Change search
Refine search result
1234 1 - 50 of 157
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Ahlquist, Mårten S. G.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Marcos-Escartin, Rocio
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bicarbonate hydrogenation by iron: Effects of solvent and ligand on the mechanism2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
  • 2.
    Ahlquist, Mårten
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhan, Shaoqi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Modeling molecular water oxidation catalysts at interfaces2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
  • 3.
    Baryshnikov, Gleb V.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia..
    Sunchugashev, Dmitry A.
    Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia..
    Valiev, Rashid R.
    Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia..
    Minaev, Boris F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Vibronic absorption spectra of the angular fused bisindolo- and biscarbazoloanthracene blue fluorophores for OLED applications2018In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 513, p. 105-111Article in journal (Refereed)
    Abstract [en]

    An in-depth analysis of the vibronic absorption spectra for the recently synthesized blue-fluorescent OLED emitters bis[(1,2)(5,6)]indoloanthracene and biscarbazolo[3,4-a:3',4'-h]anthracene has been carried out computationally at the density functional theory level within the Franck-Condon approximation. These molecules are characterized by extended and rich electronic absorption spectra with most absorption bands being of vibronic origin. The first excited singlet state of bis[(1,2)(5,6)]indoloanthracene compound demonstrates a clear observable double-peak vibronic progression for two different active modes in the absorption spectrum, while the S-2 state is vibronically inactive. In contrast, for the larger biscarbazolo[3,4-a:3',4'-h]anthracene compound the S-0 -> S-2 transition demonstrates well-resolved intense vibronic bands which overlap the less intense progressions of few modes in the S-0 -> S-1 transition. We have also found, that even the higher-lying and very intense S-0 -> S-4 and S-0 -> S-5 transitions for bis[(1,2)(5,6)]indoloanthracene and biscarbazolo[3,4-a:3',4'-h]anthracene, respectively, are characterized by clear vibronic progressions in excellent agreement with experimental spectra.

  • 4.
    Baryshnikov, Gleb V.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Valiev, R. R.
    Natl Res Tomsk Polytech Univ, Res Sch Chem & Appl Biomed Sci, Lenin Ave 30, Tomsk 634050, Russia.;Univ Helsinki, Dept Chem, FIN-00014 Helsinki, Finland..
    Cherepanov, V. N.
    Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia..
    Karaush-Karmazin, N. N.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Minaeva, V. A.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Minaev, B. F.
    Bohdan Khmelnytsky 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.
    Aromaticity and photophysics of tetrasila- and tetragerma-annelated tetrathienylenes as new representatives of the hetero[8]circulene family2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 18, p. 9246-9254Article in journal (Refereed)
    Abstract [en]

    The electronic structure, absorption and emission spectra, aromaticity and photophysical behavior of the recently synthesized tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene compounds have been studied computationally. Both compounds demonstrate a specific bifacial aromaticity, which is unusual for hetero[8]circulenes; the inner eight-membered core sustains an expected strong paratropic magnetically-induced ring current, while the outer perimeter contains saturated Si(Et)(2) and Ge(Et)(2) moieties which break the conjugation between the thiophene rings. The overall magnetically-induced ring current for both studied circulenes is close to zero because of the strong local diatropic currents in each thiophene ring that compensate the paratropic counterpart. The electronic absorption and emission spectra of tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene demonstrate a clear visible vibronic progression. The 0-0 band is the most active one in the absorption spectra, while in the fluorescence spectra the 0-1 band composed of several normal vibrations is more intense compared with the 0-0 band in excellent agreement with experiment. Accounting for spin-orbit coupling effects, an analysis of the photophysical constants for the two compounds demonstrates: (1) a clear manifestation of the internal heavy atom effect on the inter-system crossing efficiency; (2) one to two order domination of non-radiative rates over the fluorescence rate; and (3) that the S-1-S-0 internal conversion is extremely slow and can not compete with the fluorescence, while the S-1-T-n inter-system crossing is a main deactivation channel of the S-1 excited state. These results provide new insight into the electronic structure and photophysics of tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene as novel standalone representatives of hetero[8]circulenes - tetraannelated derivatives of tetrathienylene.

  • 5. Baryshnikova, A. T.
    et al.
    Minaev, B. F.
    Baryshnikov, Gleb V.
    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.
    Computational study of the structure and magnetic properties of the weakly-coupled tetranuclear square-planar complex of Cu(II) with a tetraporphyrin sheet2019In: Inorganica Chimica Acta, ISSN 0020-1693, E-ISSN 1873-3255, Vol. 485, p. 73-79Article in journal (Refereed)
    Abstract [en]

    Owing to the fact that weakly-coupled Cu(II) complexes are potentially applicable in the fields of spintronics and single-molecule magnets we have studied one particularly conspicuous case – a tetranuclear square-planar complex of Cu(II) ions with a π-extended tetraporphyrin ligand (Tetrahedron, 2008, 64, 11433), the structural criteria of which, with very long distances between the paramagnetic centers, can sensibly define the exchange coupling constants and magnetic behaviour. We use the “broken symmetry” density functional theory formalism for various spin states (open-shell singlet, triplet and quintet states). The calculated value of the magnetic exchange integral corresponds to a very weak antiferromagnetic coupling between the neighboring Cu(II) ions (Jcalc = –1.48 cm−1(calculated) Jexp = −1.16 cm−1 (experiment)). The opposite Cu(II) ions are coupled ferromagnetically with an extremely small exchange constant (jcalc = 0.09 cm−1 (calculated) that corresponds to the open-shell singlet ground state of the following spin configuration↑↓↑↓. The exchange mechanism between the [Cu(n) + 4N] localized singly-occupied “magnetic” orbitals of the dxy(Cu) + 4sp2(N) nature indicates a diffuse non-zero overlap between them on the Carbon atoms of the organic ligand. The numerical analysis of atomic spin densities and corresponding decomposition coefficients for the singly-occupied “magnetic” orbitals confirm the proposed exchange mechanism. This superexchange pathway is mediated by the in-plane sp2-hybrid orbitals of the Carbon atoms that couple four [Cu + 4N] fragments by the σ-bond system. For more detailed characterization of the target system a topological analysis of electron density distributions in the high-spin quintet states has been carried out using the Bader's method “quantum theory of atoms in molecules”.

  • 6.
    Bergstrand, Jan
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Liu, Qingyun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Huang, Bingru
    Würth, Christian
    Resch-Genger, Ute
    Zhan, Qiuqiang
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Ågren, Hans
    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.
    On the decay time of upconversion luminescence2019In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 11, no 11, p. 4959-4969Article in journal (Refereed)
    Abstract [en]

    In this study, we systematically investigate the decay characteristics of upconversion luminescence (UCL) under anti-Stokes excitation through numerical simulations based on rate-equation models. We find that a UCL decay profile generally involves contributions from the sensitizer's excited-state lifetime, energy transfer and cross-relaxation processes. It should thus be regarded as the overall temporal response of the whole upconversion system to the excitation function rather than the intrinsic lifetime of the luminescence emitting state. Only under certain conditions, such as when the effective lifetime of the sensitizer's excited state is significantly shorter than that of the UCL emitting state and of the absence of cross-relaxation processes involving the emitting energy level, the UCL decay time approaches the intrinsic lifetime of the emitting state. Subsequently, Stokes excitation is generally preferred in order to accurately quantify the intrinsic lifetime of the emitting state. However, possible cross-relaxation between doped ions at high doping levels can complicate the decay characteristics of the luminescence and even make the Stokes-excitation approach fail. A strong cross-relaxation process can also account for the power dependence of the decay characteristics of UCL.

  • 7.
    Brumboiu, Iulia
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Korea Adv Inst Sci & Technol, Dept Chem, Daejeon 34141, South Korea..
    Eriksson, Olle
    Uppsala Univ, Dept Phys & Astron, SE-75120 Uppsala, Sweden..
    Norman, P.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Atomic photoionization cross sections beyond the electric dipole approximation2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 4, article id 044306Article in journal (Refereed)
    Abstract [en]

    A methodology is developed to compute photoionization cross sections beyond the electric dipole approximation from response theory, using Gaussian type orbitals and plane waves for the initial and final states, respectively. The methodology is applied to compute photoionization cross sections of atoms and ions from the first four rows of the periodic table. Analyzing the error due to the plane wave description of the photoelectron, we find kinetic energy and concomitant photon energy thresholds above which the plane wave approximation becomes applicable. The correction introduced by going beyond the electric dipole approximation increases with photon energy and depends on the spatial extension of the initial state. In general, the corrections are below 10% for most elements, at a photon energy reaching up to 12 keV. 2019 Author(s).

  • 8.
    Brumboiu, Iulia
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Haldar, Soumyajyoti
    Luder, Johann
    Eriksson, E.
    Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
    Herper, Heike C.
    Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
    Brena, Barbara
    Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
    Sanyal, Biplab
    Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
    Ligand Effects on the Linear Response Hubbard U: The Case of Transition Metal Phthalocyanines2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 14, p. 3214-3222Article in journal (Refereed)
    Abstract [en]

    It is established that density functional theory (DFT) + U is a better choice compared to DFT for describing the correlated electron metal center in organometallics. The value of the Hubbard U parameter may be determined from linear response, either by considering the response of the metal site alone or by additionally considering the response of other sites in the compound. We analyze here in detail the influence of ligand shells of increasing size on the U parameter calculated from the linear response for five transition metal phthalocyanines. We show that the calculated multiple-site U ligand atoms that are mainly responsible for this difference are is larger than the single-site U by as much as 1 eV and the ligand atoms that are mainly responsible for this difference are the isoindole nitrogen atoms directly bonded to the central metal atom. This suggests that a different U value may be required for computations of chemisorbed molecules compared to physisorbed and gas-phase cases.

