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  • 1.
    Bian, Qingzhen
    et al.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Ma, Fei
    Lund Univ, Div Chem Phys, S-22100 Lund, Sweden..
    Chen, Shula
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Wei, Qi
    Univ Macau, Inst Appl Phys & Mat Engn, Macau, Peoples R China..
    Su, Xiaojun
    Lund Univ, Div Chem Phys, S-22100 Lund, Sweden..
    Buyanova, Irina A.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Chen, Weimin M.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Ponseca, Carlito S.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Karki, Khadga J.
    Lund Univ, Div Chem Phys, S-22100 Lund, Sweden..
    Yartsev, Arkady
    Lund Univ, Div Chem Phys, S-22100 Lund, Sweden..
    Inganas, Olle
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Vibronic coherence contributes to photocurrent generation in organic semiconductor heterojunction diodes2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 617Article in journal (Refereed)
    Abstract [en]

    Charge separation dynamics after the absorption of a photon is a fundamental process relevant both for photosynthetic reaction centers and artificial solar conversion devices. It has been proposed that quantum coherence plays a role in the formation of charge carriers in organic photovoltaics, but experimental proofs have been lacking. Here we report experimental evidence of coherence in the charge separation process in organic donor/acceptor heterojunctions, in the form of low frequency oscillatory signature in the kinetics of the transient absorption and nonlinear two-dimensional photocurrent spectroscopy. The coherence plays a decisive role in the initial 200 femtoseconds as we observe distinct experimental signatures of coherent photocurrent generation. This coherent process breaks the energy barrier limitation for charge formation, thus competing with excitation energy transfer. The physics may inspire the design of new photovoltaic materials with high device performance, which explore the quantum effects in the next-generation optoelectronic applications.

  • 2.
    Björk, Linnea
    et al.
    Department of Physics Chemistry and Biology Linköping University SE-581 83 Linköping Sweden.
    Shirani, Hamid
    Department of Physics Chemistry and Biology Linköping University SE-581 83 Linköping Sweden.
    Todarwal, Yogesh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Vidal, Ruben
    Department of Pathology and Laboratory Medicine Indiana University School of Medicine Indianapolis 46202 Indiana USA.
    Ghetti, Bernardino
    Department of Pathology and Laboratory Medicine Indiana University School of Medicine Indianapolis 46202 Indiana USA.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Klingstedt, Therése
    Department of Physics Chemistry and Biology Linköping University SE-581 83 Linköping Sweden.
    Nilsson, K. Peter R.
    Department of Physics Chemistry and Biology Linköping University SE-581 83 Linköping Sweden.
    Distinct Heterocyclic Moieties Govern the Selectivity of Thiophene‐Vinylene‐Based Ligands towards Aβ or Tau Pathology in Alzheimer's Disease2023In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, Vol. 26, no 41, p. e202300583-Article in journal (Refereed)
    Abstract [en]

    Distinct aggregated proteins are correlated with numerous neurodegenerative diseases and the development of ligands that selectively detect these pathological hallmarks is vital. Recently, the synthesis of thiophene-based optical ligands, denoted bi-thiophene-vinyl-benzothiazoles (bTVBTs), that could be utilized for selective assignment of tau pathology in brain tissue with Alzheimer's disease (AD) pathology, was reported. Herein, we investigate the ability of these ligands to selectively distinguish tau deposits from aggregated amyloid-β (Aβ), the second AD associated pathological hallmark, when replacing the terminal thiophene moiety with other heterocyclic motifs. The selectivity for tau pathology was reduced when introducing specific heterocyclic motifs, verifying that specific molecular interactions between the ligands and the aggregates are necessary for selective detection of tau deposits. In addition, ligands having certain heterocyclic moieties attached to the central thiophene-vinylene building block displayed selectivity to aggregated Aβ pathology. Our findings provide chemical insights for the development of ligands that can distinguish between aggregated proteinaceous species consisting of different proteins and might also aid in creating novel agents for clinical imaging of tau pathology in AD.

  • 3. 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.

  • 4. Bouchet, Aude
    et al.
    Brotin, Thierry
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    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.

  • 5.
    Brossier, Mathis
    et al.
    Univ Paris Saclay, France.
    Skånberg, Robin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Besançon, Lonni
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Isenberg, Tobias
    Univ Paris Saclay, France.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Bock, Alexander
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Moliverse: Contextually embedding the microcosm into the universe2023In: Computers & graphics, ISSN 0097-8493, E-ISSN 1873-7684, Vol. 112, p. 22-30Article in journal (Refereed)
    Abstract [en]

    We present Moliverse, an integration of the molecular visualization framework VIAMD into the astronomical visualization software OpenSpace, allowing us to bridge the two extreme ends of the scale spectrum to show, for example, the gas composition in a planets atmosphere or molecular structures in comet trails and can empower the creation of educational exhibitions. For that purpose we do not use a linear scale traversal but break the scale continuity and show molecular simulations as focus in the context of celestial bodies. We demonstrate the application of our concept in two storytelling scenarios and envision the application both for science presentations to lay audiences and for dedicated exploration, potentially also in a molecule-only environment.

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  • 6. 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.

  • 7. 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.

  • 8.
    Cooper, Thomas M.
    et al.
    Air Force Res Lab, Mat & Mfg Directorate, Dayton, OH 45433 USA..
    Haley, Joy E.
    Air Force Res Lab, Mat & Mfg Directorate, Dayton, OH 45433 USA..
    Stewart, David J.
    Air Force Res Lab, Mat & Mfg Directorate, Dayton, OH 45433 USA..
    Long, Stephanie
    Air Force Res Lab, Mat & Mfg Directorate, Dayton, OH 45433 USA..
    Krein, Douglas M.
    Air Force Res Lab, Mat & Mfg Directorate, Dayton, OH 45433 USA..
    Burke, Aaron R.
    Air Force Res Lab, Mat & Mfg Directorate, Dayton, OH 45433 USA..
    Arias, Eduardo
    Ctr Invest Quim Aplicada CIQA, Blvd Enrique Reyna 140, Saltillo 25294, Coahuila, Mexico..
    Moggio, Ivana
    Ctr Invest Quim Aplicada CIQA, Blvd Enrique Reyna 140, Saltillo 25294, Coahuila, Mexico..
    Turlakov, Gleb
    Ctr Invest Quim Aplicada CIQA, Blvd Enrique Reyna 140, Saltillo 25294, Coahuila, Mexico..
    Ziolo, Ronald F.
    Ctr Invest Quim Aplicada CIQA, Blvd Enrique Reyna 140, Saltillo 25294, Coahuila, Mexico..
    Biler, Michal
    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.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Nanoscale Organization of a Platinum(II) Acetylide Cholesteric Liquid Crystal Molecular Glass for Photonics Applications2020In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 30, no 28, article id 1910562Article in journal (Refereed)
    Abstract [en]

