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  • 1. Zhu, X.
    et al.
    Zou, Rongfeng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sun, P.
    Wang, Q.
    Wu, J.
    A supramolecular peptide polymer from hydrogen-bond and coordination-driven self-assembly2018In: Polymer Chemistry, ISSN 1759-9954, E-ISSN 1759-9962, Vol. 9, no 1, p. 69-76Article in journal (Refereed)
    Abstract [en]

    A terpyridine- and guanine-functionalized peptide was developed that could form different morphologies by self-assembly or coordination with Fe2+ in dimethyl sulfoxide. The self-assembly of the peptide is attributed to the G-quartet formation of a guanine moiety and intermolecular terpyridine π-π stacking. Upon the addition of Fe2+, a Fe2+-(terpyridine)2 complex is formed that turns the square-planar self-assembly to a three-dimensional self-assembly. As a consequence, a variety of interesting morphologies and chemical properties were observed. The self-assembled polymers were studied by nuclear magnetic resonance spectroscopy, ultraviolet-visible and fluorescence spectroscopy, viscosity measurement, circular dichroism, Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, transmission electron microscopy, dynamic light scattering, and atomic force microscopy. This external stimuli driven self-assembly of a peptide may be further applied to drug delivery applications. 

  • 2. Hussain, M.
    et al.
    Zhou, Yang
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Albanova University Center.
    Song, Y.
    Hameed, H. M. A.
    Jiang, H.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Albanova University Center.
    Zhang, J.
    ATAD2 in cancer: a pharmacologically challenging but tractable target2018In: Expert opinion on therapeutic targets, ISSN 1472-8222, E-ISSN 1744-7631, Vol. 22, no 1, p. 85-96Article in journal (Refereed)
    Abstract [en]

    Introduction: ATAD2 protein is an emerging oncogene that has strongly been linked to the etiology of multiple advanced human cancers. Therapeutically, despite the fact that genetic suppression/knockdown studies have validated it as a compelling drug target for future therapeutic development, recent druggability assessment data suggest that direct targeting of ATAD2’s bromodomain (BRD) may be a very challenging task. ATAD2’s BRD has been predicted as a ‘difficult to drug’ or ‘least druggable’ target due to the concern that its binding pocket, and the areas around it, seem to be unfeasible for ligand binding. Areas covered: In this review, after shedding light on the multifaceted roles of ATAD2 in normal physiology as well as in cancer-etiology, we discuss technical challenges rendered by ATAD2’s BRD active site and the recent drug discovery efforts to find small molecule inhibitors against it. Expert opinion: The identification of a novel low-nanomolar semi-permeable chemical probe against ATAD2’s BRD by recent drug discovery campaign has demonstrated it to be a pharmacologically tractable target. Nevertheless, the development of high quality bioavailable inhibitors against ATAD2 is still a pending task. Moreover, ATAD2 may also potentially be utilized as a promising target for future development of RNAi-based therapy to treat cancers. 

  • 3. Sun, C.
    et al.
    Zhu, L.
    Zhang, C.
    Song, Ce
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, Hefei, Anhui, China.
    Wang, C.
    Zhang, M.
    Xie, Y.
    Schaefer, H. F. , I I I
    Conformers, properties, and docking mechanism of the anticancer drug docetaxel: DFT and molecular dynamics studies2018In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 39, no 15, p. 889-900Article in journal (Refereed)
    Abstract [en]

    The conformational structures and properties of the anticancer drug docetaxel (DTX) are studied theoretically. A total of 3888 trial structures were initially generated by all combinations of internal single-bond rotamers and screened with the B3LYP/3-21G* method. A total of 31 unique conformers were further optimized at the B3LYP/6-311G* method. Their relative energies, dipole moments, rotational constants, and harmonic vibrational frequencies were predicted. Single-point relative energies were then determined at the M06-L/6-311G(2df,p) level. The UV spectrum of the lowest-lying DTX conformer in methanol was investigated with the TD-CAM-B3LYP/6-311 + G(2df,p) method. The 31 unique DTX structures are mainly docked at three different sites within β-tubulin. Based on the results of molecular docking and double-float MD simulations, the lowest-lying DTX conformer consistently exhibits good docking performance with β-tubulin. We identified the residues LYS299, ARG215, GLN294, LEU275, THR216, GLU290, PRO274, and THR276 on β-tubulin as active sites forming a binding pocket responsible for locking DTX within β-tubulin to make the combination more stable. The RMSD values show that the predicted complexes are favorable, and the SASA analysis shows that the hydrophilic properties of DTX are better than paclitaxel.

  • 4. Grybauskaite-Kaminskiene, Gintare
    et al.
    Ivaniuk, Khrystyna
    Bagdziunas, Gintautas
    Turyk, Pavlo
    Stakhira, Pavlo
    Baryshnikov, Gleb V.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bohdan Khmelnytsky National University, Ukraine.
    Volyniuk, Dmytro
    Cherpak, Vladyslav
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bohdan Khmelnytsky National University, Ukraine.
    Hotra, Zenon
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University, Russian Federation.
    Grazulevicius, Juozas Vidas
    Contribution of TADF and exciplex emission for efficient "warm-white" OLEDs2018In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 6, no 6, p. 1543-1550Article in journal (Refereed)
    Abstract [en]

    The bicarbazole derivative 4,4'-(9H, 9'H-[3,3'-bicarbazole]-9,9'-diyl) bis(3-(trifluoromethyl) benzonitrile), denoted as pCNBCzoCF(3), was synthesized and tested for white OLED applications. pCNBCzoCF3 demonstrated an extremely small value of the singlet-triplet energy gap that caused intensive thermally activated delayed fluorescence (TADF). In addition, this compound is able to form exciplex-type excited states at the interface with star-shaped 4,40,400-tris[phenyl(m-tolyl) amino] triphenylamine (m-MTDATA). Combining the TADF emission of pCNBCzoCF3 with the exciplex emission from the pCNBCzoCF(3) m-MTDATA interface, we fabricated a number of highly efficient "warm-white'' OLEDs, the electroluminescence of which was close to candle emission. The best device demonstrated a very high brightness of 40 900 Cd m(-2) (at 15 V), current efficiency of 53.8 Cd A(-1) and power efficiency of 19.3 lm W-1, while the external quantum efficiency reached 18.8%. The fabricated devices demonstrated high emission characteristics even for the standard test at 1000 Cd m(-2) (current efficiency of 46.2 Cd A(-1), power efficiency of 10.6 lm W-1, EQE of 17.0%).