  • 9. Carravetta, V.
    et al.
    De Abreu Gomes, A. H.
    Monti, S.
    Mocellin, A.
    Marinho, R. R. T.
    Björneholm, O.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Naves De Brito, A.
    PH-dependent X-ray Photoelectron Chemical Shifts and Surface Distribution of Cysteine in Aqueous Solution2019In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, no 17, p. 3776-3785Article in journal (Refereed)
    Abstract [en]

    The distribution and protonation states of amino acids in water droplets are of considerable concern in studies on the formation of clouds in the atmosphere as well as in many biological contexts. In the present work we use the amino acid cysteine as a prototypical example and explore the protonation states of this molecule in aqueous solution, which are strongly affected by the acidity of the environment and also can show different distributions between surface and bulk. We use a combination of X-ray photoelectron chemical shift measurements, density functional theory calculations of the shifts, and reactive force field molecular dynamics simulations of the underlying structural dynamics. We explore how the photoelectron spectra distinctly reflect the different protonation states that are generated by variation of the solution acidity and how the distribution of these protonation states can differ between bulk and surface regions. At specific pH values, we find that the distribution of the cysteine species at the surface is quite different from that in bulk, in particular, for the appearance in the surface region of species which do not exist in bulk. Some ramifications of this finding are discussed.

  • 10.
    Ceolin, Denis
    et al.
    Synchrotron SOLEIL, F-91191 Gif Sur Yvette, France..
    Liu, Ji-Cai
    North China Elect Power Univ, Dept Math & Phys, Beijing 102206, Peoples R China..
    da Cruz, Vinicius Vaz
    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. Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
    Journel, Loic
    Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France..
    Guillemin, Renaud
    Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France..
    Marchenko, Tatiana
    Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France..
    Kushawaha, Rajesh K.
    Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France..
    Piancastelli, Maria Novella
    Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden.;Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France..
    Puettner, Ralph
    Free Univ Berlin, Fachbereich Phys, D-14195 Berlin, Germany..
    Simon, Marc
    Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France..
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Synchrotron SOLEIL, F-91191 Gif Sur Yvette, France.;Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia..
    Recoil-induced ultrafast molecular rotation probed by dynamical rotational Doppler effect2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 11, p. 4877-4882Article in journal (Refereed)
    Abstract [en]

    Observing and controlling molecular motion and in particular rotation are fundamental topics in physics and chemistry. To initiate ultrafast rotation, one needs a way to transfer a large angular momentum to the molecule. As a showcase, this was performed by hard X-ray C1s ionization of carbon monoxide accompanied by spinning up the molecule via the recoil "kick" of the emitted fast photoelectron. To visualize this molecular motion, we use the dynamical rotational Doppler effect and an X-ray "pump-probe" device offered by nature itself: the recoil-induced ultrafast rotation is probed by subsequent Auger electron emission. The time information in our experiment originates from the natural delay between the C1s photoionization initiating the rotation and the ejection of the Auger electron. From a more general point of view, time-resolved measurements can be performed in two ways: either to vary the "delay" time as in conventional time-resolved pump-probe spectroscopy and use the dynamics given by the system, or to keep constant delay time and manipulate the dynamics. Since in our experiment we cannot change the delay time given by the core-hole lifetime tau, we use the second option and control the rotational speed by changing the kinetic energy of the photoelectron. The recoil-induced rotational dynamics controlled in such a way is observed as a photon energy-dependent asymmetry of the Auger line shape, in full agreement with theory. This asymmetry is explained by a significant change of the molecular orientation during the core-hole lifetime, which is comparable with the rotational period.

  • 11. Chen, J.
    et al.
    Yang, J.
    Sun, Xianqiang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wang, Z.
    Cheng, X.
    Lu, W.
    Cai, X.
    Hu, C.
    Shen, X.
    Cao, P.
    Allosteric inhibitor remotely modulates the conformation of the orthestric pockets in mutant IDH2/R140Q2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, no 1, article id 16458Article in journal (Refereed)
    Abstract [en]

    Neomorphic mutation R140Q in the metabolic enzyme isocitrate dehydrogenase 2 (IDH2) is found to be a driver mutation in cancers. Recent studies revealed that allosteric inhibitors could selectively inhibit IDH2/R140Q and induce differentiation of TF-1 erythroleukemia and primary human AML cells. However, the allosteric inhibition mechanism is not very clear. Here, we report the results from computational studies that AGI-6780 binds tightly with the divalent cation binding helices at the homodimer interface and prevents the transition of IDH2/R140Q homodimer to a closed conformation that is required for catalysis, resulting in the decrease of the binding free energy of NADPHs. If the allosteric inhibitor is removed, the original open catalytic center of IDH2/R140Q will gradually reorganize to a quasi-closed conformation and the enzymatic activity might recover. Unlike IDH2/R140Q, AGI-6780 locks one monomer of the wild-type IDH2 in an inactive open conformation and the other in a half-closed conformation, which can be used to explain the selectivity of AGI-6780. Our results suggest that conformational changes are the primary contributors to the inhibitory potency of the allosteric inhibitor. Our study will also facilitate the understanding of the inhibitory and selective mechanisms of AG-221 (a promising allosteric inhibitor that has been approved by FDA) for mutant IDH2.

  • 12.
    Chen, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Leiden University, Leiden Observatory, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands.
    Formation of Covalently Bonded Polycyclic Aromatic Hydrocarbons in the Interstellar Medium2018In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 866, no 113Article in journal (Refereed)
    Abstract [en]

    Photo-/ion-induced ionization and dissociation processes are commonly observed for polycyclic aromatic hydrocarbon (PAH) molecules. This work performs theoretical studies of PAHs and their fragments. Molecular dynamics simulations in combination with static quantum chemical calculations reveal that following a single hydrogen atom loss, the fragments, PAH-H, are extremely reactive. They catch a neighbor molecule within picoseconds to form a covalently bonded large molecule regardless of orientations/angles and temperatures. We calculate the infrared spectra of the covalently bonded molecules, which indicate that such species could be the carrier of unidentified infrared emission bands. It also implies that regular PAHs might be less abundant in space than what is expected. 

  • 13.
    Chen, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Temperature effects on anharmonic infrared spectra of large compact polycyclic aromatic hydrocarbons2019In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 622, article id A152Article in journal (Refereed)
    Abstract [en]

    Aims. Large compact polycyclic aromatic hydrocarbon molecules (PAHs) present special interest in the astrochemical community. A key issue in analyses of large PAHs is understanding the effect that temperature and anharmonicity have on different vibrational bands, and thus interpreting the infrared (IR) spectra for molecules under various conditions. Methods. Because of the huge amount of interactions/resonances in large PAHs, no anharmonic IR spectrum can be produced with static/time-independent ab initio method, especially for the molecules with D6h symmetry, e.g., coronene and circumcoronene. In this work, we performed molecular dynamics simulations to generate anharmonic IR spectra of coronene and circumcoronene. Results. The method is validated for small PAHs, i.e., naphthalene and pyrene. We find that the semiempirical method PM3 produces accurate band positions with an error <5 cm(-1). Furthermore, we calculate the spectra at multiple temperatures and find a clear trend toward band shifting and broadening.

  • 14.
    Chen, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands.
    The Carrier of 3.3 mu m Aromatic Infrared Bands: Anharmonicity and Temperature Effects on Neutral PAHs2018In: Astrophysical Journal Supplement Series, ISSN 0067-0049, E-ISSN 1538-4365, Vol. 238, no 2, article id 18Article in journal (Refereed)
    Abstract [en]

    Anharmonic infrared (IR) spectra are crucial for the study of interstellar polycyclic aromatic hydrocarbon (PAH) molecules. This work aims to provide a comprehensive study of the features that may influence the accuracy of anharmonic IR spectra of PAHs so that a reliable spectrum that incorporates all necessary features for interpreting the observational IR spectra can be obtained. Six PAHs are investigated: naphthalene, anthracene, pyrene, chrysene, 9,10-dimethylanthracene, and 9,10-dihydroanthracene. The NIST spectra and high-resolution IR absorption spectra are utilized as the reference for the comparisons. The influences of different resonances and resonant thresholds are studied. Four methods for electronic structure calculations are tested. The quantitative comparisons indicate that for the NIST data, B3LYP/NO7D provides the best agreement with measured spectra concerning band positions and B3LYP/cc-pVTZ is superior in the description of the relative intensities. The importance of 1-3 Darling-Dennison resonances, which are required for generating triple combination bands, is investigated through a comparison to a high-resolution experimental spectrum. For interpreting the bandwidths and profiles of the observational spectra, the temperature effects are included through the Wand-Landau random walk technique. The comparisons between calculated high-temperature anharmonic and observational spectra indicate that small and compact PAHs might be responsible for the 3.3 mu m aromatic infrared bands.

