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  • 1. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Boman, Linus
    Christiansen, Ove
    Cimiraglia, Renzo
    Coriani, Sonia
    Dahle, Pal
    Dalskov, Erik K.
    Ekstrom, Ulf
    Enevoldsen, Thomas
    Eriksen, Janus J.
    Ettenhuber, Patrick
    Fernandez, Berta
    Ferrighi, Lara
    Fliegl, Heike
    Frediani, Luca
    Hald, Kasper
    Halkier, Asger
    Hattig, Christof
    Heiberg, Hanne
    Helgaker, Trygve
    Hennum, Alf Christian
    Hettema, Hinne
    Hjertenaes, Eirik
    Host, Stinne
    Hoyvik, Ida-Marie
    Iozzi, Maria Francesca
    Jansik, Branislav
    Jensen, Hans Jorgen Aa.
    Jonsson, Dan
    Jorgensen, Poul
    Kauczor, Joanna
    Kirpekar, Sheela
    Kjrgaard, Thomas
    Klopper, Wim
    Knecht, Stefan
    Kobayashi, Rika
    Koch, Henrik
    Kongsted, Jacob
    Krapp, Andreas
    Kristensen, Kasper
    Ligabue, Andrea
    Lutnaes, Ola B.
    Melo, Juan I.
    Mikkelsen, Kurt V.
    Myhre, Rolf H.
    Neiss, Christian
    Nielsen, Christian B.
    Norman, Patrick
    Olsen, Jeppe
    Olsen, Jogvan Magnus H.
    Osted, Anders
    Packer, Martin J.
    Pawlowski, Filip
    Pedersen, Thomas B.
    Provasi, Patricio F.
    Reine, Simen
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Ruden, Torgeir A.
    Ruud, Kenneth
    Rybkin, Vladimir V.
    Salek, Pawel
    Samson, Claire C. M.
    de Meras, Alfredo Sanchez
    Saue, Trond
    Sauer, Stephan P. A.
    Schimmelpfennig, Bernd
    Sneskov, Kristian
    Steindal, Arnfinn H.
    Sylvester-Hvid, Kristian O.
    Taylor, Peter R.
    Teale, Andrew M.
    Tellgren, Erik I.
    Tew, David P.
    Thorvaldsen, Andreas J.
    Thogersen, Lea
    Vahtras, Olav
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    The Dalton quantum chemistry program system2014Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, nr 3, s. 269-284Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 2. Aidas, Kestutis
    et al.
    Olsen, Jogvan Magnus H.
    Kongsted, Jacob
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics2013Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 7, s. 2069-2080Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.

  • 3.
    Aidas, Kestutis
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Kongsted, Jacob
    Laaksonen, Aatto
    Mocci, Francesca
    A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution2013Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 5, s. 1621-1631Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.

  • 4. Aldongarov, Anuar
    et al.
    Irgibaeva, Irina
    Hermansson, Kersti
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Theoretical study on passivation of small CdS clusters2014Ingår i: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 112, nr 5-6, s. 674-682Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We use density functional theory quantum chemical calculations to model optical properties of small cadmium sulphide clusters in order to explore the formation of trap states and the possibility to achieve surface passivation. The addition of capping oxygen ions on the surface of the CdS quantum dots is found to passivate the single-bonded Cd atoms. Added Cu ions resulted in the formation of deep trap states for certain locations of the copper impurity, while removal of single-bonded Cd atoms by adding S or SH groups leads to a band gap increase.

  • 5. Andersson, E.
    et al.
    Niskanen, Johannes
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Hedin, L.
    Eland, J. H. D.
    Linusson, P.
    Karlsson, L.
    Rubensson, J. -E
    Carravetta, V.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Feifel, R.
    Core-valence double photoionization of the CS2 molecule2010Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, nr 9, s. 094305-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Double photoionization spectra of the CS2 molecule have been recorded using the TOF-PEPECO technique in combination with synchrotron radiation at the photon energies h nu=220, 230, 240, 243, and 362.7 eV. The spectra were recorded in the S 2p and C 1s inner-shell ionization regions and reflect dicationic states formed out of one inner-shell vacancy and one vacancy in the valence region. MCSCF calculations were performed to model the energies of the dicationic states. The spectra associated with a S 2p vacancy are well structured and have been interpreted in some detail by comparison to conventional S 2p and valence photoelectron spectra. The lowest inner-shell-valence dicationic state is observed at the vertical double ionization energy 188.45 eV and is associated with a (2p(3/2))(-1)(2 pi(g))(-1) double vacancy. The spectrum connected to the C 1s vacancy shows a distinct line at 310.8 eV, accompanied by additional broad features at higher double ionization energies. This line is associated with a (C 1s)(-1)(2 pi(g))(-1) double vacancy.

  • 6. Andersson, E.
    et al.
    Stenrup, Michael
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Eland, J.H.D.
    Hedin, L.
    Berglund, M.
    Karlsson, L.
    Larson, Åsa
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Rubensson, Jan Erik
    Feifel, Raimund
    Single-photon core-valence double ionization of molecular oxygen2008Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 78, nr 2, s. 023409-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Single-photon core-valence double ionization of molecular oxygen has been studied using a magnetic bottle time-of-flight electron coincidence spectrometer. The K-1 V-1 double ionization electron spectrum of O2 is reported and is assigned with the aid of ab initio calculations. A direct comparison of the core-valence double ionization electron spectra with the conventional valence band photoelectron spectrum is made. The lowest core-valence double ionization energy is found to be 571.6 eV and is associated with a Π3 dicationic state.