  • 5. Zhang, Z.
    et al.
    Zhang, J.
    Wu, B.
    Li, X.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Chen, Y.
    Huang, J.
    Zhu, L.
    Tian, H.
    Diarylethenes with a Narrow Singlet–Triplet Energy Gap Sensitizer: a Simple Strategy for Efficient Visible-Light Photochromism2018In: Advanced Optical Materials, ISSN 2162-7568, E-ISSN 2195-1071, Vol. 6, no 6, article id 1700847Article in journal (Refereed)
    Abstract [en]

    All-organic visible-light photochromism is reported here via a novel strategy with narrow singlet–triplet energy gap (ΔEST) materials as a sensitizer. Taking advantage of the narrow ΔEST feature and the triplet–triplet energy transfer process, highly efficient photochromism of diarylethenes (DAEs) with both ring-open and ring-closure excitations shifted to visible light region is successfully achieved. Moreover, the wavelength of the visible excitation light can be easily modulated (e.g., from 405 to 470 nm) by elaborate selection of matched sensitized molecules. The “write-and-erase” application of this photochromic system in polymer films is further demonstrated. This strategy provides a simple and versatile selection of well-matched DAE/sensitizer couples for visible-light photochromism without complicated molecular design.

  • 6.
    Monti, Susanna
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. CNR, Inst Chem Organometall Cpds, ICCOM, I-56124 Pisa, Italy..
    Barcaro, Giovanni
    CNR, Inst Chem & Phys Proc, IPCF, I-56124 Pisa, Italy..
    Sementa, Luca
    CNR, Inst Chem & Phys Proc, IPCF, I-56124 Pisa, Italy..
    Carravetta, Vincenzo
    CNR, Inst Chem & Phys Proc, IPCF, I-56124 Pisa, Italy..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Svobodny Pr 79, Krasnoyarsk 660041, Russia..
    Dynamics and self-assembly of bio-functionalized gold nanoparticles in solution: Reactive molecular dynamics simulations2018In: Nano Reseach, ISSN 1998-0124, E-ISSN 1998-0000, Vol. 11, no 4, p. 1757-1767Article in journal (Refereed)
    Abstract [en]

    The self-assembling properties, stability, and dynamics of hybrid nanocarriers (gold nanoparticles (AuNPs) functionalized with cysteine-based peptides) in solution are studied through a series of classical molecular dynamics simulations based on a recently parametrized reactive force field. The results reveal, at the atomic level, all the details regarding the peptide adsorption mechanisms, nanoparticle stabilization, aggregation, and sintering. The data confirm and explain the experimental findings and disclose aspects that cannot be scrutinized by experiments. The biomolecules are both chemisorbed and physisorbed; self-interactions of the adsorbates and formation of stable networks of interconnected molecules on the AuNP surfaces limit substrate reconstructions, protect the AuNPs from the action of the solvent, and prevent direct interactions of the gold surfaces. The possibility of agglomeration of the functionalized nanoparticles, compared with the sintering of the bare supports in a water solution, is demonstrated through relatively long simulations and fast steered dynamics. The analysis of the trajectories reveals that the AuNPs were well stabilized by the peptides. This prevented particle sintering and kept the particles far apart; however, part of their chains could form interconnections (crosslinks) between neighboring gold vehicles. The excellent agreement of these results with the literature confirm the reliability of the method and its potential application to the modeling of more complex materials relevant to the biomedical sector.

  • 7.
    Valiev, R. R.
    et al.
    Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia.;Univ Helsinki, Dept Chem, AI Virtanens Plats 1,POB 55, FI-00014 Helsinki, Finland..
    Cherepanov, V. N.
    Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia..
    Baryshnikov, Gleb V.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia.
    Sundholm, D.
    Univ Helsinki, Dept Chem, AI Virtanens Plats 1,POB 55, FI-00014 Helsinki, Finland..
    First-principles method for calculating the rate constants of internal-conversion and intersystem-crossing transitions2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 9, p. 6121-6133Article in journal (Refereed)
    Abstract [en]

    A method for calculating the rate constants for internal-conversion (k(IC)) and intersystem-crossing (k(ISC)) processes within the adiabatic and Franck-Condon (FC) approximations is proposed. The applicability of the method is demonstrated by calculation of k(IC) and k(ISC) for a set of organic and organometallic compounds with experimentally known spectroscopic properties. The studied molecules were pyrromethene-567 dye, psoralene, hetero[8]circulenes, free-base porphyrin, naphthalene, and larger polyacenes. We also studied fac-Alq(3) and fac-Ir(ppy)(3), which are important molecules in organic light emitting diodes (OLEDs). The excitation energies were calculated at the multi-configuration quasi-degenerate second-order perturbation theory (XMC-QDPT2) level, which is found to yield excitation energies in good agreement with experimental data. Spin-orbit coupling matrix elements, non-adiabatic coupling matrix elements, Huang-Rhys factors, and vibrational energies were calculated at the time-dependent density functional theory (TDDFT) and complete active space self-consistent field (CASSCF) levels. The computed fluorescence quantum yields for the pyrromethene-567 dye, psoralene, hetero[8]circulenes, fac-Alq(3) and fac-Ir(ppy)(3) agree well with experimental data, whereas for the free-base porphyrin, naphthalene, and the polyacenes, the obtained quantum yields significantly differ from the experimental values, because the FC and adiabatic approximations are not accurate for these molecules.