  • 15.
    Chen, Tao
    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.
    Formation of polyynes and ring-polyyne molecules following fragmentation of polycyclic aromatic hydrocarbons2019In: Monthly notices of the Royal Astronomical Society, ISSN 0035-8711, E-ISSN 1365-2966, Vol. 486, no 2, p. 1875-1881Article in journal (Refereed)
    Abstract [en]

    In this work, we perform molecular dynamic (MD) simulations to investigate the stability and fragmentation processes of vibrationally excited linear polycyclic aromatic hydrocarbons (PAHs). The program of CP2K in combination with the semi-empirical method PM3 is utilized for the MD simulations. The simulations show that the formation of molecular hydrogens (H-2) is different than previous studies, in particular, different than compact PAHs. At high temperatures, linear PAHs tend to open aromatic rings and convert the sp(3) C-C or sp(2) C=C bonds to sp C C bonds by removing H-2; i.e. polyynes are formed in such process. Besides polyynes, PAHs attached with sp-bonded polyyne chains are commonly observed at high temperatures. We notice that due to the addition of flexible tails (polyynes), the ring-polyyne molecules do not dissociate for a long period of time at high temperatures. Such structures facilitate the molecules to survive in the harsh environment of the interstellar medium. In addition, the ring-polyyne structures induce dipole moments that could, in principle, be detected by radio astronomy.

  • 16.
    Chen, Tao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands..
    Mackie, Cameron
    Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands..
    Candian, Alessandra
    Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands..
    Lee, Timothy J.
    NASA, Ames Res Ctr, Moffett Field, CA 94035 USA..
    Tielens, Alexander G. G. M.
    Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands..
    Anharmonicity and the infrared emission spectrum of highly excited polycyclic aromatic hydrocarbons2018In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 618, article id A49Article in journal (Refereed)
    Abstract [en]

    Aims. Infrared (IR) spectroscopy is a powerful tool to study molecules in space. A key issue in such analyses is understanding the effect that temperature and anharmonicity have on different vibrational bands, and thus interpreting the IR spectra for molecules under various conditions. Methods. We combined second order vibrational perturbation theory and the Wang-Landau random walk technique to produce accurate IR spectra of highly excited polycyclic aromatic hydrocarbons. We fully incorporated anharmonic effects, such as resonances, overtones, combination bands, and temperature effects. Results. The results are validated against experimental results for the pyrene molecule (C16H10). In terms of positions, widths, and relative intensities of the vibrational bands, our calculated spectra are in excellent agreement with gas-phase experimental data.

  • 17.
    Chen, Tao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhen, J.
    Wang, Yin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linnartz, H.
    Tielens, A. G. G. M.
    Photodissociation processes of Bisanthenquinone cation2017In: Proceedings of the International Astronomical Union, ISSN 1743-9213, no S332, p. 353-359Article in journal (Refereed)
    Abstract [en]

    A systematic study, using ion trap time-of-flight mass spectrometry, is presented for the photo-dissociation processes of Bisanthenquinone (Bq) cations, C28H12O2+, a ketone substituted Polycyclic Aromatic Hydrocarbon (PAH). The Bq cation fragments through sequential loss of the two neutral carbonyl (CO) units upon laser (626nm) irradiation, resulting in a PAH-like derivative C26H12+. Upon further irradiation, C26H12+ exhibits both stepwise dehydrogenation and C2/C2H2 loss fragmentation channels. Quantum chemistry calculations reveal a detailed picture for the first CO-loss, which involves a transition state with a barrier of ∼ 3.4 eV, which is lower than the energy required for the lowest H-loss pathway (∼ 5.0 eV). The barrier for the second CO-loss is higher (∼ 4.9 eV). The subsequent loss of this unit changes the Bq geometry from a planar to a bent one. It is concluded that the photodissociation mechanism of the substituted PAH cations studied here is site selective in the substituted subunit. This work also shows that an acetone substituted PAH cation is not photo-stable upon irradiation. 

  • 18. Chen, X.
    et al.
    Zhu, L.
    Wang, D.
    Zou, Q.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Chen, W.
    A unimolecular platform based on diarylethene with multiple stimuli-gated photochromism2019In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 164, p. 91-96Article in journal (Refereed)
    Abstract [en]

    The gated photochromic systems have attracted great interest in scientific researches due to their merits in the opto-electronic fields, whereas the multi-stimuli gating function in a unimolecular platform has rarely been addressed. Herein, a new strategy to realize multi-stimuli gated photochromic function was devised relying on a simple Schiff-based diarylethene derivative. The compound shows no photoswitching properties in solution under irradiation with any wavelength of light. It is noteworthy that mecury(II) ions, water and protons can trigger its photo-reactivity independently with different absorption changes, respectively. Therefore, a molecular logic circuit with four inputs, including mecury(II) ions, water, protons and UV light, was fabricated on the basis of the unimolecular platform, suggesting promise for application in multi-controlled photoswitchings. These results could be valuable for the further development of photoswitchings with multiple stimuli responses.

  • 19.
    Cornelissen, Tim D.
    et al.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Urbanaviciute, Indre
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Kemerink, Martijn
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Kinetic Monte Carlo simulations of organic ferroelectrics2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 3, p. 1375-1383Article in journal (Refereed)
    Abstract [en]

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

  • 20. Céolin, Denis
    et al.
    Liu, Ji-Cai
    Vaz da Cruz, Vinicius
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Journel, Loïc
    Guillemin, Renaud
    Marchenko, Tatiana
    Kushawaha, Rajesh K.
    Piancastelli, Maria-Novella
    Püttner, Ralph
    Simon, Marc
    Gel'mukhanov, Faris
    Recoil-induced ultrafast molecular rotation probed by dynamical rotational Doppler effectManuscript (preprint) (Other academic)
    Abstract [en]

    Observing and controlling molecular motion, and in particular rotation,is a fundamental topic in physics and chemistry. In order toinitiate ultrafast rotation, one needs a way to transfer a large angularmomentum to the molecule. As a showcase, this was performedby hard x-ray C1s ionization of carbon monoxide, accompanied byspinning-up the molecule via the recoil “kick” of the emitted fast photoelectron.To visualize this molecular motion, we use the dynamicalrotational Doppler effect and an X-ray “pump-probe” device offeredby nature itself: the recoil-induced ultrafast rotation is probed by subsequentAuger electron emission. The time information in our experimentorigins from the natural delay between the C1s photoionizationinitiating the rotation and the ejection of the Auger electron. From amore general point of view, time-resolved measurements can be performedin two ways: either to vary the "delay" time as in conventionaltime-resolved pump-probe spectroscopy and to use the dynamicsgiven by the system, or to keep constant "delay" time and to manipulatethe dynamics. Since in our experiment we cannot change the delaytime given by the core-hole lifetime $\tau$, we use the second optionand control the rotational speed by changing the kinetic energy of thephotoelectron. The recoil-induced rotational dynamics controlled insuch a way is observed as a photon-energy dependent asymmetryof the Auger lineshape, in full agreement with theory. This asymmetryis explained by a significant change of the molecular orientationduring the core-hole lifetime, which is comparable with the rotationalperiod.

  • 21.
    da Cruz, Vinicius Vaz
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Royal Inst Technol, Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Ertan, Emelie
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Ignatova, Nina
    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..
    Couto, Rafael C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Polyutov, Sergey
    Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    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. Royal Inst Technol, Theoret Chem & Biol, S-10691 Stockholm, Sweden.
    Anomalous polarization dependence in vibrationally resolved resonant inelastic x-ray scattering of H2O2018In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 98, no 1, article id 012507Article in journal (Refereed)
    Abstract [en]

    It is well established that different electronic channels, in resonant inelastic x-ray scattering (RIXS), display different polarization dependences due to different orientations of their corresponding transition dipole moments in the molecular frame. However, this effect does not influence the vibrational progression in the Franck-Condon approximation. We have found that the transition dipole moments of core excitation and deexcitation experience ultrafast rotation during dissociation in the intermediate core-excited state. This rotation makes the vibrational progression in RIXS sensitive to the polarization of the x-ray photons. We study the water molecule, in which the effect is expressed in RIXS through the dissociative core-excited state where the vibrational scattering anisotropy is accompanied also by violation of parity selection rules for the vibrations.

  • 22.
    da Cruz, Vinicius Vaz
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Lab Nonlinear Opt & Spect, Krasnoyarsk 660041, Russia.
    Eckert, Sebastian
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Iannuzzi, Marcella
    Univ Zurich, Phys Chem Inst, CH-8057 Zurich, Switzerland..
    Ertan, Emelie
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Pietzsch, Annette
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Couto, Rafael C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Niskanen, Johannes
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Turku, Dept Phys & Astron, FI-20014 Turunyliopisto, Finland..
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Dantz, Marcus
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Schmitt, Thorsten
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Lu, Xingye
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    McNally, Daniel
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Jay, Raphael M.
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Kimberg, Victor
    Foehlisch, Alexander
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Odelius, Michael
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scattering2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 1013Article in journal (Refereed)
    Abstract [en]

    Local probes of the electronic ground state are essential for understanding hydrogen bonding in aqueous environments. When tuned to the dissociative core-excited state at the O1s pre-edge of water, resonant inelastic X-ray scattering back to the electronic ground state exhibits a long vibrational progression due to ultrafast nuclear dynamics. We show how the coherent evolution of the OH bonds around the core-excited oxygen provides access to high vibrational levels in liquid water. The OH bonds stretch into the long-range part of the potential energy curve, which makes the X-ray probe more sensitive than infra-red spectroscopy to the local environment. We exploit this property to effectively probe hydrogen bond strength via the distribution of intramolecular OH potentials derived from measurements. In contrast, the dynamical splitting in the spectral feature of the lowest valence-excited state arises from the short-range part of the OH potential curve and is rather insensitive to hydrogen bonding.