    The fabrication, molecular structure, and spectroscopy of a stable cholesteric liquid crystal platinum acetylide glass obtained from trans-Pt(PEt3)(2)(C(sic)C-C6H5-C(sic)N)(C(sic)C-C6H5-COO-Cholesterol), are described and designated as PE1-CN-Chol. Polarized optical microscopy, differential scanning calorimetry, and wide-angle X-ray scattering experiments show room temperature glassy/crystalline texture with crystal formation upon heating to 165 degrees C. Further heating results in conversion to cholesteric phase. Cooling to room temperature leads to the formation of a cholesteric liquid crystal glass. Scanning tunneling microscopy of a PE1-CN-Chol monolayer reveals self-assembly at the solid-liquid interface with an array of two molecules arranged in pairs, oriented head-to-head through the CN groups, giving rise to a lamella arrangement. The lamella structure obtained from molecular dynamics calculations shows a clear phase separation between the conjugated platinum acetylide and the hydrophobic cholesterol moiety with the lamellae separation distance being 4.0 nm. Ultrafast transient absorption and flash photolysis spectra of the glass show intersystem crossing to the triplet state occurring within 100 ps following excitation. The triplet decay time of the film compared to aerated and deoxygenated solutions is consistent with oxygen quenching at the film surface but not within the film. The high chromophore concentration, high glass thermal stability, and long triplet lifetime in air show that these materials have potential as nonlinear absorbing materials.

  • 9.
    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.

  • 10. 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.

  • 11.
    De Oliveira, Danilo Hirabae
    et al.
    KTH Royal Inst Technol, Sweden.
    Biler, Michal
    KTH Royal Inst Technol, Sweden.
    Mim, Carsten
    Royal Tech Inst KTH, Sweden.
    Enstedt, Linnea
    KTH Royal Inst Technol, Sweden.
    Kvick, Mathias
    Spiber Technol AB, Sweden.
    Norman, Patrick
    KTH Royal Inst Technol, Sweden.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Hedhammar, My
    KTH Royal Inst Technol, Sweden.
    Silk Assembly against Hydrophobic Surfaces?Modeling and Imaging of Formation of Nanofibrils2023In: ACS Applied Bio Materials, E-ISSN 2576-6422, Vol. 6, no 3, p. 1011-1018Article in journal (Refereed)
    Abstract [en]

    A detailed insight about the molecular organization behind spider silk assembly is valuable for the decoding of the unique properties of silk. The recombinant partial spider silk protein 4RepCT contains four poly-alanine/glycine-rich repeats followed by an amphiphilic C-terminal domain and has shown the capacity to self-assemble into fibrils on hydrophobic surfaces. We herein use molecular dynamic simulations to address the structure of 4RepCT and its different parts on hydrophobic versus hydrophilic surfaces. When 4RepCT is placed in a wing arrangement model and periodically repeated on a hydrophobic surface, fi-sheet structures of the poly-alanine repeats are preserved, while the CT part is settled on top, presenting a fibril with a height of similar to 7 nm and a width of similar to 11 nm. Both atomic force microscopy and cryo-electron microscopy imaging support this model as a possible fibril formation on hydrophobic surfaces. These results contribute to the understanding of silk assembly and alignment mechanism onto hydrophobic surfaces.

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  • 12. 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.

  • 13.
    Giobbio, Ginevra
    et al.
    Tech Univ Munich, Germany; Normandie Univ, France.
    Cavinato, Luca M. M.
    Tech Univ Munich, Germany.
    Fresta, Elisa
    Tech Univ Munich, Germany; Heidelberg Univ, Germany.
    Montrieul, Anais
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering. Normandie Univ, France.
    Umuhire Mahoro, Gilbert
    Normandie Univ, France.
    Lohier, Jean-Francois
    Normandie Univ, France.
    Renaud, Jean-Luc
    Normandie Univ, France.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Gaillard, Sylvain
    Normandie Univ, France.
    Costa, Ruben D.
    Tech Univ Munich, Germany.
    Design Rule Hidden from The Eye in S/N-Bridged Ancillary Ligands for Copper(I) Complexes Applied to Light-Emitting Electrochemical Cells2023In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 33, no 50, article id 2304668Article in journal (Refereed)
    Abstract [en]

    Enhancing low-energy emitting Cu(I)-ionic transition metal complexes (iTMCs) light-emitting electrochemical cells (LECs) is of utmost importance towards Cu(I)-iTMC-based white-emitting LECs. Here, the ancillary ligand design includes (i) extension of & pi;-systems and (ii) insertion of S-bridge between heteroaromatics rings. This led to two novel heteroleptic Cu(I)-iTMCs: 2-(pyridin-2-yl-l2-azanyl)quinoline (CuN2) and 2-(naphthalen-2-ylthio)quinoline (CuS2) as N<^>N and bis[(2-diphenylphosphino)phenyl] ether as P<^>P, exhibiting improved photoluminescence quantum yields (& phi;) and thermally activated delayed fluorescence processes compared to their reference Cu(I)-iTMCs: di(pyridin-2-yl)-l2-azane (CuN1) and di(pyridin-2-yl)sulfane (CuS1). Despite CuS2 stands out with the highest & phi; (38% vs 17 / 14 / 1% for CuN1 / CuN2 / CuS1), only CuN2-LECs show the expected enhanced performance (0.35 cd A(-1) at luminance of 117 cd m(-2)) compared to CuN1-LECs (0.02 cd A(-1) at6 cd m(-2)), while CuS2-LECs feature low performances (0.04 cd A(-1) at 10 cd m(-2)). This suggests that conventional chemical design rules are not effective towards enhancing device performance. Herein, nonconventional multivariate statistical analysis and electrochemical impedance spectroscopy studies allow to rationalize the mismatch between chemical design and device performance bringing to light a hidden design rule: polarizability of the ancillary ligand is key for an efficient Cu(I)-iTMC-LECs. All-in-all, this study provides fresh insights for the design of Cu-iTMCs fueling research on sustainable ion-based lighting sources.

