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  • 1. Wei, X.
    et al.
    Bu, L.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Y.
    Full color emissions based on intramolecular charge transfer effect modulated by formyl and boron-dipyrromethene moieties2017In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 136, 480-487 p.Article in journal (Refereed)
    Abstract [en]

    From the simple one-pot Vilsmeier formylation of 9-diphenylaminoanthracence, mono-, di- and tri-formyl products were successfully synthesized and the yields for the individual products can be optimized by varying the equivalents of the Vilsmeier reagent and changing the reaction temperature. The four obtained aldehydes exhibit distinct optical properties, with the emission maxima varying in a large wavelength range of 455–593 nm, despite their similar structures. The intramolecular charge transfer effect can be effectively modulated by varying the numbers and positions of the formyl groups, resulting in the observed distinct optical properties. Based on the aldehydes, the corresponding boron-dipyrromethenes were also synthesized. Similarly, the intramolecular charge transfer effect and the optical properties can be effectively modulated by the numbers and positions of the boron-dipyrromethene moieties. To further modulate the intramolecular charge transfer effect and red shift the emission, the dimethoxy-substituted 9-diphenylaminoanthracence was also used for synthesizing the corresponding aldehyde and boron-dipyrromethene. Thus, full color emissions within the wavelength range of 455–704 nm were successfully achieved based on modulating the intramolecular charge transfer. © 2016 Elsevier Ltd

  • 2. Bu, L.
    et al.
    Chen, J.
    Wei, X.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Y.
    An AIE and ICT based NIR florescent probe for cysteine and homocysteine2017In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 136, 724-731 p.Article in journal (Refereed)
    Abstract [en]

    A combination of aggregation-induced emission and intramolecular charge transfer was achieved by using a triphenylamine analogue and a dicyanovinyl moiety as the electron donating and accepting units, respectively. Hence, we designed and synthesized a probe with a D-π-A framework as a near-infrared fluorescence turn-on probe for biothiols (cysteine and homocysteine). Owing to the remarkable intramolecular charge transfer effect as well as intramolecular rotations associated with the donor moiety, the probe exhibits extremely weak fluorescence, which becomes a good starting point for developing fluorescence “turn-on” probes. Upon reaction with cysteine or homocysteine utilizing the dicyanovinyl moiety, the intramolecular charge transfer character was weakened, and the reacting products were observed to aggregate in aqueous solutions, resulting in the aggregation-induced emission effect with red fluorescence at 651 and 656 nm, respectively. Hence, the probe could be used as a fluorescence “turn-on” sensor for cysteine and homocysteine, with the sensing time of less than 4 min and the detection limits of 8.4 μM and 5.7 μM towards cysteine and homocysteine, respectively. The probe could distinguish cysteine and homocysteine from glutathione. The sensing mechanism was systematically investigated by employing high resolution mass spectrometry, 1H NMR and density functional theory calculations as well as checking the solvent viscosity dependent fluorescence, and thus the nucleophilic addition products, the intramolecular charge transfer character, and the aggregation-induced emission behaviour were clearly elucidated. It is noteworthy that the low cytotoxicity, the intrinsic aggregation-induced emission nature and near-infrared emissions enable the application of the probe in living cell imaging. © 2016 Elsevier Ltd

  • 3. Kong, Jiahui
    et al.
    Li, Qizhao
    Li, Minzhi
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liang, Xu
    Zhu, Weihua
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Yongshu
    Modulation of the structures and properties of bidipyrrin zinc complexes by introducing terminal alpha-methoxy groups2017In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 137, 430-436 p.Article in journal (Refereed)
    Abstract [en]

    A bidipyrrin nickel complex was synthesized in a high yield by oxidatively coupling between the ligands in the corresponding 2:1 (L:M) type of dipyrrin nickel complex, and further demetallation afforded the free bidipyrrin ligand. Interestingly, when treating the bidipyrrin nickel complex or the free bidipyrrin with FeCl3 in CH2Cl2/MeOH, the symmetric di-alpha-methoxy bidipyrrin could be synthesized in a high yield, with two methoxy groups attached to the terminal pyrrolic alpha-positions. Moreover, the coordination of the unsubstituted and disubstituted bidipyrrins with Zn(OAc)(2),2H(2)O afforded two similar M2L2 type of bidipyrrin helical complexes with different ligand conformations and different Zn center dot center dot center dot Zn distances of 5.353 and 3.357 angstrom, respectively. The difference in the conformations may be related to the electrostatic repulsions between the methoxy substituents. These results indicate that the dyes based on helical bidipyrrin zinc complexes with tunable structures and photophysical properties may be developed simply by modulating the terminal alpha-substituents.

  • 4. Song, Heli
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Yongshu
    Branched and linear alkoxy chains-wrapped push-pull porphyrins for developing efficient dye-sensitized solar cells2017In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 137, 421-429 p.Article in journal (Refereed)
    Abstract [en]

    Four alkoxy-wrapped push-pull porphyrin dyes containing the phenothiazine derived donor and the ethynylbenzoic acid acceptor have been designed, synthesized and used as sensitizers for fabricating efficient dye-sensitized solar cells (DSSCs). Branched or linear alkoxy chains were introduced to the ortho-positions of the meso-phenyl moieties to suppress the dye aggregation and charge recombination. The effect of alkoxy chains were investigated in the absence and presence of an additional electron withdrawing benzothiadiazole unit. In the former cases, almost identical photovoltaic efficiencies of similar to 8.3% were achieved for both the branched and the linear alkoxy chains, while in the latter cases, the planar benzothiadiazole unit induces serious dye aggregation and charge recombination, resulting in lower efficiencies of 6.46% and 7.50% for the linear and branched chains, respectively, even though broader absorption was achieved. The relatively higher efficiency achieved for the dyes with branched chains may be related to the better effect of suppressing the dye aggregation and charge recombination. Furthermore, the coadsorption approach was employed, and a highest efficiency of 9.62% was achieved for the dye that features branched chains and the benzothiadiazole unit. These results compose a novel approach for developing efficient DSSCs by combining the coadsorbent with a porphyrin dye containing both the additional benzothiadiazole acceptor and branched alkoxy chains.

  • 5. Li, A.
    et al.
    Song, Ce
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.
    Lin, Z.
    A multiphysics fully coupled modeling tool for the design and operation analysis of planar solid oxide fuel cell stacks2017In: Applied Energy, ISSN 0306-2619, E-ISSN 1872-9118, Vol. 190, 1234-1244 p.Article in journal (Refereed)
    Abstract [en]

    A planar SOFC stack is an integral but basic power generation unit with physical conditions completely different from that of a laboratory button cell. The ability to reliably predict the operating behaviors of SOFC stacks is crucial for the technology advancement. The existing stack models either rely on simplified geometries, or handle a few selected fields that are relatively easy to couple. This paper reports the first successful development of a high geometry resolution, multiphysics fully coupled numerical model for production scale planar SOFC stacks. The computational model is developed through in-house developed multiphysics modules combined with commercial software FLUENT®. All stack components such as flow channels, manifolds, cathode-electrolyte-anode assemblies, interconnects, seals and frames are resolved in the numerical grids. The mathematical model includes the fully coupled equations of momentum, mass, species, heat and charge transports, electrochemical reaction, and methane steam reforming and shift reactions. An accurate relationship between the O2 transport and electrochemistry within the cathode-rib structure is established and used to enhance the numerical efficiency of the stack model. The stack model is validated with the experimental data. The numerical stability and modeling capability of this multiphysics stack model are illustrated by simulating a 30-cell stack of 27 million grid points. Detailed information about the distributions of flows, temperature, current and chemical species, etc, is revealed. Comparative studies show that the results obtained by simplifications of stack geometries or reductions of multiphysics couplings are unreliable, illustrating the necessity of employing a true multiphysics computational tool.