  • 23.
    da Cruz, Vinicius Vaz
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Couto, Rafael C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fedotov, Daniil A.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia..
    Rehn, Dirk R.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Savchenko, Viktoriia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Norman, Patrick
    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. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Polyutov, Sergey
    Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Niskanen, Johannes
    Univ Turku, Dept Phys & Astron, FI-20014 Turun, Finland.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Eckert, Sebastian
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Jay, Raphael M.
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Schmitt, Thorsten
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Pietzsch, Annette
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Foehlisch, Alexander
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Kimberg, Victor
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Nuclear dynamics in resonant inelastic X-ray scattering and X-ray absorption of methanol2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 23, article id 234301Article in journal (Refereed)
    Abstract [en]

    We report on a combined theoretical and experimental study of core-excitation spectra of gas and liquid phase methanol as obtained with the use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). The electronic transitions are studied with computational methods that include strict and extended second-order algebraic diagrammatic construction [ADC(2) and ADC(2)-x], restricted active space second-order perturbation theory, and time-dependent density functional theory-providing a complete assignment of the near oxygen K-edge XAS. We show that multimode nuclear dynamics is of crucial importance for explaining the available experimental XAS and RIXS spectra. The multimode nuclear motion was considered in a recently developed "mixed representation" where dissociative states and highly excited vibrational modes are accurately treated with a time-dependent wave packet technique, while the remaining active vibrational modes are described using Franck-Condon amplitudes. Particular attention is paid to the polarization dependence of RIXS and the effects of the isotopic substitution on the RIXS profile in the case of dissociative core-excited states. Our approach predicts the splitting of the 2a RIXS peak to be due to an interplay between molecular and pseudo-atomic features arising in the course of transitions between dissociative core- and valence-excited states. The dynamical nature of the splitting of the 2a peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical results are in good agreement with our liquid phase measurements and gas phase experimental data available from the literature.

  • 24.
    Daniel, Quentin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Duan, Lele
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Timmer, Brian J. J.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Chen, Hong
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Luo, Xiaodan
    Peking Univ, Coll Chem & Mol Engn, Beijing 100871, Peoples R China..
    Ambre, Ram
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Wang, Ying
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Zhang, Biaobiao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Zhang, Peili
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Wang, Lei
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Li, Fusheng
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Sun, Junliang
    Peking Univ, Coll Chem & Mol Engn, Beijing 100871, Peoples R China..
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Water Oxidation Initiated by In Situ Dimerization of the Molecular Ru(pdc) Catalyst2018In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 8, no 5, p. 4375-4382Article in journal (Refereed)
    Abstract [en]

    The mononuclear ruthenium complex [Ru(pdc)L-3] (H(2)pdc = 2,6-pyridinedicarboxylic acid, L = N-heterocycles such as 4-picoline) has previously shown promising catalytic efficiency toward water oxidation, both in homogeneous solutions and anchored on electrode surfaces. However, the detailed water oxidation mechanism catalyzed by this type of complex has remained unclear. In order to deepen understanding of this type of catalyst, in the present study, [Ru(pdc)(py)(3)] (py = pyridine) has been synthesized, and the detailed catalytic mechanism has been studied by electrochemistry, UV-vis, NMR, MS, and X-ray crystallography. Interestingly, it was found that once having reached the Ru-IV state, this complex promptly formed a stable ruthenium dimer [Ru-III(pdc)(py)(2)-O-Ru-IV(pdc)(py)(2)](+). Further investigations suggested that the present dimer, after one pyridine ligand exchange with water to form [Ru-III(pdc)(py)(2)-O-Ru-IV(pdc)(py)(H2O)](+), was the true active species to catalyze water oxidation in homogeneous solutions.

  • 25.
    Duan, Sai
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Synerget Innovat Ctr Quantum Informat & Quantum P, Hefei 230026, Anhui, Peoples R China..
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre. Kaunas Univ Technol, Dept Phys, LT-51368 Kaunas, Lithuania..
    Tian, Guangjun
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Hebei, Peoples R China..
    Luo, Yi
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Synerget Innovat Ctr Quantum Informat & Quantum P, Hefei 230026, Anhui, Peoples R China..
    Optomagnetic Effect Induced by Magnetized Nanocavity Plasmon2019In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 35, p. 13795-13798Article in journal (Refereed)
    Abstract [en]

    We propose a new type of optomagnetic effect induced by a highly confined plasmonic field in a nanocavity. It is shown that a very large dynamic magnetic field can be generated as the result of the inhomogeneity of nanocavity plasmons, which can directly activate spin-forbidden transitions in molecules. The dynamic optomagnetic effects on optical transitions between states of different spin multiplicities are illustrated by first-principles calculations for C-60. Remarkably, the intensity of spin forbidden singlet-to-triplet transitions can even be stronger than that of singlet-to-singlet transitions when the spatial distribution of plasmon is comparable with the molecular size. This approach not only offers a powerful optomagnetic means to rationally fabricate molecular excited states with different multiplicities but also provides a groundbreaking concept of the light-matter interaction that could lead to the observation of new physical phenomena and the development of new techniques.

  • 26.
    Eckert, Sebastian
    et al.
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    da Cruz, Vinicius Vaz
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    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.
    Ertan, Emelie
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden.
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Polyutov, Sergey
    Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia..
    Couto, Rafael C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Dantz, Marcus
    PSI, Res Dept Synchrotron Radiat & Nanotechnol, CH-5232 Villigen, Switzerland..
    Kennedy, Brian
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Schmitt, Thorsten
    PSI, Res Dept Synchrotron Radiat & Nanotechnol, CH-5232 Villigen, Switzerland..
    Pietzsch, Annette
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Foehlisch, Alexander
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    One-dimensional cuts through multidimensional potential-energy surfaces by tunable x rays2018In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 97, no 5, article id 053410Article in journal (Refereed)
    Abstract [en]

    The concept of the potential-energy surface (PES) and directional reaction coordinates is the backbone of our description of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to (near) degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close-lying vibrational levels. We show here that resonant inelastic x-ray scattering (RIXS) constitutes an ideal probe for revealing one-dimensional cuts through the ground-state PES of molecular systems, even far away from the equilibrium geometry, where the independent-mode picture is broken. We strictly link the center of gravity of close-lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one-dimensional Hamiltonian along the propagation coordinate of the core-excited wave packet. This concept, combined with directional and site selectivity of the core-excited states, allows us to experimentally extract cuts through the ground-state PES along three complementary directions for the showcase H2O molecule.

  • 27. Eckert, Sebastian
    et al.
    Vaz da Cruz, Vinicius
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Polyutov, Sergey
    Carvalho Couto, Rafael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    Odelius, Michael
    Föhlisch, Alexander
    One-dimensional cuts through multidimensional potential energy surfaces by tunable X-rays2018Manuscript (preprint) (Other academic)
    Abstract [en]

    The concept of the potential-energy surface (PES) and directional reaction coordinates is the backbone of ourdescription of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to (near) degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close-lying vibrational levels. We show here that resonant inelastic x-ray scattering (RIXS) constitutes an ideal probe for revealing one-dimensional cuts through the ground-state PES of molecular systems, even far away from the equilibrium geometry, where the independent-mode picture is broken. We strictly link the center of gravity of close-lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one-dimensional Hamiltonian along the propagation coordinate of the core-excited wave packet. This concept, combined with directional and site selectivity of the core-excited states, allows us to experimentally extract cuts through the ground-state PES along three complementary directions for the showcase H2O molecule.

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

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

  • 29.
    Ertan, Emelie
    et al.
    Stockholm university.
    Savchenko, Viktoriia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Federal University.
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Federal University.
    da Cruz, Vinicius Vaz
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Couto, Rafael C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Eckert, Sebastian
    Institut für Physik und Astronomie, Universität Potsdam.
    Fondell, Mattis
    Dantz, Marcus
    Research Department Synchrotron Radiation and Nanotechnology, Paul Scherrer Institut.
    Kennedy, Brian
    Institute for Methods and Instrumentation in Synchrotron Radiation Research G- ISRR, Helmholtz-Zentrum Berlin für Materialien und Energie.
    Schmitt, Thorsten
    Research Department Synchrotron Radiation and Nanotechnology, Paul Scherrer Institut.
    Pietzsch, Annette
    Institute for Methods and Instrumentation in Synchrotron Radiation Research G- ISRR, Helmholtz-Zentrum Berlin für Materialien und Energie.
    Föhlisch, Alexander
    Institut für Physik und Astronomie, Universität Potsdam.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Odelius, Michael
    Stockholm university.
    Kimberg, Victor
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ultrafast dissociation features in RIXS spectra of the water molecule2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)
    Abstract [en]

    In this combined theoretical and experimental study we report on an analysis of the resonant inelastic X-ray scattering spectra (RIXS) of gas phase water via the lowest dissociative core-excited state |1sO-14a11〉. We focus on the spectral feature near the dissociation limit of the electronic ground state. We show that the narrow atomic-like peak consists of the overlapping contribution from the RIXS channels back to the ground state and to the first valence excited state |1b1-14a11〉 of the molecule. The spectral feature has signatures of ultrafast dissociation (UFD) in the core-excited state, as we show by means of ab initio calculations and time-dependent nuclear wave packet simulations. We show that the electronically elastic RIXS channel gives substantial contribution to the atomic-like resonance due to the strong bond length dependence of the magnitude and orientation of the transition dipole moment. By studying the RIXS for an excitation energy scan over the core-excited state resonance, we can understand and single out the molecular and atomic-like contributions in the decay to the lowest valence-excited state. Our study is complemented by a theoretical discussion of RIXS in the case of the isotope substituted water (HDO and D2O) where the nuclear dynamics is significantly affected by the heavier fragments' mass.

