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  • 51.
    Li, Daobin
    et al.
    Univ Sci & Technol China, China.
    Li, Xiyu
    Univ Sci & Technol China, China.
    Chen, Shuangming
    Univ Sci & Technol China, China.
    Yang, Huan
    Univ Sci & Technol China, China.
    Wang, Changda
    Univ Sci & Technol China, China.
    Wu, Chuanqiang
    Univ Sci & Technol China.
    Haleem, Yasir A.
    Univ Sci & Technol China.
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Lu, Junling
    Univ Sci & Technol China, China.
    Ge, Binghui
    Chinese Acad Sci, China.
    Ajayan, Pulickel M.
    Rice Univ, USA.
    Luo, Yi
    Univ Sci & Technol China, China.
    Jiang, Jun
    Univ Sci & Technol China, China.
    Song, Li
    Univ Sci & Technol China, China.
    Atomically dispersed platinum supported on curved carbon supports for efficient electrocatalytic hydrogen evolution2019In: Nature Energy, ISSN 0028-212X, E-ISSN 2213-0217, Vol. 4, no 6, p. 512-518Article in journal (Refereed)
    Abstract [en]

    Dispersing catalytically active metals as single atoms on supports represents the ultimate in metal utilization efficiency and is increasingly being used as a strategy to design hydrogen evolution reaction (HER) electrocatalysts. Although platinum (Pt) is highly active for HER, given its high cost it is desirable to find ways to improve performance further while minimizing the Pt loading. Here, we use onion-like nanospheres of carbon (OLC) to anchor stable atomically dispersed Pt to act as a catalyst (Pt-1/OLC) for the HER. In acidic media, the performance of the Pt-1/OLC catalyst (0.27 wt% Pt) in terms of a low overpotential (38 mV at 10 mA cm(-2)) and high turnover frequencies (40.78 H-2 s(-1) at 100 mV) is better than that of a graphene-supported single-atom catalyst with a similar Pt loading, and comparable to a commercial Pt/C catalyst with 20 wt% Pt. First-principle calculations suggest that a tip-enhanced local electric field at the Pt site on the curved support promotes the reaction kinetics for hydrogen evolution.

  • 52.
    Li, Deyang
    et al.
    Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China.
    Chen, Guanying
    Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China..
    Near infrared harvesting dye-sensitized solar cells enabled by rare-earth upconversion materials2018In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 47, no 26, p. 8526-8537Article, review/survey (Refereed)
    Abstract [en]

    Dye-sensitized solar cells (DSSCs) have been deemed as promising alternatives to silicon solar cells for the conversion of clean sunlight energy into electricity. A major limitation to their conversion efficiency is their inability to utilize light in the infrared (IR) spectral range, which constitutes almost half the energy of the sun's radiation. This fact has elicited motivations and endeavors to extend the response wavelength of DSSCs to the IR range. Photon upconversion through rare-earth ions constitutes one of the most promising approaches toward the goal of converting near-IR (NIR) or IR light into visible or ultraviolet light, where DSSCs typically have high sensitivity. In the present review, we summarize recent progress based on the utilization of various upconversion materials and device structures to improve the performance of dye-sensitized solar cells.

  • 53.
    Li, Junfeng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Theoretical Studies on Vibrationally Resolved Optical Spectra of Polycyclic Aromatic Molecules2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Polycyclic aromatic molecules are of great interest owing to their many important applications in chemistry and have therefore been the focus of investigations for over half a century with spectroscopic techniques. This thesis is devoted to the modeling of vibrationally resolved optical spectra of polycyclic aromatic molecules. The general goal is to demonstrate the importance of nuclear motion on the electronic spectra and provide reliable spectral assignments and spectral fingerprints to distinguish different molecular isomers that are often not possible to be identified by experiments alone. In this thesis, four sets of polycyclic aromatic molecules have been systematically studied by using quantum chemistry methods. The simulated vibronic spectra are in good agreement with their experimental counterparts, which enables to provide correct reassignments for the electronic spectra.

  • 54.
    Li, Junfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhang, Jinglai
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    A theoretical study on vibronic spectra and photo conversation process of protonated naphthalenes2018In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 205, p. 520-527Article in journal (Refereed)
    Abstract [en]

    The equilibrium structures and vibrational frequencies of the ground state and several singlet low-lying excited states of alpha-and beta-protonated naphthalenes (alpha-and beta-HN+) have been studied by time -dependent density -functional theory (TD-DFT). Within the Franck -Condon approximation, vibronic absorption spectra of alpha-HN+ and beta-HN+, together with the vibronic emission spectrum of alpha-HN+, have been calculated. The obtained good agreement between the theoretical and experimental spectra enables to correctly assign vibronic features in both absorption and emission spectra. Moreover, the non -radiative deactivation pathway from the low-lying excite states to the ground state in alpha-HN+ and beta-HN+, as well as the photo-induce proton transfer pathway, are investigated at the CASPT2/CASSCF/6-31G* level. Our study is helpful for understanding the photochemical behavior of these important polycyclic aromatic hydrocarbon molecules.

  • 55.
    Li, Junfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhang, Jinglai
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    The assignment of optical absorption spectra of protonated anthracene isomers:revisitedManuscript (preprint) (Other academic)
  • 56.
    Li, Junhao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China.
    Zhang, Hongxiao
    East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China..
    Liu, Guixia
    East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China..
    Tang, Yun
    East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China..
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Li, Weihua
    East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China..
    Computational Insight Into Vitamin K-1 omega-Hydroxylation by Cytochrome P450 4F22018In: Frontiers in Pharmacology, ISSN 1663-9812, E-ISSN 1663-9812, Vol. 9, article id 1065Article in journal (Refereed)
    Abstract [en]

    Vitamin K-1 (VK1) plays an important role in the modulation of bleeding disorders. It has been reported that omega-hydroxylation on the VK1 aliphatic chain is catalyzed by cytochrome P450 4F2 (CYP4F2), an enzyme responsible for the metabolism of eicosanoids. However, the mechanism of VK1 omega-hydroxylation by CYP4F2 has not been disclosed. In this study, we employed a combination of quantum mechanism (QM) calculations, homology modeling, molecular docking, molecular dynamics (MD) simulations, and combined quantum mechanism/molecular mechanism (QM/MM) calculations to investigate the metabolism profile of VK1 omega-hydroxylation. QM calculations based on the truncated VK1 model show that the energy barrier for omega-hydroxylation is about 6-25 kJ/mol higher than those at other potential sites of metabolism. However, results from the MD simulations indicate that hydroxylation at the omega-site is more favorable than at the other potential sites, which is in accordance with the experimental observation. The evaluation of MD simulations was further endorsed by the QM/MM calculation results. Our studies thus suggest that the active site residues of CYP4F2 play a determinant role in the omega-hydroxylation. Our results provide structural insights into the mechanism of VK1 omega-hydroxylation by CYP4F2 at the atomistic level and are helpful not only for characterizing the CYP4F2 functions but also for looking into the omega-hydroxylation mediated by other CYP4 enzymes.

  • 57.
    Li, Qizhao
    et al.
    East China Univ Sci & Technol, Key Lab Adv Mat, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Joint Int Res Lab Precis Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Ishida, Masatoshi
    Kyushu Univ, Dept Chem & Biochem, Grad Sch Engn, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka 8190395, Japan..
    Kai, Hiroto
    Kyushu Univ, Dept Chem & Biochem, Grad Sch Engn, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka 8190395, Japan..
    Gu, Tingting
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Li, Chengjie
    East China Univ Sci & Technol, Key Lab Adv Mat, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Joint Int Res Lab Precis Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Li, Xin
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Baryshnikov, Glib
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liang, Xu
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Zhu, Weihua
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH Royal Inst Technol, Dept Theoret Chem & Biol, Sch Biotechnol, S-10691 Stockholm, Sweden..
    Furuta, Hiroyuki
    Kyushu Univ, Dept Chem & Biochem, Grad Sch Engn, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka 8190395, Japan..
    Xie, Yongshu
    East China Univ Sci & Technol, Key Lab Adv Mat, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Joint Int Res Lab Precis Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Skeletal Rearrangement of Twisted Thia-Norhexaphyrin: Multiply Annulated Polypyrrolic Aromatic Macrocycles2019In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 58, no 18, p. 5925-5929Article in journal (Refereed)
    Abstract [en]

    A hybrid thia-norhexaphyrin comprising a directly linked N-confused pyrrole and thiophene unit (1) revealed unique macrocycle transformations to afford multiply inner-annulated aromatic macrocycles. Oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone triggered a cleavage of the C-S bond of the thiophene unit, accompanied with skeletal rearrangement to afford unique pi-conjugated products: a thiopyrrolo-pentaphyrin embedded with a pyrrolo[1,2]isothiazole (2), a sulfur-free pentaphyrin incorporating an indolizine moiety (3), and a thiopyranyltriphyrinoid containing a 2H-thiopyran unit (4). Furthermore, 2 underwent desulfurization reactions to afford a fused pentaphyrin containing a pyrrolizine moiety (5) under mild conditions. Using expanded porphyrin scaffolds, oxidative thiophene cleavage and desulfurization of the hitherto unknown N-confused core-modified macrocycles would be a practical approach for developing unique polypyrrolic aromatic macrocycles.