  • 6. Liu, Lingling
    et al.
    Li, Xiao-Fei
    Yan, Qing
    Li, Qin-Kun
    Zhang, Xiang-Hua
    Deng, Mingsen
    Qiu, Qi
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Uniform and perfectly linear current-voltage characteristics of nitrogen-doped armchair graphene nanoribbons for nanowires2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 1, 44-48 p.Article in journal (Refereed)
    Abstract [en]

    Metallic nanowires with desired properties for molecular integrated circuits (MICs) are especially significant in molectronics, but preparing such wires at a molecular level still remains challenging. Here, we propose, from first principles calculations, experimentally realizable edge-nitrogen-doped graphene nanoribbons (N-GNRs) as promising candidates for nanowires. Our results show that edge N-doping has distinct effects on the electronic structures and transport properties of the armchair GNRs and zigzag GNRs (AGNRs, ZGNRs), due to the formation of pyridazine and pyrazole rings at the edges. The pyridazine rings raise the Fermi level and introduce delocalized energy bands near the Fermi level, resulting in a highly enhanced conductance in N-AGNRs at the stable nonmagnetic ground state. Especially for the family of AGNRs with widths of n = 3p + 2, their semiconducting characteristics are transformed to metallic characteristics via N-doping, and they exhibit perfectly linear current-voltage (I-V) behaviors. Such uniform and excellent features indicate bright application prospects of the N-AGNRs as nanowires and electrodes in molectronics.

  • 7. Wang, Shangshang
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Wandong
    Chen, Xuanying
    Zhang, Junji
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zou, Qi
    Zhu, Liangliang
    Chen, Wenbo
    Cu2+-Selectivity gated photochromism in Schiff-modified diarylethenes with a star-shaped structure2017In: Journal of Materials Chemistry C, ISSN 2050-7526, Vol. 5, no 2, 282-289 p.Article in journal (Refereed)
    Abstract [en]

    A great deal of effort has been devoted to developing gated photochromic systems due to their advantages in the smart materials and opto-electronic fields, whereas the gating function through certain ions has rarely been addressed. Since the photochromic materials gated by ions can be readily further processed into a multi-functional molecular switch and probe, we herein designed and conveniently synthesized a star-shaped Schiff-based diarylethene derivative showing typical photochromic properties in solution. This compound possesses two response channels (colorimetric and fluorogenic) to Cu2+ ions with photoswitching characteristics, making it a viable photochromic probe. It is noteworthy that its photochromic reactivity can be locked when Cu2+ ions are introduced into the solution. Moreover, the photoinactive and photoactive states can be interchanged reversibly by binding Cu2+ ions and unbinding Cu2+ ions using EDTA, which shows promise for application in multi-controlled molecular switches and smart materials. The mechanism of the photochromic properties locked by Cu2+ ions is reasonably proposed by theoretical simulations. These results could be valuable for the further development of molecular switching systems with multiple stimuli responses.

  • 8. Wang, Shangshang
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Wandong
    Chen, Xuanying
    Zhang, Junji
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Zou, Qi
    Zhu, Liangliang
    Chen, Wenbo
    Cu2+-Selectivity gated photochromism in Schiff-modified diarylethenes with a star-shaped structure2017In: Journal of Materials Chemistry C, ISSN 2050-7526, Vol. 5, no 2, 282-289 p.Article in journal (Refereed)
    Abstract [en]

    A great deal of effort has been devoted to developing gated photochromic systems due to their advantages in the smart materials and opto-electronic fields, whereas the gating function through certain ions has rarely been addressed. Since the photochromic materials gated by ions can be readily further processed into a multi-functional molecular switch and probe, we herein designed and conveniently synthesized a star-shaped Schiff-based diarylethene derivative showing typical photochromic properties in solution. This compound possesses two response channels (colorimetric and fluorogenic) to Cu2+ ions with photoswitching characteristics, making it a viable photochromic probe. It is noteworthy that its photochromic reactivity can be locked when Cu2+ ions are introduced into the solution. Moreover, the photoinactive and photoactive states can be interchanged reversibly by binding Cu2+ ions and unbinding Cu2+ ions using EDTA, which shows promise for application in multi-controlled molecular switches and smart materials. The mechanism of the photochromic properties locked by Cu2+ ions is reasonably proposed by theoretical simulations. These results could be valuable for the further development of molecular switching systems with multiple stimuli responses.

  • 9.
    C. Couto, Rafael
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vaz da Cruz, Vinícius
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Eckert, Sebastian
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    F. Guimarães, Freddy
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel’mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Föhlisch, Alexander
    Selective gating to vibrational modes through resonant X-ray scattering2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, 14165-1-14165-7 p.Article in journal (Refereed)
    Abstract [en]

    The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.

  • 10. Naruse, M.
    et al.
    Kim, S. -J
    Takahashi, T.
    Aono, M.
    Akahane, K.
    D'Acunto, M.
    Hori, H.
    Thylén, Lars
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Hewlett-Packard Laboratories, USA.
    Katori, M.
    Ohtsu, M.
    Percolation of optical excitation mediated by near-field interactions2017In: Physica A: Statistical Mechanics and its Applications, ISSN 0378-4371, Vol. 471, 162-168 p.Article in journal (Refereed)
    Abstract [en]

    Optical excitation transfer in nanostructured matter has been intensively studied in various material systems for versatile applications. Herein, we theoretically and numerically discuss the percolation of optical excitations in randomly organized nanostructures caused by optical near-field interactions governed by Yukawa potential in a two-dimensional stochastic model. The model results demonstrate the appearance of two phases of percolation of optical excitation as a function of the localization degree of near-field interaction. Moreover, it indicates sublinear scaling with percolation distances when the light localization is strong. Furthermore, such a character is maximized at a particular size of environments. The results provide fundamental insights into optical excitation transfer and will facilitate the design and analysis of nanoscale signal-transfer characteristics.

  • 11.
    Vaz da Cruz, Vinicius
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    C. Couto, Rafael
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Eckert, Sebastian
    Fondell, Mattis
    Dantz, Marcus
    O'Cinneide, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    F. Guimarães, Freddy
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Föhlisch, Alexander
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    A study of the water molecule using frequency control over nuclear dynamics in resonant X-ray scattering2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)
    Abstract [en]

    In this combined theoretical and experimental study we report a full analysis of the resonant inelastic X-ray scattering (RIXS) spectra of H2O, D2O and HDO. We demonstrate that electronically-elastic RIXS has an inherent capability to map the potential energy surface and to perform vibrational analysis of the electronic ground state in multimode systems. We show that the control and selection of vibrational excitation can be performed by tuning the X-ray frequency across core-excited molecular bands and that this is clearly reflected in the RIXS spectra. Using high level ab initio electronic structure and quantum nuclear wave packet calculations together with high resolution RIXS measurements, we discuss in detail the mode coupling, mode localization and anharmonicity in the studied systems.

  • 12. Nørby, M. S.
    et al.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden .
    Kongsted, J.
    Assessing frequency-dependent site polarisabilities in linear response polarisable embedding2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, 39-47 p.Article in journal (Refereed)
    Abstract [en]

    In this paper, we discuss the impact of using a frequency-dependent embedding potential in quantum chemical embedding calculations of response properties. We show that the introduction of a frequency-dependent embedding potential leads to further model complications upon solving the central equations defining specific molecular properties. On the other hand, we also show from a numerical point of view that the consequences of using such a frequency-dependent embedding potential is almost negligible. Thus, for the kind of systems and processes studied in this paper the general recommendation is to use frequency-independent embedding potentials since this leads to less complicated model issues. However, larger effects are expected if the absorption bands of the environment are closer to that of the region treated using quantum mechanics.