  • 7. Augustsson, A.
    et al.
    Kashtanov, Stepan
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Luo, Yi
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Chang, C.L.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Rubensson, J.-E.
    Nordgren, J.
    Conformations and core-excitation dynamics liquid water.Manuskript (preprint) (Övrigt vetenskapligt)
  • 8. Baev, A.
    et al.
    Feifel, R.
    Gel'mukhanov, Faris
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Piancastelli, M. N.
    Bassler, M.
    Miron, C.
    Sorensen, S. L.
    de Brito, A. N.
    Bjorneholm, O.
    Karlsson, L.
    Svensson, S.
    Geometrical information on core-excited states obtained from interference quenching of vibrational states in resonant x-ray photoemission2003Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 67, nr 2Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An interference quenching of the m=1 final state vibrational line in the resonant Auger decay of N 1s-->pi(*) core-excited N-2 is observed and analyzed. The intensity ratio between the m=1 and m=0 vibrational levels of the X (2)Sigma(g)(+) final state shows a surprising nonmonotonic variation as a function of frequency detuning, going through a minimum with a complete suppression of m=1. We have developed a simple model which indicates a linear relation between the value of the detuning frequency for this minimum and the equilibrium bond distance of the core-excited state. This implies the possibility of determining the equilibrium bond distances for core-excited states to a high degree of accuracy. Simultaneously with the simple model we present a strict theory of the studied effect. This strict theory allows us to explore the accuracy of determining the bond length of the core-excited state from resonant Auger spectra. We obtain a weak influence of the core-hole lifetime on the determined bond length, whereas the number of intermediate vibrational states accounted for in the numerical simulations seems to be quite important.

  • 9. Baev, A.
    et al.
    Gelmukhanov, Faris
    KTH, Tidigare Institutioner, Kemi.
    Kimberg, Viktor
    KTH, Tidigare Institutioner, Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner, Bioteknologi.
    Nonlinear propagation of strong multi-mode fields2003Ingår i: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 36, s. 3761-3774Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We develop a strict theory of nonlinear propagation of few interacting stronglight beams. The key idea of our approach is a self-consistent solution ofthe nonlinear wave equation and the density matrix equations of the materialbeyond the rotatory wave approximation. We assume a Fourier expansion ofthe density matrixwhich goes beyond the conventionalTaylor expansions of thepolarization over the field amplitudeswhich is inadequate for the field strengthsthat we are interested in. Two qualitatively different situations are considered,with and without phase matching. Unlike in our previous paper (Baev et al2003 J. Opt. Soc. Am. B at press) devoted to the three-photon (TP) absorptioninduced upconverted lasing, we obtain here a strict solution for the nonlinearinteraction between different light beams. The general theory is applied to anumerical study of the role of saturation in TP photoabsorption by an organicchromophore in solution.

  • 10. Baev, A.
    et al.
    Gel'mukhanov, Faris
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Macak, P.
    Luo, Yi
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    General theory for pulse propagation in two-photon active media2002Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 117, nr 13, s. 6214-6220Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The propagation of laser pulses of different lengths in nonlinear media of organic absorbers is described starting out from a recently suggested dynamical theory for two-photon absorption (TPA) of molecules in solutions [J. Opt. Soc. Am. B 19, 937 (2002)]. The roles of saturation effects and pulse duration on the suppression of TPA are emphasized. The numerical simulations of the pulse propagation are performed for a two-photon active charge transfer molecule using molecular parameters obtained from first principle calculations.

  • 11. Baev, A.
    et al.
    Gel'mukhanov, Faris
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Salek, Pawel
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Ueda, K.
    de Fanis, A.
    Okada, K.
    Sorensen, S.
    Doppler interference in dissociative resonant photoemission2002Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 66, nr 2Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Resonant photoemission involving dissociative core excited states has been the subject of a great number of experimental and theoretical investigations in recent time. The resonant decay of such dissociating systems has been shown to lead to semiatomic Auger electron emission spectra, with particular angular behavior. In the present paper a detailed theoretical analysis of dissociative resonant photoemission spectra of homonuclear diatomic molecules is presented. The theory addresses both fixed in space and randomly oriented homonuclear molecules and emphasizes the Doppler effect and the role of the interference between channels referring to the Doppler split atomic fragments. It is shown that peaks originating from decay in the atomic fragments can be asymmetric and structured due to the Doppler interference effect. The predicted strong non-Lorentzian behavior of the substructure on the top of the Doppler broadened atomiclike contribution is traced to the interplay between decay channels leading to gerade and ungerade final states. Simulations based on wave-packet theory are compared with experimental data for molecular oxygen. Our numerical simulations of the atomiclike resonance of fixed in space molecules show that the spectral profile is very sensitive to the shape of interatomic potentials of core excited and final states. It is shown that the Doppler effect in the decay spectra depends upon the symmetry of the core excited state.

  • 12. Baev, A.
    et al.
    Kimberg, Viktor
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Polyutov, Sergey
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Gelmukhanov, Faris
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Bi-directional description of amplified spontaneous emission induced by three-photon absorption2005Ingår i: Journal of the Optical Society of America. B, Optical physics, ISSN 0740-3224, E-ISSN 1520-8540, Vol. 22, nr 2, s. 385-393Artikel i tidskrift (Refereegranskat)
    Abstract [en]

     A semiclassical dynamic theory of the nonlinear propagation of a few interacting intense light pulses is applied to study the nonlinear counterpropagation of amplified spontaneous emission (ASE) induced by three-photon absorption of short intense laser pulses in a chromophore solution. Several important results from the modeling are reached for the ASE process developing in the regime of strong saturation. Accounting for ASE in both forward and backward directions with respect to the pump pulse results in a smaller efficiency of nonlinear conversion for the forward ASE compared with the case in which forward emission is considered alone, something that results from the partial repump of the absorbed energy to the backward ASE component; the overall efficiency is nevertheless higher than for the forward emission considered alone. The efficiency of nonlinear conversion of the pump energy to the counterpropagating ASE pulses is strongly dependent on the concentration of active molecules so that a particular combination of concentration versus cell length optimizes the conversion coefficient. Under certain specified conditions, the ASE effect is found to be oscillatory; the origin of oscillations is dynamical competition between stimulated emission and off-resonant absorption. This result can be considered one of the possible explanations of the temporal fluctuations of the forward ASE pulse [Nature 415, 767 (2002)].