  • 8.
    Chen, Tao
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Leiden Observatory, Leiden University, PO Box 9513, NL 2300 RA Leiden, The Netherlands.
    Zhen, J.
    Wang, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Linnartz, H.
    Tielens, A. G. G. M.
    From planes to bowls: Photodissociation of the bisanthenequinone cation2018In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 692, p. 298-303Article in journal (Refereed)
    Abstract [en]

    We present a combined experimental and theoretical study of the photodissociation of the bisanthenequinone (C28H12O2) cation, Bq+. The experiments show that, upon photolysis, the Bq+ cation does not dehydrogenate, but instead fragments through the sequential loss of the two neutral carbonyl groups, causing the formation of five-membered carbon cycles. Quantum chemical calculations confirm this Bq+ → [Bq - CO]+ → [Bq - 2CO]+ sequence as the energetically most favorable reaction pathway. For the first CO loss, a transition state with a barrier of ∼3.2 eV is found, substantially lower than the lowest calculated H loss dissociation pathway (∼4.9 eV). A similar situation applies for the second CO loss channel (∼3.8 eV vs. ∼4.7 eV), but where the first dissociation step does not strongly alter the planar PAH geometry, the second step transforms the molecule into a bowl-shaped one. 

  • 9. Wang, J.
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, J.
    Tian, H.
    Modulating a D-Π-A type diarylethene for on-demand Cu2+ check via photo-switchable detection range and sensitivity2018In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 257, p. 77-86Article in journal (Refereed)
    Abstract [en]

    Detection range and sensitivity are two important parameters in a sensing system. Unfortunately, in common sensory systems, wide detection range always suffers from low sensitivity and vice versa. Thus, it becomes more and more desirable to design sensors with both wide detection range and high sensitivity. Here, we report a sensory system based on a photo-switchable D-π-A type diarylethene (SDE), which presents both wide detection range and high sensitivity under alternate light modulation. The D-π-A structure endows the sensor with high energy level of HOMO, which enabled the oxidation of both photoisomer SDEo/SDEc by Cu2+. While the discrepancy in energy levels of oxidation potentials in SDE photoisomers leads to their different reactivity, or in another word, sensitivity towards Cu2+. The inherent oxidative cycloreversion of SDEc to SDEo, on the other hand, provides a possibility that two photoisomers would detect Cu2+ in different working concentrations. The open form was employed for the detection of Cu2+ in a wider concentration range (0–13.0 equivalent) with relatively lower sensitivity (6.4 × 10−7 M). While the closed form was able to probe Cu2+ in lower concentration (0–3.0 equivalent) with higher sensitivity (6.6 × 10−9 M). Based on this photo-switchable sensing activity, a molecular multimeter of variable detection range for Cu2+ was then constructed.

  • 10.
    Baryshnikov, Gleb V.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Tomsk State University, Russian Federation.
    Valiev, Rashid R.
    Minaev, Boris F.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University, Russian Federation.
    Optical tuning of tetrabenzo[8]circulene derivatives through pseudorotational conformational isomerization2018In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 151, p. 372-379Article in journal (Refereed)
    Abstract [en]

    In order to further search efficient [8]circulene materials for OLED applications we have theoretically investigated the structure and electronic, absorption spectra of functionalized tetrabenzo[8]circulenes with different substituents in the outer perimeter. These hydrocarbon materials complement the wide family of [8]circulenes which earlier have been demonstrated to possess promising emissive and exciplex-forming properties suitable for organic light emitting diodes. The hydrocarbon tetrabenzo[8]circulenes show saddle shape of the molecular skeleton which can exist in two different conformations with different curvatures of the macrocycle. The aromaticity, electronic structure and orbital pattern are found to be principally different for these two isomers, where the global minimum isomer is weakly antiaromatic and electronically less stable comparing with the non-aromatic local minimum structure. The absorption spectra are also very different: the global minimum structure is more active in the long-wavelength region while the local minimum isomer shows absorption only at short wavelengths. Our computational findings suggest a new concept for optical tuning of curved [8]circulenes through conformational isomerization and aromaticity control, thus through structural variations without changing the molecular composition. Based on this principle we have designed novel functionalized [8]circulenes with promising fluorescence activity.

  • 11.
    Liu, Haichun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Institute of Technology.
    Huang, Kai
    Valiev, Rashid R.
    Zhan, Qiuqiang
    Zhang, Yong
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Photon Upconversion Kinetic Nanosystems and Their Optical Response2018In: Laser & Photonics reviews, ISSN 1863-8880, E-ISSN 1863-8899, Vol. 12, no 1, article id 1700144Article, review/survey (Refereed)
    Abstract [en]

    Lanthanide-doped photon upconversion nanoparticles (UCNPs) are capable of converting low-intensity near-infrared light to UV and visible emission through the synergistic effects of light excitation and mutual interactions between doped ions. UCNPs have attracted strong interest as unique spectrum converters and found a multitude of applications in areas like biomedical imaging, energy harvesting and information technology. UCNPs are distinct from many other types of luminescent materials in terms of the involvement of a host lattice and multiple optical centers, i.e., trivalent lanthanide ions with manyfolds of accessible long-lived energy states, in individual nanoparticles. The mutual interactions between these optical centers, i.e., sequential energy transfers, make them operate as an integrated unit and co-determine the luminescence kinetics and other optical properties of the individual nanoparticle. Thus, each nanoparticle consititutes a kinetic optical system. In this work, we explore UCNPs from the outset of being such kinetic optical systems and review their physical formation, the underlying photophysics, macroscopic statistical description, and their response to various optical stimuli in the spectral, polarization, intensity, temporal and frequency domains, and demonstrate ways that their optical output can be optimized by manipulating the excitation schemes. Our review highlights upconversion nanotechnology as an interdisciplinary field across chemistry, physics and biomedical engineering, with great future possibilities, flexibility and ramifications. We outline some of the potential directions of upconversion nanoparticle research.