  • 13.
    Valiev, Rashid R.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Eland, J. H. D.
    Feifel, R.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Optimization of core–valence states of molecules2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 1-2, 252-259 p.Article in journal (Refereed)
    Abstract [en]

    Core–valence double-electron ionisation spectra of a few small molecules–carbon monoxide, ammonia, methyl fluoride and thiophene–are presented and analysed using the self-consistent field algorithm introduced by Hans Jørgen Jensen 30 years ago. It confirms the utility of this algorithm, frequently employed to obtain stable and sharp convergence of wave functions for the benefit of calculations of a great variety of molecular properties, thus also for optimisation of core–valence states and for the interpretation of the corresponding spectra.

  • 14.
    Sun, Xu
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Optics and Photonics, OFO. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP.
    Thylén, Lars
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP.
    Wosinski, L.ech
    KTH, School of Engineering Sciences (SCI), Applied Physics, Optics and Photonics, OFO. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP.
    Hollow hybrid plasmonic Mach-Zehnder sensor2017In: Optics Letters, ISSN 0146-9592, E-ISSN 1539-4794, Vol. 42, no 4Article in journal (Refereed)
    Abstract [en]

    A Mach–Zehnder interferometer (MZI)-based liquid refractiveindex sensor, utilizing a hollow hybrid plasmonic (HP)waveguide as the sensing element, has been investigated,showing large sensitivity to the refractive index changesof the tested liquids, as well as lower propagation loss incomparison to typical plasmonic waveguide-based ones.The sensor is fabricated using conventional silicon-oninsulator(SOI) technology; therefore, it is compatible toother standard SOI devices. The waveguide sensitivity, Sw,is experimentally demonstrated to be 0.64, with a propagationloss less than 0.25 dB/μm. Using a 20 μm long hollowHP waveguide in the sensing arm, the sensitivity of the MZIsensor (device sensitivity, Sd ) is about 160 nm/RIU, with anextinction ratio larger than 40 dB.

  • 15. Deksnys, T.
    et al.
    Simokaitiene, J.
    Keruckas, J.
    Volyniuk, D.
    Bezvikonnyi, O.
    Cherpak, V.
    Stakhira, P.
    Ivaniuk, K.
    Helzhynskyy, I.
    Baryshnikov, Glib
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Minaev, B.
    Grazulevicius, J. V.
    Synthesis and characterisation of a carbazole-based bipolar exciplex-forming compound for efficient and color-tunable OLEDs2017In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, no 2, 559-568 p.Article in journal (Refereed)
    Abstract [en]

    A new ambipolar fluorophore, 3,6-di(4,4′-dimethoxydiphenylaminyl)-9-(1-naphthyl)carbazole, was synthesized and its physical properties were studied by differential scanning calorimetry, thermogravimetric analysis, UV-vis absorption, luminescence and photoelectron emission spectroscopy, cyclic voltammetry and a time of flight method. The latter technique indicates that the compound demonstrates bipolar semiconducting properties. Using the synthesized compound as an emissive material, a single-layer OLED with an electroluminescence spectrum containing a voltage-dependent electroplex emission band in the region of 550-650 nm was fabricated. Another OLED was fabricated with an additional electron transporting bathophenanthroline layer that forms a direct interface with the layer of 3,6-di(4,4′-dimethoxydiphenylaminyl)-9-(1-naphthyl)carbazole. A strong exciplex-type band in the electroluminescence spectrum of this OLED with an emission maximum at ca. 540 nm was observed. The electroluminescence spectra of both devices were found to be clearly dependent on the applied bias. This effect can be useful for the development of efficient and colour-tunable OLEDs.

  • 16.
    Lobov, Gleb S.
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Optics and Photonics, OFO.
    Marinins, Aleksandrs
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Optics and Photonics, OFO.
    Etcheverry, Sebastian
    Zhao, Yichen
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Vasileva, Elena
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Sugunan, Abhilash
    Laurell, Fredrik
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
    Thylén, Lars
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Hewlett Packard Enterprise Labs, USA.
    Wosinski, Lech
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Östling, Mikael
    KTH, School of Information and Communication Technology (ICT), Elektronics, Integrated devices and circuits.
    Toprak, Muhammet S.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Popov, Sergei
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Optics and Photonics, OFO.
    Direct birefringence and transmission modulation via dynamic alignment of P3HT nanofibers in an advanced opto-fluidic component2017In: Optical Materials Express, ISSN 2159-3930, E-ISSN 2159-3930, Vol. 7, no 1, 52-61 p.Article in journal (Refereed)
    Abstract [en]

    Poly-3-hexylthiophene (P3HT) nanofibers are semiconducting high-aspect ratio nanostructures with anisotropic absorption and birefringence properties found at different regions of the optical spectrum. In addition, P3HT nanofibers possess an ability to be aligned by an external electric field, while being dispersed in a liquid. In this manuscript we show that such collective ordering of nanofibers, similar to liquid crystal material, significantly changes the properties of transmitted light. With a specially fabricated opto-fluidic component, we monitored the phase and transmission modulation of light propagating through the solution of P3HT nanofibers, being placed in the electric field with strength up to 0.1 V/mu m. This report describes a technique for light modulation, which can be implemented in optical fiber-based devices or on-chip integrated components.

  • 17.
    Lobov, G. S.
    et al.
    KTH, School of Information and Communication Technology (ICT).
    Marinins, A.
    KTH, School of Information and Communication Technology (ICT).
    Etcheverry, S.
    Zhao, Yichen
    KTH, School of Information and Communication Technology (ICT).
    Vasileva, Elena
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Sugunan, A.
    Laurell, F.
    Thylén, Lars
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wosinski, L.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Östling, Mikael
    KTH, School of Information and Communication Technology (ICT).
    Toprak, M. S.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Popov, Sergei
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Optics and Photonics, OFO.
    Direct birefringence and transmission modulation via dynamic alignment of P3HT nanofibers in an advanced opto-fluidic component2017In: Optical Materials Express, ISSN 2159-3930, E-ISSN 2159-3930, Vol. 7, no 1, 52-61 p.Article in journal (Refereed)
    Abstract [en]

    Poly-3-hexylthiophene (P3HT) nanofibers are semiconducting high-aspect ratio nanostructures with anisotropic absorption and birefringence properties found at different regions of the optical spectrum. In addition, P3HT nanofibers possess an ability to be aligned by an external electric field, while being dispersed in a liquid. In this manuscript we show that such collective ordering of nanofibers, similar to liquid crystal material, significantly changes the properties of transmitted light. With a specially fabricated opto-fluidic component, we monitored the phase and transmission modulation of light propagating through the solution of P3HT nanofibers, being placed in the electric field with strength up to 0.1 V/μm. This report describes a technique for light modulation, which can be implemented in optical fiber-based devices or on-chip integrated components.

  • 18.
    Wang, Yan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bergenstråhle-Wohlert, Malin
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Berglund, Lars A.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Wohlert, Jakob
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Swelling and dimensional stability of xyloglucan/montmorillonite nanocomposites in moist conditions from molecular dynamics simulations2017In: Computational Materials Science, ISSN 0927-0256, Vol. 128, 191-197 p.Article in journal (Refereed)
    Abstract [en]

    Nacre-mimetic biocomposites made from the combination of montmorillonite clay and the hemicellulose xyloglucan give materials that retain much of their material properties even at high relative humidity. Here, a model composite system consisting of two clay platelets intercalated by xyloglucan oligomers was studied at different levels of hydration using molecular dynamics simulations, and compared to the pure clay. It was found that xyloglucan inhibits swelling of the clay at low water contents by promoting the formation of nano-sized voids that fill with water without affecting the material's dimensions. At higher water contents the XG itself swells, but at the same time maintaining contact with both platelets across the gallery, thereby acting as a physical cross-linker in a manner similar to the role of XG in the plant cell wall.