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  • 14.
    Gonzalez-Sanchez, Marina
    et al.
    Univ Autoonoma Madrid, Spain.
    Mayoral, Mariia J.
    Univ Complutense Madrid, Spain.
    Vazquez-Gonzalez, Violeta
    Univ Autoonoma Madrid, Spain.
    Paloncyova, Marketa
    KTH Royal Inst Technol, Sweden; Palackyy Univ Olomouc, Czech Republic.
    Sancho-Casado, Irene
    Univ Autoonoma Madrid, Spain.
    Aparicio, Fatima
    Univ Autoonoma Madrid, Spain.
    de Juan, Alberto
    Univ Autoonoma Madrid, Spain.
    Longhi, Giovanna
    Univ Brescia, Italy.
    Norman, Patrick
    KTH Royal Inst Technol, Sweden.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Gonzalez-Rodriguez, David
    Univ Autoonoma Madrid, Spain; Univ Autonoma Madrid, Spain.
    Stacked or Folded? Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers2023In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 145, no 32, p. 17805-17818Article in journal (Refereed)
    Abstract [en]

    Self-assembled nanotubesexhibit impressive biologicalfunctionsthat have always inspired supramolecular scientists in their effortsto develop strategies to build such structures from small moleculesthrough a bottom-up approach. One of these strategies employs moleculesendowed with self-recognizing motifs at the edges, which can undergoeither cyclization-stacking or folding-polymerizationprocesses that lead to tubular architectures. Which of these self-assemblypathways is ultimately selected by these molecules is, however, oftendifficult to predict and even to evaluate experimentally. We showhere a unique example of two structurally related molecules substitutedwith complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway takenis determined by chelate cooperativity, that is, by their propensityto assemble in specific cyclic structures through Watson-Crickpairing. Because of chelate cooperativities that differ in severalorders of magnitude, these molecules exhibit distinct supramolecularscenarios prior to their polymerization that generate self-assemblednanotubes with different internal monomer arrangements, either stackedor coiled, which lead at the same time to opposite helicities andchiroptical properties.

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  • 15.
    Gonzalez-Sanchez, Marina
    et al.
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    Mayoral, Mariia J.
    Univ Complutense Madrid, Dept Inorgan Chem, Madrid 28040, Spain..
    Vazquez-Gonzalez, Violeta
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    Paloncyova, Marketa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Palackyy Univ Olomouc, Czech Adv Technol & Res Inst CATRIN, Reg Ctr Adv Technol & Mat, Olomouc 77900, Czech Republic..
    Sancho-Casado, Irene
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    Aparicio, Fatima
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    de Juan, Alberto
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    Longhi, Giovanna
    Univ Brescia, Dept Mol & Translat Med, I-25123 Brescia, Italy..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, Mathieu
    Linköping Univ, Lab Organ Elect, S-58183 Linköping, Sweden.;Linköping Univ, Swedish Esci Res Ctr SeRC, S-58183 Linköping, Sweden.;Linköping Univ, Sci Visualizat Grp, ITN, Campus Norrköping, S-58183 Linköping, Sweden..
    Gonzalez-Rodriguez, David
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain.;Univ Autonoma Madrid, Inst Adv Res Chem Sci IAdChem, Madrid 28049, Spain..
    Stacked or Folded?: Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers2023In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 145, no 32, p. 17805-17818Article in journal (Refereed)
    Abstract [en]

    Self-assembled nanotubesexhibit impressive biologicalfunctionsthat have always inspired supramolecular scientists in their effortsto develop strategies to build such structures from small moleculesthrough a bottom-up approach. One of these strategies employs moleculesendowed with self-recognizing motifs at the edges, which can undergoeither cyclization-stacking or folding-polymerizationprocesses that lead to tubular architectures. Which of these self-assemblypathways is ultimately selected by these molecules is, however, oftendifficult to predict and even to evaluate experimentally. We showhere a unique example of two structurally related molecules substitutedwith complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway takenis determined by chelate cooperativity, that is, by their propensityto assemble in specific cyclic structures through Watson-Crickpairing. Because of chelate cooperativities that differ in severalorders of magnitude, these molecules exhibit distinct supramolecularscenarios prior to their polymerization that generate self-assemblednanotubes with different internal monomer arrangements, either stackedor coiled, which lead at the same time to opposite helicities andchiroptical properties.

  • 16.
    Gowda, Vasantha
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Filippov, Andrei
    Luleå Univ Technol, Chem Interfaces, Luleå, Sweden.;Kazan State Med Univ, Dept Med & Biol Phys, Kazan 420012, Russia..
    Mantonico, Malisa, V
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Ornithopoulou, Eirini
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Linköping Univ, Lab Organ Elect, S-60174 Norrköping, Sweden.;Linköping Univ, Grp Sci Visualizat, ITN, S-60174 Norrköping, Sweden.;Linköping Univ, Swedish E Sci Res Ctr SeRC, S-60174 Norrköping, Sweden..
    Antzutkin, Oleg N.
    Luleå Univ Technol, Chem Interfaces, Luleå, Sweden.;Univ Warwick, Dept Phys, Coventry, W Midlands, England..
    Lendel, Christofer
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Structural characterisation of amyloid-like fibrils formed by an amyloidogenic peptide segment of beta-lactoglobulin2021In: RSC Advances, E-ISSN 2046-2069, Vol. 11, no 45, p. 27868-27879Article in journal (Refereed)
    Abstract [en]

    Protein nanofibrils (PNFs) represent a promising class of biobased nanomaterials for biomedical and materials science applications. In the design of such materials, a fundamental understanding of the structure-function relationship at both molecular and nanoscale levels is essential. Here we report investigations of the nanoscale morphology and molecular arrangement of amyloid-like PNFs of a synthetic peptide fragment consisting of residues 11-20 of the protein beta-lactoglobulin (beta-LG(11-20)), an important model system for PNF materials. Nanoscale fibril morphology was analysed by atomic force microscopy (AFM) that indicates the presence of polymorphic self-assembly of protofilaments. However, observation of a single set of C-13 and N-15 resonances in the solid-state NMR spectra for the beta-LG(11-20) fibrils suggests that the observed polymorphism originates from the assembly of protofilaments at the nanoscale but not from the molecular structure. The secondary structure and inter-residue proximities in the beta-LG(11-20) fibrils were probed using NMR experiments of the peptide with C-13- and N-15-labelled amino acid residues at selected positions. We can conclude that the peptides form parallel beta-sheets, but the NMR data was inconclusive regarding inter-sheet packing. Molecular dynamics simulations confirm the stability of parallel beta-sheets and suggest two preferred modes of packing. Comparison of molecular dynamics models with NMR data and calculated chemical shifts indicates that both packing models are possible.

