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  • 101. Ding, Yubin
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hill, Jonathan P.
    Ariga, Katsuhiko
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Andreasson, Joakim
    Zhu, Weihong
    Tian, He
    Xie, Yongshu
    Acid/Base Switching of the Tautomerism and Conformation of a Dioxoporphyrin for Integrated Binary Subtraction2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 40, p. 12910-12916Article in journal (Refereed)
    Abstract [en]

    Compared with most of the reported logic devices based on the supramolecular approach, systems based on individual molecules can avoid challenging construction requirements. Herein, a novel dioxoporphyrin DPH22 was synthesized and two of its tautomers were characterized by single-crystal X-ray diffraction studies. Compound DPH22 exhibits multichannel controllable stepwise tautomerization, protonation, and deprotonation processes through interactions with H and F- ions. By using the addition of H+ and F- ions as inputs and UVNis absorption values at.1=412, 510, 562, and 603 nm as outputs, the controlled tautomerism of DPH22 has been successfully used for the construction of an integrated molecular level half-subtractor and comparator. In addition, this acid/base-switched tautomerism is reversible, thus endowing the system with ease of reset and recycling; consequently, there is no need to modulate complicated intermolecular interactions and electron-/chargetransfer processes.

  • 102. Ekström, Ulf
    et al.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH.
    Carravetta, Vincenzo
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Polarization propagator for X-ray spectra2006In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 97, no 14Article in journal (Refereed)
    Abstract [en]

    A polarization propagator for x-ray spectra is outlined and implemented in density functional theory. It rests on a formulation of a resonant-convergent first-order polarization propagator approach which makes it possible to directly calculate the x-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted x-ray spectrum relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects.

  • 103. Engstrom, M.
    et al.
    Himo, Fahmi
    KTH, Superseded Departments, Biotechnology.
    Graslund, A.
    Minaev, B.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Hydrogen bonding to tyrosyl radical analyzed by ab initio g-tensor calculations2000In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 104, no 21, p. 5149-5153Article in journal (Refereed)
    Abstract [en]

    Hydrogen bonding to the tyrosyl radical in ribonucleotide reductase (RNR) has been simulated by a complex between the phenoxyl radical and a water molecule. Multiconfigurational self-consistent field linear response theory was used to calculate the g-tensor of the isolated phenoxyl radical and of the phenoxyl-water model. The relevance of the model was motivated by the fact that spin density distributions and electron paramagnetic resonance (EPR) spectra of the phenoxyl and tyrosyl radicals are very similar. The calculated g-tensor anisotropy of the phenoxyl radical was comparable with experimental findings for tyrosyl in those RNRs where the H-bond is absent: g(x) = 2.0087(2.0087), g(y) = 2.0050(2.0042), and g(z) = 2.0025(2.0020), where the tyrosyl radical EPR data from Escherichia coli RNR are given in parentheses. The hydrogen bonding models reproduced a shift toward a lower g(x) value that was observed experimentally for mouse and herpes simplex virus RNR where the H-bond was detected by electron-nuclear double resonance after deuterium exchange. This decrease could be traced to lower angular momentum and spin-orbit coupling matrix elements between the ground B-2(1) and the first excited B-2(2) states (oxygen lone-pair n to pi(SOMO) excitation) upon hydrogen bonding in a linear configuration. The g(x) value was further decreased by hydrogen bonding in bent configurations due to a blue shift of this excitation.

  • 104. Engstrom, M.
    et al.
    Himo, Fahmi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Ab initio g-tensor calculations of the thioether substituted tyrosyl radical in galactose oxidase2000In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 319, no 04-mar, p. 191-196Article in journal (Refereed)
    Abstract [en]

    The tyrosyl radical in galactose oxidase is covalently cross-linked to a neighboring cysteine residue through a thioether bond. The role of this sulfur cross-link has been discussed ever since the crystal structure of the enzyme was solved. In the present work, the ab initio multiconfigurational linear response method is applied to calculate the g-tensor of unsubstituted and thioether substituted phenoxyl radicals. In contrast to some previous interpretations, but in agreement with recent EPR measurements, we find that the sulfur substitution induces only minor shifts in the g-tensor components. The spin distribution retains the odd-alternant pattern of the unsubstituted radical and only a small amount of spin is localized to the sulfur center.