  • 19.
    Liu, Haichun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Jayakumar, Muthu K. G.
    Huang, Kai
    Wang, Zi
    Zheng, Xiang
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Yong
    Phase angle encoded upconversion luminescent nanocrystals for multiplexing applications2017In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 9, no 4, 1676-1686 p.Article in journal (Refereed)
    Abstract [en]

    Lanthanide-doped upconversion nanoparticles (UCNPs) are increasingly used as luminescent candidates in multiplexed applications due to their excellent optical properties. Inthepast,several encodingidentities havebeen proposedforUCNPs,includingemissioncolour,intensity ratio between different emissionbands, colourspatial distribution, and luminescencelifetime.In this paper, a new optical encoding dimension for upconversion nanomaterials is developed by exploring their luminescence kinetics, i.e., the phase angle of upconversion luminescence in response to a harmonic-wave excitation. Our theoretical derivation shows that the phase angle is governed jointly by the rise and decay times, characterizing the upconversion luminescence kinetics. Experimentally, a full set of methods are developed to manage the upconversion luminescence kinetics, through which the rise and decay times can be manipulated dependently or independently. Furthermore,a large phase-angle space is achieved in which tens of unique codes can be potentially generated in the same colour channel. Our work greatly extends the multiplexing capacity of UCNPs,and offers newopportunities for their applicationsin a wide range such as microarray assays, bioimaging, anti-counterfeiting, deep tissue multiplexed labelling/detectionand high-density data storage.In addition, the development of thisluminescence kinetics-based optical encoding strategy is also instructive for developing multiplexing techniques using other cascade luminescent systems that inherently lack multi-spectral channels, such as triplet-triplet annihilation molecule pairs.

  • 20.
    Ignatova, Nina
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University.
    V. Cruz, Vinícius
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Couto, Rafael C.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Zimin, Andrey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    F. Guimarães, Freddy
    Polyutov, Sergey
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Gel’mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gradual collapse of nuclear wavefunctions regulated by frequencytuned X-ray scattering2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, ISSN 2045-2322, Vol. 7, no 43891, 10.1038/srep43891Article in journal (Refereed)
    Abstract [en]

    As is well established, the symmetry breaking by isotope substitution in the water molecule results in localisation of the vibrations along one of the two bonds in the ground state. In this study we find that this localisation may be broken in excited electronic states. Contrary to the ground state, the stretching vibrations of HDO are delocalised in the bound core-excited state in spite of the mass difference between hydrogen and deuterium. The reason for this effect can be traced to the narrow “canyon-like” shape of the potential of the state along the symmetric stretching mode, which dominates over the localisation mass-difference effect. In contrast, the localisation of nuclear motion to one of the HDO bonds is preserved in the dissociative core-excited state . The dynamics of the delocalisation of nuclear motion in these core-excited states is studied using resonant inelastic X-ray scattering of the vibrationally excited HDO molecule. The results shed light on the process of a wave function collapse. After core-excitation into the state of HDO the initial wave packet collapses gradually, rather than instantaneously, to a single vibrational eigenstate.

  • 21.
    Hu, Wei
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Duan, Sai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical modeling of surface and tip-enhanced Raman spectroscopies2017In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 7, no 2, UNSP e1293Article, review/survey (Refereed)
    Abstract [en]

    Raman spectroscopy is a powerful technique in molecular science because of the ability of providing vibrational 'finger-print'. The developments of the surfaceenhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have significantly improved the detection sensitivity and efficiency. However, they also introduce complications for the spectral assignments, for which advanced theoretical modeling has played an important role. Here we summarize some of our recent progresses for SERS and TERS, which generally combine both solid-state physics and quantum chemistry methods with two different schemes, namely the cluster model and the periodic boundary condition (PBC) model. In the cluster model, direct Raman spectra calculations are performed for the cluster taken from the accurate PBC structure. For PBC model, we have developed a quasianalytical approach that enables us to calculate the Raman spectra of entire system. Under the TERS condition, the non-uniformity of plasmonic field in real space can drastically alter the interaction between the molecule and the light. By taking into account the local distributions of the plasmonic field, a new interaction Hamiltonian is constructed and applied to model the super-high-resolution Raman images of a single molecule. It shows that the resonant Raman images reflect the transition density between ground and excited states, which are generally vibrational insensitive. The nonresonant Raman images, on the other hand, allow to visualize the atomic movement of individual vibrational modes in real space. The inclusion of non-uniformity of plasmonic field provides ample opportunities to discover new physics and new applications in the future. 

  • 22.
    Fan, Ting
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Duan, Lele
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Huang, Ping
    Chen, Hong
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Daniel, Quentin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Ahlquist, Mårten S. G.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    The Ru-tpc Water Oxidation Catalyst and Beyond: Water Nucleophilic Attack Pathway versus Radical Coupling Pathway.2017In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 7, no 4, 2956-2966 p.Article in journal (Refereed)
    Abstract [en]

    Many Ru water oxidation catalysts have been documented in the literature. However, only a few can catalyze the O-O bond formation via the radical coupling pathway, while most go through the water nucleophilic attack pathway. Understanding the electronic effect on the reaction pathway is of importance in design of active water oxidation catalysts. The Ru-bda (bda = 2,2'-bipyridine-6,6'-dicarboxylate) catalyst is one example that catalyzes the 0-0 bond formation via the radical coupling pathway. Herein, we manipulate the equatorial backbone ligand, change the doubly charged bda(2-) ligand to a singly charged tpc- (2,2':6',2 ''-terpyridine-6-carboxylate) ligand, and study the structure activity relationship. Surprisingly, kinetics measurements revealed that the resulting Ru-tpc catalyst catalyzes water oxidation via the water nucleophilic attack pathway, which is different from the Ru-bda catalyst. The O-O bond formation Gibbs free energy of activation (AGO) at T = 298.15 K was 20.2 +/- 1.7 kcal mol(-1). The electronic structures of a series of Ru-v=O species were studied by density function theory calculations, revealing that the spin density of O-Ru=O of Ru-v=O is largely dependent on the surrounding ligands. Seven coordination configuration significantly enhances the radical character of Ru-v=O.

  • 23. Kagalwala, Husain N.
    et al.
    Tong, Lianpeng
    Zong, Ruifa
    Kohler, Lars
    Ahlquist, Mårten S. G.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fan, Ting
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gagnon, Kevin J.
    Thummel, Randolph P.
    Evidence for Oxidative Decay of a Ru-Bound Ligand during Catalyzed Water Oxidation2017In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 7, no 4, 2607-2615 p.Article in journal (Refereed)
    Abstract [en]

    In the evaluation of systems designed for 800 catalytic water oxidation, ceric ammonium nitrate (CAN) is often used as a sacrificial electron acceptor. One of the sources of failure for such systems is oxidative decay of the catalyst in the presence of the strong oxidant CAN (E-ox = +1.71 V). Little progress has been made in understanding the circumstances behind this decay. In this study we show that a 2-(2'-hydroxphenyl) derivative (LH) of 1,10-phenanthroline (phen) in the complex [Ru(L)(tpy)](+) (tpy = 2,2';6',2 ''-terpyridine) can be oxidized by CAN to a 2-carboxy-phen while still bound to the metal. This complex is, in fact, a very active water oxidation catalyst. The incorporation of a methyl substituent on the phenol ring of LH slows down the oxidative decay and consequently slows down the catalytic oxidation. An analogous system based on bpy (2,2'-bipyridine) instead of phen shows much lower activity under the same conditions. Water molecule association to the Ru center of [Ru(L)(tpy)](+) and carboxylate donor dissociation were proposed to occur at the trivalent state. The resulting [Ru-III-OH2] was further oxidized to [Ru-IV=O] via a PCET process.