  • 12. Sun, Yu-Ping
    et al.
    Miao, Quan
    Zhou, Ai-Ping
    Liu, Rui-Jin
    Liu, Bo
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Institute of Nanotechnology, Spectroscopy and Quantum Chemistry, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Suppression of resonant auger effect with chirped x-ray free-electron laser pulse2018In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 51, no 3, article id 035602Article in journal (Refereed)
    Abstract [en]

    We study the Auger effect in the presence of strong x-ray free-electron lasers (XFELs) propagating through resonant argon vapors by solving the Maxwell-Bloch equations numerically. The simulations are based on the three-level system with the carrier frequency tuned in the 2p(3/2)-4s resonance. It is shown that the Auger branching is sensitive to the pulse area and duration. The relative Auger yield can be suppressed in the course of pulse propagation due to the interplay between the Auger decay and stimulated emission. Further suppression can be achieved by chirping the initial pulse, which is more effective for the long-pulse case. In addition, the sign and magnitude of the chirp rate play important roles in pulse reshaping and Auger emission.

  • 13.
    Baryshnikov, Glib V.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Minaeva, Valentina A.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Grigoras, M.
    The Electronic Structure and Spectra of Triphenylamines Functionalized by Phenylethynyl Groups2018In: Optics and Spectroscopy, ISSN 0030-400X, E-ISSN 1562-6911, Vol. 124, no 1, p. 57-64Article in journal (Refereed)
    Abstract [en]

    We study the features of the electronic structure and the IR, UV, and visible spectra of a series of triphenylamines substituted with phenylethynyl groups. The analysis is performed at the level of the density functional theory (DFT) and its nonstationary version in comparison with the experimental data of IR and electron spectroscopy. It is shown that, in the excited state, there is a change in the alternation of single, double, and triple bonds in accordance with the character of bonding and antibonding in the lowest vacant molecular orbital. The gradual introduction of additional phenylethynyl groups does not cause frequency shifts in the IR spectra of the molecules under study, but significantly affects the intensity of the corresponding IR bands. A similar effect is also observed in the electronic-absorption spectra of these compounds. This can be used for optical tuning of triphenylamines as promising materials for organic light-emitting diodes and solar cells.

  • 14. Zhang, Lin
    et al.
    Kang, Zheng-Zhong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang Univ, Dept Chem, Zheda Rd 38, Hangzhou 310027, Zhejiang, Peoples R China.
    Qi, Shi-Chao
    Liu, Xiao-Qin
    Wang, Zhi-Min
    Sun, Lin-Bing
    Ultradeep Removal of Moisture in Gases to Parts-per-Billion Levels: The Exploration of Adsorbents2018In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 5, p. 2840-2847Article in journal (Refereed)
    Abstract [en]

    Owing to the rigid standards of manufacturing semiconductor components, decrease of the moisture to parts-per-billion (ppb), at a global level, is always vital but extremely nerve-racking in the production of high-purity gases. Herein, typical adsorbents including oxides (SiO2 and gamma-Al2O3), zeolites (4A and NaX), and metal-organic frameworks (MOFs; HKUST-1, UiO-66, and ZIF-8) are investigated with respect to the abilities of ultradeep dewatering from N-2. Compared with other adsorbents, NaX performs much better on both dewatering efficiency (DE, from 2750 to 66 ppb) and the adsorption capacity (AC, 1.55 x 10(4) L N-2.g(-1)). Moreover, it is for the first time experimentally and theoretically proved that the dewatering ability of X zeolite mainly depends on its cation species (Na+, Li+, K+, Cs+, Mg2+, Ca2+, Sr2+, or Ba2+), the forces between the zeolite and H2O, and the number of H2O molecules per cell of the zeolite. CaX thus shows a fascinating DE from 2750 to 33 ppb, a huge AC of 9.08 x 10(4) L N-2.g(-1), and an ideal reusability, compared with results of the scarce contributions reported to date.

  • 15.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Oliveira, Marcelo
    Fdez. Galvan, Ignacio
    Baader, Wilhelm J.
    A combined theoretical and experimental study onthe mechanism of spiro-adamantyl-1,2-dioxetanone decomposition2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, p. 17462-17472Article in journal (Refereed)
    Abstract [en]

    1,2-Dioxetanones have been considered as model compounds for bioluminescence processes. Theunimolecular decomposition of these prototypes leads mainly to the formation of triplet excited stateswhereas in the catalysed decomposition of these peroxides singlet states are formed preferentially.Notwithstanding, these cyclic peroxides are important models to understand the general principles ofchemiexcitation as they can be synthesised, purified and characterised. We report here results ofexperimental and theoretical approaches to investigating the decomposition mechanism of spiroadamantyl-1,2-dioxetanone. The activation parameters in the unimolecular decomposition of thisderivative have been determined by isothermal kinetic measurements (30–70 C) and thechemiluminescence activation energy calculated from the correlation of emission intensities. Theactivation energy for peroxide decomposition proved to be considerably lower than thechemiluminescence activation energy indicating the existence of different reaction pathways for groundand excited state formation. These experimental results are compared with the calculations at thecomplete active space second-order perturbation theory (CASPT2), which reveal a two-step biradicalmechanism starting by weak peroxide bond breakage followed by carbon–carbon elongation. Thetheoretical findings also indicate different transition state energies on the excited and ground statesurfaces during the C–C bond cleavage in agreement with the experimental activation parameters.

  • 16.
    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, p. 2717-2723Article 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.