  • 13. Baev, A.
    et al.
    Salek, Pawel
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Gel'mukhanov, Faris
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Quantum-classical modeling of nonlinear pulse propagation in a dissolved two-photon active chromophore2006Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 11, s. 5379-5385Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the present work we outline the implications of a quantum-classical approach for modeling two-photon absorption of organic chromophores in solution. The approach joins many-photon absorption dynamic simulations with quantum chemical first principles calculations of corresponding excitation energies and transition matrix elements. Among a number of conclusions of the study, we highlight three: (i) The use of either short- or long-pulse excitation is demonstrated to switch the absorptive capacity of the nonlinear medium owing to enhancement of the nonlinear stepwise processes; (ii) The two-photon cross section strongly depends on the way in which the dephasing rate decays when the laser frequency is tuned off-resonant with the corresponding molecular transition; (iii) The results of the pulse propagation simulations based on electronic structure data obtained with a new Coulomb attenuated functional is shown to be in much better agreement with the experimental results than those based on data received with traditional density functionals.

  • 14. Baev, A
    et al.
    Salek, Pawel
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Gelmukhanov, Faris
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    de Brito, N
    Bjorneholm, O
    Svensson, S
    Picturing molecular femtosecond processes through an ultra-fast controllable X-ray shutter2003Ingår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 289, nr 1, s. 51-56Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We show that frequency detuning in a resonant X-ray scattering experiment acts as an X-ray camera shutter by regulating the duration time of the scattering process. The camera shutter can be used to select processes at different time scales for observation. This is illustrated by a resonant Auger study of the ultra-fast dissociation of the core-excited HF molecule. We present experimental results and first principle simulations of the molecular fraction in the resonant Auger spectra of HF which is a dynamical parameter that well illustrates X-ray shutter controlled dissociation.

  • 15. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    A quantum mechanical - Electrodynamical approach to nonlinear properties: Application to optical power limiting with platinum-organic compounds2007Ingår i: Journal of nonlinear optical physics and materials, ISSN 0218-8635, Vol. 16, nr 2, s. 157-169Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Light propagation in a medium is sensitively dependent on the shape and intensity of the optical pulse as well as on the electronic and vibrational structure of the basic molecular units. We review in this paper the results of systematic studies of this problem for isotropic media. Our theoretical approach - the quantum mechanical-electrodynamical (QMED) approach - is based on a quantum mechanical account of the many-level electron-nuclear medium coupled to a numerical solution of the density matrix and Maxwell's equations. This allows us to accommodate a variety of nonlinear effects which accomplish the propagation of strong light pulses. Particular attention is paid to the understanding of the role of coherent and sequential excitations of electron-nuclear degrees of freedom. The QMED combination of quantum chemistry with classical pulse propagation enables us to estimate the optical transmission from cross sections of multi-photon absorption processes and from considerations of propagation effects, saturation and pulse effects. Results of the theory suggest that in the nonlinear regime, it is often necessary to simultaneously account for coherent one-step and incoherent step-wise multi-photon absorption, as well as for off-resonant excitations even when resonance conditions prevail. The dynamic theory of nonlinear propagation of a few interacting intense light pulses is highlighted here in a study of the optical power limiting with platinum-organic molecular compounds. © World Scientific Publishing Company.

  • 16. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Light-matter interaction of strong laser pulses in the micro-, nano-, and picosecond regimes2007Ingår i: Materials Research Society Symposium Proceedings, 2007, s. 12-29Konferensbidrag (Refereegranskat)
    Abstract [en]

    Light propagation in a medium is sensitively dependent on the shape and intensity of the optical pulse as well as on the electronic and vibrational structure of the basic molecular units. We review in this paper results of systematic studies of this problem for isotropic media. Our theoretical approach-the quantum mechanical-electrodynamical (QMED) approach-is based on a quantum mechanical account of the many-level electron-nuclear medium coupled to a numerical solution of the density matrix and Maxwell s equations. This allows to accommodate a variety of nonlinear effects which accomplish the propagation of strong light pulses. Particular attention is paid to the understanding of the role of coherent and sequential excitations of electron-nuclear degrees of freedom. The QMED combination of quantum chemistry with classical pulse propagation allows to estimate the optical transmission from cross sections of multi-photon absorption processes and from considerations of propagation effects, saturation and pulse effects. Results of the theory suggest that in the nonlinear regime it is often necessary to account simultaneously for coherent one-step and incoherent step-wise multi-photon absorption, as well as for off-resonant excitations even when resonance conditions prevail. The dynamic theory of nonlinear propagation of a few interacting intense light pulses is here highlighted in a study of the optical power limiting with platinum-organic molecular compounds. © 2007 Materials Research Society.

  • 17.
    Baev, Alexander
    et al.
    KTH, Tidigare Institutioner, Bioteknologi.
    Gel'mukhanov, Faris
    KTH, Tidigare Institutioner, Bioteknologi.
    Rubio-Pons, Oscar
    KTH, Tidigare Institutioner, Bioteknologi.
    Cronstrand, Peter
    KTH, Tidigare Institutioner, Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner, Bioteknologi.
    Upconverted lasing based on many-photon absorption: an all dynamic description2004Ingår i: Journal of the Optical Society of America. B, Optical physics, ISSN 0740-3224, E-ISSN 1520-8540, Vol. 21, nr 2, s. 384-396Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A theory is developed for the propagation through a nonlinear medium of strong pump and amplifiedspontaneous-emission pulses. The theory is based on a solution of the density matrix equations that aims at providing an adequate treatment of the nonlinear polarization of the material without addressing the Taylor expansion over the powers of intensity. The theory has been applied for modeling of three-photon absorption induced upconverted stimulated emission of organic molecules in solvents. Numerical results are presented for the organic chromophore 4-[N-(2-hydroxyethyl)-N-(methyl)amino phenyl]-4'-(6-hydroxyhexyl sulfonyl) stilbene dissolved in dimethyl sulfoxide. The results are in good agreement with available experimental results.

  • 18. Baev, Alexander
    et al.
    Norman, Patrick
    Henriksson, Johan
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Theoretical Simulations of clamping levels in optical power limiting2006Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 42, s. 20912-20916Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Multiphysics modeling, combining quantum mechanical and classical wave mechanical theories, of clamping levels has been performed for a platinum(II) organic compound in a sol-gel glass matrix. A clamping level of 2.5 mu J is found for a pulse duration of 10 ns. The excited-state absorption in the triplet manifold is shown to be crucial for clamping to occur.