  • 17.
    Gustafsson, Camilla
    et al.
    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.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    QM/MM Density Functional Theory Simulations of the Optical Properties Fingerprinting the Ligand-binding of Pentameric Formyl Thiophene Acetic Acid in Amyloid-β(1–42)Manuscript (preprint) (Other academic)
  • 18.
    Gustafsson, Camilla
    et al.
    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.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Quantum Mechanics/Molecular Mechanics Density Functional Theory Simulations of the Optical Properties Fingerprinting the Ligand-Binding of Pentameric Formyl Thiophene Acetic Acid in Annyloid-beta(1-42)2020In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 124, no 5, p. 875-888Article in journal (Refereed)
    Abstract [en]

    The binding pocket proposed by Konig et al. [Chem. Commun. 2018, 54, 3030-3033] for the biomarker pentameric formyl thiophene acetic acid (p-FTAA) in the fibrillar structure of amyloid-beta(1-42) has been put to the test by the comparison of theoretical and experimental optical absorption and fluorescence spectra obtained in a water environment and inside the protein scaffold. The optical absorption/emission properties of this luminescent conjugated oligothiophene were studied by means of classical force field molecular dynamics simulations to account for the sampling of configuration space in conjunction with polarizable embedding time-dependent density functional theory calculations of spectra. The nuclear motions of residues in the beta-sheet were found to be modest, and the time dependence of embedding parameters was shown to be negligible so that a time-independent parameter set could be derived and used for all 300 snapshots considered in the spectrum averaging. In regard to linear absorption spectra, the calculated red shift due to protein binding for the dominant S-1 <- S-0 transition in p-FTAA was found to be equal to 23 nm (0.17 eV), which is in excellent agreement with the corresponding experimental result of 18 nm and taken as corroborating evidence for having correctly identified the binding pocket of p-FTAA in the amyloid. The underlying mechanisms for the calculated red shift were disentangled, and it is shown that some 20 nm (0.15 eV) of the total 23 nm (0.17 eV) is associated with increased planarity of p-FTAA in the binding pocket, whereas a mere 3 nm (0.02 eV) is associated with changes in the environment. In regard to emission spectra, we demonstrate that intersystem crossing from the excited S-1 state to the triplet manifold of states is a less likely event for p-FTAA in the binding pocket as compared to in the aqueous solution, and we thereby partly explain the much higher quantum yield of fluorescence for the more rigid p-FTAA in the binding pocket. Two-photon absorption in p-FTAA is shown to predominantly occur to an overall symmetric excited state and be more than twice as strong for the biomarker in the binding pocket as compared to in water. The corresponding red shift, on the other hand, is very small. Earlier experimental two-photon fluorescence imaging using p-FTAA is shown not to target the dominant two-photon state, and ways to reach a higher image quality (lower signal-to-noise ratio) are proposed in terms of tuning the laser wavelength toward the region of 600 nm or the synthesis of asymmetric ligands with S-1 states that are both one- and two-photon allowed.

  • 19.
    Gustafsson, Camilla
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Shirani, H.
    Leira, P.
    Rehn, Dirk Robert
    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.
    Nilsson, K. P. R.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Lindgren, M.
    Deciphering the Electronic Transitions of Thiophene-Based Donor-Acceptor-Donor Pentameric Ligands Utilized for Multimodal Fluorescence Microscopy of Protein Aggregates2021In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 22, no 3, p. 323-335Article in journal (Refereed)
    Abstract [en]

    Anionic pentameric thiophene acetates can be used for fluorescence detection and diagnosis of protein amyloid aggregates. Replacing the central thiophene unit by benzothiadiazole (BTD) or quinoxaline (QX) leads to large emission shifts and basic spectral features have been reported [Chem. Eur. J. 2015, 21, 15133-13137]. Here we present new detailed experimental results of solvent effects, time-resolved fluorescence and examples employing multi-photon microscopy and lifetime imaging. Quantum chemical response calculations elucidate how the introduction of the BTD/QX groups changes the electronic states and emissions. The dramatic red-shift follows an increased conjugation and quinoid character of the π-electrons of the thiophene backbone. An efficient charge transfer in the excited states S1 and S2 compared to the all-thiophene analogue makes these more sensitive to the polarity and quenching by the solvent. Taken together, the results guide in the interpretation of images of stained Alzheimer disease brain sections employing advanced fluorescence microscopy and lifetime imaging, and can aid in optimizing future fluorescent ligand development.

  • 20.
    Gustafsson, Camilla
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Shirani, Hamid
    Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University.
    Konsmo, Audun
    Department of Physics, Norwegian University of Science and Technology.
    Rhen, Dirk
    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.
    Nilsson, Peter
    Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Lindgren, Mikael
    Department of Physics, Norwegian University of Science and Technology.
    Deciphering the electronic transitions of thiophene-based donor-acceptor-donor pentameric ligands utilized for multimodal fluorescence microscopy of protein aggregatesManuscript (preprint) (Other academic)
  • 21.
    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.

  • 22. 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.

  • 23.
    König, Carolin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Skanberg, Robin
    Linköpings Univ, Dept Media & Informat Technol, Norrköping, Sweden..
    Hotz, Ingrid
    Linköpings Univ, Dept Media & Informat Technol, Norrköping, Sweden..
    Ynnerman, Anders
    Linköpings Univ, Dept Media & Informat Technol, Norrköping, 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), 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.

  • 24.
    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).

  • 25.
    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.

  • 26.
    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, Patrick
    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.