  • 58.
    Li, Qizhao
    et al.
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Li, Chengjie
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Kim, Jinseok
    Yonsei Univ, Dept Chem, Seoul 03722, South Korea.;Yonsei Univ, Spect Lab Funct Elect Syst, Seoul 03722, South Korea..
    Ishida, Masatoshi
    Kyushu Univ, Grad Sch Engn, Dept Chem & Biochem, Fukuoka, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka, Fukuoka 8190395, Japan..
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Gu, Tingting
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Liang, Xu
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Zhu, Weihua
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Kim, Dongho
    Yonsei Univ, Dept Chem, Seoul 03722, South Korea.;Yonsei Univ, Spect Lab Funct Elect Syst, Seoul 03722, South Korea..
    Furuta, Hiroyuki
    Kyushu Univ, Grad Sch Engn, Dept Chem & Biochem, Fukuoka, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka, Fukuoka 8190395, Japan..
    Xie, Yongshu
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Regioselectively Halogenated Expanded Porphyrinoids as Building Blocks for Constructing Porphyrin-Porphyrinoid Heterodyads with Tunable Energy Transfer2019In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 13, p. 5294-5302Article in journal (Refereed)
    Abstract [en]

    Expanded porphyrins have been attracting increasing attention owing to their unique optical and electrochemical properties as well as switchable aromaticity. Toward material applications, regioselective functionalization of the expanded porphyrins at their periphery is indeed challenging due to the presence of multiple reactive sites. Herein, a set of regioselective halogenated isomers (L5-Br-A/B/C) of neo-confused isosmaragdyrin (L5) are synthesized by a combination of the halogenation reaction of L5 and sequential macrocycleto-macrocycle transformation reactions of its halogenated isomers. On this basis, the regioselectively functionalized isosmaragdyrins are utilized as building blocks for constructing multichromophoric porphyrinoids, specifically, heterodyads L5-ZnP-A/B/C, in which a common zinc porphyrin is linked at three different pyrrolic positions of isosmaragdyrins, respectively, by Sonogashira coupling reactions. The highly efficient energy cascade from porphyrin to isosmaragdyrin is elucidated using steady-state/time-resolved spectroscopies and theoretical calculations. Notably, the energy transfer processes from the porphyrin to the isosmaragdyrin moieties as well as the excitation energy transfer rates in L5-ZnP-A/B/C are highly dependent on the linking sites by through-bond and Forster-type resonance energy transfer mechanisms. The site-selective functionalization and subsequent construction of a set of heterodyads of the expanded porphyrinoid would provide opportunities for developing new materials for optoelectronic applications.

  • 59. Li, S.
    et al.
    Zou, Rongfeng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wu, J.
    Landry, M. P.
    Cholesterol-directed nanoparticle assemblies based on single amino acid peptide mutations activate cellular uptake and decrease tumor volume2017In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 8, no 11, p. 7552-7559Article in journal (Refereed)
    Abstract [en]

    Peptide drugs have been difficult to translate into effective therapies due to their low in vivo stability. Here, we report a strategy to develop peptide-based therapeutic nanoparticles by screening a peptide library differing by single-site amino acid mutations of lysine-modified cholesterol. Certain cholesterol-modified peptides are found to promote and stabilize peptide α-helix formation, resulting in selectively cell-permeable peptides. One cholesterol-modified peptide self-assembles into stable nanoparticles with considerable α-helix propensity stabilized by intermolecular van der Waals interactions between inter-peptide cholesterol molecules, and shows 68.3% stability after incubation with serum for 16 h. The nanoparticles in turn interact with cell membrane cholesterols that are disproportionately present in cancer cell membranes, inducing lipid raft-mediated endocytosis and cancer cell death. Our results introduce a strategy to identify peptide nanoparticles that can effectively reduce tumor volumes when administered to in in vivo mice models. Our results also provide a simple platform for developing peptide-based anticancer drugs.

  • 60.
    Li, Xiyu
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Theoretical Computer Science, TCS.
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liu, Haichun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Chen, Guanying
    Harbin Inst Technol, Sch Chem Engn & Technol, Harbin 150001, Heilongjiang, Peoples R China..
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Mechanism for the Extremely Efficient Sensitization of Yb(3+)Luminescence in CsPbCl3 Nanocrystals2019In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 3, p. 487-492Article in journal (Refereed)
    Abstract [en]

    Rare earth ion (RE3+)-doped inorganic CsPbX3 (X = Cl or Cl/Br) nanocrystals have been presented as promising materials for applications in solar-energy conversion technology. An extremely efficient sensitization of Yb3+ luminescence in CsPbCl3 nanoparticles (NCs) was very recently demonstrated where quantum cutting is responsible for the performance of photoluminescence quantum yields over 100% (T. J. Milstein, et al. Nano Letters 2018, 18, 3792). In the present work, based on the cubic phase of inorganic perovskite, we seek to obtain atom-level insight into the basic mechanisms behind these observations in order to boost the further development of RE3+-doped CsPbX3 NCs for optoelectronics. In our calculations of cubic crystal structure, we do not find any energy level formed in the middle of the band gap, which disfavors a mechanism of stepwise energy transfer from the perovskite host to two Yb3+ ions. Our work indicates that the configuration with "right-angle" Yb3+-V-Pb-Yb3+ couple is most likely to form in Yb3+-doped CsPbCl3. Associated with this "right-angle" couple, the "right-angle" Pb atom with trapped excited states would localize the photogenerated electrons and act as the energy donor in a quantum cutting process, which achieves simultaneous sensitization of two neighboring Yb3+ ions.

  • 61.
    Li, Xiyu
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liu, Haichun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Chen, Guanying
    Harbin Inst Technol, Sch Chem Engn & Technol, Harbin 150001, Heilongjiang, Peoples R China.
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China ; Federal Siberian Research Clinical Centre under FMBA of Russia, 26 Kolomenskaya, Krasnoyarsk 660037, Russia.
    On the Mechanism for the Extremely Efficient Sensitization of Yb3+ Luminescence in CsPbCl3 Nanocrystals2019In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 3, p. 487-492Article in journal (Refereed)
    Abstract [en]

    Rare earth ion (RE3+)-doped inorganic CsPbX3 (X = Cl or Cl/Br) nanocrystals have been presented as promising materials for applications in solar-energy conversion technology. An extremely efficient sensitization of Yb3+ luminescence in CsPbCl3 nanoparticles (NCs) was very recently demonstrated where quantum cutting is responsible for the performance of photoluminescence quantum yields over 100% (T. J. Milstein, et al. Nano Letters 2018, 18, 3792). In the present work, based on the cubic phase of inorganic perovskite, we seek to obtain atom-level insight into the basic mechanisms behind these observations in order to boost the further development of RE3+-doped CsPbX3 NCs for optoelectronics. In our calculations of cubic crystal structure, we do not find any energy level formed in the middle of the band gap, which disfavors a mechanism of stepwise energy transfer from the perovskite host to two Yb3+ ions. Our work indicates that the configuration with "right-angle" Yb3+-V-Pb-Yb3+ couple is most likely to form in Yb3+-doped CsPbCl3. Associated with this "right-angle" couple, the "right-angle" Pb atom with trapped excited states would localize the photogenerated electrons and act as the energy donor in a quantum cutting process, which achieves simultaneous sensitization of two neighboring Yb3+ ions.

  • 62.
    Li, Xuping
    et al.
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Deng, Chao
    Zhejiang Univ, Dept Polymer Sci & Engn, MOE Key Lab Macromol Synth & Functionalizat, Hangzhou 310027, Zhejiang, Peoples R China..
    Bao, Xiaoyan
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Wu, Bin
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Zhou, Yunyun
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhu, Liangliang
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    A three-dimensional ratiometric sensing strategy on unimolecular fluorescence-thermally activated delayed fluorescence dual emission2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 731Article in journal (Refereed)
    Abstract [en]

    Visualized sensing through fluorescence signals is a powerful method for chemical and physical detection. However, the utilization of fluorescent molecular probes still suffers from lack of precise signal self-calibration in practical use. Here we show that fluorescence and thermally activated delayed fluorescence can be simultaneously produced at the single-molecular level. The thermally activated delayed fluorescence serves as a sensing signal with its wavelength and lifetime both altered correlating to polarity, whereas the fluorescence always remains unchanged as an internal reference. Upon the establishment of a three-dimensional working curve upon the ratiometric wavelength and photoluminescence lifetime vs. polarity, disturbance factors during a relevant sensing process can be largely minimized by such a multiple self-calibration. This strategy was further applied into a precise detection of the microenvironmental polarity variation in complex phospholipid systems, towards providing new insights for convenient and accurate diagnosis of membrane lesions.