  • 19. Baev, Alexander
    et al.
    Prasad, Paras N.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Samoc, Marek
    Wegener, Martin
    Metaphotonics: An emerging field with opportunities and challenges2015Ingår i: Physics reports, ISSN 0370-1573, E-ISSN 1873-6270, Vol. 594, s. 1-60Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Metaphotonics is an emerging multidisciplinary field that deals with manipulation of electro-magnetic fields in nanoengineered (meta)materials using both electric and magnetic interactions and their cross-coupling. It offers unprecedented control of both linear and nonlinear optical functions for applications ranging from optical switching, to negative- and near-zero refractive index metamaterials, to chiral bioimaging, to cloaking. However, realization of such applications requires physics-guided nanoengineering of appropriate artificial media with electro-magnetic properties at visible and infrared wavelengths that are tailored to surpass those of any naturally-occurring material. Here, we review metaphotonics with a broadened vision and scope, introduce potential applications, describe the role of theoretical physics through multiscale modeling, review the materials development and current status, and outline opportunities in this fertile emerging field.

  • 20.
    Baev, Alexander
    et al.
    KTH, Tidigare Institutioner, Bioteknologi.
    Rubio-Pons, Oscar
    KTH, Tidigare Institutioner, Bioteknologi.
    Gel'Mukhanov, Faris
    KTH, Tidigare Institutioner, Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner, Bioteknologi.
    Optical limiting properties of Zinc- and Platinum-based organometallic compounds2004Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, nr 36, s. 7406-7416Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Optical power limiting is theoretically studied using an approach that combines quantum electronic structure calculations of multiphoton excitations and classical calculations of dynamical wave propagation. We illustrate the capability of such a combined approach by presenting results for a couple of organometallic compounds; basic metal-base porphyrins, vinylphenylamine porhyrin, and the so-called type IVc platinum compound. A comparative analysis of their electronic properties related to nonlinear absorption of electromagnetic radiation and their optical limiting capability has been performed based on dynamical simulations of the nonlinear pulse propagation taking account of resonant as well as off-resonant effects. Several key features and rate-limiting steps in the transmission have been examined in relation to various characteristics of the pulse. It is found that the resonant vs off-resonant conditions, the saturation conditions and the dephasing play critical roles for the nonlinear transmission. The saturation effects are sensitive to the pulse duration, the inter-system crossing rate and the quenching of the higher triplet state. The inter-system crossing rate has to be comparable with the inverse pulse duration in order to boost the stepwise two-photon channel associated with singlet-singlet followed by triplet-triplet transitions. It is illustrated that structure-to-property relations of the rate-limiting steps serve as important criteria for choices of compounds suitable for the application of interest.

  • 21. Bai, Linyi
    et al.
    Zhu, Liangliang
    Ang, Chung Yen
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Wu, Shaojue
    Zeng, Yongfei
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Zhao, Yanli
    Iron( III)-Quantity-Dependent Aggregation-Dispersion Conversion of Functionalized Gold Nanoparticles2014Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, nr 14, s. 4032-4037Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Developing gold nanoparticles (AuNPs) with well-designed functionality is highly desirable for boosting the performance and versatility of inorganic-organic hybrid materials. In an attempt to achieve ion recognition with specific signal expressions, we present here 4-piperazinyl-1,8-naphthalimide-functionalized AuNPs for the realization of quantitative recognition of Fe-III ions with dual (colorimetric and fluorescent) output. The research takes advantage of 1)quantity-controlled chelation-mode transformation of the piperazinyl moiety on the AuNPs towards Fe-III, thereby resulting in an aggregation-dispersion conversion of the AuNPs in solution, and 2)photoinduced electron transfer of a naphthaimide fluorophore on the AuNPs, thus leading to reversible absorption and emission changes. The functional AuNPs are also responsive to pH variations. This strategy for realizing the aggregation-dispersion conversion of AuNPs with returnable signal output might exhibit application potential for advanced nanoscale chemosensors.

  • 22.
    Balamurugan, Kanagasabai
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512). KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Multistep Modeling Strategy To Improve the Binding Affinity Prediction of PET Tracers to A beta(42): Case Study with Styrylbenzoxazole Derivatives2016Ingår i: ACS CHEMICAL NEUROSCIENCE, ISSN 1948-7193, Vol. 7, nr 12, s. 1698-1705Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Positron emission tomography (PET) tracers play an important role in the diagnosis of Alzheimer's disease, a condition that leads to progressive dementia and memory loss. A high binding affinity and specificity of the PET tracers to amyloid oligomers and fibrils are crucial for their successful application as diagnostic agents. In this sense, it is essential to design PET tracers with enhanced binding affinities, which can lead to more precise and earlier detection of Alzheimer's disease conditions. The application of in silico methodology for the design and development of efficient PET tracers may serve as an important route to improved Alzheimer's disease diagnosis. In this work, the performance of widely used computational methods is explored for predicting experimental binding affinities of styrylbenzoxazole (SB) derivatives against a common amyloid protofibril. By performing docking, molecular dynamics, and quantum chemistry calculations in sequence their combined predictive performance is explored. The present work emphasizes the merits as well as limitations of these simulation strategies in the realm of designing PET tracers for Alzheimer's disease diagnosis.

  • 23.
    Banerjee, Saikat
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, Nordic Institute for Theoretical Physics NORDITA. Institute for Materials Science, Los Alamos National Laboratory, USA.
    Fransson, J.
    Black-Schaffer, A. M.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Balatsky, A. V.
    Granular superconductor in a honeycomb lattice as a realization of bosonic Dirac material2016Ingår i: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 93, nr 13, artikel-id 134502Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We examine the low-energy effective theory of phase oscillations in a two-dimensional granular superconducting sheet where the grains are arranged in a honeycomb lattice structure. Using the example of graphene, we present evidence for the engineered Dirac nodes in the bosonic excitations: the spectra of the collective bosonic modes cross at the K and K' points in the Brillouin zone and form Dirac nodes. We show how two different types of collective phase oscillations are obtained and that they are analogous to the Leggett and the Bogoliubov-Anderson-Gorkov modes in a two-band superconductor. We show that the Dirac node is preserved in the presence of an intergrain interaction, despite induced changes of the qualitative features of the two collective modes. Finally, breaking the sublattice symmetry by choosing different on-site potentials for the two sublattices leads to a gap opening near the Dirac node, in analogy with fermionic Dirac materials. The Dirac node dispersion of bosonic excitations is thus expanding the discussion of the conventional Dirac cone excitations to the case of bosons. We call this case as a representative of bosonic Dirac materials (BDM), similar to the case of Fermionic Dirac materials extensively discussed in the literature.