  • 105. Engstrom, M.
    et al.
    Vaara, J.
    Schimmelpfennig, B.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Density functional theory calculations of electron paramagnetic resonance parameters of a nitroxide spin label in tissue factor and factor VIIa protein complex2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 47, p. 12354-12360Article in journal (Refereed)
    Abstract [en]

    The electron paramagnetic resonance (EPR) g and N-14 hyperfine coupling (A) tensors of a nitroxide spin label are calculated with density-functional theory (DFT). The influence on the spin label from nearby amino acids in the extracellular part of tissue factor (sTF) and activated factor VII (FVIIa) protein complex is investigated. For that purpose, the nitroxide unit and six surrounding amino acids within 5 Angstrom are selected on the basis of a molecular mechanics structure of the protein complex. The effects of the surroundings on the EPR parameters of the spin label can be divided into indirect effects caused by the induced structure changes of the spin label and direct effects. The structural changes are larger in the present case. The experimentally measurable hyperfine tensor component perpendicular to the molecular plane of the spin label, A(zz), as well as the g tensor component along the NO direction, g,,, are significant probes of the intramolecular structure of the spin label. This indicates the possibility of relating EPR properties to the geometric structure of radical sites. The direct environmental effects on the g tensor from the surrounding amino acids mainly affect the second-order spin-orbit/orbital Zeeman cross-term contributions from the spin label itself. The direct effects originating elsewhere in the model are small. Neither the g nor A tensors display additivity of the effects of individual amino acids on the final observable. The results underline the feasibility of DFT calculations of the EPR parameters in large molecular systems, such as spin labels and other radicals in proteins.

  • 106. Engstrom, M.
    et al.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    MCSCF and DFT calculations of EPR parameters of sulfur centered radicals2000In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 328, no 06-apr, p. 483-491Article in journal (Refereed)
    Abstract [en]

    The EPR parameters of sulfur centered radicals are different depending on the radical structure, charge and solvent. That is, the g- and A-tensor components provide significant patterns which may distinguish sulfur radical structures from each other. In the present work, these EPR parameters were calculated for monosulfide radicals (RS'), disulfide radicals (RSS.), radical cations ((RSSR+)-S-.) and anions ((RSSR-)-S-.), with R = CH3, using the MCSCF linear response and DFT/B3LYP methods. Results were in agreement with experimental data for the cases when well-resolved EPR spectra are available. Especially, the assignment of the disulfide anion in ribonucleotide reductase was confirmed. The results indicate that investigations with the present computational methods on refined structures and solvent modeling may provide interpretations of experimental data on unassigned radical species.

  • 107. Eriksen, Janus J.
    et al.
    Olsen, Jogvan Magnus H.
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mikkelsen, Kurt V.
    Kongsted, Jacob
    Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 13, p. 2853-2864Article in journal (Refereed)
    Abstract [en]

    In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.

  • 108. Fahleson, Tobias
    et al.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Linköping University, Sweden.
    A Polarization Propagator for Nonlinear X-ray Spectroscopies2016In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 7, no 11, p. 1991-1995Article in journal (Refereed)
    Abstract [en]

    A complex polarization propagator approach has been developed to third order and implemented in density functional theory (DFT), allowing for the direct calculation of nonlinear molecular properties in the X-ray wavelength regime without explicitly addressing the excited-state manifold. We demonstrate the utility of this propagator method for the modeling of coherent near-edge X-ray two-photon absorption using, as an example, DFT as the underlying electronic structure model. Results are compared with the corresponding near edge X-ray absorption fine structure spectra, illuminating the differences in the role of symmetry, localization, and correlation between the two spectroscopies. The ramifications of this new technique for nonlinear X-ray research are briefly discussed.