  • 63.
    Li, Zhenyu
    et al.
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Peoples R China..
    Zhang, Wenhua
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Peoples R China..
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Yang, Jinlong
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Peoples R China..
    A first principles study on atomic structure of graphene oxide and the mechanism of oxidation induced cutting2009In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 238Article in journal (Other academic)
  • 64. Liang, Lijun
    et al.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Theoretical insights into aggregation-induced helicity modulation of a perylene bisimide derivative2018In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 24, no 3, article id 51Article in journal (Refereed)
    Abstract [en]

    Formation of helical chiroptical self-assemblies via noncovalent interaction is a widely observed phenomenon in nature, the mechanism of which remains insufficiently understood. Employing an amphiphilic perylene-sugar dyad molecule (PBI-HAG) as an example, we report that the modulatable supramolecular helicity may emerge from an aggregating process that is dominated by competition between two types of noncovalent interaction: hydrogen bonding and pi-pi stacking. The interplay between these two driving forces, which is greatly affected by the solvent environment, determines the morphology the supramolecular assembly of PBI-HAGs. In particular, a non-layered supramolecular structure was formed in octane owing to stabilization effects of intermolecular hydrogen bonds, whereas a layered supramolecular structure was formed in water because of energetically favorable pi-pi stacking of aromatic rings. The formation of distinct supramolecular architectures in different solvents was reinforced by simulated circular dichroism spectra, which show opposite signals consistent with experimental observations. The results of this study could help us understand aggregation-induced supramolecular chirality of noncovalent self-assemblies.

  • 65.
    Linares, Mathieu
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sun, Haofan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. East China Univ Sci & Technol, Shanghai Key Lab Funct Mat Chem, Dept Chem & Mol Engn, Shanghai 200237, Peoples R China.
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Andreasson, Joakim
    Chalmers Univ Technol, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Norman, P.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 7, p. 3637-3643Article in journal (Refereed)
    Abstract [en]

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

  • 66.
    Litvin, Valentina A.
    et al.
    Bohdan Khmelnitsky Natl Univ, Dept Chem, Shevchenka Bvd 81, UA-18031 Cherkassy, Ukraine..
    Minaev, Boris F.
    Bohdan Khmelnitsky Natl Univ, Dept Chem, Shevchenka Bvd 81, UA-18031 Cherkassy, Ukraine..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Bohdan Khmelnitsky Natl Univ, Dept Chem, Shevchenka Bvd 81, UA-18031 Cherkassy, Ukraine..
    Experimental and theoretical study of the mechanism formation of silver nanoclusters in the reduction reaction of Ag+ ions by alizarin solution2019In: Colloid and Interface Science Communications, ISSN 2215-0382, Vol. 29, p. 47-54Article in journal (Refereed)
    Abstract [en]

    For the study of the processes of the Ag+ ions interaction with humic substances a low molecular weight model compound - alizarin - was used for the first time in the present work. It has been established that alizarin carries out a double role in the process of synthesis of silver nanoparticles: reducing agent of Ag+ ions and a stabilizer of the formed nanoparticles. Based on the analysis of experimental data a mechanism of silver nanoparticles formation was proposed. In particular, at the moment of mixing of the reagents, a microphase Ag2O is formed and becomes a source of silver ions in solution. Alizarin molecules form a complex with silver ions, which provide the centres of primary clusters formation. The growth of primary clusters occurs through the reduction of Ag+ ions from the solution. Organic component of the complex undergoes oxidative hydroxylation by the Elbs reaction type.

  • 67.
    Liu, Juzhe
    et al.
    Beihang Univ, Beijing Adv Innovat Ctr Biomed Engn, Sch Chem, Beijing 100191, Peoples R China..
    Ji, Yongfei
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Nai, Jianwei
    Beihang Univ, Beijing Adv Innovat Ctr Biomed Engn, Sch Chem, Beijing 100191, Peoples R China..
    Niu, Xiaogang
    Beihang Univ, Beijing Adv Innovat Ctr Biomed Engn, Sch Chem, Beijing 100191, Peoples R China..
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Anhui, Peoples R China..
    Guo, Lin
    Beihang Univ, Beijing Adv Innovat Ctr Biomed Engn, Sch Chem, Beijing 100191, Peoples R China..
    Yang, Shihe
    Hong Kong Univ Sci & Technol, Dept Chem, Kowloon, Hong Kong, Peoples R China.;Peking Univ, Shenzhen Grad Sch, Sch Chem Biol & Biotechnol, Guangdong Key Lab Nano Micromat Res, Shenzhen, Peoples R China..
    Ultrathin amorphous cobalt-vanadium hydr(oxy)oxide catalysts for the oxygen evolution reaction2018In: Energy & Environmental Science, ISSN 1754-5692, E-ISSN 1754-5706, Vol. 11, no 7, p. 1736-1741Article in journal (Refereed)
    Abstract [en]

    Cost efficient and long-term stable catalysts are in great demand for the oxygen evolution reaction (OER), a key process involved in water splitting cells and metal-air batteries. Here, we demonstrate that the ultrathin amorphous cobalt-vanadium hydr(oxy)oxide we synthesized is a highly promising electrocatalytic material for the OER with a low overpotential of 0.250 V (even lower down to 0.215 V when supported on Au foam) at 10 mA cm(-2) and a long stable operation time (170 h) in alkaline media. In combination with in situ X-ray absorption spectral characterization and first-principles simulations, we reveal that the ultrathin, amorphous and alloyed structural characteristics have enabled its facile transformation to the desirable active phase, leading to a dramatically enhanced catalytic activity. Our finding highlights the remarkable advantages of the two-dimensional amorphous material and sheds new light on the design of high-performance electrocatalysts.

  • 68.
    Löytynoja, Tuomas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. University of Oulu.
    Quantum and quantum-classical calculations of core-ionized molecules in varied environments2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Computational quantum chemistry methods have been applied in two particular cases: to provide insight to photoionization induced fragmentation of HgBr2 and HgCl2 molecules, and to study core-electron binding energies and chemical shifts of molecules in liquid, surface adsorbed and polymeric environments in the framework of quantum mechanics/molecular mechanics (QM/MM). In the photodissociation studies the computational work is based on the relativistic Dirac equation as the systems present strong spin-orbit interaction affecting the fragmentation processes. In the QM/MM studies of ethanol-water mixtures and molecules physisorbed on silver surfaces the structures are provided by classical molecular dynamics simulations to analyze the distribution of the binding energies of core-orbitals and effects of their surroundings. In the case of polymethyl methacrylate polymer the impact of a QM-MM boundary and a polymeric environment are studied. The theoretical backgrounds of the computational methods applied and the obtained results are discussed.

  • 69.
    Ma, Yong
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Lin, J.
    Song, X. -N
    Wang, C. -K
    Hua, W.
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Local structures of nitrogen doped graphdiynes determined by computational X-ray spectroscopy2019In: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 149, p. 672-678Article in journal (Refereed)
    Abstract [en]

    Nitrogen doping is an important method to modulate electronic structure of two-dimensional carbon materials. The properties of the doped systems are heavily dependent on the local structure of nitrogen dopants involved, which are often determined by experimental X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) at the nitrogen K-edge. In the present work, the N1s XPS and NEXAFS spectra of nitrogen-doped graphdiynes have been accurately calculated at the density functional theory level. Five representative nitrogen-dopants in graphdiynes, namely [pyridinic, amino, graphitic, and two sp-hybridized N (sp-N-1 and sp-N-2) local structures], are fully examined, from which all experimental features could be correctly assigned. The calculated results can be used to determine the ratio of different nitrogen dopants in graphdiyne at different elevated temperatures reported in previous experiments. Our findings provide the basic references for structure determination of nitrogen doped graphdiyne and new understanding of the underlying structure-property relationships.

  • 70.
    Ma, Yong
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, P. R. China.
    Wang, S. -Y
    Hu, J.
    Zhou, Y.
    Song, X. -N
    Wang, C. -K
    Theoretical Identification of the Six Stable C84 Isomers by IR, XPS, and NEXAFS Spectra2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 4, p. 1019-1026Article in journal (Refereed)
    Abstract [en]

    Six stable C84 isomers satisfying isolated pentagon rule (IPR) have been theoretically identified by infrared (IR), X-ray photoelectron (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra. The XPS and NEXAFS spectra at the K-edge for all nonequivalent carbon atoms were simulated by the density functional theory method. NEXAFS spectra show stronger dependence than IR and XPS spectra on the six C84 isomers, which can be properly used for isomer identification. Furthermore, spectral components of total spectra for carbon atoms in different local environment have been explored.

  • 71.
    Ma, Yong
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wang, Sheng-Yu
    Hu, Jing
    Song, Xiu-Neng
    Zhou, Yong
    Wang, Chuan-Kui
    Theoretical N K-edge NEXAFS spectroscopy study for configuration of a dipolar molecule on graphene2018In: Materials Chemistry and Physics, ISSN 0254-0584, E-ISSN 1879-3312, Vol. 207, p. 309-314Article in journal (Refereed)
    Abstract [en]

    The landscape of the chromophore-functionalized molecule on graphene surface is of much significance in terms of the application of doped graphene. By means of the N1s near-edge X-ray absorption fine structure (NEXAFS) spectroscopy in density functional theory (DFT), the landscape of a dipolar molecule pyrene-tethered Disperse Red 1 (DRIP) on graphene surface was systematically analyzed. The azo pi* and nitro pi* peaks in experimental spectra were well assigned as the resonances from 1s of N atoms in different compounds to the lowest unoccupied molecular orbital (LUMO). The intensities of the two above peaks are influenced by the incidence angles of X-ray. By comparing the theoretical spectra with the experimental spectra, the most possible geometric configurations of DR1 P molecule on Graphene surface are determined.