  • 24.
    Banerjee, Saikat
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, Nordic Institute for Theoretical Physics NORDITA. Los Alamos Natl Lab, USA.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Balatsky, Alexander V.
    KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Landau-like states in neutral particles2016Ingår i: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 93, nr 23, artikel-id 235134Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We show the emergence of a new type of dispersion relation for neutral atoms with an interesting similarity to the spectrum of two-dimensional electrons in an applied perpendicular constant magnetic field. These neutral atoms can be confined in toroidal optical traps and give quasi-Landau spectra. In strong contrast to the equidistant infinitely degenerate Landau levels for charged particles, the spectral gap for such two-dimensional neutral particles increases in particular electric-field configurations. The idea in the paper is motivated by the development in cold atom experiments and builds on the seminal paper of Aharonov and Casher.

  • 25. Baryshnikov, G. V.
    et al.
    Minaev, B. F.
    Minaeva, V. A.
    Podgornaya, A. T.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Application of Bader's atoms in molecules theory to the description of coordination bonds in the complex compounds of Ca2+ and Mg2+ with methylidene rhodanine and its anion2012Ingår i: Russian journal of general chemistry, ISSN 1070-3632, E-ISSN 1608-3350, Vol. 82, nr 7, s. 1254-1262Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the framework of Bader's atoms in molecules theory a complete analysis of the distribution function of electron density in molecules of complexes of Ca2+ and Mg2+ with methylidene rhodanine and its anion was carried out. The role of mutual polarization of the metal cation and the ligand in the formation of coordination bonds was demonstrated. The accumulation of electron density in the interatomic space of coordination bonds is assumed to be a consequence of the deformation of the ligand electron shell under the influence of the cation electric field. Based on the magnitude and sign of the Laplacian and the electron energy density at the critical points of coordination bonds the interactions were classified the in terms of the atoms in molecules theory. The energy of the coordination bonds was evaluated using the Espinoza's formula. The stability of metal-containing rings was considered basing on the values of the bond ellipticity.

  • 26. Baryshnikov, G. V.
    et al.
    Minaev, B. F.
    Minaeva, V. A.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Theoretical study of the conformational structure and thermodynamic properties of 5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine and ethyl-5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine-3-acetic acid as acceptor groups of indoline dyes2010Ingår i: Journal of Structural Chemistry, ISSN 0022-4766, E-ISSN 1573-8779, Vol. 51, nr 5, s. 817-823Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The quantum chemical DFT method with the B3LYP hybrid functional in 6-31++G(d,p) and 6-311+G(d,p) basis sets is used to calculate the equilibrium geometric parameters of different conformations of 5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine and its substituted form ethyl-5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine-3'-acetic acid applied in the synthesis of indoline and some other sensitizing dyes for solar cells. The thermodynamic parameters of four conformers and their synthesis reactions are calculated. The effect of substituents on the thermodynamic stability of the studied isomers is shown.

  • 27.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. 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, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Centra, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Vibronic absorption spectra of the angular fused bisindolo- and biscarbazoloanthracene blue fluorophores for OLED applications2018Ingår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 513, s. 105-111Artikel i tidskrift (Refereegranskat)
    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.

  • 28.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Valiev, R. R.
    Natl Res Tomsk Polytech Univ, Res Sch Chem & Appl Biomed Sci, Lenin Ave 30, Tomsk 634050, Russia.;Univ Helsinki, Dept Chem, FIN-00014 Helsinki, Finland..
    Cherepanov, V. N.
    Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia..
    Karaush-Karmazin, N. N.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Minaeva, V. A.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Minaev, B. F.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Ågren, Hans
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Aromaticity and photophysics of tetrasila- and tetragerma-annelated tetrathienylenes as new representatives of the hetero[8]circulene family2019Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, nr 18, s. 9246-9254Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 29.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bogdan Khmelnitsky Natl Univ.
    Valiev, Rashid R.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Tomsk State Univ; Tomsk Polytech Univ.
    Karaush, Nataliya N.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Minaeva, Valentina A.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Sinelnikov, Alexandr N.
    Pedersen, Stephan K.
    Pittelkow, Michael
    Minaev, Boris F.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Benzoannelated aza-, oxa- and azaoxa[8]circulenes as promising blue organic emitters2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 40, s. 28040-28051Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the present work, we studied the synergetic effect of benzoannelation and NH/O-substitution for enhancing the absorption intensity in a series of novel designed benzoannelated aza- and oxa[8]circulenes. Semi-empirical estimations of the fluorescence rate constants allowed us to determine the most promising fluorophores among all the possible benzoannelated aza-, oxa- and mixed azaoza[8]circulenes. Among them, para-dibenzoannelated [8]circulenes demonstrated the most intense light absorption and emission due to the prevailing role of the linear acene chromophore. Calculated phi(fl) values are in complete agreement with experimental data for a number of already synthesized circulenes. Thus, we believe that the most promising circulenes designed in this study can demonstrate an intensive fluorescence in the case of their successful synthesis, which in turn could be extremely useful for the fabrication of future blue OLEDs. Special attention is devoted to the aromaticity features and peculiarities of the absorption spectra for the two highly-symmetrical (D-4h ground state symmetry) pi-isoelectronic species as well as the so-called tetrabenzotetraaza[8]circulene and tetrabenzotetraoxa[8]circulene molecules. Both of them are characterized by rich electronic spectra, which can be assigned only by taking into account the vibronic coarse structure of the first electronic absorption band; the 0-1 and 0-2 transitions were found to be active in the absorption spectrum in complete agreement with experimental data obtained for both energy and intensity. The corresponding promotive vibrational modes have been determined and their vibronic activity estimated using the Franck-Condon approximation.