  • 30.
    Fahleson, Tobias
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Derivation and application of response functions for nonlinear absorption and dichroisms2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is titled ’Derivation and application of response functions for nonlinear absorption and dichroisms’ and was written by Tobias Fahleson at the Division of Theoretical Chemistry & Biology at KTH Royal Institute of Technology in Sweden. It explores and expands upon theoretical means of quantifying a number of nonlinear spectroscopies, including two-photon absorption, resonant inelastic x-ray scattering, Jones birefringence, and magnetic circular dichroism. Details are provided for the derivation and program implementation of complex-valued (damped) cubic response functions that have been implemented in the quantum chemistry package DALTON [1], based on working equations formulated for an approximate-state wave function. This is followed by an assessment of the implementation. It is demonstrated how two-photon absorption (TPA) can be described either through second-order transition moments or the damped cubic response function. A set of illustrative TPA profiles are produced for smaller molecules. In addition, resonant inelastic x-ray scattering (RIXS) is explored in a similar manner as two-photon absorption. It is shown for small systems how RIXS spectra may be obtained using a reduced form of the cubic response function. Linear birefringences are investigated for noble gases, monosubstituted benzenes, furan homologues, and liquid acetonitrile. Regarding the noble gases, the Jones effect is shown to be proportional to a power series with respect to atomic radial sizes. For monosubstituted benzenes, a linear relation between the Jones birefringence and the empirical para-Hammett constant as well as the permanent electric dipole moment is presented. QM/MM protocols are applied for a pure acetonitrile liquid, including polarizable embedding and polarizable-density embedding models. The final chapter investigates magnetically induced circular dichroism (MCD). A question regarding relative stability of the first set of excited states for DNA-related molecular systems is resolved through MCD by exploiting the signed nature of circular dichroisms. Furthermore, to what extent solvent contributions affect MCD spectra and the effect on uracil MCD spectrum due to thionation is studied.

  • 31.
    Fahleson, Tobias
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Olsen, Jogvan Magnus Haugaard
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Rizzo, Antonio
    A QM/MM and QM/QM/MM study of Kerr, Cotton-Mouton and Jones linear birefringences in liquid acetonitrile2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 5, p. 3831-3840Article in journal (Refereed)
    Abstract [en]

    QM/MM and QM/QM/MM protocols are applied to the ab initio study of the three linear birefringences Kerr, Cotton-Mouton, and Jones, as shown by acetonitrile in the gas and pure liquid phases. The relevant first-order properties as well as linear, quadratic, and cubic frequency-dependent response functions were computed using time-dependent Kohn-Sham density-functional theory with use of the standard CAM-B3LYP functional. In the liquid phase, a series of room temperature (293.15 K) molecular dynamics snapshots were selected, for which averaged values of the observables were obtained at an optical wavelength of 632.8 nm. The birefringences were computed for electric and magnetic induction fields corresponding to the laboratory setup previously employed by T. Roth and G. L. J. A. Rikken in Phys. Rev. Lett., 2000, 85, 4478. Under these conditions, acetonitrile is shown to exhibit a weak Jones response-in fact roughly 6.5 times smaller than the limit of detection of the apparatus employed in the measurements mentioned above. A comparison is made with the corresponding gas-phase results and an assessment is made of the index of measurability, estimating the degree of overlap of the three birefringences in actual measurements. For acetonitrile, it is shown that this index is a factor of 3.6 and 6.7 larger than that of methylcyclopentadienyl-Mn-tricarbonyl and cyclohexadienyl-Fe-tricarbonyl, respectively-two compounds reported in Phys. Rev. Lett., 2000, 85, 4478 to exhibit a strong Jones signal.

  • 32.
    Fu, Yao
    et al.
    Zhejiang Univ, Ctr Chem High Performance & Novel Mat, Dept Chem, Hangzhou 310027, Zhejiang, Peoples R China. u, Yao.
    Kang, Zhengzhong
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Zhejiang Univ, Dept Chem, Hangzhou 310027, Zhejiang, Peoples R China.
    Yin, Jinglin
    Cao, Weicheng
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wang, Qi
    Kong, Xueqian
    Duet of Acetate and Water at the Defects of Metal-Organic Frameworks2019In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 19, no 3, p. 1618-1624Article in journal (Refereed)
    Abstract [en]

    Metal-organic frameworks (MOFs) are porous crystalline materials with promising applications in molecular adsorption, separation, and catalysis. It has been discovered recently that structural defects introduced unintentionally or by design could have a significant impact on their properties. However, the exact chemical composition and structural evolution under different conditions at the defects are still under debate. In this study, we performed multidimensional solid-state nuclear magnetic resonance (SSNMR) coupled with computer simulations to elucidate an important scenario of MOF defects, uncovering the dynamic interplay between residual acetate and water. Acetate, as a defect modulator, and water, as a byproduct, are prevalent defect-associated species, which are among the key factors determining the reactivity and stability of defects. We discovered that acetate molecules coordinate to a single metal site monodentately and pair with water at the neighboring position. The acetates are highly flexible, which undergo fast libration as well as a slow kinetic exchange with water through dynamic hydrogen bonds. The dynamic processes under variable temperatures and different hydration levels have been quantitatively analyzed across a broad time scale from microseconds to seconds. The integration of SSNMR and computer simulations allows a precision probe into defective MOF structures with intrinsic dynamics and disorder.

  • 33. Giussani, Angelo
    et al.
    Farahani, Pooria
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Martinez-Munoz, Daniel
    Lundberg, Marcus
    Lindh, Roland
    Roca-Sanjuan, Daniel
    Molecular Basis of the Chemiluminescence Mechanism of Luminol2019In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 25, no 20, p. 5202-5213Article in journal (Refereed)
    Abstract [en]

    Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.

  • 34.
    Guanglin, Kuang
    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. College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan, 475004P. R. China.
    Mechanistic Insight into the Binding Profile of DCVJ and alpha-Synuclein Fibril Revealed by Multiscale Simulations2019In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 10, no 1, p. 610-617Article in journal (Refereed)
    Abstract [en]

    Parkinson's disease (PD) is a serious neuro-degenerative disease and is characterized by abnormal alpha-synuclein (alpha-syn) accumulation in Lewy bodies (LB) and 2 Lewy neurites (LN), which makes alpha-syn an important imaging target for PD. An imaging probe that quantifies fibrillar alpha-syn can enhance the clinical diagnosis of PD and can also be used to evaluate the efficacy of therapeutics aimed at reducing the abnormal aggregation of the alpha-syn fibril in the brain. In this paper, we study the binding profile of fibrillar alpha-syn with a fluorescent probe 4-(dicyanovinyl)julolidine (DCVJ), which is being explored for identifying alpha-syn imaging agents. A multiscale simulation workflow including molecular docking, molecular dynamics, metadynamics, and QM/MM calculations was implemented. We find that DCVJ can bind to multiple sites of alpha-syn which are located either at the surface or in the core. Free energy calculations using implicit solvent models reveal that the most favorable binding mode for DCVJ is associated with the core binding site and is further confirmed by metadyamics simulation. Besides, a dynamic binding pathway is discovered, which reveals that DCVJ binds gradually into the core of the fibril passing through several intermediate states. The conformational arrest of the dicyano vinyl group in the fibrillar environment could explain the reason behind the fibril-specific fluorescence of DCVJ. Furthermore, based on hybrid QM/MM calculations, the molecular geometry of the dicyano vinyl group is found to be environment specific which explains why DCVJ serves as a staining agent for such fibrillar-like environments. Our results could be helpful for elucidating the binding mechanism of imaging tracers with the fibrillar form of alpha-syn and explain their fibrillar-specific optical properties, a knowledge that in turn can be used to guide the design and development of compounds with higher affinity and selectivity for alpha-syn using structure-based strategies.

  • 35. Gusev, A. N.
    et al.
    Shul'gin, V. F.
    Braga, E. V.
    Nemec, I.
    Minaev, Boris F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Trávníček, Z.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
    Eremenko, I. L.
    Lyssenko, K. A.
    Linert, W.
    Synthesis and photophysical properties of Zn(II) Schiff base complexes possessing strong solvent-dependent solid-state fluorescence2018In: Polyhedron, ISSN 0277-5387, E-ISSN 1873-3719, Vol. 155, p. 202-208Article in journal (Refereed)
    Abstract [en]

    The present article reports on the syntheses, crystal structures and luminescence properties of three solvate forms of a zinc(II) complex containing 4-{(E)-[(2-fluorophenyl)imino]methyl}-5-methyl-2-phenyl-2,4-dihydro-3H-pyrazol-3-one (HL). The reaction of zinc(II)acetate with the HL ligand in ethanol and acetonitrile led to the formation of two solvate analogues [Zn(L)2]·Solv (Solv – ethanol (1) and acetonitrile (2)). The properties of the [Zn(L)2]·Solv complexes were investigated by UV–Vis absorption and fluorescence emission spectroscopy, and the density functional theory calculations. Bader's topological analysis was performed to investigate the electronic peculiarities of Zn(II) polyhedra and non-covalent interactions within crystal packing of studied solvates.