  • 72.
    Ma, Yong
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China.
    Wang, Sheng-Yu
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Hu, Jing
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Zhang, Jun-Rong
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Lin, Juan
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Yang, Shu-Qiong
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Song, Xiu-Neng
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Identification of Four C-40 Isomers by Means of a Theoretical XPS/ NEXAFS Spectra Study2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 20, p. 4750-4755Article in journal (Refereed)
    Abstract [en]

    XPS and NEXAFS spectra of four stable C-40 isomers [29(C-2), 31 (C-s), 38(D-2), and 39(D-sd)] have been investigated theoretically. We combined density functional theory and the full core hole potential method to simulate C 1s XPS and NEXAFS spectra for nonequivalent carbon atoms of four stable C-40 fullerene isomers. The NEXAFS showed obvious dependence on the four C-40 isomers, and XPS spectra are distinct for all four isomers, which can be employed to identify the four stable structures of C-40. Furthermore, the individual components of the spectra according to different categories have been investigated, and the relationship between the spectra and the local structures of C atoms was also explored.

  • 73.
    Mackie, Cameron J.
    et al.
    Lawrence Berkeley Natl Lab, Chem Sci Div, Berkeley, CA 94720 USA.;Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands..
    Chen, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands.
    Candian, Alessandra
    Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands..
    Lee, Timothy J.
    NASA, Ames Res Ctr, Moffett Field, CA 94035 USA..
    Tielens, Alexander G. G. M.
    Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands..
    Fully anharmonic infrared cascade spectra of polycyclic aromatic hydrocarbons2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 149, no 13, article id 134302Article in journal (Refereed)
    Abstract [en]

    The infrared (IR) emission of polycyclic aromatic hydrocarbons (PAHs) permeates our universe; astronomers have detected the IR signatures of PAHs around many interstellar objects. The IR emission of interstellar PAHs differs from their emission as seen under conditions on Earth as they emit through a collisionless cascade down through their excited vibrational states from high internal energies. The difficulty in reproducing interstellar conditions in the laboratory results in a reliance on theoretical techniques. However, the size and complexity of PAHs require careful consideration when producing the theoretical spectra. In this work, we outline the theoretical methods necessary to lead to fully theoretical IR cascade spectra of PAHs including: an anharmonic second order vibrational perturbation theory treatment, the inclusion of Fermi resonances through polyads, and the calculation of anharmonic temperature band shifts and broadenings (including resonances) through a Wang-Landau approach. We also suggest a simplified scheme to calculate vibrational emission spectra that retain the essential characteristics of the full IR cascade treatment and can directly transform low temperature absorption spectra in IR cascade spectra. Additionally we show that past astronomical models were in error in assuming a 15 cm(-1) correction was needed to account for anharmonic emission effects.

  • 74. Madsen, Diana
    et al.
    Christiansen, Ove
    König, Carolin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Anharmonic vibrational spectra from double incremental potential energy and dipole surfaces2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 5, p. 3445-3456Article in journal (Refereed)
    Abstract [en]

    We extend the fragmentation-based double incremental expansion in FALCON coordinates (DIF) and its linear-scaling analogue [C. Konig and O. Christiansen, J. Chem. Phys., 2016, 145, 064105] to dipole surfaces. Thereby, we enable the calculation of intensities in vibrational absorption spectra from these cost-efficient property surfaces. We validate the obtained potential energy and dipole surfaces by vibrational spectra calculations employing damped response theory for correlated vibrational coupled cluster wave functions. Our largest calculation on a hexa-phenyl includes all 180 vibrational degrees of freedom of the system, which illustrates the potential of both the DIF schemes for property surface generation and the use of damped response theory from high-dimensional correlated vibrational wave functions. Generally, we obtain good agreement between the spectra calculated from the DIF property surfaces and the non-fragmented analogues. Moreover, when adopting suitable electronic structure methods, good agreement with respect to the experiment can be obtained, as shown for the example of 5-methylfurfural and RI-MP2. In conclusion, our results illustrate that the presented scheme with linearly scaling surfaces enables high quality spectra, as long as reasonably sized fragments can be defined. With this work, we push the realistic limits of vibrational spectra calculations from vibrational wave function methods and accurate electronic structure calculations to significantly larger systems than currently accessible.

  • 75.
    Madsen, Diana
    et al.
    Aarhus Univ, Dept Chem, Langelandsgade 140, DK-8000 Aarhus C, Denmark..
    Christiansen, Ove
    Aarhus Univ, Dept Chem, Langelandsgade 140, DK-8000 Aarhus C, Denmark..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Koenig, Carolin
    Christian Albrechts Univ Kiel, Inst Phys Chem, Max Eyth Str 1, D-24118 Kiel, Germany..
    Vibrationally resolved emission spectra of luminescent conjugated oligothiophenes from anharmonic calculations2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 31, p. 17410-17422Article in journal (Refereed)
    Abstract [en]

    We report on accurate and efficient calculations of vibrationally resolved emission spectra for oligothiophenes from anharmonic vibrational configuration interaction wave-function calculations in reduced vibrational spaces. These reduced spaces are chosen based on the independent mode displaced harmonic oscillator model. Good agreement with experiment is obtained for all-trans oligothiophenes with two to five rings also when employing only a few active modes. Vibrational modes incorporating inter-ring carbon-carbon stretches and a ring breathing mode are found to be the main players in the vibrational progression for the emission from the first excited electronic state for all investigated oligothiophene derivatives. The presented framework is here illustrated for oligothiophenes, but we have made no underlying system-dependent assumptions and believe it to become a valuable tool for the rational design of fluorescence biomarkers.

  • 76.
    Makafe, Gaelle G.
    et al.
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Hussain, Muzammal
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Chinese Acad Sci, Guangdong Prov Key Lab Biocomp, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Surineni, Goverdhan
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Tan, Yaoju
    Guangzhou Chest Hosp, Dept Clin Lab, State Key Lab Resp Dis, 62 Hengzhigang Rd, Guangzhou 510095, Guangdong, Peoples R China..
    Wong, Nai-Kei
    Southern Univ Sci & Technol, Hosp 2, Shenzhen Peoples Hosp 3, Key Discipline Infect Dis, 29 Bulan Rd, Shenzhen 518112, Peoples R China..
    Julius, Mugweru
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Embu, Dept Biol Sci, Embu 660100, Kenya..
    Liu, Lanying
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Gift, Chiwala
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Jiang, Huofeng
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Sci & Technol China, Sch Life Sci, 96 Jinzhai Rd, Hefei 230027, Anhui, Peoples R China..
    Tang, Yunxiang
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Anhui Univ, Inst Phys Sci & Informat Technol, 111 Jiulong Rd, Hefei 230009, Anhui, Peoples R China..
    Liu, Jianxiong
    Guangzhou Chest Hosp, Dept Clin Lab, State Key Lab Resp Dis, 62 Hengzhigang Rd, Guangzhou 510095, Guangdong, Peoples R China..
    Tan, Shouyong
    Guangzhou Chest Hosp, Dept Clin Lab, State Key Lab Resp Dis, 62 Hengzhigang Rd, Guangzhou 510095, Guangdong, Peoples R China..
    Yu, Zhijun
    Chinese Acad Sci, Guangdong Prov Key Lab Biocomp, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Liu, Zhiyong
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China..
    Lu, Zhili
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China..
    Fang, Cuiting
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Zhou, Yang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhang, Jiancun
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Chinese Acad Sci, Guangdong Prov Key Lab Biocomp, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Zhu, Qiang
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Liu, Jinsong
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Chinese Acad Sci, Guangdong Prov Key Lab Biocomp, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Zhang, Tianyu
    Chinese Acad Sci, State Key Lab Resp Dis, Guangzhou Inst Biomed & Hlth, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Guangzhou Regenerat Med & Hlth Guangdong Lab GRM, 190 Kaiyuan Ave,Sci Pk, Guangzhou 510530, Guangdong, Peoples R China.;Univ Chinese Acad Sci, 19 Yuquan Rd, Beijing 100049, Peoples R China..
    Quinoline Derivatives Kill Mycobacterium tuberculosis by Activating Glutamate Kinase2019In: Cell Chemical Biology, ISSN 2451-9456, E-ISSN 2451-9448, Vol. 26, no 8, p. 1187-+Article in journal (Refereed)
    Abstract [en]

    There is a great need for identification and development of new anti-tuberculosis drugs with novel targets. Recent drug-discovery efforts typically focus on identifying inhibitors but not activators that perturb metabolic enzymes' functions as a means to kill Mycobacterium tuberculosis (Mtb). Here, we describe a class of quinoline compounds, Z0933/Z0930, which kill Mtb by acting as activators of glutamate kinase (GK), a previously untargeted enzyme catalyzing the first step of proline biosynthesis. We further show that Z0933/Z0930 augment proline production and induce Mtb killing via proline-derived redox imbalance and production of reactive oxygen species. This work highlights the effectiveness of gain-of-function probes against Mtb and provides a framework for the discovery of next-generation allosteric activators of GK.