  • 17.
    Baryshnikov, Glib V.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Cherkasy National University, Ukraine.
    Minaev, B. F.
    Baryshnikova, A. T.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University, Russian Federation.
    A computational study of structural and magnetic properties of bi- and trinuclear Cu(II) complexes with extremely long Cu–-Cu distances2017In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 491, p. 48-55Article in journal (Refereed)
    Abstract [en]

    Three recently synthesized copper(II) complexes with aroylhydrazones of trifluoroacetic and benzenecarboxylic acids (Dalton Trans., 2013, 42, 16878) have been computationally investigated by density functional theory within the broken symmetry approximation accounting for empirical dispersion corrections. A topological analysis of electron density distributions has been carried out using Bader's “quantum theory of atoms in molecules” formalism. The calculated values of spin-spin exchange for the studied dinuclear complexes indicate a very weak ferromagnetic coupling of the unpaired electrons in good agreement with experimental data. At the same time, the trinuclear copper(II) complex possesses a low-spin doublet ground state with one ferromagnetic and two antiferromagnetic spin projections between the triangular-positioned Cu2+ ions. The estimated values of the coupling constants for the spin-spin exchange in this trinuclear complex are in a good agreement with experimental observations. The calculations support a mechanism of exchange coupling through the aromatic links in these strongly spin-separated systems.

  • 18. 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, p. 1934-1941Article 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.

  • 19. Chen, S.
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Song, L.
    A fluorescent photochromic diarylethene based on naphthalic anhydride with strong solvatochromism2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 47, p. 29854-29859Article in journal (Refereed)
    Abstract [en]

    A novel "push-pull" diarylethene molecule consisting of an electron withdrawing ethene bridge (1,8-naphthalic anhydride) and two moderate electron donating side chains (2,5-dimethylthiophene) has been designed and synthesized. The photochromism study, together with density functional theory calculations, revealed that the molecule exhibits reversible fluorescence switching capacity upon photo-isomerization and remarkable solvatochromism with red shift of the fluorescence maximum by more than 150 nm owing to intramolecular charge transfer.

  • 20. 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, p. 1234-1244Article 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.

  • 21. Luo, Shenzheng
    et al.
    Zou, Rongfeng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wu, Junchen
    Landry, Markita P.
    A Probe for the Detection of Hypoxic Cancer Cells2017In: ACS SENSORS, ISSN 2379-3694, Vol. 2, no 8, p. 1139-1145Article in journal (Refereed)
    Abstract [en]

    Hypoxia is a common feature of tumor cells. Nitroreductase (NTR), a common biomarker of hypoxia, has been widely used to evaluate the extent of tumor hypoxia. In this study, three fluorescent probes (FBN-1-3) were synthesized to monitor the extent of hypoxia in cancer cells in real time. FBN-1-3 were composed of a fluorescein analogue and one of three different aromatic nitro groups. Of these probes, FBN-1 showed excellent sensitivity and selectivity in detecting hypoxia via a reduction in O-2 concentration. Confocal fluorescence imaging and flow cytometry demonstrated that HepG-2, A549, and SKOV-3 cells incubated with FBN-1 under reduced oxygen conditions showed significantly enhanced fluorescence. A mouse HepG-2 tumor model confirmed that FBN-1 responds rapidly to NTR and can be used to evaluate the degree of tumor hypoxia. The changes in intra- and extracellular NTR in tumor cells were also concurrently monitored, which did not reveal a link between NTR concentration and degree of hypoxia. Our work provides a functional probe for tumor hypoxia, and our results suggest the fluorescent response of our probe is due to a decrease in O-2 concentration, and not NTR concentration.

  • 22. Fahleson, Tobias
    et al.
    Olsen, Jógvan Magnus Haugaard
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rizzo, Antonio
    A QM/MM and QM/QM/MM study of Kerr, Cotton--Mouton and Jones linear birefringences in liquid acetonitrile2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)
    Abstract [en]

    QM/MM and QM/QM/MM protocols are applied to the ab initio study of the three linear bire-fringences Kerr, Cotton–Mouton, and Jones, as shown by acetonitrile in the gas and pureliquid phases. The relevant first-order properties as well as linear, quadratic, and cubicfrequency-dependent response functions were computed using time-dependent Kohn–Shamdensity-functional theory with use of the standard CAM-B3LYP functional. In the liquid phase,a series of room temperature (293.15 K) molecular dynamics snapshots were selected, for whichaveraged values of the observables were obtained at an optical wavelength of 632.8 nm. Thebirefringences were computed for electric and magnetic induction fields corresponding to the lab-oratory setup previously employed by Roth and Rikken in Phys. Rev. Lett. 85, 4478, (2000).Under these conditions, acetonitrile is shown to exhibit a weak Jones response — in fact roughly6.5 times smaller than the limit of detection of the apparatus employed in the measurementsmentioned above. A comparison is made with the corresponding gas-phase results and an as-sessment is made of the index of measureability, estimating the degree of overlap of the threebirefringences in actual measurements. For acetonitrile, it is shown that this index is a factorof 3.6 and 6.7 larger than that of methylcyclopentadienyl-Mn-tricarbonyl and cyclohexadienyl-Fe-tricarbonyl, respectively — two compounds reported in Phys. Rev. Lett. 85, 4478, (2000) to exhibita strong Jones signal.

    The full text will be freely available from 2018-12-31 12:00
  • 23.
    Holmgaard List, Nanna
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, J.
    Jensen, H. J
    A quantum-mechanical perspective on linear response theory within polarizable embedding2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 23, article id 234101Article in journal (Refereed)
    Abstract [en]

    We present a derivation of linear response theory within polarizable embedding starting from a rigorous quantum-mechanical treatment of a composite system. To this aim, two different subsystem decompositions (symmetric and nonsymmetric) of the linear response function are introduced and the pole structures as well as residues of the individual terms are discussed. In addition to providing a thorough justification for the descriptions used in polarizable embedding models, this theoretical analysis clarifies which form of the response function to use and highlights complications in separating out subsystem contributions to molecular properties. The basic features of the presented expressions and various approximate forms are illustrated by their application to a composite model system.

  • 24.
    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 1463-9084, Vol. 19, no 30, p. 19573-19589Article 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.