  • 30.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bogdan Khmelnitsky National University, Ukraine; Tomsk State University, Russian Federation.
    Valiev, Rashid R.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Tomsk State University, Russian Federation; Tomsk Polytechnic University, Russian Federation.
    Minaev, Boris F.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bogdan Khmelnitsky National University, Ukraine; Tomsk State University, Russian Federation.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    A computational study of aromaticity and photophysical properties of unsymmetrical azatrioxa[8]circulenes2017Ingår i: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, nr 7, s. 2717-2723Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 31.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Valiev, Rashid R.
    Minaev, Boris F.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Substituent-sensitive fluorescence of sequentially N-alkylated tetrabenzotetraaza[8]circulenes2017Ingår i: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, nr 15, s. 7621-7625Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We explore the use of substituent-sensitive balance between fluorescence and non-radiative decay as a tool for optical tuning of promising materials for organic light emitting diode applications. A series of N-butylated tetrabenzotetraaza[8]circulenes is studied computationally in order to explain the gradual decrease of fluorescence intensity with the increase of the substituent number. The inter-system crossing probability is found to increase upon the gradual substitution of the circulene macrocycle as a result of the decrease of the S-1-T-1 energy gap due to the deformation of the tetrabenzotetraaza[8] circulenes and therefore the distortion of the pi-conjugation within the macrocycles. In contrast, the S-1-T-1 spin-orbit coupling matrix elements are quite insensitive to the number of outer substituents. As a result, the fluorescence-responsible pi pi(star) transition becomes less intense and the fluorescence rate constant decreases.

  • 32.
    Baryshnikov, Glib V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. V. D. Kuznetsov Siberian Physical-Technical Institute at National Research Tomsk State University, Russian Federation.
    Minaev, Boris F.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. V. D. Kuznetsov Siberian Physical-Technical Institute at National Research Tomsk State University, Russian Federation.
    Baryshnikova, A. A.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Anion-induced exchange interactions in binuclear complexes of Cu(II) with flexible hexadentate bispicolylamidrazone ligands2016Ingår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 661, s. 48-52Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Two recently synthesized copper(II) complexes with spacer-armed bispicolylamidrazone ligands have been theoretically studied at the density functional theory (DFT) level accounting for empirical dispersion correction and intrinsic anionic environment by perchlorate ions. The exchange parameter between the open-shell singlet and triplet states of the studied complexes has been estimated by broken symmetry DFT calculations. The mechanism of spin-spin exchange interaction between the unpaired electrons via the σ-bond aliphatic chain (Gusev et al., 2015) is confirmed. Instead, a anion-induced mechanism is proposed which means that the anionic grid participates in the exchange interaction between the unpaired electrons.

  • 33. Baryshnikova, A. T.
    et al.
    Minaev, B. F.
    Baryshnikov, Gleb V.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Computational study of the structure and magnetic properties of the weakly-coupled tetranuclear square-planar complex of Cu(II) with a tetraporphyrin sheet2019Ingår i: Inorganica Chimica Acta, ISSN 0020-1693, E-ISSN 1873-3255, Vol. 485, s. 73-79Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 34. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Odelius, Michael
    Elucidating the Mechanism of Zn2+ Sensing by a Bipyridine Probe Based on Two-Photon Absorption2016Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, nr 34, s. 9067-9075Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this work, we examine, by means of computational methods, the mechanism of Zn2+ sensing by a bipyridine-centered, D-pi-A-pi-D-type-ratiometric molecular probe. According to recently published experimental data [Divya, K. P.; Sreejith, S.; Ashokkumar, P.; Yuzhan, K.; Peng, Q; Maji, S. K.; Tong, Y.; Yu, H.; Zhao, Y.; Ramamurthy, P.; Ajayaghosh, A. A ratiometric fluorescent molecular -probe with enhanced two-photon response upon Zn2+ binding for in vitro and in vivo: bioimaging.= Chem. Sci. 2014, S, 3469-3474], after coordination to zinc ions the -probe exhibits a large enhancement of the two -photon absorption cross section. The goal of our investigation was to elucidate the mechanism behind this phenomenon. For this purpose, linear and nonlinear optical properties of -the unbound (cation-free) and bound probe were calculated, including the influence of solute Solvent interactions, implicitly using a polarizable continuum model and exp-licitely employing the QM/MM approach. Because the results of the calculations indicate that many conformers of the probe are energetically accessible at room temperature in solution and hence contribute to the Signal, structurepteperty relationships were also taken into account. Results of our simulations-demonstrate that the one-photon absorption bands for both the unbound -and bound forms correspond to the bright pi -> pi* transition to the first excited state; which, on the other hand,. exhibits negligible two-photon activity. On the basis of the results of the quadratic respOnse calculations, we put forward-notion that it is the second excited state that gives the strong signal in the experimental nonlinear spectrum. To explain the differenCes in the two-photon absorption activity for the two lowest-lying excited states and nonlinear response enhancement upon binding, we employed the generalized few -state model including the ground, first, and- second excited states. The analysis of the optical channel suggests that the large two-photon response is due to the coordination -induced increase of the, transition- moment from the first to the second excited state.

  • 35. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Tian, Guangjun
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Bartkowiak, Wojciech
    Nonempirical Simulations of Inhomogeneous Broadening of Electronic Transitions in Solution: Predicting Band Shapes in One- and Two-Photon Absorption Spectra of Chalcones2017Ingår i: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 22, nr 10, artikel-id 1643Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have examined several approaches relying on the Polarizable Embedding (PE) scheme to predict optical band shapes for two chalcone molecules in methanol solution. The PE-TDDFT and PERI-CC2 methods were combined with molecular dynamics simulations, where the solute geometry was kept either as rigid, flexible or partly-flexible (restrained) body. The first approach, termed RBMD-PE-TDDFT, was employed to estimate the inhomogeneous broadening for subsequent convolution with the vibrationally-resolved spectra of the molecule in solution determined quantum-mechanically (QM). As demonstrated, the RBMD-PE-TDDFT/QM-PCM approach delivers accurate band widths, also reproducing their correct asymmetric shapes. Further refinement can be obtained by the estimation of the inhomogeneous broadening using the RBMD-PERI-CC2 method. On the other hand, the remaining two approaches (FBMD-PE-TDDFT and ResBMD-PE-TDDFT), which lack quantum-mechanical treatment of molecular vibrations, lead to underestimated band widths. In this study, we also proposed a simple strategy regarding the rapid selection of the exchange-correlation functional for the simulations of vibrationally-resolved one-and two-photon absorption spectra based on two easy-to-compute metrics.

