelu 27, Olomouc 78371, Czech Republic..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Moucheron, Cecile
    Univ Libre Bruxelles, Chim Organ & Photochim CP160 08, 50 Ave FD Roosevelt, B-1050 Brussels, Belgium..
    Surin, Mathieu
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium..
    Binding Modes and Selectivity of Ruthenium Complexes to Human Telomeric DNA G-Quadruplexes2018In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 24, no 58, p. 15577-15588Article in journal (Refereed)
    Abstract [en]

    Metal complexes constitute an important class of DNA binders. In particular, a few ruthenium polyazaaromatic complexes are attractive as light switches because of their strong luminescence enhancement upon DNA binding. In this paper, a comprehensive study on the binding modes of several mononuclear and binuclear ruthenium complexes to human telomeric sequences, made of repeats of the d(TTAGGG) fragment is reported. These DNA sequences form G-quadruplexes (G4s) at the ends of chromosomes and constitute a relevant biomolecular target in cancer research. By combining spectroscopy experiments and molecular modelling simulations, several key properties are deciphered: the binding modes, the stabilization of G4 upon binding, and the selectivity of these complexes towards G4 versus double-stranded DNA. These results are rationalized by assessing the possible deformation of G4 and the binding free energies of several binding modes via modelling approaches. Altogether, this comparative study provides fundamental insights into the molecular recognition properties and selectivity of Ru complexes towards this important class of DNA G4s.

  • 19. Selegard, Robert
    et al.
    Rouhbalchsh, Zeinab
    Shirani, Hamid
    Johanson, Leif B. G.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Aili, Daniel
    Nilsson, K. Peter R.
    Distinct Electrostatic Interactions Govern the Chiro-Optical Properties and Architectural Arrangement of Peptide-Oligothiophene Hybrid Materials2017In: Macromolecules, ISSN 0024-9297, E-ISSN 1520-5835, Vol. 50, no 18, p. 7102-7110Article in journal (Refereed)
    Abstract [en]

    The development of chiral optoelectronic materials is of great interest due to their potential of being utilized in electronic devices, biosensors, and artificial enzymes. Herein, we report the chiral optical properties and architectural arrangement of optoelectronic materials generated from noncovalent self-assembly of a cationic synthetic peptide and five chemically defined anionic pentameric oligothiophenes. The peptide-oligothiophene hybrid materials exhibit a three-dimensional ordered helical structure and optical activity in the pi-pi* transition region that are observed due to a single chain induced chirality of the conjugated thiophene backbone upon interaction with the peptide. The latter property is highly dependent on electrostatic interactions between the peptide and the oligothiophene, verifying that a distinct spacing of the carboxyl groups along the thiophene backbone is a major chemical determinant for having a hybrid material with distinct optoelectronic properties. The necessity of the electrostatic interaction between specific carboxyl functionalities along the thiophene backbone and the lysine residues of the peptide, as well as the induced circular dichroism of the thiophene backbone, was also confirmed by theoretical calculations. We foresee that our findings will aid in designing optoelectronic materials with dynamic architectonical precisions as well as offer the possibility to create the next generation of materials for organic electronics and organic bioelectronics.

  • 20.
    Urbanaviciute, Indre
    et al.
    Linkoping Univ, Complex Mat & Devices, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Bhattacharjee, Subham
    Eindhoven Univ Technol, Lab Macromol & Organ Chem, POB 513, NL-5600 MB Eindhoven, Netherlands..
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Lugger, Jody A. M.
    Eindhoven Univ Technol, Lab Macromol & Organ Chem, POB 513, NL-5600 MB Eindhoven, Netherlands..
    Cornelissen, Tim D.
    Linkoping Univ, Complex Mat & Devices, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sijbesma, Rint P.
    Eindhoven Univ Technol, Lab Macromol & Organ Chem, POB 513, NL-5600 MB Eindhoven, Netherlands..
    Kemerink, Martijn
    Linkoping Univ, Complex Mat & Devices, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Suppressing depolarization by tail substitution in an organic supramolecular ferroelectric2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 4, p. 2069-2079Article in journal (Refereed)
    Abstract [en]

    Despite being very well established in the field of electro-optics, ferroelectric liquid crystals so far lacked interest from a ferroelectric device perspective due to a typically high operating temperature, a modest remnant polarization and/or poor polarization retention. Here, we experimentally demonstrate how simple structural modification of a prototypical ferroelectric liquid-crystal benzene-1,3,5-trisamide (BTA) - introduction of branched-tail substituents - results in materials with a wide operating temperature range and a data retention time of more than 10 years in thin-film solution-processed capacitor devices at room temperature. The observed differences between linear- and branched-tail compounds are analyzed using density functional theory (DFT) and molecular dynamics (MD) simulations. We conclude that morphological factors like improved packing quality and reduced disorder, rather than electrostatic interactions or intra/inter-columnar steric hindrance, underlay the superior properties of the branched-tailed BTAs. Synergistic effects upon blending of compounds with branched and linear side-chains can be used to further improve the materials' characteristics.

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