  • 24. Minaeva, V. A.
    et al.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Baryshnikov, Gleb V.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Calculation of the optical spectra of the copper(I) complex with triphenylphosphine, iodine, and 3-pyridine-2-yl-5-phenyl-1H-1,2,4-triazole by the DFT method2017In: Optics and Spectroscopy, ISSN 0030-400X, E-ISSN 1562-6911, Vol. 122, no 2, 175-183 p.Article in journal (Refereed)
    Abstract [en]

    The IR and UV spectra of the [CuIL(PPh3)] complex (PPh3 = triphenylphosphine, L = 3-pyridine- 2-yl-5-phenyl-1De-1,2,4-triazole) have been analyzed in detail within the density functional theory (DFT) and its time-dependent version TD DFT. The standard functional B3LYP and sets of basis orbitals 6-311G(d,p) and Lanl2DZ are used for the atoms of the elements of periods I and II and for the iodine atom, respectively. The calculated IR spectra of the complex and free ligands coincide with the observed IR bands, due to which one can completely interpret all normal modes and confirm X-ray diffraction (XRD) data. Particular attention is paid to the structure of excited triplet (D cent (1)) state in order to explain the role of copper and iodine ions in the formation of photo- and electroluminescence spectra. It is shown that the equilibrium D cent (1) state undergoes structural relaxation after the vertical excitation and significantly changes its electronic nature and the charge transfer structure.

  • 25.
    Sun, Xianqiang
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Laroch, Genevieve
    Wang, Xu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bowman, Gregory R.
    Giguõre, Patrick M.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Propagation of the Allosteric Modulation Induced by Sodium in the delta-Opioid Receptor2017In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 23, no 19, 4615-4624 p.Article in journal (Refereed)
    Abstract [en]

    Allosteric sodium in the helix bundle of a G protein-coupled receptor (GPCR) can modulate the receptor activation on the intracellular side. This phenomenon has confounded the GPCR community for decades. In this work, we present a theoretical model that reveals the mechanism of the allosteric modulation induced by sodium in the delta-opioid receptor. We found that the allosteric sodium ion exploits a distinct conformation of the key residue Trp2746.48 to propagate the modulation to helices 5 and 6, which further transmits along the helices and regulates their positions on the intracellular side. This mechanism is supported by subsequent functional assays. Remarkably, our results highlight the contrast between the allosteric effects towards two GPCR partners, the G protein and b-arrestin, as indicated by the fact that the allosteric modulation initiated by the sodium ion significantly affects the b-arrestin recruitment, while it alters the G protein signaling only moderately. We believe that the mechanism revealed in this work can be used to explain allosteric effects initiated by sodium in other GPCRs since the allosteric sodium is highly conserved across GPCRs. 

  • 26. Yu, Shujun
    et al.
    Wang, Xiangxue
    Yao, Wen
    Wang, Jian
    Ji, Yongfei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ai, Yuejie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Alsaedi, Ahmed
    Hayat, Tasawar
    Wang, Xiangke
    Macroscopic, Spectroscopic, and Theoretical Investigation for the Interaction of Phenol and Naphthol on Reduced Graphene Oxide2017In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 51, no 6, 3278-3286 p.Article in journal (Refereed)
    Abstract [en]

    Interaction of phenol and naphthol with reduced graphene oxide (rGO), and their competitive behavior on rGO were examined by batch experiments, spectroscopic analysis and theoretical calculations. The batch sorption showed that the removal percentage of phenol or naphthol on rGO in bisolute systems was significantly lower than those of phenol or naphthol in single-solute systems. However, the overall sorption capacity of rGO in bisolute system was higher than single-solute system, indicating that the rGO was a very suitable material for the simultaneous elimination of organic pollutants from aqueous solutions. The interaction mechanism was mainly pi-pi interactions and hydrogen bonds, which was evidenced by FTIR, Raman and theoretical calculation. FTIR and Raman showed that a blue shift of C=C and -OH stretching modes and the enhanced intensity ratios of I-D/I-G after phenols sorption. The theoretical calculation indicated that the total hydrogen bond numbers, diffusion constant and solvent accessible surface area of naphthol were higher than those of phenol, indicating higher sorption affinity of rGO for naphthol as compared to phenol. These findings were valuable for elucidating the interaction mechanisms between phenols and graphene-based materials, and provided an essential start in simultaneous removal of organics from wastewater.

  • 27. Bondarchuk, Sergey V.
    et al.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Super high-energy density single-bonded trigonal nitrogen allotrope-a chemical twin of the cubic gauche form of nitrogen2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 9, 6698-6706 p.Article in journal (Refereed)
    Abstract [en]

    A new ambient- pressure metastable single- bonded 3D nitrogen allotrope (TrigN) of trigonal symmetry (space group R(-)3) was calculated using density functional theory (DFT). A comprehensive characterization of this material, comprising thermodynamic, elastic, and spectral (vibrational, UV-vis absorption, and nuclear magnetic resonance) properties, was performed. Using high-throughput band structure calculation, the TrigN phase was characterized as an insulator with an indirect band gap of 2.977 eV. Phonon dispersion calculations justified that this structure is vibrationally stable at ambient pressure. The calculated Raman activities at the Gamma-point demonstrated a rich pattern, whereas no relatively intense transitions were observed in its IR absorption spectrum. The TrigN material is almost transparent to visible light as well as to ultraviolet A and B. The main absorption peaks appeared within the range of 50-200 nm. The electron arrangement of the nitrogen nuclei in the studied nitrogen allotrope is much denser compared to that of the molecular nitrogen, which is in agreement with the calculated magnetic shielding tensor values. Robust mechanical stability is revealed from the elastic constants calculation. Due to strong anisotropy, the values of the Young's moduli vary from 281 to 786 GPa. A huge amount of internal energy is enclosed in the TrigN material. Upon decomposition to molecular nitrogen, the energy release is expected to be 11.01 kJ g(-1) compared to the value of 10.22 kJ g(-1) for the cubic gauche form of nitrogen. The TrigN allotrope possesses unique detonation characteristics with a detonation pressure of 146.06 GPa and velocity of 15.86 km s(-1).

  • 28. Ru, Xiao
    et al.
    Song, Ce
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Lin, Zijing
    Structural Information-Based Method for the Efficient and Reliable Prediction of Oligopeptide Conformations2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 12, 2525-2533 p.Article in journal (Refereed)
    Abstract [en]

    Predictions of structures of biomolecules are challenging due to the high dimensionalities of the potential energy surfaces (PESs) involved. Reducing the necessary PES dimensionality is helpful for improving the computational efficiency of all relevant structure prediction methods. For that purpose, a systematic analysis of the backbone dihedral angles (DAs) in the low energy conformations of amino acids, di-, tri-, and tetrapeptides is performed. The analysis reveals that the DAs can be represented by a set of discretized values. Moreover, there are rules limiting the combinations of neighboring DA states. The DA combination rules are used to formulate a path matrix scheme for locating the low energy conformations of peptides. Comparing with the full DA combinations, the PES dimensionality in the path matrix method is reduced by a factor of 2.5 '', where n is the number of amino acid residues in a peptide. The path matrix method is validated by applications to find the conformations of representative tri-, tetra-, and pentapeptides and comparison with the best literature results. All the tests show that the path matrix method is very efficient and highly reliable by producing the best search results for the low energy peptide conformations.