  • 36. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Wielgus, Malgorzata
    Jedrzejewska, Beata
    Puttreddy, Rakesh
    Rissanen, Kari
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Osmialowski, Borys
    Two-photon absorption of BF2-carrying compounds: insights from theory and experiment2017Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, nr 8, s. 5705-5708Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 37. Belyanin, Maxim L.
    et al.
    Stepanova, Elena V.
    Valiev, Rashid R.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. National Research Tomsk Polytechnic University, Russian Federation.
    Filimonov, Victor D.
    Usov, Vladimir Y.
    Borodin, Oleg Y.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Design, synthesis and evaluation of a new Mn - Contrast agent for MR imaging of myocardium based on the DTPA-phenylpentadecanoic acid complex2016Ingår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 665, s. 111-116Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the present paper we describe the first synthesis and evaluation of a novel Mn (II) complex (DTPA-PPDA Mn (II)) which contains a C-15 fatty acid moiety that has high affinity to the heart muscle. The complexation energy of DTPA-PPDA Mn (II) evaluated by quantum chemistry methodology indicates that it essentially exceeds the corresponding value for the known DTPA Mn (II) complex. Molecular docking revealed that the affinity of the designed complex to the heart-type transport protein H-FABP well exceeds that of lauric acid. Phantom experiments in low-field MRI the designed contrast agent provides MR imaging comparable to gadopentetic acid.

  • 38. Birgerson, J.
    et al.
    Keil, M.
    Luo, Yi
    KTH, Tidigare Institutioner, Bioteknologi.
    Svensson, S.
    Ågren, Hans
    KTH, Tidigare Institutioner, Bioteknologi.
    Salaneck, W. R.
    A study of the electronic structure of ethylenedioxythiophene in gas phase using NEXAFS and quantum chemical calculations2004Ingår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 392, nr 1-3, s. 100-104Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Near-edge X-ray absorption fine structure spectroscopy spectra of ethylenedioxythiophene has been recorded in gas phase at the carbon K-edge, sulphur L-edge and oxygen, K-edge. The experimental data has been interpreted with the help of a modified density functional code deMon. The good agreement between the calculated spectra and the measured one allows us to assign all observed resonances. The existence of pi* resonances in both the measured and the calculated OK-edge adsorption spectrum demonstrate that the delocalized pi-system of the thiophene part of the molecule is extended up to the oxygen atoms of the molecule.

  • 39. Bjorneholm, O.
    et al.
    Bassler, M.
    Ausmees, A.
    Hjelte, I.
    Feifel, R.
    Wang, H.
    Miron, C.
    Piancastelli, M. N.
    Svensson, S.
    Sorensen, S. L.
    Gel'mukhanov, Faris
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Doppler splitting of in-flight auger decay of dissociating oxygen molecules: The localization of delocalized core holes2000Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 84, nr 13, s. 2826-2829Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    By exploiting the core-excitation-induced dissociation of O-2, we find that the Auger emission exhibits a Doppler-like energy shift. We show this to be a manifestation of localization of the core hole and propose that the problem of core-hole localization versus delocalization in core-hole spectroscopies may be resolved by considering the nature of the measurement.

  • 40.
    Bondesson, Laban
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Frediani, Luca
    Department of Chemistry, University of Tromsø, Norway.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Mennucci, Bendetta
    Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Italy.
    Solvation of N3- at the water surface: the Polarizable Continuum Model approach2006Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 23, s. 11361-11368Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a new quantum mechanical model to introduce Pauli repulsion interaction between a molecular solute and the surrounding solvent in the framework of the Polarizable Continuum Model. The new expression is derived in a way to allow naturally for a position-dependent solvent density. This development makes it possible to employ the derived expression for the calculation of molecular properties at the interface between two different dielectrics. The new formulation has been tested on the azide anion (N-3(-)) for which we have calculated the solvation energy, the dipole moment, and the static polarizability at the interface as a function of the ion position. The calculations have been carried out for different ion-surface orientations, and the results have also been compared with the parallel electrostatic-only solvation model.

  • 41.
    Bondesson, Laban
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Mikkelsen, Kurt V.
    Department of Chemistry, University of Copenhagen.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Garberg, Per
    Biovitrum AB, Stockholm.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Density functional theory calculations of hydrogen bonding energies of drug molecules2006Ingår i: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 776, nr 1-3, s. 61-68Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Hydrogen bonding energies of several drug molecules have been calculated using hybrid density functional theory with inclusion of basis set superposition error corrections. The calculated total hydrogen bonding energy of each drug molecule has been compared with the result of a conceptually simple additive model, from which the summation of hydrogen bonding energies of individual polar groups present in the drug molecule are considered. It is shown that the validity of the additive model is strongly conditional, and to some extent predictable: In cases where the hydrogen bonding group is isolated the addition model can be of relevance, while in cases where the hydrogen bonding groups are interconnected through pi-conjugation rings or chains of the drug molecules it introduces substantial errors. It is suggested that such strong cooperative effects of hydrogen bonds should always be taken into account for evaluation of the hydrogen bonding energies of drug molecules.

  • 42.
    Bondesson, Laban
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Mikkelsen, Kurt V.
    Department of Chemistry, University of Copenhagen.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Garberg, Per
    Biovitrum AB, Stockholm.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Hydrogen bonding effects on infrared and Raman spectra of drug molecules2007Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 66, nr 2, s. 213-224Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Infrared and Raman spectra of three drug molecules, aspirin, caffeine and ibuprofen, in gas phase and in aqueous solution have been simulated using hybrid density functional theory. The long range solvent effect is modelled by the polarizable continuum model, while the short range hydrogen bonding effects are taken care of by the super-molecular approach with explicit inclusion of water molecules. The calculated spectra are found to compare well with available experimental results. The agreement obtained make grounds for proposing theoretical modeling as a tool for characterizing changes in the bonding environments of drug molecules in terms of particular variations in their IR and Raman spectra.