  • 25. Osikoya, Adeniyi Olugbenga
    et al.
    Parlak, Onur
    Murugan, Natarajan. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Dikio, Ezekiel Dixon
    Moloto, Harry
    Uzun, Lokman
    Turner, Anthony P. F.
    Tiwari, Ashutosh
    Acetylene-sourced CVD-synthesised catalytically active graphene for electrochemical biosensing2017In: Biosensors and Bioelectronics, ISSN 0956-5663, Vol. 89, p. 496-504Article in journal (Refereed)
    Abstract [en]

    In this study, we have demonstrated the use of chemical vapour deposition (CVD) grown-graphene to develop a highly-ordered graphene-enzyme electrode for electrochemical biosensing. The graphene sheets were deposited on 1.00 mm thick copper sheet at 850 degrees C using acetylene (C2H2) as carbon source in an argon (Ar) and nitrogen (N-2) atmosphere. An anionic surfactant was used to increase wettability and hydrophilicity of graphene; thereby facilitating the assembly of biomolecules on the electrode surface. Meanwhile, the theoretical calculations confirmed the successful modification of hydrophobic nature of graphene through the anionic surface assembly, which allowed high-ordered immobilisation of glucose oxidase (GOx) on the graphene. The electrochemical sensing activities of the graphene-electrode was explored as a model for bioelectrocatalysis. The bioelectrode exhibited a linear response to glucose concentration ranging from 0.2 to 9.8 mM, with sensitivity of 0.087 A/M/cm(2) and a detection limit of 0.12 mu M (S/N=3). This work sets the stage for the use of acetylene-sourced CVD-grown graphene as a fundamental building block in the fabrication of electrochemical biosensors and other bioelectronic devices.

  • 26. Zhan, Qiuqiang
    et al.
    Liu, Haichun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Baoju
    Wu, Qiusheng
    Pu, Rui
    Zhou, Chao
    Huang, Bingru
    Peng, Xingyun
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering. South China Normal University, China.
    Achieving high-efficiency emission depletion nanoscopy by employing cross relaxation in upconversion nanoparticles2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, no 1, article id 1058Article in journal (Refereed)
    Abstract [en]

    Stimulated emission depletion microscopy provides a powerful sub-diffraction imaging modality for life science studies. Conventionally, stimulated emission depletion requires a relatively high light intensity to obtain an adequate depletion efficiency through only light–matter interaction. Here we show efficient emission depletion for a class of lanthanide-doped upconversion nanoparticles with the assistance of interionic cross relaxation, which significantly lowers the laser intensity requirements of optical depletion. We demonstrate two-color super-resolution imaging using upconversion nanoparticles (resolution ~ 66 nm) with a single pair of excitation/depletion beams. In addition, we show super-resolution imaging of immunostained cytoskeleton structures of fixed cells (resolution ~ 82 nm) using upconversion nanoparticles. These achievements provide a new perspective for the development of photoswitchable luminescent probes and will broaden the applications of lanthanide-doped nanoparticles for sub-diffraction microscopic imaging.

  • 27. 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, p. 2717-2722Article 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.

  • 28. 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, p. 724-731Article 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

  • 29. Shi, Leilei
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhou, Min
    Muhammad, Faheem
    Ding, Yubin
    Wei, Hui
    An arylboronate locked fluorescent probe for hypochlorite2017In: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 142, no 12, p. 2104-2108Article in journal (Refereed)
    Abstract [en]

    An unusual arylboronate based fluorescent probe R1 was synthesized for the selective and sensitive detection of ClO-. A detailed mechanistic study revealed that R1 reacted with ClO- through an oxidation to chlorination mechanism, and the arylboronate moiety in R1 acted as a "lock" to eliminate the effects of pH fluctuations. With this design strategy, R1 was successfully used to detect as low as 6.4 nM of ClO- over other ROS species in a wide pH range from 4.5 to 9.0.

  • 30. Witzke, Sarah
    et al.
    Holmgaard List, Nanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Olsen, Jogvan Magnus Haugaard
    Steinmann, Casper
    Petersen, Michael
    Beerepoot, Maarten T. P.
    Kongsted, Jacob
    An Averaged Polarizable Potential for Multiscale Modeling in Phospholipid Membranes2017In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 38, no 9, p. 601-611Article in journal (Refereed)
    Abstract [en]

    A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl-2-oleoylsn- glycerol-3-phospho-L-serine given their common use both in experimental and computational studies. The charges, and to a lesser extent the polarizabilities, are found to depend strongly on the molecular conformation of the lipids. Furthermore, the importance of explicit polarization is underlined for the description of larger assemblies of lipids, that is, membranes. In conclusion, we find that specially developed polarizable parameters are needed for embedding calculations in membranes, while common non-polarizable point-charge force fields usually perform well enough for structural and dynamical studies.

  • 31. 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, p. 39-47Article 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.

  • 32.
    Jena, Naresh K.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Lyne, ÅL.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Birgisson, B.
    Atomic level simulations of the interaction of asphaltene with quartz surfaces: role of chemical modifications and aqueous environment2017In: Materials and Structures, ISSN 1359-5997, E-ISSN 1871-6873, Vol. 50, no 1, article id 99Article in journal (Refereed)
    Abstract [en]

    Understanding the properties of bitumen and its interaction with mineral aggregates is crucial for future strategies to improve roads and highways. Knowledge of basic molecular and electronic structures of bitumen, one out of the two main components of asphalt, poses a major step towards achieving such a goal. In the present work we employ atomistic simulation techniques to study the interaction of asphaltenes, a major constituent of bitumen, with quartz surfaces. As an effective means to tune adhesion or cohesion properties of asphaltenes and mineral surfaces, we propose chemical modification of the pristine asphaltene structure. By the choice of substituent and site of substitution we find that adhesion between the asphaltene molecule and the quartz surface can easily be improved at the same time as the cohesive interaction between the asphaltene units is reduced, while other substituents may lead to the opposite effect. We also provide insight at the molecular level into how water molecules affect interactions between asphaltenes and quartz. Our approach emphasizes a future role for advanced atomistic modeling to understand the properties of bitumen and suggest further improvements.