  • 77.
    Marcos, Rocio
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bertini, Federica
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Peruzzini, Maurizio
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Gonsalvi, Luca
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Mechanistic Studies on NaHCO3 Hydrogenation and HCOOH Dehydrogenation Reactions Catalysed by a Fe-II Linear Tetraphosphine Complex2018In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 24, no 20, p. 5366-5372Article in journal (Refereed)
    Abstract [en]

    We present a theoretical extension of the previously published bicarbonate hydrogenation to formate and formic acid dehydrogenation catalysed by Fe-II complexes bearing the linear tetraphosphine ligand tetraphos-1. The hydrogenation reaction was found to proceed at the singlet surface with two competing pathways: A)H-2 association to the Fe-H species followed by deprotonation to give a Fe(H)(2) intermediate, which then reacts with CO2 to give formate. B)CO2 insertion into the Fe-H bond, followed by H-2 association and subsequent deprotonation. B was found to be slightly preferred with an activation energy of 22.8kcalmol(-1), compared to 25.3 for A. Further we have reassigned the Fe-H complex, as a Fe(H)(H-2), which undergoes extremely rapid hydrogen exchange.

  • 78.
    Minaev, Boris F.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Minaeva, Valentina A.
    Spin-orbit coupling in enzymatic reactions and the role of spin in biochemistry2017In: Handbook of Computational Chemistry, Springer International Publishing , 2017, p. 1557-1587Chapter in book (Other academic)
    Abstract [en]

    We review the general concept of nonadiabatic quantum spin transitions in biochemistry. A few important examples are highlighted to illustrate the concept: the role of spin effects in oxidases, cytochromes, in dioxygen binding to heme, in photosynthesis, and in tentative models of consciousness. The most thoroughly studied of these effects are connected with dioxygen activation by enzymes. Discussion on the mechanisms of overcoming spin prohibitions in dioxygen reactions with flavin-dependent oxygenases and with hemoglobin and myoglobin is presented in some detail. We consider spin-orbit coupling (SOC) between the starting triplet state from the entrance channel of the O2 binding to glucose oxidase, to ferrous heme, and the final singlet open-shell state in these intermediates. Both triplet (T) and singlet (S) states in these examples are dominated by the radical-pair structures D+O2induced by charge transfer; the peculiarities of their orbital configurations are essential for the SOC analysis. An account of specific SOC in the open πg-shell of dioxygen helps to explain the probability of T-S transitions in the active site near the transition state. Simulated potential energy surface cross-sections along the reaction coordinates for these multiplets, calculated by density functional theory, agree with the notion of a relatively strong SOC induced inside the oxygen moiety by an orbital angular momentum change in the πg-shell during the T-S transition. The SOC model explains well the efficient spin inversion during the O2 binding with heme and glucose oxidase, which constitutes a key mechanism for understanding metabolism. Other examples of nontrivial roles of spin effects in biochemistry are briefly discussed. 

  • 79.
    Minaeva, Valentina
    et al.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Karaush-Karmazin, Nataliya
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Minaev, Boris
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    A complete characterization of vibrational IR and Raman spectra of the highly-symmetrical octathia[8]circulene2019In: Vibrational Spectroscopy, ISSN 0924-2031, E-ISSN 1873-3697, Vol. 100, p. 107-116Article in journal (Refereed)
    Abstract [en]

    The highly-symmetrical octathia[8]circulene molecule (8S) was synthesized and well studied 10 years ago in Moscow, including X-ray diffraction, IR and Raman spectra assignment on the ground of molecular DFT calculation. Nevertheless, this comprehensive study could not explain a big number of interesting deviations from the DFT predictions based on the molecular Dsh symmetry restriction being specific for a free species in a gas phase. In present work we have performed DFT optimization of the 8S tetramer starting with the X-ray diffraction analysis of a similar crystal structure. DFT calculation of IR and Raman spectra of such a huge system provides a good assignment of the crystal-field splitting and new band occurrence. The force-field distortions, electric charges and polarizability dependence on the tetramer structure are well reproduced by the B3LYP functional with the dispersion correction. Thus, the small shifts of IR and Raman bands, their splitting and intensity redistribution upon weak intermolecular interactions in crystal packing are explained and full assignment of all observed bands is presented.

  • 80. Mishra, Y. K.
    et al.
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Kotakoski, J.
    Adam, J.
    Progress in electronics and photonics with nanomaterials2017In: Vacuum, ISSN 0042-207X, E-ISSN 1879-2715, Vol. 146, p. 304-307Article in journal (Refereed)
    Abstract [en]

    Nanomaterials have been at the center of attraction for almost five decades as their contributions to different disciplines such as electronics, photonics and medicine are enormous. Various kinds of nanomaterials have been developed and are currently utilized in innumerable applications. Nevertheless, their simple realization and easy and efficient upscaling are topics under intense investigation. Innovative strategies have been adopted for nanomaterial synthesis and their usability. Here, we provide a brief overview on nanomaterials ranging from basic understanding of their structure-property relationship to advanced applications. This editorial covers various aspects about nanomaterials, which will be useful/attractive for beginners in the field of nanotechnology as well as for experts and for industrialists looking forward to exploit them for real world applications.

  • 81.
    Mudedla, Sathish Kumar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Murugan, Natarajan Arul
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Effect of Familial Mutations on the Interconversion of alpha-Helix to beta-Sheet Structures in an Amyloid-Forming Peptide: Insight from Umbrella Sampling Simulations2019In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 10, no 3, p. 1347-1354Article in journal (Refereed)
    Abstract [en]

    Understanding the initial events of aggregation of amyloid beta monomers to form beta-sheet rich fibrils is useful for the development of therapeutics for Alzheimer's disease. In this context, the changes in energetics involved in the aggregation of helical amyloid beta monomers into beta-sheet rich dimers have been investigated using umbrella sampling simulations and density functional theory calculations. The results from umbrella sampling simulations for the free energy profile for the interconversion closely agree with the results of density functional theory calculations. The results reveal that helical peptides converted to beta-sheet structures through coil-like conformations as intermediates that are mostly stabilized by intramolecular hydrogen bonds. The stabilization of intermediate structures could be a possible way to inhibit fibril formation. Mutations substantially decrease the height of the energy barrier for interconversion from alpha-helix to beta-sheet structure when compared to that of the wild type, something that is attributed to an increase in the number of intramolecular hydrogen bonds between backbone atoms in the coil structures that correspond to a maximum value on the free energy surface. The reduction of the energy barrier leads to an enhancement of the rate of aggregation of amyloid beta monomers upon introduction of various familial mutations, which is consistent with previous experimental reports.

  • 82.
    Mudedla, Sathish Kumar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Subramanian, Venkatesan
    Cent Leather Res Inst, CSIR, Chem Lab, Chennai 600020, India..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Destabilization of amyloid fibrils on interaction with MoS2-based nanomaterials2019In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 9, no 3, p. 1613-1624Article in journal (Refereed)
    Abstract [en]

    The present work is motivated by the established concept that the structure and energetics of biomacromolecules can be modulated by confining their dimensions in the nanoscale. In particular, here we use force-field methods to understand the stability of amyloid fibrils at nanostructured interfaces, which can be useful for the development of new therapeutics for Alzheimer's disease. We explore the binding modes and structural properties of fibrils at the interface of molybdenum disulphide nanotubes and the nanosurface using classical molecular dynamics simulations. We find that in general the MoS2 materials induces disruptions in the structure of the amyloid fibrils where the beta sheet conformation of the fibrils changes to a turned conformation, and it is large in the case of nanotubes in comparison to the nanosurfaces. The intermolecular hydrogen bonds, hydrophilic and hydrophobic contacts between the monomer peptides in the fibril are reduced due to their adsorption onto the MoS2 materials, which results in a destabilization of the fibril. The destabilization of fibril is to some extent compensated for by the van der Waals interactions between the fibril and MoS2. Overall the results indicate that MoS2-based materials can be useful in inhibiting the aggregation of smaller protofibrils to matured fibrils and to bust the already formed fibrils. Therapeutic materials should not exhibit any cross interaction with other off-targets compounds. In order to test whether the MoS2 nanomaterial has any such effect we have studied its interaction with two additional biomacromolecules, the human serum albumin and p53 protein, and we report no significant changes in the secondary structure of these biomolecules. Through molecular docking studies we also established that the drug binding ability of HSA is not altered by its surface binding to MoS2 nanosurface.