  • 29. Fransson, Thomas
    et al.
    Rehn, Dirk Robert
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Norman, P.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Static polarizabilities and C-6 dispersion coefficients using the algebraic-diagrammatic construction scheme for the complex polarization propagator2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 9, 094301Article in journal (Refereed)
    Abstract [en]

    An implementation of the damped linear response function, or complex polarization propagator, using the algebraic-diagrammatic construction (ADC) scheme has been developed and utilized for the calculation of electric-dipole polarizabilities and C-6 dispersion coefficients. Four noble gases (He, Ne, Ar, and Kr), five n-alkanes (methane, ethane, propane, butane, and pentane), three carbonyls (formaldehyde, acetaldehyde, and acetone), and three unsaturated hydrocarbons (ethene, acetylene, and benzene) have been treated with the hierarchical set of models ADC(2), ADC(2)-x, and ADC(3/2), and comparison has been made to results obtained with damped linear response Hartree-Fock (HF) and coupled cluster singles and doubles (CCSD) theory as well as high-quality experimental estimates via the dipole oscillator strength distribution approach. This study marks the first ADC calculations of C-6 dispersion coefficients and the first ADC(3/2) calculations of static polarizabilities. Results at CCSD and ADC(3/2) levels of theory are shown to be of similar quality, with electron correlation effects increasing the molecular property values for all calculations except CCSD considerations of ethene and acetylene (attributed to an overestimation of bond electron density at HF level of theory). The discrepancies betweenCCSDand ADC(3/2) are partially due toADCoverestimating anisotropies, and discrepancies with respect to experimental values are partially due to the lack of zero-point vibrational effects in the present study.

  • 30. Chen, S.
    et al.
    Li, W.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhu, W. -H
    Aggregation-controlled photochromism based on a dithienylethene derivative with aggregation-induced emission2017In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 5, no 10, 2717-2722 p.Article in journal (Refereed)
    Abstract [en]

    We report novel aggregation-induced emission (AIE) characteristics involving aggregation-controlled photochromism properties of a dithienylethene derivative, BTE-EQ, where two quinolinemalononitrile (EQ) units are covalently attached to a dithienylethene core. The typical AIE effect of BTE-EQ has been found to originate from the AIE character of the EQ units with respect to the reference compound BTE, which does not contain an EQ unit. The photochromism study, together with density functional theory calculations, reveals that the photochromic activity of BTE-EQ can be reversibly switched off and on by controlling the aggregation state during the AIE process, which provides a novel route to controlling the photochromism of diarylethenes.

  • 31. Wu, H.
    et al.
    Hang, C.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Yin, L.
    Zhu, M.
    Zhang, J.
    Zhou, Y.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Q.
    Zhu, L.
    Molecular stacking dependent phosphorescence-fluorescence dual emission in a single luminophore for self-recoverable mechanoconversion of multicolor luminescence2017In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 53, no 18, 2661-2664 p.Article in journal (Refereed)
    Abstract [en]

    A self-recoverable mechanoconversion of multicolor luminescence was observed by crystallization-induced self-assembly. Such a self-assembly led to the formation of nanorods with different molecular stacking modes, thus making the phosphorescence/fluorescence proportion alterable. Therefore, multicolor luminescence of the single luminophore can be achieved by a straightforward reversible mechanical stimulus.

  • 32.
    Minaeva, Valentina A.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Karaush, N. N.
    Minaev, B. F.
    Baryshnikov, Gleb V.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Chen, F.
    Tanaka, T.
    Osuka, A.
    Comparative study of the structural and spectral properties of tetraaza- and tetraoxaannelated tetracirculenes2017In: Optics and Spectroscopy, ISSN 0030-400X, E-ISSN 1562-6911, Vol. 122, no 4, 523-540 p.Article in journal (Refereed)
    Abstract [en]

    The IR spectrum of a recently synthesized tetraaza[8]circulene (4N) molecule has been investigated and completely interpreted based on the calculation of the molecular structure and force field within the density functional theory (DFT) using the B3LYP/6-311G(d,p) method. The calculation has also successfully explained the X-ray diffraction data. The same method has been used to calculate the tetraoxa[8]circulene (4D) molecule and perform a comparative analysis of the IR spectra of both molecules. In contrast to 4D, the 4N molecule exhibits strong fluorescence, which hinders measurement of its Raman spectrum; hence, it is only predicted based on the DFT calculation in this study. A comparison of the IR and Raman spectra of the 4N molecule with the experimental and theoretical analogs for the 4D molecule has made it possible to assign all the observed vibrational transitions and explain the nature of normal vibrations in these complex molecules.

  • 33. Gerasimov, V. S.
    et al.
    Ershov, A. E.
    Karpov, S. V.
    Gavrilyuk, A. P.
    Zakomirnyi, Vadim
    KTH. Siberian Federal University, Russian Federation.
    Rasskazov, I. L.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Polyutov, S. P.
    Thermal effects in systems of colloidal plasmonic nanoparticles in high-intensity pulsed laser fields [Invited]2017In: Optical Materials Express, ISSN 2159-3930, E-ISSN 2159-3930, Vol. 7, no 2, 555-568 p.Article in journal (Refereed)
    Abstract [en]

    We have studied light induced processes in nanocolloids and composite materials containing ordered and disordered aggregates of plasmonic nanoparticles accompanied by their strong heating. A universal comprehensive physical model that combines mechanical, electrodynamical, and thermal interactions at nanoscale has been developed as a tool for investigations. This model was used to gain deep insight on phenomena that take place in nanoparticle aggregates under high-intensity pulsed laser radiation resulting in the suppression of nanoparticle resonant properties. Verification of the model was carried out with single colloidal Au and Ag nanoparticles and their aggregates.

  • 34. Shao, Wei
    et al.
    Chen, Guanying
    Ohulchanskyy, Tymish Y.
    Yang, Chunhui
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Prasad, Paras N.
    A core-multiple shell nanostructure enabling concurrent upconversion and quantum cutting for photon management2017In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 9, no 5, 1934-1941 p.Article in journal (Refereed)
    Abstract [en]

    Photon management enables the manipulation of the number of input photons by conversion of two or more light quanta into one (upconversion) or vice versa (quantum cutting). Simultaneous realization of both these processes in a single unit provides unique opportunities of efficient utilization of photons throughout a broad spectral range. Yet, concurrent realization of these two parallel optical processes in one single unit remains elusive, limiting its impact on many existing or possible future applications such as for panchromatic photovoltaics. Here, we describe an epitaxial active core/inert shell/active shell/inert shell fluoride nanostructure to implement upconversion and quantum cutting within spatially confined and isolated rare-earth-doped active domains. The core area transforms infrared photons through trivalent erbium (Er3+) ions into three-and two-photon upconverted visible and near infrared luminescence, while the second shell domain splits an excitation photon into two near infrared photons through cooperative quantum cutting from one trivalent terbium ion (Tb3+) to two trivalent ytterbium ions (Yb3+). The inert layer in between the active domains is able to effectively suppress the destructive interference between upconversion and quantum cutting, while the outermost inert shell is able to eliminate surfacerelated quenching. This design enables the colloidal core/multishell nanoparticles to have an upconversion quantum yield of similar to 1.6%, and to have a luminescence yield of the quantum cutting process as high as similar to 130%. This work constitutes a solid step for flexible photon management in a single nanostructure, and has an implication for photonic applications beyond photovoltaics.

  • 35.
    Baryshnikov, Glib V.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bogdan Khmelnitsky Cherkasy National University, Ukraine.
    Bondarchuk, S. V.
    Minaeva, V. A.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bogdan Khmelnitsky Cherkasy National University, Ukraine.
    Solvatochromic effect in absorption and emission spectra of star-shaped bipolar derivatives of 1,3,5-triazine and carbazole. A time-dependent density functional study2017In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 23, no 2, 55Article in journal (Refereed)
    Abstract [en]

    A series of three star-shaped compounds containing both donor (carbazole) and acceptor (2,4,6-triphenyl-1,3,5-triazine) moieties linked through various linking bridges was studied theoretically at the linear response TD-DFT level of theory to describe their absorption and fluorescence spectra. The concept of a localized charge-transfer excited state has been applied successfully to explain the observed strong solvatochromic effect in the emission spectra of the studied molecules, which can be utilized for the fabrication of color tunable solution-processable OLEDs. The concept is in particularly applicable to donor–acceptor species with a C3 symmetry point group where the static dipole moment changes dramatically upon electronic excitation. An important peculiarity of the studied molecules is that they are characterized by non-zero values of the HOMO and LUMO orbitals in the same common part of molecular space that provides a large electric dipole transition moment for both light absorption and emission. [Figure not available: see fulltext.]