  • 33. Rajasekhar, K.
    et al.
    Narayanaswamy, N.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Viccaro, K.
    Lee, H. -G
    Shah, K.
    Govindaraju, T.
    Aβ plaque-selective NIR fluorescence probe to differentiate Alzheimer's disease from tauopathies2017In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 98, p. 54-61Article in journal (Refereed)
    Abstract [en]

    Selective detection and staining of toxic amyloid plaques, a potential biomarker present in the Alzheimer's disease (AD) brain is crucial for both clinical diagnosis and monitoring AD disease progression. Herein, we report a coumarin-quinoline (CQ) conjugate-based turn-on near-infrared (NIR) fluorescence probe for specific detection of β-amyloid (Aβ) aggregates. CQ probe is highly sensitive and exhibits ~100-fold fluorescence enhancement in vitro upon binding Aβ aggregates with enhanced quantum yield. Furthermore, the probe has ~10-fold higher binding affinity towards Aβ aggregates (86 nM) compared to commonly used Thioflavin T. Most importantly, CQ probe displays unambiguous selectivity towards Aβ aggregates compared to other toxic protein aggregates such as tau, α-synuclein (α-Syn) and islet amyloid polypeptide (IAPP). In addition, CQ is nontoxic to neuronal cells and shows significant blood brain barrier permeability. Remarkably, CQ stains Aβ plaques in human brain tissue over co-existing tau aggregates and neurofibrillary tangles (NFTs), which are associated in AD and tauopathies. This is a highly desirable attribute to distinguish AD from tau pathology and mixed dementia.

  • 34. Ivaniuk, K.
    et al.
    Cherpak, V.
    Stakhira, P.
    Baryshnikov, Gleb
    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.
    Hotra, Z.
    Turyk, P.
    Zhydachevskii, Y.
    Volyniuk, D.
    Aksimentyeva, O.
    Penyukh, B.
    Lazauskas, A.
    Tamulevičius, S.
    Grazulevicius, J. V.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University, Russian Federation.
    BaZrO3 perovskite nanoparticles as emissive material for organic/inorganic hybrid light-emitting diodes2017In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 145, p. 399-403Article in journal (Refereed)
    Abstract [en]

    In the present work we have demonstrated double-channel emission from organic exciplexes coupled to inorganic nanoparticles. The process is demonstrated by yellow-green emission in light-emitting diodes based on organic exciplexes hybridized with perovskite-type dispersed BaZrO3 nanoparticles. Such double-channel emission provides a broadening of the electroluminescence spectrum and a resultant yellow-green emission color of the device. We have realized an energy transfer from the exciplexes arranged by the interface between two organic layers and the spherical-shaped BaZrO3 nanoparticles randomly deposited on the organic interface constructed of the tris(4-carbazoyl-9-ylphenyl)amine and 4,7-diphenyl-1,10-phenanthroline molecules. The fabricated device exhibits a current efficiency value of 3.88 C d/A, maximum brightness of 3465 cd/m2 (at 15 V), and external quantum efficiency of about 1.26%. In order to estimate the efficiency of the energy transfer from the exciplex to the BaZrO3 nanoparticles we have applied the Förster model for the dipole-dipole energy transfer accounting for the mutual overlap of the exciplex emission spectrum and the absorption spectrum of the BaZrO3 nanoparticles.

  • 35. 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, p. 421-429Article 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.

  • 36. 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, p. 175-183Article 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.

  • 37.
    Zhan, Shaoqi
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mårtensson, Daniel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Purg, Miha
    Kamerlin, Shina C. L.
    Ahlquist, Mårten S. G.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Capturing the Role of Explicit Solvent in the Dimerization of Ru-V(bda) Water Oxidation Catalysts2017In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 56, no 24, p. 6962-6965Article in journal (Refereed)
    Abstract [en]

    A ground-breaking empirical valence bond study for a soluble transition-metal complex is presented. The full reaction of catalyst monomers approaching and reacting in the Ru-V oxidation state were studied. Analysis of the solvation shell in the reactant and along the reaction coordinate revealed that the oxo itself is hydrophobic, which adds a significant driving force to form the dimer. The effect of the solvent on the reaction between the prereactive dimer and the product was small. The solvent seems to lower the barrier for the isoquinoline (isoq) complex while it is increased for pyridines. By comparing the reaction in the gas phase and solution, the proposed p-stacking interaction of the isoq ligands is found to be entirely driven by the water medium.

  • 38. Monti, Susanna
    et al.
    Barcaro, Giovanni
    Sementa, Luca
    Carravetta, Vincenzo
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Characterization of the adsorption dynamics of trisodium citrate on gold in water solution2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 78, p. 49655-49663Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations (MDs) based on a reactive force field (ReaxFF) are carried out to investigate typical adsorption modes of trisodium citrate (CIT) on gold nanoparticles (AuNPs). All possible configurations of CIT on a model AuNP in solution are identified and the stabilizing role played by the adsorbate on the AuNP structure is disclosed by analyzing protonation state, dynamics and interactions of the molecules with the surrounding environment. A realistic scenario is created by sampling extensively the conformational space of citrate and by validating the simulation results against data extracted from the literature. Carboxyl moieties are found in contact with the gold substrate through one or both oxygens and Na+ ions are present in the adsorbed citrate layer. Citrate binding is relatively strong and its action as a chelator stabilizes surface reconstructions. The molecules have the tendency to self-assemble and form a stable cover, which is reinforced by adatoms. All the results are in perfect agreement with experimental observations and theoretical data.

  • 39.
    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, p. 19787-19793Article 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.

  • 40.
    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, p. 523-540Article 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.