  • 43. Bouchet, Aude
    et al.
    Brotin, Thierry
    Linares, Mathieu
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Cavagnat, Dominique
    Buffeteaeu, Thierry
    Enantioselective Complexation of Chiral Propylene Oxide by an Enantiopure Water-Soluble Cryptophane2011Ingår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, nr 10, s. 4178-4181Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    ECD and NMR experiments show that the complexation of propylene oxide (PrO) within the cavity of an enantiopure water-soluble cryptophane 1 in NaOH solution is enantioselective and that the (R)-PrO@PP-1 diastereomer is more stable than the (S)-PrO@PP-1 diastereomer with a free energy difference of 1.7 kJ/mol. This result has been confirmed to by molecular dynamics (MD) and ab initio calculations. The enantioselectivity is preserved in LiOH and KOH solutions even though the binding constants decrease, whereas PrO is not complexed in CsOH solution.

  • 44. Bouchet, Aude
    et al.
    Brotin, Thierry
    Linares, Mathieu
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Cavagnat, Dominique
    Buffeteau, Thierry
    Conformational Effects Induced by Guest Encapsulation in an Enantiopure Water-Soluble Cryptophane2011Ingår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, nr 5, s. 1372-1383Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A new water-soluble cryptophane 1 derivative (penta-hydroxyl cryptophane-A) has been synthesized from cryptophanol-A and the chiroptical properties of its two enantiomers M M-1 and P P-1 have been studied by polarimetry, electronic circular dichroism (ECD), and vibrational circular dichroism (VCD). Cryptophane 1 shows specific circular dichroism responses upon complexation that depend on the size of the guest and on the nature of the counterion (Li+, Na+, K+, Cs+) present in the solution. In LiOH and NaOH solutions, chiroptical changes induced by the encapsulation of guests and by the presence of cations in the vicinity of hosts can be interpreted from molecular dynamics (MD) and ab initio calculations by subtle conformational changes of the bridges. In KOH solution, the exchange dynamics is dependent on the size of the guest molecules, whereas in CsOH solution no encapsulation effect is observed whatever the size of the guest molecule. This last behavior comes from the fact that host 1 exhibits a very high affinity for cesium cations.

  • 45. Bratkovsky, Alexander
    et al.
    Ponizovskaya, Ekaterina
    Wang, Shih-Yuan
    Holmström, Petter
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Fotonik och optik.
    Thylén, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Fotonik och optik.
    Fu, Ying
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    A metal-wire/quantum-dot composite metamaterial with negative epsilon and compensated optical loss2008Ingår i: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 93, nr 19, s. 193106-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Numerical simulations of a binary mixture of quantum dots exhibiting gain with silver nanorods are performed, showing the feasibility of lossless negative epsilon operation for realistic material structures and parameters.

  • 46. Brena, Barbara
    et al.
    Siegbahn, Per E. M.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Modeling Near-Edge Fine Structure X-ray Spectra of the Manganese Catalytic Site for Water Oxidation in Photosystem II2012Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, nr 41, s. 17157-17167Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Mn Is near-edge absorption fine structure (NEXAFS) has been computed by means of transition-state gradient-corrected density functional theory (DFT) on four Mn4Ca clusters modeling the successive S-0 to S-3 steps of the oxygen-evolving complex (OEC) in photosystem II (PSII). The model clusters were obtained from a previous theoretical study where they were determined by energy minimization. They are composed of Mn(III) and Mn(IV) atoms, progressing from Mn(III)(3)Mn(IV) for S-0 to Mn(III)(2)Mn(IV)(2) for S-1 to Mn(III)Mn(IV)(3) for S-2 to Mn(IV)(4) for S-3, implying an Mn-centered oxidation during each step of the photosynthetic oxygen evolution. The DFT simulations of the Mn Is absorption edge reproduce the experimentally measured curves quite well. By the half-height method, the theoretical IPEs are shifted by 0.93 eV for the S-0 -> S-1 transition, by 1.43 eV for the S-1 -> S-2 transition, and by 0.63 eV for the S-2 -> S-3 transition. The inflection point energy (IPE) shifts depend strongly on the method used to determine them, and the most interesting result is that the present clusters reproduce the shift in the S-2 -> S-3 transition obtained by both the half-height and second-derivative methods, thus giving strong support to the previously suggested structures and assignments.

  • 47. Bu, L.
    et al.
    Chen, J.
    Wei, X.
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Xie, Y.
    An AIE and ICT based NIR florescent probe for cysteine and homocysteine2017Ingår i: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 136, s. 724-731Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 48.
    C. Couto, Rafael
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Vaz da Cruz, Vinícius
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ertan, Emelie
    Eckert, Sebastian
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    F. Guimarães, Freddy
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Gel’mukhanov, Faris
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Odelius, Michael
    Kimberg, Victor
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Föhlisch, Alexander
    Selective gating to vibrational modes through resonant X-ray scattering2017Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, s. 14165-1-14165-7Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 49. Carniato, S.
    et al.
    Luo, Yi
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Theoretical study of the near-edge Cu L x-ray absorption spectrum of copper phthalocyanine2001Ingår i: Physical Review B Condensed Matter, ISSN 0163-1829, E-ISSN 1095-3795, Vol. 6308, nr 8Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Copper tetraazaporphyrin is used as a model for copper phthalocyanine in theoretical simulations of the features observed at the Cu L-2,L-3 near-edge x-ray absorption spectra. Theoretical results obtained by a density-functional theory approach provided interpretations of the different features observed experimentally, including the so-called white line and the satellite structures, leading to the conclusion that the solid phase arrangement exerts no significant influence on the shape of the Cu L-2,L-3 copper molecular spectrum. The calculations show that the unoccupied 3d levels are essentially located in the plane (3d(x2y2)) of the molecule with a small contribution that has an out-of-plane 3d(z2-y2) and 3d(xz,yz) character. The angular dependence of the copper unoccupied electronic levels could be used to confirm the orientation of the copper tetraazaporphyrin on the substrates.

  • 50. Carravetta, V.
    et al.
    De Abreu Gomes, A. H.
    Monti, S.
    Mocellin, A.
    Marinho, R. R. T.
    Björneholm, O.
    Ågren, Hans
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Naves De Brito, A.
    PH-dependent X-ray Photoelectron Chemical Shifts and Surface Distribution of Cysteine in Aqueous Solution2019Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, nr 17, s. 3776-3785Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

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