  • 83.
    Mudedla, Sathish Kumar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden.;Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Free Energy Landscape for Alpha-Helix to Beta-Sheet Interconversion in Small Amyloid Forming Peptide under Nanoconfinement2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 42, p. 9654-9664Article in journal (Refereed)
    Abstract [en]

    Understanding the mechanism of fibrillization of amyloid forming peptides could be useful for the development of therapeutics for Alzheimer's disease (AD). Taking this standpoint, we have explored in this work the free energy profile for the interconversion of monomeric and dimeric forms of amyloid forming peptides into different secondary structures namely beta-sheet, helix, and random coil in aqueous solution using umbrella sampling simulations and density functional theory calculations. We show that the helical structures of amyloid peptides can form beta sheet rich aggregates through random coil conformations in aqueous condition. Recent experiments (Chem. Eur. J. 2018, 24, 3397-3402 and ACS Appl. Mater. Interfaces 2017, 9, 21116-21123) show that molybdenum disulfide nanosurface and nanoparticles can reduce the fibrillization process of amyloid beta peptides. We have unravelled the free energy profile for the interconversion of helical forms of amyloid forming peptides into beta-sheet and random coil in the presence of a two-dimensional nanosurface of MoS2. Results indicate that the monomer and dimeric forms of the peptides adopt the random coil conformation in the presence of MoS2 while the helical form is preferable for the monomeric form and that the beta-sheet and helix forms are the preferable forms for dimers in aqueous solution. This is due to strong interaction with MoS2 and intramolecular hydrogen bonds of random coil conformation. The stabilization of random coil conformation does not lead to a beta sheet like secondary structure for the aggregate. Thus, the confinement of MoS2 promotes deaggregation of amyloid beta peptides rather than aggregation, something that could be useful for the development of therapeutics for AD.

  • 84.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Chiotis, Konstantinos
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Ctr Alzheimer Res, Div Clin Geriatr, Stockholm, Sweden.;Karolinska Univ Hosp, Theme Neurol, Stockholm, Sweden..
    Rodriguez-Vieitez, Elena
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Ctr Alzheimer Res, Div Clin Geriatr, Stockholm, Sweden..
    Lemoine, Laetitia
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Ctr Alzheimer Res, Div Clin Geriatr, Stockholm, Sweden..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Nordberg, Agneta
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Ctr Alzheimer Res, Div Clin Geriatr, Stockholm, Sweden.;Karolinska Univ Hosp, Theme Aging, Stockholm, Sweden..
    Cross-interaction of tau PET tracers with monoamine oxidase B: evidence from in silico modelling and in vivo imaging2019In: European Journal of Nuclear Medicine and Molecular Imaging, ISSN 1619-7070, E-ISSN 1619-7089, Vol. 46, no 6, p. 1369-1382Article in journal (Refereed)
    Abstract [en]

    PurposeSeveral tracers have been designed for tracking the abnormal accumulation of tau pathology in vivo. Recently, concerns have been raised about the sources of off-target binding for these tracers; inconclusive data propose binding for some tracers to monoamine oxidase B (MAO-B).MethodsMolecular docking and dynamics simulations were used to estimate the affinity and free energy for the binding of several tau tracers (FDDNP, THK523, THK5105, THK5317, THK5351, T807 [aka AV-1451, flortaucipir], T808, PBB3, RO-948, MK-6240, JNJ-311 and PI-2620) to MAO-B. These values were then compared with those for safinamide (MAO-B inhibitor). PET imaging was used with the tau tracer [F-18]THK5317 and the MAO-B tracer [C-11]DED in five patients with Alzheimer's disease to investigate the MAO-B binding component of this first generation tau tracer in vivo.ResultsThe computational modelling studies identified a binding site for all the tau tracers on MAO-B; this was the same site as that for safinamide. The binding affinity and free energy of binding for the tau tracers to MAO-B was substantial and in a similar range to those for safinamide. The most recently developed tau tracers MK-6240, JNJ-311 and PI-2620 appeared, in silico, to have the lowest relative affinity for MAO-B. The in vivo investigations found that the regional distribution of binding for [F-18]THK5317 was different from that for [C-11]DED, although areas of suspected off-target [F-18]THK5317 binding were detected. The binding relationship between [F-18]THK5317 and [C-11]DED depended on the availability of the MAO-B enzyme.ConclusionsThe developed tau tracers show in silico and in vivo evidence of cross-interaction with MAO-B; the MAO-B component of the tracer binding was dependent on the regional concentration of the enzyme.

  • 85.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Nordberg, Agneta
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Different Positron Emission Tomography Tau Tracers Bind to Multiple Binding Sites on the Tau Fibril: Insight from Computational Modeling2018In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 9, no 7, p. 1757-1767Article in journal (Refereed)
    Abstract [en]

    Using the recently reported cryo-EM structure for the tau fibril [Fitzpatrick et al. (2017) Nature 547, 185-190], which is a potential target concerning Alzheimer's disease, we present the first molecular modeling studies on its interaction with various positron emission tomography (PET) tracers. Experimentally, based on the binding assay studies, at least three different high affinity binding sites have been reported for tracers in the tau fibril. Herein, through integrated modeling using molecular docking, molecular dynamics, and binding free energy calculations, we provide insight into the binding patterns of various tracers to the tau fibril. We suggest that there are four different high affinity binding sites available for many of the studied tracers showing varying binding affinity to different binding sites. Thus, PBB3 binds most strongly to site 4, and interestingly, this site is not a preferable site for any other tracers. For THIC5351, our data show that it strongly binds to sites 3 and 1, the former one being more preferable. We also find that MK6240 and T807 bind to site 1 specifically. The modeling data also give some insight into whether a tracer bound to a specific site can be replaced by others or not. For example, the displacement of T807 by PBB3 as reported experimentally can also be explained and attributed to the larger binding affinity of the latter compound in all binding sites. The binding free energy results explain very well the small binding affinity of THK523 compared to all the aryl quinoline moieties containing THK tracers. The ability of certain tau tracers, like FDDNP and THK523, to bind to amyloid fibrils has also been investigated. Furthermore, such off-target interaction of tau tracers with amyloid beta fibrils has been validated using a quantum mechanical fragmentation approach.

  • 86.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zalesny, Robert
    Wroclaw Univ Sci & Technol, Fac Chem, Dept Phys & Quantum Chem, Wyb Wyspianskiego 27, PL-50370 Wroclaw, Poland..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Unusual binding-site-specific photophysical properties of a benzothiazole-based optical probe in amyloid beta fibrils2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 31, p. 20334-20339Article in journal (Refereed)
    Abstract [en]

    Optical imaging of amyloid fibrils serves as a cost-effective route for the diagnosis of Alzheimer-like conformational diseases. However, the challenge here is to optimize the binding affinity and photophysical properties of the optical imaging agents in a way specific to certain types of amyloids. In a few occasions it is shown that novel optical imaging agents can be designed to bind to a particular type of amyloid fibril with larger binding affinity and specificity. There is also a recent report on photoluminescent polythiophenes which display photophysical properties that can be used to distinguish the variants or subtypes of amyloids (J. Rasmussen et al., Proc. Natl. Acad. Sci. U. S. A., 2017, 114(49), 13018-13023). Based on a multiscale modeling approach, here, we report on the complementary aspect that the photophysical properties of a benzothiazole based optical probe (referred to as BTA-3) can be specific to the binding sites in the same amyloid fibrils and we attribute this to its varying electronic structure in different sites. As reported experimentally from competitive binding assay studies for many amyloid staining molecules and tracers, we also show multiple binding sites in amyloid fibrils for this probe. In particular, BTA-3 displayed a red-shift in its low-frequency absorption band only in site-4, a surface site of amyloid fibrils when compared to the spectra in water solvent. In the remaining sites, it exhibited a less significant blue shift for the same absorption band.

  • 87.
    Niskanen, Johannes
    et al.
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.;Univ Turku, Dept Phys & Astron, FI-20014 Turun, Finland..
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Sahle, Christoph J.
    European Synchrotron Radiat Facil 71, F-38043 Grenoble 9, France..
    Eckert, Sebastian
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany..
    Jay, Raphael M.
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany..
    Gilmore, Keith
    European Synchrotron Radiat Facil 71, F-38043 Grenoble 9, France..
    Pietzsch, Annette
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Dantz, Marcus
    Paul Scherrer Inst, Photon Sci Div, Swiss Light Source, CH-5232 Villigen, Switzerland..
    Lu, Xingye
    Paul Scherrer Inst, Photon Sci Div, Swiss Light Source, CH-5232 Villigen, Switzerland..
    McNally, Daniel E.
    Paul Scherrer Inst, Photon Sci Div, Swiss Light Source, CH-5232 Villigen, Switzerland..
    Schmitt, Thorsten
    Paul Scherrer Inst, Photon Sci Div, Swiss Light Source, CH-5232 Villigen, Switzerland..
    da Cruz, Vinicius Vaz
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Kimberg, Victor
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia..
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia..
    Foehlisch, Alexander
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany..
    Compatibility of quantitative X-ray spectroscopy with continuous distribution models of water at ambient conditions2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 10, p. 4058-4063Article in journal (Refereed)
    Abstract [en]

    The phase diagram of water harbors controversial views on underlying structural properties of its constituting molecular moieties, its fluctuating hydrogen-bonding network, as well as pair-correlation functions. In this work, long energy-range detection of the X-ray absorption allows us to unambiguously calibrate the spectra for water gas, liquid, and ice by the experimental atomic ionization cross-section. In liquid water, we extract the mean value of 1.74 +/- 2.1% donated and accepted hydrogen bonds per molecule, pointing to a continuous-distribution model. In addition, resonant inelastic X-ray scattering with unprecedented energy resolution also supports continuous distribution of molecular neighborhoods within liquid water, as do X-ray emission spectra once the femtosecond scattering duration and proton dynamics in resonant X-ray-matter interaction are taken into account. Thus, X-ray spectra of liquid water in ambient conditions can be understood without a two-structure model, whereas the occurrence of nanoscale-length correlations within the continuous distribution remains open.