  • 109. Feifel, R.
    et al.
    Baev, Alexander
    KTH, Superseded Departments, Chemistry.
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Chemistry.
    Ågren, Hans
    KTH, Superseded Departments, Chemistry.
    Andersson, M.
    Ohrwall, G.
    Piancastelli, M. N.
    Miron, C.
    Sorensen, S. L.
    de Brito, A. N.
    Bjorneholm, O.
    Karlsson, L.
    Svensson, S.
    Role of stray light in the formation of high-resolution resonant photoelectron spectra: an experimental and theoretical study of N-22004In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 134, no 1, p. 49-65Article in journal (Refereed)
    Abstract [en]

    We show that the undular stray light, diffusely scattered by the optical system of a synchrotron beamline, can play an important role in the formation of high-resolution resonant photoelectron (RPE) spectra. The influence of the stray light is mediated through the Stokes doubling effect, with the Lorentzian tail of the spectral function being replaced by a more complicated form. This effect is shown to appear in the high-resolution resonant photoelectron spectrum of the N-2 molecule in which the spectral shape of the non-Raman (NR) bands differs qualitatively for the A(2)Pi(u) and X(2)Sigma(g)(+) final states. A particularly large enhancement of the non-Raman Stokes line is observed for the A-state while the picture is inverted for the X-state where the non-Raman band is suppressed. It is shown that the resonant photoemission profile is affected by two qualitatively different detunings, the detuning of the monochromatized line relative to the photoabsorption line and the detuning of the undulator harmonic relative to the same reference line. The experimental data show that the relative intensity of the non-Raman line strongly depends on the tuning of the undulator harmonic with respect to the selected monochromator bandpass, leading to a strong decrease of the Stokes line intensity for certain undulator detunings. A clear red-shift asymmetry for the decrease in the Stokes line intensity is observed when the monochromator line is detuned towards negative photon frequencies, whereas the picture is reverted for the situation of a positively detuned monochromator line. The results show the necessity to control the stray light and to investigate both the Raman and non-Raman contributions to the spectral profiles in order to avoid misinterpretation and in order to make full use of the information available in resonant photoemission spectra of molecules.

  • 110. Feifel, R.
    et al.
    Baev, Alexander
    KTH, Superseded Departments, Biotechnology.
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Piancastelli, M. N.
    Andersson, M.
    Öhrwall, G.
    Miron, C.
    Meyer, M.
    Sorensen, S. L.
    de Brito, A. N.
    Björneholm, O.
    Karlsson, L.
    Svensson, S.
    Generalization of the duration-time concept for interpreting high-resolution resonant photoemission spectra2004In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 69, no 2, p. 022707-Article in journal (Refereed)
    Abstract [en]

    The duration-time concept, vastly successful for interpreting the frequency dependence of resonant radiative and nonradiative x-ray scattering spectra, is tested for fine-scale features that can be obtained with state of the art high-resolution spectroscopy. For that purpose resonant photoelectron (RPE) spectra of the first three outermost singly ionized valence states X (2)Sigma(g)(+), A (2)Pi(u), and B (2)Sigma(u)(+), are measured for selective excitations to different vibrational levels (up to n=13) of the N 1s-->pi(*) photoabsorption resonance in N-2 and for negative photon frequency detuning relative to the adiabatic 0-0 transition of this resonance. It is found that different parts of the RPE spectrum converge to the spectral profile of direct photoionization (fast scattering) for different detunings, and that the RPE profiles are asymmetrical as a function of frequency detuning. The observed asymmetry contradicts the picture based on the simplified notation of a common scattering duration time, but is shown to agree with the here elaborated concept of partial and mean duration times. Results of the measurements and the simulations show that the duration time of the scattering process varies for different final electronic and different final vibrational states. This owes to two physical reasons: one is the competition between the fast vertical and the slow resonant scattering channels and the other is the slowing down of the scattering process near the zeros of the real part of the scattering amplitude.