  • 27. Minh, Nghia Nguyen Thi
    et al.
    Begum, Afshan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    Zhang, Jun
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    Leira, Petter
    Norwegian Univ Sci & Technol, Dept Phys, N-7491 Trondheim, Norway..
    Todarwal, Yogesh
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Linares, Mathieu
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden.;Linkooping Univ, Lab Organ Elect, ITN, SE-58183 Linkooping, Sweden.;Linköping Univ, Sci Visualizat Grp, ITN, SE-58183 Linköping, Sweden..
    Norman, Patrick
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Derbyshire, Dean
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    von Castelmur, Eleonore
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    Lindgren, Mikael
    Norwegian Univ Sci & Technol, Dept Phys, N-7491 Trondheim, Norway..
    Hammarstroem, Per
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    Koenig, Carolin
    Leibniz Univ Hannover, Inst Phys Chem & Electrochem, D-30167 Hannover, Germany..
    Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study2023In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 127, no 30, p. 6628-6635Article in journal (Refereed)
    Abstract [en]

    Misfolding and aggregation of transthyretin (TTR) causeseveralamyloid diseases. Besides being an amyloidogenic protein, TTR hasan affinity for bicyclic small-molecule ligands in its thyroxine (T4)binding site. One class of TTR ligands are trans-stilbenes. The trans-stilbenescaffold is also widely applied for amyloid fibril-specific ligandsused as fluorescence probes and as positron emission tomography tracersfor amyloid detection and diagnosis of amyloidosis. We have shownthat native tetrameric TTR binds to amyloid ligands based on the trans-stilbenescaffold providing a platform for the determination of high-resolutionstructures of these important molecules bound to protein. In thisstudy, we provide spectroscopic evidence of binding and X-ray crystallographicstructure data on tetrameric TTR complex with the fluorescent salicylicacid-based pyrene amyloid ligand (Py1SA), an analogue of the Congored analogue X-34. The ambiguous electron density from the X-ray diffraction,however, did not permit Py1SA placement with enough confidence likelydue to partial ligand occupancy. Instead, the preferred orientationof the Py1SA ligand in the binding pocket was determined by moleculardynamics and umbrella sampling approaches. We find a distinct preferencefor the binding modes with the salicylic acid group pointing intothe pocket and the pyrene moiety outward to the opening of the T4binding site. Our work provides insight into TTR binding mode preferencefor trans-stilbene salicylic acid derivatives as well as a frameworkfor determining structures of TTR-ligand complexes.

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  • 28.
    Minh, Nghia Nguyen Thi
    et al.
    Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstr. 3A, Hannover, 30167, Germany.
    Begum, Afshan
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden.;Uppsala Univ, Dept Cell & Mol Biol Mol Biophys, S-75237 Uppsala, Sweden..
    Zhang, Jun
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    Leira, Petter
    Norwegian Univ Sci & Technol, Dept Phys, N-7491 Trondheim, Norway..
    Todarwal, Yogesh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Linköping Univ, Lab Organ Elect, ITN, SE-58183 Linköping, Sweden.;Linköping Univ, Sci Visualizat Grp, ITN, SE-58183 Linköping, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Derbyshire, Dean
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    von Castelmur, Eleonore
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    Lindgren, Mikael
    Norwegian Univ Sci & Technol, Dept Phys, N-7491 Trondheim, Norway..
    Hammarstroem, Per
    Linköping Univ, Dept Phys Chem & Biol, Div Chem, S-58183 Linköping, Sweden..
    Koenig, Carolin
    Leibniz Univ Hannover, Inst Phys Chem & Electrochem, D-30167 Hannover, Germany..
    Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study2023In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 127, no 30, p. 6628-6635Article in journal (Refereed)
    Abstract [en]

    Misfolding and aggregation of transthyretin (TTR) causeseveralamyloid diseases. Besides being an amyloidogenic protein, TTR hasan affinity for bicyclic small-molecule ligands in its thyroxine (T4)binding site. One class of TTR ligands are trans-stilbenes. The trans-stilbenescaffold is also widely applied for amyloid fibril-specific ligandsused as fluorescence probes and as positron emission tomography tracersfor amyloid detection and diagnosis of amyloidosis. We have shownthat native tetrameric TTR binds to amyloid ligands based on the trans-stilbenescaffold providing a platform for the determination of high-resolutionstructures of these important molecules bound to protein. In thisstudy, we provide spectroscopic evidence of binding and X-ray crystallographicstructure data on tetrameric TTR complex with the fluorescent salicylicacid-based pyrene amyloid ligand (Py1SA), an analogue of the Congored analogue X-34. The ambiguous electron density from the X-ray diffraction,however, did not permit Py1SA placement with enough confidence likelydue to partial ligand occupancy. Instead, the preferred orientationof the Py1SA ligand in the binding pocket was determined by moleculardynamics and umbrella sampling approaches. We find a distinct preferencefor the binding modes with the salicylic acid group pointing intothe pocket and the pyrene moiety outward to the opening of the T4binding site. Our work provides insight into TTR binding mode preferencefor trans-stilbene salicylic acid derivatives as well as a frameworkfor determining structures of TTR-ligand complexes.

  • 29.
    Minh, Nghia Nguyen Thi
    et al.
    Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Hannover, Germany.
    Begum, Afshan
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. Uppsala Univ, Sweden.
    Zhang, Jun
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Leira, Petter
    Norwegian Univ Sci & Technol, Norway.
    Todarwal, Yogesh
    KTH Royal Inst Technol, Sweden.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering. KTH Royal Inst Technol, Sweden.
    Norman, Patrick
    KTH Royal Inst Technol, Sweden.
    Derbyshire, Dean
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    von Castelmur, Eleonore
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Lindgren, Mikael
    Norwegian Univ Sci & Technol, Norway.
    Hammarström, Per
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Koenig, Carolin
    Leibniz Univ Hannover, Germany.
    Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study2023In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 127, no 30, p. 6628-6635Article in journal (Refereed)
    Abstract [en]

    Misfolding and aggregation of transthyretin (TTR) causeseveralamyloid diseases. Besides being an amyloidogenic protein, TTR hasan affinity for bicyclic small-molecule ligands in its thyroxine (T4)binding site. One class of TTR ligands are trans-stilbenes. The trans-stilbenescaffold is also widely applied for amyloid fibril-specific ligandsused as fluorescence probes and as positron emission tomography tracersfor amyloid detection and diagnosis of amyloidosis. We have shownthat native tetrameric TTR binds to amyloid ligands based on the trans-stilbenescaffold providing a platform for the determination of high-resolutionstructures of these important molecules bound to protein. In thisstudy, we provide spectroscopic evidence of binding and X-ray crystallographicstructure data on tetrameric TTR complex with the fluorescent salicylicacid-based pyrene amyloid ligand (Py1SA), an analogue of the Congored analogue X-34. The ambiguous electron density from the X-ray diffraction,however, did not permit Py1SA placement with enough confidence likelydue to partial ligand occupancy. Instead, the preferred orientationof the Py1SA ligand in the binding pocket was determined by moleculardynamics and umbrella sampling approaches. We find a distinct preferencefor the binding modes with the salicylic acid group pointing intothe pocket and the pyrene moiety outward to the opening of the T4binding site. Our work provides insight into TTR binding mode preferencefor trans-stilbene salicylic acid derivatives as well as a frameworkfor determining structures of TTR-ligand complexes.