  • 88.
    Norman, P.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205, D-69120 Heidelberg, Germany..
    Simulating X-ray Spectroscopies and Calculating Core-Excited States of Molecules2018In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 118, no 15, p. 7208-7248Article, review/survey (Refereed)
    Abstract [en]

    During the past decade, the research field of computational X-ray spectroscopy has witnessed an advancement triggered by the development of advanced synchrotron light sources and X-ray free electron lasers that in turn has enabled new sophisticated experiments with needs for supporting theoretical investigations. Following a discussion about fundamental conceptual aspects of the physical nature of core excitations and the concomitant requirements on theoretical methods, an overview is given of the major developments made in electronic-structure theory for the purpose of simulating advanced X-ray spectroscopies, covering methods based on density-functional theory as well as wave function theory. The capabilities of these theoretical approaches are illustrated by an overview of simulations of selected linear and nonlinear X-ray spectroscopies, including X-ray absorption spectroscopy (XAS), X-ray natural circular dichroism (XNCD), X-ray emission spectroscopy (XES), resonant inelastic X-ray scattering (RIXS), and X-ray two-photon absorption (XTPA).

  • 89.
    Norman, Patrick
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ruud, K.
    Saue, T.
    Principles and practices of molecular properties: Theory, modeling and simulations2018Book (Other academic)
    Abstract [en]

    A comprehensive yet accessible exploration of quantum chemical methods for the determination of molecular properties of spectroscopic relevance Molecular properties can be probed both through experiment and simulation. This book bridges these two worlds, connecting the experimentalist's macroscopic view of responses of the electromagnetic field to the theoretician's microscopic description of the molecular responses. Comprehensive in scope, it also offers conceptual illustrations of molecular response theory by means of time-dependent simulations of simple systems. This important resource in physical chemistry offers: A journey in electrodynamics from the molecular microscopic perspective to the conventional macroscopic viewpoint The construction of Hamiltonians that are appropriate for the quantum mechanical description of molecular properties Time- and frequency-domain perspectives of light-matter interactions and molecular responses of both electrons and nuclei An introduction to approximate state response theory that serves as an everyday tool for computational chemists A unified presentation of prominent molecular properties Principles and Practices of Molecular Properties: Theory, Modeling and Simulations is written by noted experts in the field. It is a guide for graduate students, postdoctoral researchers and professionals in academia and industry alike, providing a set of keys to the research literature. 

  • 90. Orms, Natalie
    et al.
    Rehn, Dirk R.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Krylov, Anna I.
    Characterizing Bonding Patterns in Diradicals and Triradicals by Density-Based Wave Function Analysis: A Uniform Approach2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 2, p. 638-648Article in journal (Refereed)
    Abstract [en]

    Density-based wave function analysis enables unambiguous comparisons of the electronic structure computed by different methods and removes ambiguity of orbital choices. We use this tool to investigate the performance of different spin flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high- and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such as polyradicals. We show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of the bonding pattern.

  • 91.
    Osella, Silvio
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Warsaw, Ctr New Technol, Banacha 2C, PL-02097 Warsaw, Poland.
    Di Meo, Florent
    Limoges Univ, Fac Pharm, INSERM, UMR 1248, 2 Rue Docteur Marcland, F-87025 Limoges, France..
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fabre, Gabin
    Limoges Univ, LCSN EA1069, Fac Pharm, 2 Rue Dr Marcland, F-87025 Limoges, France..
    Ameloot, Marcel
    Hasselt Univ, Biomed Res Inst, B-3590 Diepenbeek, Belgium..
    Trouillas, Patrick
    Limoges Univ, Fac Pharm, INSERM, UMR 1248, 2 Rue Docteur Marcland, F-87025 Limoges, France.;Palacky Univ, Ctr Adv Technol & Mat, Fac Sci, Tr 17 Listopadu 12, Olomouc 77146, Czech Republic..
    Knippenberg, Stefan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Hasselt Univ, Biomed Res Inst, B-3590 Diepenbeek, Belgium..
    Combining (Non)linear Optical and Fluorescence Analysis of DiD To Enhance Lipid Phase Recognition2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 10, p. 5350-5359Article in journal (Refereed)
    Abstract [en]

    The widespread interest in phase recognition of lipid membranes has led to the use of different optical techniques to enable differentiation of healthy and not fully functional cells. In this work, we show how the combination of different (non)linear optical methods such as one-photon absorption (OPA), two-photon absorption (TPA), and second harmonic generation (SHG) as well as the study of the fluorescence decay time leads to an enhanced screening of membrane phases using a fluorescent 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiD) probe. In the current study we consider the pure liquid disordered phases of DOPC (dioleoyl-sn-glycero-3-phosphocholine, room temperature) and DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 323 K), the solid gel phase of DPPC (298 K), and the liquid ordered phase of a 2:1 binary mixture of sphingomyelin and cholesterol. By means of extensive hybrid quantum mechanics molecular mechanics calculations and based upon the (non)linear absorption of the embedded probes, it is found that DiD can be used to identify the lipid bilayer phase. The joint TPA and SHG as well as fluorescence analyses qualifies DiD as a versatile probe for phase recognition. In particular, the SHG data obtained by means of hyper-Rayleigh scattering and by electric field induced second harmonic generation reveal differences in polarization of the probe in the different environments. The TPA results finally confirm the particular location of the probe in between the polar headgroup region of the 2:1 SM:Chol mixture in the liquid ordered phase.

  • 92.
    Osella, Silvio
    et al.
    Univ Warsaw, Chem & Biol Syst Simulat Lab, Ctr New Technol, Banacha 2C, PL-02097 Warsaw, Poland..
    Knippenberg, Stefan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Hasselt Univ, Biomed Res Inst, Agoralaan,Bldg C, Diepenbeek, Belgium.
    Environmental effects on the charge transfer properties of Graphene quantum dot based interfaces2019In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 119, no 10, article id e25882Article in journal (Refereed)
    Abstract [en]

    Graphene quantum dots (GQD) are interesting materials due to the confined sizes which allow to exploit their optoelectronic properties, especially when they interface with organic molecules through physisorption. In particular, when interfaces are formed, charge transfer (CT) processes can occur, in which electrons can flow either from the GQD to the absorbed molecule, or vice versa. These processes are accessible by modeling and computational analysis. Yet, the presence of different environments can strongly affect the outcome of such simulations which, in turn, can lead to wrong results if not taken into account. In this multiscale study, we assess the sensibility of the computational approach and compute the CT, calculated at interfaces composed by GQD and amino-acene derivatives. The hole transfer is strongly affected by dynamic disorder and the nature of the environment, and imposes stringent descriptions of the modeled systems to ensure enhanced accuracy of the transfer of charges.

  • 93.
    $$$Paloncyova, Marketa
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ameloot, Marcel
    Hasselt Univ, Biomed Res Inst, Agoralaan Bldg C, B-3590 Diepenbeek, Belgium..
    Knippenberg, Stefan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Orientational distribution of DPH in lipid membranes: a comparison of molecular dynamics calculations and experimental time-resolved anisotropy experiments2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 14, p. 7594-7604Article in journal (Refereed)
    Abstract [en]

    Characterization of the membrane phases is a crucial task in cell biology. Cells differ in composition of the lipids and consequently in adopted phases. The phases can be discriminated based upon lipid ordering and molecular diffusion and their identification could be used for characterization of cell membranes. Here we used molecular dynamics (MD) simulations to study the behavior of the fluorescent reporter molecule diphenylhexatriene (DPH) in different lipid phases - liquid disordered (L-d), liquid ordered (L-o), and solid ordered (S-o) composed of phosphatidylcholines (L-d and S-o) or a sphingomyelin/cholesterol (SM/Chol) mixture (L-o). To the best of our knowledge, this is the first simulation of DPH in L-o SM/Chol and S-o DPPC membranes. For the considered membrane compositions DPH is mostly oriented parallel to lipid tails. In the L-o phase we observed a significant fraction of DPH positioned in between membrane leaflets, which agrees with experimental findings, but which has not been observed in previous MD simulations of DPH in phosphatidylcholine membranes. Further, we calculated rotational autocorrelation functions (ROTACF) from our MD simulations in order to model the time-resolved fluorescence anisotropy decay. We observed that order parameters P-2 and P-4 are sufficient to fully describe the orientation distribution of DPH. We analyzed the ROTACFs by a so-called general model for the time-resolved fluorescence anisotropy [W. van der Meer et al., Biophys. J., 1984, 46, 515] and observed an overestimation of P-4. We suggest a rescaling of the recovered P-4 yielding an orientation distribution of DPH close to the one observed in our MD simulations.