  • 41. Wang, Xiaolin
    et al.
    Yang, Huiqing
    Wen, Yaping
    Wang, Li
    Li, Junfeng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Jinglai
    Comprehension of the Effect of a Hydroxyl Group in Ancillary Ligand on Phosphorescent Property for Heteroleptic Ir(III) Complexes: A Computational Study Using Quantitative Prediction2017In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 56, no 15, p. 8986-8995Article in journal (Refereed)
    Abstract [en]

    A new Ir(III) complex (dfpypya)(2)Ir(pic-OH) (2) is theoretically designed by introduction of a simple hydroxyl group into the ancillary ligand on the basis of (dfpypya)(2)Ir(pic) (1) with the aim to get the high efficiency and stable blue-emitting phosphors, where dfpypya is 3-methyl-6-(2',4'-difluoro-pyridinato)pyridazine, pic is picolinate, and pic OH is 3-hydroxypicolinic acid. The other configuration (dfpypya)(2)Ir(pic OH)' (3) is also investigated to compare with 2. The difference between 2 and 3 is whether the intramolecular hydrogen bond is formed in the (dfpypya)(2)Ir(pic OH). The quantum yield is determined by three different methods including the semiquantitative and quantitative methods. To quantitatively determine the quantum yield is still not an easy task to be completed. This work would provide some useful advices to select the suitable method to reliably evaluate the quantum yield. Complex 2 has larger quantum yield and more stability as compared with 1 and 3. The formation of intramolecular hydrogen bond would become a new method to design new phosphor with the desired properties.

  • 42. 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, p. 719-726Article 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.

  • 43. Zhang, T.
    et al.
    Brumboiu, Iulia
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Lanzilotto, V.
    Luder, J.
    Grazioli, C.
    Giangrisostomi, E.
    Ovsyannikov, R.
    Sass, Y.
    Bidermane, I.
    Stupar, M.
    de Simone, M.
    Coreno, M.
    Ressel, B.
    Pedio, M.
    Rudolf, P.
    Brena, B.
    Puglia, C.
    Conclusively Addressing the CoPc Electronic Structure: A Joint Gas-Phase and Solid-State Photoemission and Absorption Spectroscopy Study2017In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 121, no 47, p. 26372-26378Article in journal (Refereed)
    Abstract [en]

    The occupied and empty densities of states of cobalt phthalocyanine (CoPc) were investigated by photoelectron and X-ray absorption spectroscopies in the gas phase and in thin films deposited on a Au(111) surface. The comparison between the gas-phase results and density functional theory single-molecule simulations confirmed that the CoPc ground state is correctly described by the (2)A(1g) electronic configuration. Moreover, photon-energy-dependent valence photoemission spectra of both the gas phase and thin film confirmed the atomic character of the highest occupied molecular orbital as being derived from the organic ligand, with dominant contributions from the carbon atoms. Multiplet ligand-field theory was employed to simulate the Co L-edge X-ray absorption spectroscopy results.

  • 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, 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, p. 501-507Article 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. Ahlstrand, David A.
    et al.
    Polukeev, Alexey V.
    Marcos, Rocio
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wendt, Ola F.
    Csp(3)-H Activation without Chelation Assistance in an Iridium Pincer Complex Forming Cyclometallated Products2017In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 23, no 8, p. 1748-1751Article in journal (Refereed)
    Abstract [en]

    Cyclometallation of 8-methylquinoline and 2-(dimethylamino)-pyridine in an iridium-based pincer complex is described. The C-H activation of 2-(dimethylamino) pyridine is not chelation assisted, which has not been described before for Csp(3)-H bonds in cyclometallation reactions. The mechanism of the cyclometallation of 2-(dimethylamino) pyridine was studied by DFT calculations and kinetic measurements.

  • 46. 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, E-ISSN 2050-7534, Vol. 5, no 2, p. 282-289Article 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.

  • 47. 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, E-ISSN 2050-7534, Vol. 5, no 2, p. 282-289Article 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.

  • 48. Manchineella, Shivaprasad
    et al.
    Murugan, Natarajan Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Govindaraju, Thimmaiah
    Cyclic Dipeptide-Based Ambidextrous Supergelators: Minimalistic Rational Design, Structure-Gelation Studies, and In Situ Hydrogelation2017In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 18, no 11, p. 3581-3590Article in journal (Refereed)
    Abstract [en]

    Ambidextrous supergelators are developed through structure-gelation screening of rationally designed cyclic dipeptides (CDPs). The organo- and hydrogels of CDPs were thoroughly characterized by their minimal gelation concentration (MGC) for organic and aqueous solvents, thermal stability (T-g), and viscoelastic properties. Intermo-lecular hydrogen bonding, the major driving force for gelation was evaluated using temperature-dependent nuclear magnetic resonance (NMR) spectroscopy. The contribution of attractive van der Waals interaction of tBoc group in driving CDP gelation was ascertained using beta-cyclodextrin (beta-CD)-adamantane carboxylic acid (AC)-based host guest gelation and H-1 NMR. studies. The self-assembled fibrous network of CDPs in organic and aqueous solvents responsible for the molecular gelation was elucidated using field emission scanning electron microscopy (FESEM) analysis. Among the CDPs studied CDP-2 found to be supergelator with MGC of 0.3 wt % and form in situ hydrogels under simulated physiological conditions. The in situ gelation property was evaluated by the incorporation of curcumin, as a model study to demonstrate the drug delivery application. Furthermore, supergelator CDP-2 was found to exhibit in cellulo cytocompatibility. Moreover, density functional theory (DFT) calculations were carried out to propose the microscopic structure for the self-assembly of CDP compounds and intermolecular N-H center dot center dot center dot O hydrogen bonding interactions appear to stabilize the fibrous network. The hydrophobic interactions among the tert-butyloxycarbonyl (tBoc) groups and pi-pi stacking interactions between phenyl rings contribute to the further stabilization of self-assembled 2D fibrous networks of CDPs. Overall, the present study highlights the in situ gelation property of CDP-based supergelators and their potential for biomedical and regenerative medicine applications.

  • 49. 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, p. 755-763Article 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 a