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  • 30.
    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.

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  • 31.
    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.

  • 32.
    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.

  • 33.
    Proietti, Giampiero
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Axelsson, Anton
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Capezza, Antonio Jose
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Polymeric Materials.
    Todarwal, Yogesh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Szabo, Zoltan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Lendel, Christofer
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Olsson, Richard
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Polymeric Materials.
    Dinér, Peter
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Ultralight aerogels via supramolecular polymerization of a new chiral perfluoropyridin-based sulfonimidamide organogelatorManuscript (preprint) (Other academic)
  • 34.
    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, E-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.

  • 35.
    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.

  • 36.
    Sedghamiz, Tahereh
    et al.
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Mehandzhiyski, Alexandar
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Modarresi, Mohsen
    Ferdowsi Univ Mashhad, Iran.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Zozoulenko, Igor
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    What Can We Learn about PEDOT:PSS Morphology from Molecular Dynamics Simulations of Ionic Diffusion?2023In: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 35, no 14, p. 5512-5523Article in journal (Refereed)
    Abstract [en]

    Poly(3,4-ethylenedioxythiophene) polystyrene sulfonate(PEDOT:PSS)is one of the most important mixed electron-ion conducting polymers,where the efficiency of the ion transport is crucial for many of itsapplications. Despite the impressive experimental progress in thedetermination of ionic mobilities in PEDOT:PSS, the fundamentals ofion transport in this material remain poorly understood, and the theoreticalinsight into the ion diffusion on the microscopical level is completelymissing. In the present paper, a Martini 3 coarse-grained moleculardynamics (MD) model for PEDOT:PSS is developed and applied to calculatethe ion diffusion coefficients and ion distribution in the film. Wefind that the ion diffusion coefficients for Na+ ions arepractically the same in the PEDOT-rich and PSS-rich regions and donot show sensitivity to the oxidation level. We compare the calculateddiffusion coefficients with available experimental results. Basedon this comparison and based on the MD morphology simulation of PEDOT:PSSrevealing the formation of pores inside the film, we revise a commonlyaccepted granular morphological model of PEDOT:PSS. Namely, we arguethat PEDOT:PSS films, in addition to PEDOT-rich and PSS-rich regions,must contain a network of pores where the ion diffusion takes place.

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  • 37. 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.

  • 38.
    Sharma, Mohit
    et al.
    Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sidwall Thygesen, Signe
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Media and Information Technology.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Natarajan, Vijay
    Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India.
    Continuous Scatterplot Operators for Bivariate Analysis and Study of Electronic Transitions2023In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506Article in journal (Refereed)
    Abstract [en]

    Electronic transitions in molecules due to the absorption or emission of light is a complex quantum mechanical process. Their study plays an important role in the design of novel materials. A common yet challenging task in the study is to determine the nature of electronic transitions, namely which subgroups of the molecule are involved in the transition by donating or accepting electrons, followed by an investigation of the variation in the donor-acceptor behavior for different transitions or conformations of the molecules. In this paper, we present a novel approach for the analysis of a bivariate field and show its applicability to the study of electronic transitions. This approach is based on two novel operators, the continuous scatterplot (CSP) lens operator and the CSP peel operator, that enable effective visual analysis of bivariate fields. Both operators can be applied independently or together to facilitate analysis. The operators motivate the design of control polygon inputs to extract fiber surfaces of interest in the spatial domain. The CSPs are annotated with a quantitative measure to further support the visual analysis. We study different molecular systems and demonstrate how the CSP peel and CSP lens operators help identify and study donor and acceptor characteristics in molecular systems.

  • 39. Skånberg, R.
    et al.
    König, Carolin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    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.
    Jönsson, D.
    Hotz, I.
    Ynnerman, A.
    VIA-MD: Visual Interactive Analysis of Molecular Dynamics2018In: MolVA 2018 - Workshop on Molecular Graphics and Visual Analysis of Molecular Data, The Eurographics Association , 2018, p. 19-27Conference paper (Refereed)
    Abstract [en]

    We present a visual exploration environment tailored for large-scale spatio-temporal molecular dynamics simulation data. The environment is referred to as VIA-MD (visual interactive analysis of molecular dynamics) and has been developed in a participatory design process with domain experts on molecular dynamics simulations of complex molecular systems. A key feature of our approach is the support for linked interactive 3D exploration of geometry and statistical analysis using dynamic temporal windowing and animation. Based on semantic level descriptions and hierarchical aggregation of molecular properties we enable interactive filtering, which enables the user to effectively find spatial, temporal and statistical patterns. The VIA-MD environment provides an unprecedented tool for analysis of complex microscopic interactions hidden in large data volumes. We demonstrate the utility of the VIA-MD environment with four use cases. The first two deal with simulation of amyloid plaque associated with development of Alzheimer's, and we study an aqueous solution of 100 probes and an amyloid fibril. The identification of interaction "hotspots" is achieved with the use of combined filter parameters connected with probe molecular planarity and probe-fibril interaction energetics. The third and fourth examples show the wide applicability of the environment by applying it to analysis of molecular properties in material design.

  • 40.
    Skånberg, Robin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics2023In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 63, no 23, p. 7382-7391Article in journal (Refereed)
    Abstract [en]

    The typical workflow in molecular dynamics (MD) analysis requires several separate tools, often resulting in a lack of synergy and interaction between the individual analysis steps. This article presents VIAMD, an application designed to address this issue by integrating a 3D visualization of molecular trajectories with flexible analysis components. VIAMD uses an interactive scripting interface, allowing for property definition and evaluation. The application provides context-aware suggestions and expression feedback through information and visualizations. The user-defined properties can be explored and analyzed through the various components. This enables correlation with spatial conformations, statistical analysis of distributions, and powerful aggregation of multidimensional properties such as spatial distribution functions. VIAMD has the potential to advance research in many scientific disciplines and is a promising solution for improving the workflow of MD visualization and analysis.