  • 36.
    Gusev, Alexey
    et al.
    Russian Acad Sci, NS Kurnakov Inst Gen & Inorgan Chem, Moscow 119991, Russia. ryukova, Mariya.
    Braga, Elena
    Zamnius, Ekaterina
    Kiskin, Mikhail
    Kryukova, Mariya
    Baryshnikova, Alina
    Minaev, Boris F.
    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. Bohdan Khmelnytsky 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.
    Linert, Wolfgang
    Structure and excitation-dependent emission of novel zinc complexes with pyridyltriazoles2019In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 9, no 38, p. 22143-22152Article in journal (Refereed)
    Abstract [en]

    A series of Zn(ii) complexes with 5-(4-R-phenyl)-3-(pyridin-2-yl)-1,2,4-triazoles have been synthesized and subsequently characterized by single crystal X-ray diffraction, H-1-NMR, FT-IR spectroscopy, elemental analyses, ESI-MS, and PXRD. The X-ray diffraction analyses revealed that the complexes have a similar molecular structure and their supramolecular frameworks are constructed by hydrogen bonds and pi center dot center dot center dot pi interaction scaffolds. Upon irradiation with UV light, the studied complexes display deep blue emission at 396-436 nm in the solid state. The compounds show an unexpected excitation-dependent emission phenomenon which is detected by a change in the emission color (from blue to yellow) upon increase of the excitation wavelength. The conducted quantum-chemical calculations indicate that supramolecular differences in the single-crystal architecture of the synthesized complexes play a crucial role for this photophysical behaviour.

  • 37.
    Gusev, Alexey N.
    et al.
    Russian Acad Sci, NS Kurnakov Inst Gen & Inorgan Chem, Moscow 119991, Russia..
    Kiskin, Mikhail A.
    Russian Acad Sci, NS Kurnakov Inst Gen & Inorgan Chem, Moscow 119991, Russia..
    Braga, Elena V.
    Russian Acad Sci, NS Kurnakov Inst Gen & Inorgan Chem, Moscow 119991, Russia..
    Chapran, Marian
    Lodz Univ Technol, Dept Mol Phys, Zeromskiego 116, PL-90924 Lodz, Poland..
    Wiosna-Salyga, Gabriela
    Lodz Univ Technol, Dept Mol Phys, Zeromskiego 116, PL-90924 Lodz, Poland..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia..
    Minaeva, Valentina A.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Minaev, Boris F.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Ivaniuk, Khrystyna
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Stakhira, Pavlo
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia..
    Linert, Wolfgang
    Vienna Univ Technol, Inst Appl Synthet Chem, Getreidemarkt 9-163 AC, A-1060 Vienna, Austria..
    Novel Zinc Complex with an Ethylenediamine Schiff Base for High-Luminance Blue Fluorescent OLED Applications2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 18, p. 11850-11859Article in journal (Refereed)
    Abstract [en]

    To explore the photophysical properties of coordination compounds with bright blue fluorescence, an azomethin-zinc complex was synthesized and characterized by various techniques (elemental analysis, thermogravimetry, and IR-mass-spectroscopy). The crystal structure was determined by X-ray diffraction analysis. Through thermal characterization, this complex was proved to have good thermal stability. Photoluminescence spectra were recorded, both in solution and in the solid state, and the complexes showed noteworthy photoluminescence with a maximum in the blue region. The results of time-dependent density functional theory calculations indicated that the origin of luminescence for the title complex is a combination of monomer and excimer emissions. The light emission performance of the zinc complex in organic light emitting diodes was investigated, and the results indicated superior electroluminescence properties as a blue fluorescent light source (max. brightness 17 000 cd/m(2), max. EQE = 5%).

  • 38. Hodecker, M.
    et al.
    Rehn, Dirk Robert
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dreuw, A.
    Algebraic-diagrammatic construction scheme for the polarization propagator including ground-state coupled-cluster amplitudes. II. Static polarizabilities2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 17, article id 174105Article in journal (Refereed)
    Abstract [en]

    The modification of the algebraic-diagrammatic construction (ADC) scheme for the polarization propagator using ground-state coupled-cluster (CC) instead of Møller-Plesset (MP) amplitudes, referred to as CC-ADC, is extended to the calculation of molecular properties, in particular, dipole polarizabilities. Furthermore, in addition to CC with double excitations (CCD), CC with single and double excitations (CCSD) amplitudes can be used, also in the second-order transition moments of the ADC(3/2) method. In the second-order CC-ADC(2) variants, the MP correlation coefficients occurring in ADC are replaced by either CCD or CCSD amplitudes, while in the F/CC-ADC(2) and F/CC-ADC(3/2) variants, they are replaced only in the second-order modified transition moments. These newly implemented variants are used to calculate the static dipole polarizability of several small- to medium-sized molecules, and the results are compared to the ones obtained by full configuration interaction or experiment. It is shown that the results are consistently improved by the use of CC amplitudes, in particular, for aromatic systems such as benzene or pyridine, which have proven to be difficult cases for standard ADC approaches. In this case, the second-order CC-ADC(2) and F/CC-ADC(2) variants yield significantly better results than the standard third-order ADC(3/2) method, at a computational cost amounting to only about 1% of the latter.

  • 39.
    Hu, Wei
    et al.
    Qilu Univ Technol, Shandong Prov Key Lab Mol Engn, Sch Chem & Pharmaceut Engn, Jinan 250353, Shandong, Peoples R China.;Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Collaborat Innovat Ctr Chem Energy Mat, Sch Chem & Mat Sci, Hefei 230026, Anhui, Peoples R China..
    Cao, Xinrui
    Xiamen Univ, Dept Phys, Inst Theoret Phys & Astrophys, Xiamen 361005, Peoples R China..
    Zhang, Yujin
    Qilu Univ Technol, Dept Phys, Sch Elect & Informat Engn, Jinan 250353, Shandong, Peoples R China..
    Li, Tianduo
    Qilu Univ Technol, Shandong Prov Key Lab Mol Engn, Sch Chem & Pharmaceut Engn, Jinan 250353, Shandong, Peoples R China..
    Jiang, Jun
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Collaborat Innovat Ctr Chem Energy Mat, Sch Chem & Mat Sci, Hefei 230026, Anhui, Peoples R China..
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tunable Single-Photon Emission by Defective Boron-Nitride Nanotubes for High-Precision Force Detection2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 14, p. 9624-9628Article in journal (Refereed)
    Abstract [en]

    Boron-nitride nanotubes (BNNTs) hold great potential for electronic, optical, and mechanical applications. By introducing a NBVN defect of removing one nitrogen atom while replacing one boron by nitrogen atom, we examined the use of defective NBVN@BNNTs as a novel type of single-photon emission (SPE) material. Using first-principles calculations to reveal the electronic structures of NBVN@BNNTs, we found that SPE with 1.45-2.29 eV energy can be generated in NBVN@BNNTs with size ranging from (5,0) to (10,0). It is also intriguing to find that their SPE responses are sensitive to the external forces, as indicated by the computed potential energy surfaces and dielectric tensors. Specifically, the (7,0) NBVN@BNNT can serve as an ideal force detector due to its sensitivity and linear response to external force. However, the (5,0) and (6,0) NBVN@BNNTs exhibit insensitive SPE with respect to force applied, and the detection ability of the (8,0), (9,0), and (10,0) NBVN@BNNTs are limited due to the emergence of new photon emissions when tensions become larger than 10 nN. These findings would open a new door for utilizing defective BNNTs for SPE and mechanical detection applications.

  • 40.
    Huang, Bingru
    et al.
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Guangdong Prov Key Lab Opt Informat Mat & Technol, Guangzhou 510006, Guangdong, Peoples R China.
    Bergstrand, Jan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhan, Qiuqiang
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Guangdong Prov Key Lab Opt Informat Mat & Technol, Guangzhou 510006, Guangdong, Peoples R China.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Ågren, Hans
    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.
    Overtone Vibrational Transition-Induced Lanthanide Excited-State Quenching in Yb3+/Er3+-Doped Upconversion Nanocrystals2018In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 12, p. 10572-10575Article in journal (Refereed)
  • 41.
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Federal University.
    Multimode resonant X-ray scattering of free molecules2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is focused on the role that nuclear dynamics plays in the formation of X-ray absorption (XAS) and resonant inelastic X-ray scattering (RIXS) spectra of multimode free molecules. A combined approach based on ab initio electronic structure methods and quantum nuclear wave packet dynamics is applied to two systems -- water and methanol in the gas phase. An IR-pump – X-ray-probe spectroscopy of vibrationally excited water and its isotope substitutions is employed to explore different vibrational progressions of the final electronic state due to a spatial filtration of the vibrations in the core-excited state and selection rules. It was demonstrated the possibility to use RIXS as a tool to study X-ray absorption from a selected vibrational level of the ground state. IR-pump – X-ray-probe spectroscopy applied to the HDO molecule sheds light on the old classical problem of wave function collapse: we demonstrate numerically the gradual collapse of the initially localised vibrational wave function in the HDO molecule. It is also explained the dynamical nature of the splitting of the 1b1 peak in the RIXS spectrum of H2O, HDO and D2O molecules. This splitting is referred to close-lying molecular and atomic-like peaks. In order to study the methanol molecule a special theoretical tool for studies of multimode molecules has been developed. This approach combines the advantages of the quantum wave packet technique for simulations of the dynamics in dissociative states with the efficiency of the Franck-Condon method for computing transitions between bound states. It is shown that the multimode nuclear dynamics plays an important role in XAS and RIXS spectra of methanol. The XAS and RIXS spectra formation was explained taking into account different dynamics in different core-excited potential energy surfaces, as well as the entanglement of vibrational modes by anharmonicity and by the life-time vibrational interference.