  • 36. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Wielgus, Malgorzata
    Jedrzejewska, Beata
    Puttreddy, Rakesh
    Rissanen, Kari
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Osmialowski, Borys
    Two-photon absorption of BF2-carrying compounds: insights from theory and experiment2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 8, 5705-5708 p.Article in journal (Refereed)
    Abstract [en]

    This communication presents a structure-property study of a few novel pyridine-based difluoroborate compounds with a N-BF2-O core, which exhibit outstanding fluorescence properties. To exploit their potential for two-photon bioimaging, relationships between the two-photon action cross section and systematic structural modifications have been investigated and unravelled.

  • 37.
    Zhang, Rui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Xianbiao
    Wang, Huifang
    Zhang, Yao
    Jiang, Song
    Hu, Chunrui
    Zhang, Yang
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Dong, Zhenchao
    Distinguishing Individual DNA Bases in a Network by Non-Resonant Tip-Enhanced Raman Scattering2017In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 56, no 20, 5561-5564 p.Article in journal (Refereed)
    Abstract [en]

    The importance of identifying DNA bases at the single-molecule level is well recognized for many biological applications. Although such identification can be achieved by electrical measurements using special setups, it is still not possible to identify single bases in real space by optical means owing to the diffraction limit. Herein, we demonstrate the outstanding ability of scanning tunneling microscope (STM)-controlled non-resonant tip-enhanced Raman scattering (TERS) to unambiguously distinguish two individual complementary DNA bases (adenine and thymine) with a spatial resolution down to 0.9 nm. The distinct Raman fingerprints identified for the two molecules allow to differentiate in real space individual DNA bases in coupled base pairs. The demonstrated ability of non-resonant Raman scattering with super-high spatial resolution will significantly extend the applicability of TERS, opening up new routes for singlemolecule DNA sequencing.

  • 38.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhou, Yang
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zou, Rongfeng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Halldin, C.
    Nordberg, A.
    Långström, B.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University, Russian Federation.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Characterization of the binding mode of the PET tracer [18F]ASEM to a chimera structure of the α7 nicotinic acetylcholine receptor2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 32, 19787-19793 p.Article in journal (Refereed)
    Abstract [en]

    The α7 nicotinic acetylcholine receptor (α7-nAChR) is assumed to be implicated in a variety of neurological disorders, such as schizophrenia and Alzheimer's disease (AD). The progress of these disorders can be studied through imaging α7-nAChR with positron emission tomography (PET). [18F]ASEM is a novel and potent α7-nAChR PET radioligand showing great promise in recent tests. However, the mechanism of the molecular interaction between [18F]ASEM and α7-nAChR is still unclear. In this paper, the binding profile of [18F]ASEM to a chimera structure of α7-nAChR was investigated with molecular docking, molecular dynamics, and metadynamics simulation methods. We found that [18F]ASEM binds at the same site as the crystallized agonist epibatidine but with a different binding mode. The dibenzo[b,d]thiophene ring has a different orientation compared to the pyridine ring of epibatidine and has van der Waals interactions with residues from loop C on one side and π-π stacking interaction with Trp53 on the other side. The conformation of Trp53 was found to have a great impact on the binding of [18F]ASEM. Six binding modes in terms of the side chain dihedral angles χ1 and χ2 of Trp53 were discovered by metadynamics simulation. In the most stable binding mode, Trp53 adopts a different conformation from that in the crystalline structure and has a rather favorable π-π stacking interaction with [18F]ASEM. We believe that these discoveries can be valuable for the development of novel PET radioligands.

  • 39. Aaldering, L. J.
    et al.
    Poongavanam, V.
    Langkjær, N.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Jørgensen, P. T.
    Wengel, J.
    Veedu, R. N.
    Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule2017In: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 18, no 8, 755-763 p.Article in journal (Refereed)
    Abstract [en]

    The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C3), unlocked nucleic acid (UNA) and 3′-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  • 40. Nåbo, L. J.
    et al.
    Holmgaard List, Nanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Steinmann, C.
    Kongsted, J.
    Computational Approach to Evaluation of Optical Properties of Membrane Probes2017In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 2, 719-726 p.Article in journal (Refereed)
    Abstract [en]

    Computed optical properties of membrane probes are typically evaluated in the gas phase, i.e. neglecting the influence of the membrane. In this study, we examine how and to what extent a membrane influences the one- and two-photon absorption (1PA and 2PA, respectively) properties for a number of cholesterol analogs and thereby also evaluate the validity of the common gas phase approach. The membrane is modeled using the polarizable embedding scheme both with and without the effective external field extension of the polarizable embedding model. The shifts in excitation energies and 1PA oscillator strengths compared to the gas phase are relatively small, while the 2PA cross section is more affected. The electric field inside the membrane induces a larger change in the permanent electric dipole moment upon excitation of the analogs compared to the gas phase, which leads to an almost 2-fold increase in the 2PA cross section for one cholesterol analog. The relative trends observed in the membrane are the same as in the gas phase, and the use of gas phase calculations for qualitative comparison and design of cholesterol membrane probes is thus a useful and computationally efficient strategy.

  • 41.
    Baryshnikov, Gleb V.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bogdan Khmelnitsky National University, Ukraine; Tomsk State University, Russian Federation.
    Valiev, Rashid R.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Tomsk State University, Russian Federation; Tomsk Polytechnic University, Russian Federation.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bogdan Khmelnitsky National University, Ukraine; Tomsk State University, Russian Federation.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    A computational study of aromaticity and photophysical properties of unsymmetrical azatrioxa[8]circulenes2017In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, no 7, 2717-2723 p.Article in journal (Refereed)
    Abstract [en]

    Owing to their potential use in organic light-emitting diodes and field-effect transistors we present a theoretical study of a series of unsymmetrical azatrioxa[8]circulenes in order to explain the impact of outer substituents and benzoannelation on photophysical constants and aromaticity of these compounds in terms of spin-orbit coupling perturbation and magnetically-induced ring currents. It is argued that the S1-Tn inter-system crossing processes constitute the main deactivation pathways for the fluorescence quenching, something that is supported by a good agreement obtained with experimental data on fluorescence quantum yields. The concept of the gauge-including magnetically induced currents has been applied in order to estimate the role of substituents and benzoannelated fragments on the aromaticity and particularly on the overall balance between the diatropic “aromatic” and paratropic “antiaromatic” current strengths. While a variation of the substituents in the outer perimeter of the studied circulenes does not provide a clear effect on their aromaticity, it is demonstrated that an additional benzoannelation (π-extension) of the azatrioxa[8]circulene macrocycle induces a significant aromaticity enhancement.