  • 94. Peng, Xingyun
    et al.
    Huang, Bingru
    Pu, Rui
    Liu, Haichun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhang, Tao
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Zhan, Qiuqiang
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fast upconversion super-resolution microscopy with 10 μs per pixel dwell times2019In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 11, no 4, p. 1563-1569Article in journal (Refereed)
  • 95. Pershoguba, S. S.
    et al.
    Banerjee, Saikat
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Lashley, J. C.
    Park, J.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Aeppli, G.
    Balatsky, Alexander V.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Los Alamos National Laboratory, USA.
    Dirac Magnons in Honeycomb Ferromagnets2018In: Physical Review X, ISSN 2160-3308, E-ISSN 2160-3308, Vol. 8, no 1, article id 011010Article in journal (Refereed)
    Abstract [en]

    The discovery of the Dirac electron dispersion in graphene [A. H. Castro Neto, The Electronic Properties of Graphene, Rev. Mod. Phys. 81, 109 (2009)RMPHAT0034-686110.1103/RevModPhys.81.109] led to the question of the Dirac cone stability with respect to interactions. Coulomb interactions between electrons were shown to induce a logarithmic renormalization of the Dirac dispersion. With a rapid expansion of the list of compounds and quasiparticle bands with linear band touching [T. O. Wehling, Dirac Materials, Adv. Phys. 63, 1 (2014)ADPHAH0001-873210.1080/00018732.2014.927109], the concept of bosonic Dirac materials has emerged. We consider a specific case of ferromagnets consisting of van der Waals-bonded stacks of honeycomb layers, e.g., chromium trihalides CrX3 (X=F, Cl, Br and I), that display two spin wave modes with energy dispersion similar to that for the electrons in graphene. At the single-particle level, these materials resemble their fermionic counterparts. However, how different particle statistics and interactions affect the stability of Dirac cones has yet to be determined. To address the role of interacting Dirac magnons, we expand the theory of ferromagnets beyond the standard Dyson theory [F. J. Dyson, General Theory of Spin-Wave Interactions, Phys. Rev. 102, 1217 (1956)PHRVAO0031-899X10.1103/PhysRev.102.1217, F. J. Dyson, Thermodynamic Behavior of an Ideal Ferromagnet, Phys. Rev. 102, 1230 (1956)PHRVAO0031-899X10.1103/PhysRev.102.1230] to the case of non-Bravais honeycomb layers. We demonstrate that magnon-magnon interactions lead to a significant momentum-dependent renormalization of the bare band structure in addition to strongly momentum-dependent magnon lifetimes. We show that our theory qualitatively accounts for hitherto unexplained anomalies in nearly half-century-old magnetic neutron-scattering data for CrBr3 [W. B. Yelon and R. Silberglitt, Renormalization of Large-Wave-Vector Magnons in Ferromagnetic CrBr3 Studied by Inelastic Neutron Scattering: Spin-Wave Correlation Effects, Phys. Rev. B 4, 2280 (1971)PLRBAQ0556-280510.1103/PhysRevB.4.2280, E. J. Samuelsen, Spin Waves in Ferromagnetic CrBr3 Studied by Inelastic Neutron Scattering, Phys. Rev. B 3, 157 (1971)PLRBAQ0556-280510.1103/PhysRevB.3.157]. We also show that honeycomb ferromagnets display dispersive surface and edge states, unlike their electronic analogs.

  • 96.
    Pidluzhna, A.
    et al.
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Ivaniuk, K.
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Stakhira, P.
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Hotra, Z.
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine.;Rzeszow Univ Technol, Al Powstancow Warszawy 12, PL-35959 Rzeszow, Poland..
    Chapran, M.
    Lodz Univ Technol, Dept Mol Phys, Zeromskiego 116, PL-90924 Lodz, Poland..
    Ulanski, J.
    Lodz Univ Technol, Dept Mol Phys, Zeromskiego 116, PL-90924 Lodz, Poland..
    Tynkevych, O.
    Yuriy Fedkovych Chernivtsi Natl Univ, Kotsiubynsky Str 2, UA-58012 Chernovtsy, Ukraine..
    Khalavka, Y.
    Yuriy Fedkovych Chernivtsi Natl Univ, Kotsiubynsky Str 2, UA-58012 Chernovtsy, Ukraine..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Minaev, B. F.
    Bohdan Kitmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Multi-channel electroluminescence of CdTe/CdS core-shell quantum dots implemented into a QLED device2019In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 162, p. 647-653Article in journal (Refereed)
    Abstract [en]

    CdTe/CdS core-shell quantum dots were synthesized and implemented into a light emitting device resulting in multi-channel electroluminescence with a light-green emission color. The main electroluminescence band at about 530 nm corresponds to the emission by the CdTe core (type I core/shell structure), while the next emission band at 595 nm is assigned to the crossed recombination of electrons from the conduction band of the CdS shell and holes from the valence band of the CdTe core (type II core/shell structure). At the same time, the photoluminescence spectrum of the synthesized CdTe/CdS core-shell quantum dots contains only one emission band distinctive for type II structures. This behavior of CdTe/CdS core-shell quantum dots upon the electroexcitation allows the extension of the electroluminescence spectrum in the optical region in a way that is useful for lighting source applications. Such multi-channel electroluminescence can most probably also be reproduced in related core-shell systems accounting for size-confinement between the core size and shell thickness.

  • 97. Poongavanam, Vasanthanathan
    et al.
    Namasivayam, Vigneshwaran
    Vanangamudi, Murugesan
    Al Shamaileh, Hadi
    Veedu, Rakesh N.
    Kihlberg, Jan
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Integrative approaches in HIV-1 non-nucleoside reverse transcriptase inhibitor design2018In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 8, no 1, article id e1328Article in journal (Refereed)
    Abstract [en]

    The design of inhibitors for human immunodeficiency virus type-1 reverse transcriptase (HIV-1 RT) is one of the most successful approaches for the treatment of HIV infections. Among the HIV-1 RT inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTIs) constitute a prominent drug class, which includes nevirapine, delavirdine, efavirenz, etravirine, and rilpivirine approved for clinical use. However, the efficiency of many of these drugs has been undermined by drug-resistant variants of HIV-1 RT, and it therefore becomes inevitable to design novel drugs to cope with resistance. Here, we discuss various drug design strategies, which include traditional medicinal chemistry, computational chemistry, and chemical biology approaches. In particular, computational modeling approaches, including machine learning, empirical descriptors-based, force-field, ab initio, and hybrid quantum mechanics/molecular mechanics-based methods are discussed in detail. We foresee that these methods will have a major impact on efforts to guide the design and discovery of the next generation of NNRTIs that combat RT multidrug resistance.

  • 98.
    Qian, Zhengliang
    et al.
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Yuan, Tao
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Huang, Xinghua
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Wang, Qiaochun
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Agren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tian, He
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Divalent Pseudorotaxane with Polarized Plug-Socket and Padlock Functions2018In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 20, no 6, p. 1487-1490Article in journal (Refereed)
    Abstract [en]

    A dual-pore structured host composed of one 24-crown-8 and one 34-crown-10, and a "U"-shaped guest consisting of two different recognition units, one dibenzylammonium and one viologen, were synthesized and bound 1:1 into a divalent pseudorotaxane P1. P1 can mimic the inserting and pulling out functions of a polarized plug-socket system under solvent driven stimulus and can also realize the locking and unlocking actions of a padlock under pH stimulus.

  • 99.
    Qiu, Feifei
    et al.
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Peoples R China..
    Song, Ce
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Li, Li
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Peoples R China..
    Wei, Yong
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Peoples R China..
    Tian, Guangjun
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Peoples R China..
    First-principles study on vibrationallv resolved fluorescence of fused 5,15-(diphenyl)-10,20-(dibromo)porphyrin molecule2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 149, no 7, article id 074312Article in journal (Refereed)
    Abstract [en]

    The vibrationally resolved fluorescence spectrum of a narrow-line single-molecule transducer, fused 5,15-(diphenyl)-10,20-(dibromo)porphyrin (fused-H2P) molecule, has been calculated by time-dependent density functional theory with the inclusion of both Franck-Condon and Herzberg-Teller contributions. Analytical transition dipole derivatives are used for the calculations of Herzberg-Teller terms to eliminate the possible errors caused by numerical differentials. The performance of different exchange-correlation functionals including B3LYP, omega B97X-D, and M06-2X has been examined. The comparison with the high-resolution experimental emission spectrum indicates that all three functionals can satisfactorily describe the fluorescence spectral profile, while omega B97X-D and M06-2X give slightly better excitation energy than B3LYP. Detailed analysis shows that the fluorescence spectrum is dominated by the Franck-Condon contribution, while the Herzberg-Teller term contributes mostly to its low energy tail. It is found that the size of the basis set has limited influence on the fluorescence spectrum, and a standard 6-31G(d, p) basis set is adequate for the purpose. The substitution of terthiophene side chains is found to have minor effects on the fluorescence spectrum. Our study provides unambitious assignments for all the vibronic structures in the experimental spectrum.

  • 100.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Quantum chemistry on Intel Xeon Phi processors: Opportunities and challenges2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
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