  • 42.
    Ignatova, Nina
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Federal University.
    V. Cruz, Vinícius
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Couto, Rafael C.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Zimin, Andrey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    F. Guimarães, Freddy
    Polyutov, Sergey
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Gel’mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gradual collapse of nuclear wave functions regulated by frequency tuned X-ray scattering2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, no 43891Article in journal (Refereed)
    Abstract [en]

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

  • 43.
    Ji, Yongfei
    et al.
    Guangzhou Univ, Dept Chem & Chem Engn, Guangzhou 510006, Guangdong, Peoples R China..
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Direct Donation of Protons from H2O to CO2 in Artificial Photosynthesis on the Anatase TiO2(101) Surface2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 5, p. 3019-3023Article in journal (Refereed)
    Abstract [en]

    Conversion of CO2 and H2O into value-added organic molecules via artificial photosynthesis is a promising solution to current energy and environment problems. In the reaction, it is generally believed that CO2 is converted into organic molecules by photogenerated electrons and protons that result from photo-oxidation of H2O. In this work, we investigate the possibility that H2O, without being oxidized, directly donates protons to CO2 and other intermediates adsorbed at the oxygen vacancy on the anatase TiO2(101) surface. We found that this can greatly lower the barriers (by about 0.3 eV) for the hydrogenation of CO2, CO, H2CO, and CH3O because less energy is required to displace these adsorbates to accept the proton (in H2O). The OH- group produced in these reactions can recombine with a surface-adsorbed proton to form a new H2O molecule, making H2O a shuttling center of the adsorbed protons, or it can take part in the oxygen evolution reaction with a lower barrier. The results suggest that H2O can play multiple roles in artificial photosynthesis and the reduction and oxidation parts of the reaction may have synergistic effects.

  • 44.
    Kang, Dongwei
    et al.
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Zhang, Heng
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Wang, Zhao
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Zhao, Tong
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Ginex, Tiziana
    Univ Barcelona, Inst Biomed IBUB, Fac Pharm, Dept Nutr Food Sci & Gastron, Campus Torribera, Santa Coloma De Gramenet 08921, Spain.;Univ Barcelona, Inst Theoret & Computat Chem IQTCUB, Campus Torribera, Santa Coloma De Gramenet 08921, Spain..
    Luque, Francisco Javier
    Univ Barcelona, Inst Biomed IBUB, Fac Pharm, Dept Nutr Food Sci & Gastron, Campus Torribera, Santa Coloma De Gramenet 08921, Spain.;Univ Barcelona, Inst Theoret & Computat Chem IQTCUB, Campus Torribera, Santa Coloma De Gramenet 08921, Spain..
    Yang, Yang
    Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA..
    Wu, Gaochan
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Feng, Da
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Wei, Fenju
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Zhang, Jian
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    De Clercq, Erik
    Katholieke Univ Leuven, Rega Inst Med Res, Lab Virol & Chemotherapy, Herestr 49 Postbus 1043 09-A097, B-3000 Leuven, Belgium..
    Pannecouque, Christophe
    Katholieke Univ Leuven, Rega Inst Med Res, Lab Virol & Chemotherapy, Herestr 49 Postbus 1043 09-A097, B-3000 Leuven, Belgium..
    Chen, Chin Ho
    Duke Univ, Med Ctr, Surg Oncol Res Facil, Box 2926, Durham, NC 27710 USA..
    Lee, Kuo-Hsiung
    Univ N Carolina, Eshelman Sch Pharm, Nat Prod Res Labs, Chapel Hill, NC 27599 USA.;China Med Univ & Hosp, Chinese Med Res & Dev Ctr, Taichung 40402, Taiwan..
    Murugan, N. Arul
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Steitz, Thomas A.
    Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA..
    Zhan, Peng
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Liu, Xinyong
    Shandong Univ, Sch Pharmaceut Sci, Minist Educ, Dept Med Chem,Key Lab Chem Biol, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China..
    Identification of Dihydrofuro[3,4-d]pyrimidine Derivatives as Novel HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors with Promising Antiviral Activities and Desirable Physicochemical Properties2019In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 62, no 3, p. 1484-1501Article in journal (Refereed)
    Abstract [en]

    To address drug resistance to HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), a series of novel diarylpyrimidine (DAPY) derivatives targeting "tolerant region I" and "tolerant region II" of the NNRTIs binding pocket (NNIBP) were designed utilizing a structure-guided scaffold-hopping strategy. The dihydrofuro[3,4-d]pyrimidine derivatives 13c2 and 13c4 proved to be exceptionally potent against a wide range of HIV-1 strains carrying single NNRTI-resistant mutations (EC50 = 0.9-8.4 nM), which were remarkably superior to that of etravirine (ETV). Meanwhile, both compounds exhibited comparable activities with ETV toward the virus with double mutations F227L+V106A and K103N+Y181C. Furthermore, the most active compound 13c2 showed favorable pharmacokinetic properties with an oral bioavailability of 30.96% and a half-life of 11.1 h, which suggested that 13c2 is worth further investigation as a novel NNRTI to circumvent drug resistance. [GRAPHICS]

  • 45.
    Karaush, N. N.
    et al.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Minaeva, V. A.
    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. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.
    Minaev, Boris F.
    Bohdan Khmelnytsky 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. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Identification of tautomeric intermediates of a novel thiazolylazonaphthol dye - A density functional theory study2018In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 203, p. 324-332Article in journal (Refereed)
    Abstract [en]

    The recently synthesized thiazolylazo dye, 1-(5-benzy1-1,3-thiazol-2-yl)diazenyllnaphthalene-2-ol called shortly BnTAN, is studied by density functional theory (DFT) in three tautomeric forms in order to explain the available H-1 NMR, UV-Vis and FTIR spectra. An experimentally observed IR band at 1678 cm(-1), assigned to the C=O bond stretching vibration, supports the notion that BnTAN retains in the less stable keto-form even in the solid state due to an ultrafast single-coordinate intramolecular proton transfer. This finding is also in a good agreement with an X-ray crystallography analysis which indicates an intermediate position of the proton between the OH and -N=N-groups. Calculations also show that some experimentally observed H-I NMR signals could be considered as being averaged values between theoretically calculated chemical shifts for the corresponding protons in the keto- and enol-tautomers. At the same time the UV-Vis spectra are almost insensitive to the tautomerization processes as the main single band absorption at 500 nm is present in all tautomers according to our TD DFT simulations. The minor differences in spectral features of the long-wavelength visible region are also noted and discussed with respect to the manifestation of the less stable tautomer form.

  • 46.
    Karaush, Nataliya N.
    et al.
    Bogdan Khmelnitsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Baryshnikov, Gleb V.
    Bogdan Khmelnitsky 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. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Minaev, Boris F.
    Bogdan Khmelnitsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    A theoretical study of new representatives of closed- and open-circle benzofuran and benzocyclopentadienone oligomers2018In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 42, no 14, p. 11493-11505Article in journal (Refereed)
    Abstract [en]

    Owing to their potential use as materials for strong optical rotation, circular dichroism and circularly polarized luminescence, the structure and energetic stability of novel closed- and open-circle benzofuran and benzocyclopentadienone oligomers have been studied computationally using the DFT method. It is found that an extension of the macrocycle size (n = 10-30) for the closed-circle species leads to a gradual transformation of their structure from saddle- to helical- and then to a wing-like shape. At the same time, the smaller closed-circle representatives with n = 4 and 6 exhibit a bowl-shaped structure due to the high energy strain of their molecular structures. Application of the NICS (nucleus-independent chemical shift) criterion to the here studied open-circle benzofuran and benzocyclopentadienone species with planar linear, planar fan-shape and helical molecular topology indicates that for the planar benzofuran series the inner benzene ring is more aromatic than the outer hexagons, while the aromaticity of the outer and inner furan rings is insensitive to the molecular size variations. The replacement of the aromatic furan rings by antiaromatic cyclopentadienone fragments for the planar linear species leads to a decrease of aromaticity of the benzene rings from the edge to the center of the benzocyclopentadienone chain. On the other hand, for the planar fan-shape benzocyclopentadienone series a zigzag trend in the NICS values is observed for the benzene rings. Loss of planarity only slightly affects the aromaticity of the helical open-circle benzofuran and benzocyclopentadienone oligomers. We propose that an increase of the NICS indices for the outer and inner rings of the macromolecular helical species is due to the magnetic couplings between the superimposed benzene and furan/cyclopentadienone rings.