  • 42. Wu, Hongwei
    et al.
    Zhao, Pei
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Chen, Wenbo
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Qing
    Zhu, Liangliang
    Tuning for Visible Fluorescence and Near-Infrared Phosphorescence on a Unimolecular Mechanically Sensitive Platform via Adjustable CH-pi Interaction2017In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 9, no 4, 3865-3872 p.Article in journal (Refereed)
    Abstract [en]

    CH-pi interaction-assisted alignment of organic conjugated systems has played an important role to regulate molecular electronic and photophysical properties, whereas harnessing such a smart noncovalent interaction into the tuning of unimolecular complex emissive bands covering a wide spectral region remains a challenging research topic. Since the tuning for visible and near-infrared emissive properties in a single pi-functional platform relates to its multicolor luminescent behaviors and potential superior application in analysis, bioimaging, and sensing, herein, we report a proportional control of the singlet and triplet emissions that cover visible and near-infrared spectral regions, respectively, can be straightforwardly achieved by CH-pi interaction-assisted self-assembly at the unimolecular level. Employing an octathionaphthalene-based single luminophore as a prototype, we find that a strength-adjustable CH-pi interaction-assisted self-assembly can be established in mixed DMF/H2O and in the film state. The hybridization of planar local excited and intramolecular charge transfer transitions occurs on the basis, allowing a competitive inhibition to the intersystem crossing process to generate a complex emission composed of visible fluorescence and near-infrared phosphorescence. Furthermore, reversible mechanochromic and mechanoluminescent conversions of the corresponding solid sample can both be observed to rely on a corresponding self-assembly alternation. These results can probably provide new visions for the development of future intelligent and multifunctional luminescent materials.

  • 43. Mao, Wenxuan
    et al.
    Zhang, Junji
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, Chen
    Tian, He
    Regioisomerically pure multiaryl coronene derivatives: highly efficient synthesis via bay-extended perylene tetrabutylester2017In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 53, no 36, 5052-5055 p.Article in journal (Refereed)
    Abstract [en]

    By a facile strategy, we obtained three pure regioisomers of multiaryl coronene bisimide (CBI) derivatives via IBr-mediated annelation and subsequent Suzuki coupling reactions with high yields. A series of aromatic groups with different electron properties were efficiently introduced to obtain functional CBI derivatives under mild conditions with good yields. Furthermore, the annelation mechanism as well as the optical and electrochemical properties of CBI derivatives were further investigated.

  • 44. Chen, H.
    et al.
    Gao, Y.
    Lu, Z.
    Ye, L.
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD. KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry. KTH, Superseded Departments, Chemistry. KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP. State Key Laboratory of Fine Chemicals, Institute of Artificial Photosynthesis, DUT-KTH Joint Education and Research Center on Molecular Devices, Dalian University of Technology (DUT), Dalian 116024, China.
    Copper Oxide Film In-situ Electrodeposited from Cu(II) Complex as Highly Efficient Catalyst for Water Oxidation2017In: Electrochimica Acta, ISSN 0013-4686, E-ISSN 1873-3859, Vol. 230, 501-507 p.Article in journal (Refereed)
    Abstract [en]

    Water splitting is deemed as an effective pathway for producing ideal clean energy, such as hydrogen. Here, a copper oxide film (Cu-Tris film) was prepared in-situ from a 0.2 M phosphate buffer solution (pH = 12.0) containing 1.0 mM Cu2+ and 2.0 mM Tris via controlled-potential electrodeposition. The Cu-Tris film showed a significantly low overpotential of 390 mV at a current density of 1.0 mA/cm2 for electrocatalytic water oxidation. Simultaneously, a considerably low Tafel slope of 41 mV/decade was achieved. This Cu-Tris film also exhibited a high and stable current density of ca. 7.5 mA/cm2 at 1.15 V vs. NHE for long-term electrocatalysis (10 h). These results demonstrated the superior performance of the developed Cu-Tris film, which should be attributed to the regulating effect of the five coordinated planar structure of the Cu-Tris complex precursor during the process of electrodeposition.

  • 45.
    Duan, Sai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    Xie, Zhen
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.
    Gauge invariant theory for super high resolution Raman images2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 19, 194106Article in journal (Refereed)
    Abstract [en]

    The use of a highly localized plasmonic field has enabled us to achieve sub-nanometer resolution of Raman images for single molecules. The inhomogeneous spatial distribution of plasmonic field has become an important factor that controls the interaction between the light and the molecule. We present here a gauge invariant interaction Hamiltonian (GIIH) to take into account the nonuniformity of the electromagnetic field distribution in the non-relativistic regime. The theory has been implemented for both resonant and nonresonant Raman processes within the sum-over-state framework. It removes the gauge origin dependence in the phenomenologically modified interaction Hamiltonian (PMIH) employed in previous studies. Our calculations show that, in most resonant cases, the Raman images from GIIH are similar to those from PMIH when the origin is set to the nuclear charge center of the molecule. In the case of nonresonant Raman images, distinct differences can be found from two different approaches, while GIIH calculations provide more details and phase information of the images. Furthermore, the results from GIIH calculations are more stable with respect to the computational parameters. Our results not only help to correctly simulate the resonant and nonresonant Raman images of single molecules but also lay the foundation for developing gauge invariant theory for other linear and nonlinear optical processes under the excitation of non-uniform electromagnetic field. Published by AIP Publishing.

  • 46.
    Baryshnikov, Gleb
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bohdan Khmelnytsky National University, Ukraine.
    Minaev, Boris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bohdan Khmelnytsky National University, Ukraine.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University, Russia.
    Theory and Calculation of the Phosphorescence Phenomenon2017In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 117, no 9, 6500-6537 p.Article, review/survey (Refereed)
    Abstract [en]

    Phosphorescence is a phenomenon of delayed luminescence that corresponds to the radiative decay of the molecular triplet state. As a general property of molecules, phosphorescence represents a cornerstone problem of chemical physics due to the spin prohibition of the underlying triplet-singlet emission and because its analysis embraces a deep knowledge of electronic molecular structure. Phosphorescence is the simplest physical process which provides an example of spin-forbidden transformation with a characteristic spin selectivity and magnetic field dependence, being the model also for more complicated chemical reactions and for spin catalysis applications. The bridging of the spin prohibition in phosphorescence is commonly analyzed by perturbation theory, which considers the intensity borrowing from spin-allowed electronic transitions. In this review, we highlight the basic theoretical principles and computational aspects for the estimation of various phosphorescence parameters, like intensity, radiative rate constant, lifetime, polarization, zero-field splitting, and spin sublevel population. Qualitative aspects of the phosphorescence phenomenon are discussed in terms of concepts like structure-activity relationships, donor-acceptor interactions, vibronic activity, and the role of spin-orbit coupling under charge-transfer perturbations. We illustrate the theory and principles of computational phosphorescence by highlighting studies of classical examples like molecular nitrogen and oxygen, benzene, naphthalene and their azaderivatives, porphyrins, as well as by reviewing current research on systems like electrophosphorescent transition metal complexes, nucleobases, and amino acids. We furthermore discuss modern studies of phosphorescence that cover topics of applied relevance, like the design of novel photofunctional materials for organic light-emitting diodes (OLEDs), photovoltaic cells, chemical sensors, and bioimaging.

  • 47. Ai-Xi, Chen
    et al.
    Hong, Wang
    Duan, Sai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hai-Ming, Zhang
    Xin, Xu
    Li-Feng, Chi
    Potential-Induced Phase Transition of N-Isobutyryl-L-cysteine Monolayers on Au(111) Surfaces2017In: Wuli huaxue xuebao, ISSN 1000-6818, Vol. 33, no 5, 1010-1016 p.Article in journal (Refereed)
    Abstract [en]

    Functional solid substrates modified by self-assembled monolayers (SAMs) have potential applications in biosensors, chromatography, and biocompatible materials. The potential-induced phase transition of N-isobutyryl-L-cysteine (L-NIBC) SAMs on Au(111) surfaces was investigated by in-situ electrochemical scanning tunneling microscopy (EC-STM) in 0.1 mol.L-1 H2SO4 solution. The NIBC SAMs with two distinct structures (alpha phase and beta phase) can be prepared by immersing the Au(111) substrate in pure NIBC aqueous solution and NIBC solution controlled by phosphate buffer at pH 7, respectively. The as-prepared a phase and beta phase of NIBC SAMs sho