  • 41.
    Skånberg, Robin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC).
    Linares, Mathieu
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Media and Information Technology. Swedish e-Science Research Centre (SeRC).
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC).
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC).
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC).
    MolFind - Integrated Multi-Selection Schemes for Complex Molecular Structures2019In: Workshop on Molecular Graphics and Visual Analysis of Molecular Data (MolVA) / [ed] J. Byška, M. Krone, and B. Sommer, The Eurographics Association , 2019Conference paper (Refereed)
    Abstract [en]

    Selecting components and observing changes ofproperties and configurations over time is an important step in the analysis of molecular dynamics (MD) data. In this paper, we present a selection tool combining text-based queries with spatial selection and filtering. Morphological operations facilitate refinement of the selection by growth operators, e.g. across covalent bonds. The combination of different selection paradigms enables flexible and intuitive analysis on different levels of detail and visual depiction of molecular events. Immediate visual feedback during interactions ensures a smooth exploration of the data. We demonstrate the utility of our selection framework by analyzing temporal changes in the secondary structure of poly-alanineand the binding ofaspirin to phospholipase A2.

  • 42.
    Strakosas, Xenofon
    et al.
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering. Lund Univ, Sweden.
    Biesmans, Hanne
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Abrahamsson, Tobias
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Hellman, Karin
    Lund Univ, Sweden.
    Silverå Ejneby, Malin
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Donahue, Mary
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Ekstrom, Peter
    Lund Univ, Sweden.
    Ek, Fredrik
    Lund Univ, Sweden.
    Savvakis, Marios
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Hjort, Martin
    Lund Univ, Sweden.
    Bliman, David
    Univ Gothenburg, Sweden; IRLAB Therapeut AB, Sweden.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Lindholm, Caroline
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Stavrinidou, Eleni
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Gerasimov, Jennifer
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Simon, Daniel
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Olsson, Roger
    Lund Univ, Sweden; Univ Gothenburg, Sweden.
    Berggren, Magnus
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Metabolite-induced in vivo fabrication of substrate-free organic bioelectronics2023In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 379, no 6634, p. 795-802Article in journal (Refereed)
    Abstract [en]

    Interfacing electronics with neural tissue is crucial for understanding complex biological functions, but conventional bioelectronics consist of rigid electrodes fundamentally incompatible with living systems. The difference between static solid-state electronics and dynamic biological matter makes seamless integration of the two challenging. To address this incompatibility, we developed a method to dynamically create soft substrate-free conducting materials within the biological environment. We demonstrate in vivo electrode formation in zebrafish and leech models, using endogenous metabolites to trigger enzymatic polymerization of organic precursors within an injectable gel, thereby forming conducting polymer gels with long-range conductivity. This approach can be used to target specific biological substructures and is suitable for nerve stimulation, paving the way for fully integrated, in vivo-fabricated electronics within the nervous system.

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  • 43.
    Todarwal, Yogesh
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gustafsson, Camilla
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Minh, Nghia Nguyen Thi
    Leibniz Univ Hannover, Inst Phys Chem & Electrochem, D-30167 Hannover, Germany..
    Ertzgaard, Ingrid
    Norwegian Univ Sci & Technol, Dept Phys, N-7491 Trondheim, Norway..
    Klingstedt, Therese
    Linköping Univ, Dept Phys Chem & Biol, SE-58183 Linköping, Sweden..
    Ghetti, Bernardino
    Indiana Univ Sch Med, Dept Pathol & Lab Med, Indianapolis, IN 46202 USA..
    Vidal, Ruben
    Indiana Univ Sch Med, Dept Pathol & Lab Med, Indianapolis, IN 46202 USA..
    Koenig, Carolin
    Leibniz Univ Hannover, Inst Phys Chem & Electrochem, D-30167 Hannover, Germany..
    Lindgren, Mikael
    Norwegian Univ Sci & Technol, Dept Phys, N-7491 Trondheim, Norway..
    Nilsson, K. Peter R.
    Linköping Univ, Dept Phys Chem & Biol, SE-58183 Linköping, Sweden..
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Linköping Univ, Lab Organ Elect, ITN, SE-58183 Linköping, Sweden.;Linköping Univ, Sci Visualizat Grp, ITN, SE-58183 Linköping, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tau Protein Binding Modes in Alzheimer's Disease for Cationic Luminescent Ligands2021In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 125, no 42, p. 11628-11636Article in journal (Refereed)
    Abstract [en]

    The bi-thiophene-vinylene-benzothiazole (bTVBT4) ligand developed for Alzheimer's disease (AD)-specific detection of amyloid tau has been studied by a combination of several theoretical methods and experimental spectroscopies. With reference to the cryo-EM tau structure of the tau protofilament (Nature 2017, 547, 185), a periodic model system of the fibril was created, and the interactions between this fibril and bTVBT4 were studied with nonbiased molecular dynamics simulations. Several binding sites and binding modes were identified and analyzed, and the results for the most prevailing fibril site and ligand modes are presented. A key validation of the simulation work is provided by the favorable comparison of the theoretical and experimental absorption spectra of bTVBT4 in solution and bound to the protein. It is conclusively shown that the ligand-protein binding occurs at the hydrophobic pocket defined by the residues Ile360, Thr361, and His362. This binding site is not accessible in the Pick's disease (PiD) fold, and fluorescence imaging of bTVBT4-stained brain tissue samples from patients diagnosed with AD and PiD provides strong support for the proposed tau binding site.

  • 44.
    Todarwal, Yogesh
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Comparative Analysis of Luminescent Cationic, Anionic, and Neutral Ligands Binding to Amyloid Fibrils in Alzheimer's Disease: A Computational InsightManuscript (preprint) (Other academic)
  • 45.
    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.