  • 47.
    Karaush-Karmazin, Nataliya N.
    et al.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    $$$Baryshnikov, Gleb V.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.;KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Div Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Valiulina, Lenara I.
    Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia..
    Valiev, Rashid
    Tomsk Polytech Univ, 36 Lenin Ave, Tomsk 634050, Russia.;Univ Helsinki, Fac Sci, Inst Atmospher & Earth Syst Res, FIN-00014 Helsinki, Finland..
    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), Theoretical Chemistry and Biology.
    Minaev, Boris F.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Impact of heteroatoms (S, Se, and Te) on the aromaticity of heterocirculenes2019In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 43, no 30, p. 12178-12190Article in journal (Refereed)
    Abstract [en]

    A series of thia[7]circulenes and novel Se-, Te-, S/Te-, and Se/Te-substituted [8]circulenes have been studied by calculations of nucleus-independent chemical shift indices and gauge including magnetically induced currents to interpret the impact of heteroatoms on the aromatic properties of these polyheterocyclic species. The calculations indicate that all the studied hetero[7]circulenes and hetero[8]circulenes consist of two concentric subsystems: an inner seven- or eight-membered core is antiaromatic because of the existence of a paratropic ring current, and an outer system of benzene and hetarene rings that exhibit aromatic behaviour due to the circulation of diatropic ring currents. Thus, most of the hetero[7]circulenes can be considered as slightly antiaromatic because of the slight domination of the paratropic ring currents over the diatropic ones, whereas hetero[8]circulenes represent aromatic species due to the prevailing contribution of the diatropic currents. The antiaromaticity gradually increases with more scattered arrangements of the thiophene and benzene rings in each series of di-, tri-, tetra-, and pentathia[7]circulenes because of the reduced conjugation effect between the neighboring thiophene and benzene rings. Loss of planarity with increased strain leads to an increased antiaromatic character of the lower representatives of the thia[n]circulenes, whereas higher thia[n]circulenes demonstrate a more pronounced aromatic nature because of the small deviation from planarity. The ring current topology is found to be quite insensitive to the heteroatom type, number of hetarene rings and the size of the inner ring; this clearly manifests the special electronic structure of hetero[n]circulenes containing two concentric cyclic subsystems.

  • 48.
    Knippenberg, S.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Hasselt Univ, Biomed Res Inst, Agoralaan Bldg C, B-3590 Diepenbeek, Belgium..
    Fabre, G.
    Limoges Univ, Fac Pharm, LCSN EA1069, 2 Rue Dr Marcland, F-87025 Limoges, France..
    Osella, S.
    Univ Warsaw, Ctr New Technol, Banacha 2C, PL-02097 Warsaw, Poland..
    Di Meo, F.
    Limoges Univ, Fac Pharm, INSERM UMR 1248, 2 Rue Docteur Marcland, F-87025 Limoges, France..
    Paloncyova, M.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ameloot, M.
    Hasselt Univ, Biomed Res Inst, Agoralaan Bldg C, B-3590 Diepenbeek, Belgium..
    Trouillas, P.
    Limoges Univ, Fac Pharm, INSERM UMR 1248, 2 Rue Docteur Marcland, F-87025 Limoges, France.;Palacky Univ, Fac Sci, Ctr Adv Technol & Mat, Tr 17 Listopadu 12, Olomouc 77146, Czech Republic..
    Atomistic Picture of Fluorescent Probes with Hydrocarbon Tails in Lipid Bilayer Membranes: An Investigation of Selective Affinities and Fluorescent Anisotropies in Different Environmental Phases2018In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 34, no 30, p. 9072-9084Article in journal (Refereed)
    Abstract [en]

    By reverting to spectroscopy, changes in the biological environment of a fluorescent probe can be monitored and the presence of various phases of the surrounding lipid bilayer membranes can be detected. However, it is currently not always clear in which phase the probe resides. The well-known orange 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbo-cyanine perchlorate (DiI-C18(5)) fluorophore, for instance, and the new, blue BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) derivative were experimentally seen to target and highlight identical parts of giant unilamellar vesicles of various compositions, comprising mixtures of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), sphingomyelin (SM), and cholesterol (Chol). However, it was not clear which of the coexisting membrane phases were visualized (Bacalum et al., Langmuir. 2016, 32, 3495). The present study addresses this issue by utilizing large-scale molecular dynamics simulations and the z-constraint method, which allows evaluating Gibbs free-energy profiles. The current calculations give an indication why, at room temperature, both BODIPY and DiI-C18(5) probes prefer the gel (S-o) phase in DOPC/DPPC (2:3 molar ratio) and the liquid-ordered (L-o) phase in DOPC/SM/Chol (1:2:1 molar ratio) mixtures. This study highlights the important differences in orientation and location and therefore in efficiency between the probes when they are used in fluorescence microscopy to screen various lipid bilayer membrane phases. Dependent on the lipid composition, the angle between the transition-state dipole moments of both probes and the normal to the membrane is found to deviate clearly from 90 degrees. It is seen that the DiI-C18(5) probe is located in the headgroup region of the SM/Chol mixture, in close contact with water molecules. A fluorescence anisotropy study also indicates that DiI-C18(5) gives rise to a distinctive behavior in the SM/Chol membrane compared to the other considered membranes. The latter behavior has not been seen for the studied BODIPY probe, which is located deeper in the membrane.

  • 49.
    Kosina, Pavel
    et al.
    Palacky Univ, Fac Med & Dent, Dept Med Chem & Biochem, Hnevotinska 3, Olomouc 77515, Czech Republic..
    Paloncyova, Marketa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Palacky Univ, Fac Sci, Dept Phys Chem, Reg Ctr Adv Technol & Mat, Tr 17 Listopadu 12, Olomouc 77146, Czech Republic..
    Svobodova, Alena Rajnochova
    Palacky Univ, Fac Med & Dent, Dept Med Chem & Biochem, Hnevotinska 3, Olomouc 77515, Czech Republic..
    Zalesak, Bohumil
    Univ Hosp Olomouc, Dept Plast & Aesthet Surg, IP Pavlova 6, Olomouc 77900, Czech Republic..
    Biedermann, David
    Acad Sci Czech Republ, Inst Microbiol, Lab Biotransformat, Videnska 1083, Prague 14220, Czech Republic..
    Ulrichova, Jitka
    Palacky Univ, Fac Med & Dent, Dept Med Chem & Biochem, Hnevotinska 3, Olomouc 77515, Czech Republic..
    Vostalova, Jitka
    Palacky Univ, Fac Med & Dent, Dept Med Chem & Biochem, Hnevotinska 3, Olomouc 77515, Czech Republic..
    Dermal Delivery of Selected Polyphenols from Silybum marianum. Theoretical and Experimental Study2019In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 24, no 1, article id 61Article in journal (Refereed)
    Abstract [en]

    Silymarin is a well-known standardized extract from the seeds of milk thistle (Silybum marianum L., Asteraceae) with a pleiotropic effect on human health, including skin anticancer potential. Detailed characterization of flavonolignans properties affecting interactions with human skin was of interest. The partition coefficients log P-ow of main constitutive flavonolignans, taxifolin and their respective dehydro derivatives were determined by a High Performance Liquid Chromatography (HPLC) method and by mathematical (in silico) approaches in n-octanol/water and model lipid membranes. These parameters were compared with human skin intake ex vivo. The experimental log P-ow values for individual diastereomers were estimated for the first time. The replacement of n-octanol with model lipid membranes in the theoretical lipophilicity estimation improved the prediction strength. During transdermal transport, all the studied compounds permeated the human skin ex vivo; none of them reached the acceptor liquid. Both experimental/theoretical tools allowed the studied polyphenols to be divided into two groups: low (taxifolin, silychristin, silydianin) vs. high (silybin, dehydrosilybin, isosilybin) lipophilicity and skin intake. In silico predictions can be usefully applied for estimating general lipophilicity trends, such as skin penetration or accumulation predictions. However, the theoretical models cannot yet provide the dermal delivery differences of compounds with very similar physico-chemical properties; e.g., between diastereomers.

  • 50. Kuklin, A. V.
    et al.
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Minaev, B. F.
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Strong Topological States and High Charge Carrier Mobility in Tetraoxa[8]circulene Nanosheets2018In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 38, p. 22216-22222Article in journal (Refereed)
    Abstract [en]

    Here we report structural and electronic properties of a new family of two-dimensional covalent metal-free organic frameworks based on tetraoxa[8]circulene with different types of fusing. All nanosheets demonstrate high thermodynamic stability and unique electronic properties depending on the fusing type. Among three types of nanosheets, only two demonstrate semiconducting properties exhibiting 1.37 and 1.84 eV direct band gaps, while another one is found to be a semimetal, which hosts strong topological states and enhances the band gap (∼87 meV) induced by spin-orbit coupling that exceeds by several orders of magnitude that gap in graphene. Tetraoxa[8]circulene-based nanosheets are also predicted to be good organic semiconductors due to a clearly observable quantum confinement effect on the band gap size in oligomers and relatively low effective masses, which result in high carrier mobility. Owing to the versatility of chemical design, these materials have the potential to expand applications beyond those of graphene.

1234 1 - 50 of 157
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf