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  • 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. KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Div Theoret Chem & Biol, S-10691 Stockholm, Sweden.;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.
    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).

  • 5. 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.

  • 6.
    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. 

  • 7.
    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.

  • 8.
    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.

  • 9.
    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 17439213, 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. 

  • 10. 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.

  • 11.
    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.

  • 12.
    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.

  • 13.
    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.

  • 14. 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.

  • 15. 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.

  • 16.
    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.

  • 17.
    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.

  • 18. 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.

  • 19. Huang, Bingru
    et al.
    Bergstrand, Jan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    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. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Liu, Haichun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Overtone Vibrational Transition-InducedLanthanide 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)
  • 20.
    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.

  • 21.
    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.

  • 22.
    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.

  • 23.
    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.

  • 24.
    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.

  • 25.
    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.

  • 26. 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.

  • 27.
    König, Carolin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Skanberg, Robin
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Hotz, Ingrid
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Ynnerman, Anders
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Norman, P.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations2018In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, no 24, p. 3030-3033Article in journal (Refereed)
    Abstract [en]

    A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol(-1) due to the interactions between the anionic carboxyl groups of the probe and the cationic epsilon-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

  • 28.
    Li, Deyang
    et al.
    Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China.
    Chen, Guanying
    Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China..
    Near infrared harvesting dye-sensitized solar cells enabled by rare-earth upconversion materials2018In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 47, no 26, p. 8526-8537Article, review/survey (Refereed)
    Abstract [en]

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

  • 29.
    Li, Junfeng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Theoretical Studies on Vibrationally Resolved Optical Spectra of Polycyclic Aromatic Molecules2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

  • 30.
    Li, Junfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhang, Jinglai
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    A theoretical study on vibronic spectra and photo conversation process of protonated naphthalenes2018In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 205, p. 520-527Article in journal (Refereed)
    Abstract [en]

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

  • 31.
    Li, Junfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhang, Jinglai
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    The assignment of optical absorption spectra of protonated anthracene isomers:revisitedManuscript (preprint) (Other academic)
  • 32.
    Li, Junhao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China.
    Zhang, Hongxiao
    East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China..
    Liu, Guixia
    East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China..
    Tang, Yun
    East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China..
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Li, Weihua
    East China Univ Sci & Technol, Shanghai Key Lab New Drug Design, Sch Pharm, Shanghai, Peoples R China..
    Computational Insight Into Vitamin K-1 omega-Hydroxylation by Cytochrome P450 4F22018In: Frontiers in Pharmacology, ISSN 1663-9812, E-ISSN 1663-9812, Vol. 9, article id 1065Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 34.
    Li, Zhenyu
    et al.
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Peoples R China..
    Zhang, Wenhua
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Peoples R China..
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Yang, Jinlong
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Peoples R China..
    A first principles study on atomic structure of graphene oxide and the mechanism of oxidation induced cutting2009In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 238Article in journal (Other academic)
  • 35. Liang, Lijun
    et al.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Theoretical insights into aggregation-induced helicity modulation of a perylene bisimide derivative2018In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 24, no 3, article id 51Article in journal (Refereed)
    Abstract [en]

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

  • 36.
    Löytynoja, Tuomas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. University of Oulu.
    Quantum and quantum-classical calculations of core-ionized molecules in varied environments2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

  • 37.
    Ma, Yong
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, P. R. China.
    Wang, S. -Y
    Hu, J.
    Zhou, Y.
    Song, X. -N
    Wang, C. -K
    Theoretical Identification of the Six Stable C84 Isomers by IR, XPS, and NEXAFS Spectra2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 4, p. 1019-1026Article in journal (Refereed)
    Abstract [en]