  • 46.
    Urbanaviciute, Indre
    et al.
    Linköping Univ, Dept Phys Chem & Biol IFM, Complex Mat & Devices, Linköping, Sweden.
    Meng, Xiao
    Eindhoven Univ Technol, Lab Macromol & Organ Chem, Eindhoven, Netherlands.
    Biler, Michal
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Wei, Yingfen
    Univ Groningen, Zernike Inst Adv Mat, Groningen, Netherlands.
    Cornelissen, Tim D.
    Linköping Univ, Dept Phys Chem & Biol IFM, Complex Mat & Devices, Linköping, Sweden.
    Bhattacharjee, Subham
    Eindhoven Univ Technol, Lab Macromol & Organ Chem, Eindhoven, Netherlands; Kazi Nazrul Univ, Dept Chem, Burdwan, W Bengal, India.
    Linares, Mathieu
    Linköping Univ, Dept Sci & Technol ITN, Campus Norrköping, Norrköping, Sweden; Linköping Univ, SeRC, Linköping, Sweden.
    Kemerink, Martijn
    Linköping Univ, Dept Phys Chem & Biol IFM, Complex Mat & Devices, Linköping, Sweden.
    Negative piezoelectric effect in an organic supramolecular ferroelectric2019In: Materials Horizons, ISSN 2051-6347, E-ISSN 2051-6355, Vol. 6, no 8, p. 1688-1698Article in journal (Refereed)
    Abstract [en]

    The vast majority of ferroelectric materials demonstrate a positive piezoelectric effect. Theoretically, the negative piezoelectric coefficient d(33) could be found in certain classes of ferroelectrics, yet in practice, the number of materials showing linear longitudinal contraction with increasing applied field (d(33) < 0) is limited to few ferroelectric polymers. Here, we measure a pronounced negative piezoelectric effect in the family of organic ferroelectric small-molecular BTAs (trialkylbenzene-1,3,5-tricarboxamides), which can be tuned by mesogenic tail substitution and structural disorder. While the large- and small-signal strain in highly-ordered thin-film BTA capacitor devices are dominated by intrinsic contributions and originates from piezostriction, rising disorder introduces additional extrinsic factors that boost the large-signal d(33) up to -20 pm V-1 in short-tailed molecules. Interestingly, homologues with longer mesogenic tails show a large-signal electromechanical response that is dominated by the quadratic Maxwell strain with significant mechanical softening upon polarization switching, whereas the small-signal strain remains piezostrictive. Molecular dynamics and DFT calculations both predict a positive d(33) for defect-free BTA stacks. Hence, the measured negative macroscopic d(33) is attributed to the presence of structural defects that enable the dimensional effect to dominate the piezoelectric response of BTA thin films.

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  • 47.
    Wang, Zhen
    et al.
    KTH Royal Inst Technol, Sweden.
    Heasman, Patrick
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Rostami, Jowan
    KTH Royal Inst Technol, Sweden.
    Benselfelt, Tobias
    KTH Royal Inst Technol, Sweden.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Li, Hailong
    Stockholm Univ, Sweden.
    Iakunkov, Artem
    KTH Royal Inst Technol, Sweden.
    Sellman, Farhiya
    KTH Royal Inst Technol, Sweden; KTH Royal Inst Technol, Sweden.
    Ostmans, Rebecca
    KTH Royal Inst Technol, Sweden; KTH Royal Inst Technol, Sweden.
    Hamedi, Mahiar Max
    KTH Royal Inst Technol, Sweden.
    Zozoulenko, Igor
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Wagberg, Lars
    KTH Royal Inst Technol, Sweden; KTH Royal Inst Technol, Sweden.
    Dynamic Networks of Cellulose Nanofibrils Enable Highly Conductive and Strong Polymer Gel Electrolytes for Lithium-Ion Batteries2023In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 33, no 30, article id 2212806Article in journal (Refereed)
    Abstract [en]

    Tunable dynamic networks of cellulose nanofibrils (CNFs) are utilized to prepare high-performance polymer gel electrolytes. By swelling an anisotropically dewatered, but never dried, CNF gel in acidic salt solutions, a highly sparse network is constructed with a fraction of CNFs as low as 0.9%, taking advantage of the very high aspect ratio and the ultra-thin thickness of the CNFs (micrometers long and 2-4 nm thick). These CNF networks expose high interfacial areas and can accommodate massive amounts of the ionic conductive liquid polyethylene glycol-based electrolyte into strong homogeneous gel electrolytes. In addition to the reinforced mechanical properties, the presence of the CNFs simultaneously enhances the ionic conductivity due to their excellent strong water-binding capacity according to computational simulations. This strategy renders the electrolyte a room-temperature ionic conductivity of 0.61 +/- 0.12 mS cm(-1) which is one of the highest among polymer gel electrolytes. The electrolyte shows superior performances as a separator for lithium iron phosphate half-cells in high specific capacity (161 mAh g(-1) at 0.1C), excellent rate capability (5C), and cycling stability (94% capacity retention after 300 cycles at 1C) at 60 degrees C, as well as stable room temperature cycling performance and considerably improved safety compared with commercial liquid electrolyte systems.

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  • 48.
    Zahabi, Najmeh
    et al.
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Baryshnikov, Glib
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Zozoulenko, Igor
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Charge carrier dynamics in conducting polymer PEDOT using ab initio molecular dynamics simulations2023In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 159, no 15, article id 154801Article in journal (Refereed)
    Abstract [en]

    As conducting polymers become increasingly important in electronic devices, understanding their charge transport is essential for material and device development. Various semi-empirical approaches have been used to describe temporal charge carrier dynamics in these materials, but there have yet to be any theoretical approaches utilizing ab initio molecular dynamics. In this work, we develop a computational technique based on ab initio Car-Parrinello molecular dynamics to trace charge carrier temporal motion in archetypical conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT). Particularly, we analyze charge dynamics in a single PEDOT chain and in two coupled chains with different degrees of coupling and study the effect of temperature. In our model we first initiate a positively charged polaron (compensated by a negative counterion) at one end of the chain, and subsequently displace the counterion to the other end of the chain and trace polaron dynamics in the system by monitoring bond length alternation in the PEDOT backbone and charge density distribution. We find that at low temperature (T = 1 K) the polaron distortion gradually disappears from its initial location and reappears near the new position of the counterion. At the room temperature (T = 300 K), we find that the distortions induced by polaron, and atomic vibrations are of the same magnitude, which makes tracking the polaron distortion challenging because it is hidden behind the temperature-induced vibrations. The novel approach developed in this work can be used to study polaron mobility along and between the chains, investigate charge transport in highly doped polymers, and explore other flexible polymers, including n-doped ones.

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