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

  • 38.
    Ma, Yong
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wang, Sheng-Yu
    Hu, Jing
    Song, Xiu-Neng
    Zhou, Yong
    Wang, Chuan-Kui
    Theoretical N K-edge NEXAFS spectroscopy study for configuration of a dipolar molecule on graphene2018In: Materials Chemistry and Physics, ISSN 0254-0584, E-ISSN 1879-3312, Vol. 207, p. 309-314Article in journal (Refereed)
    Abstract [en]

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

  • 39.
    Ma, Yong
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China.
    Wang, Sheng-Yu
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Hu, Jing
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Zhang, Jun-Rong
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Lin, Juan
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Yang, Shu-Qiong
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Song, Xiu-Neng
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techn, Jinan 250014, Shandong, Peoples R China..
    Identification of Four C-40 Isomers by Means of a Theoretical XPS/ NEXAFS Spectra Study2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 20, p. 4750-4755Article in journal (Refereed)
    Abstract [en]

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

  • 40.
    Mackie, Cameron J.
    et al.
    Lawrence Berkeley Natl Lab, Chem Sci Div, Berkeley, CA 94720 USA.;Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands..
    Chen, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands.
    Candian, Alessandra
    Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands..
    Lee, Timothy J.
    NASA, Ames Res Ctr, Moffett Field, CA 94035 USA..
    Tielens, Alexander G. G. M.
    Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands..
    Fully anharmonic infrared cascade spectra of polycyclic aromatic hydrocarbons2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 149, no 13, article id 134302Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 42.
    Marcos, Rocio
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bertini, Federica
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Peruzzini, Maurizio
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Gonsalvi, Luca
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Mechanistic Studies on NaHCO3 Hydrogenation and HCOOH Dehydrogenation Reactions Catalysed by a Fe-II Linear Tetraphosphine Complex2018In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 24, no 20, p. 5366-5372Article in journal (Refereed)
    Abstract [en]

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

  • 43.
    Minaev, Boris F.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Minaeva, Valentina A.
    Spin-orbit coupling in enzymatic reactions and the role of spin in biochemistry2017In: Handbook of Computational Chemistry, Springer International Publishing , 2017, p. 1557-1587Chapter in book (Other academic)
    Abstract [en]

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

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

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

  • 45.
    Mudedla, Sathish Kumar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Subramanian, Venkatesan
    Cent Leather Res Inst, CSIR, Chem Lab, Chennai 600020, India..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Destabilization of amyloid fibrils on interaction with MoS2-based nanomaterials2019In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 9, no 3, p. 1613-1624Article in journal (Refereed)
    Abstract [en]

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

  • 46.
    Mudedla, Sathish Kumar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden.;Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Free Energy Landscape for Alpha-Helix to Beta-Sheet Interconversion in Small Amyloid Forming Peptide under Nanoconfinement2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 42, p. 9654-9664Article in journal (Refereed)
    Abstract [en]

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

  • 47.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Nordberg, Agneta
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Different Positron Emission Tomography Tau Tracers Bind to Multiple Binding Sites on the Tau Fibril: Insight from Computational Modeling2018In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 9, no 7, p. 1757-1767Article in journal (Refereed)
    Abstract [en]

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

  • 48.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zalesny, Robert
    Wroclaw Univ Sci & Technol, Fac Chem, Dept Phys & Quantum Chem, Wyb Wyspianskiego 27, PL-50370 Wroclaw, Poland..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Unusual binding-site-specific photophysical properties of a benzothiazole-based optical probe in amyloid beta fibrils2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 31, p. 20334-20339Article in journal (Refereed)
    Abstract [en]

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

  • 49.
    Norman, P.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205, D-69120 Heidelberg, Germany..
    Simulating X-ray Spectroscopies and Calculating Core-Excited States of Molecules2018In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 118, no 15, p. 7208-7248Article, review/survey (Refereed)
    Abstract [en]

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

  • 50.
    Norman, Patrick
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ruud, K.
    Saue, T.
    Principles and practices of molecular properties: Theory, modeling and simulations2017Book (Other academic)
    Abstract [en]

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

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