  • 111. Feifel, R
    et al.
    Burmeister, F
    Salek, Pawel
    KTH, Superseded Departments, Biotechnology.
    Piancastelli, N
    Bassler, M
    Sorensen, L
    Miron, C
    Wang, H
    Hjelte, I
    Bjorneholm, O
    de Brito, N
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Svensson, S
    Observation of a continuum-continuum interference hole in ultrafast dissociating core-excited molecules2000In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 85, no 15, p. 3133-3136Article in journal (Refereed)
    Abstract [en]

    The femtosecond dissociation of HCl after core excitation has been studied through the resonant Auger decay. The spectra contain contributions from decay occurring at both "molecular" and "atomic" internuclear distances. We have observed a new interference mechanism in these spectra: An atomic spectral line develops into a negative spectral contribution, a "hole," when detuning the excitation energy from the maximum of the Cl 2p(-1)sigma* resonance. Resonant x-ray scattering theory quantitatively explains this behavior as due to a novel destructive continuum-Continuum interference between molecular and atomic contributions to the Auger decay.

  • 112. Feifel, R.
    et al.
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Baev, A.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Piancastelli, M. N.
    Bassler, M.
    Miron, C.
    Sorensen, S. L.
    de Brito, A. N.
    Bjorneholm, O.
    Karlsson, L.
    Svensson, S.
    Interference quenching of nu('')=1 vibrational line in resonant photoemission of N-2: A possibility to obtain geometrical information on the core-excited state2002In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 89, no 10Article in journal (Refereed)
    Abstract [en]

    An interference quenching of the nu=1 vibrational line in the resonant Auger decay of N 1s-->pi(*) core-excited N-2 is observed and analyzed. The intensity ratio between the nu=1 and nu=0 vibrational levels of the X(2)Sigma(g)(+) final state shows a surprising nonmonotonous variation as a function of frequency detuning, going through a minimum with a complete suppression of nu=1. We have developed a simple model which shows a linear relation between the value of the detuning frequency for this minimum and the equilibrium bond distance R-c(0) of the core-excited state. A new way is thus established of determining the equilibrium bond distance for the core-excited state with a precision deltaR(c)(0)<10(-3) Angstrom.

  • 113. Feifel, R.
    et al.
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Baev, Alexander
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Miron, C.
    Ohrwall, G.
    Piancastelli, M. N.
    Sorensen, S. L.
    Karlsson, L.
    Svensson, S.
    Profile of resonant photoelectron spectra versus the spectral function width and photon frequency detuning2004In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 70, no 3Article in journal (Refereed)
    Abstract [en]

    The outermost, singly ionized valence state of N-2, the X (2)Sigma(g)(+) state, is investigated in detail as a function of the photon frequency bandwidth for core excitation to the N 1s-->pi(*) resonance, where the photon frequency is tuned in between the first two vibrational levels of this bound intermediate electronic state. We find a strong, nontrivial dependence of the resulting resonant photoemission spectral profile on the monochromator function width and the frequency of its peak position. For narrow bandwidth excitation we observe a well resolved vibrational fine structure in the final electron spectrum, which for somewhat broader bandwidths gets smeared out into a continuous structure. For even broader monochromator bandwidths, it converts again into a well resolved vibrational progression. In addition, spectral features appearing below the adiabatic transition energy of the ground state of N-2(+) are observed for broadband excitation. A model taking into account the interplay of the partial scattering cross section with the spectral function is presented and applied to the X (2)Sigma(g)(+) final state of N-2(+).

  • 114.
    Felicissimo, V.C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Cesar, A.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Probing weak molecular orbital interactions in non-conjugated diene molecules by means of near-edge X-ray absorption spectroscopy2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 33, p. 7385-7395Article in journal (Refereed)
    Abstract [en]

    Carbon and oxygen near-edge X-ray absorption fine structure (NEXAFS) spectra of 1,4-cyclohexadiene, p-benzoquinone, norbornadiene, norbornadienone, and cis-cis-[4,4,2]propella-3,8-diene-11,12-dione were calculated by means of Hartree-Fock and hybrid density functional theory using the static-exchange (STEX) approximation. The NEXAFS spectra are used as a probe to identify weak molecular interactions between the two non-conjugated ethylenic pi* orbitals present in these molecules. We show that the X-ray absorption spectrum of 1,4-cyclohexadiene exhibits some particular spectral structures in the discrete energy region that evidence diene through-bond orbital interaction, whereas absorption peaks are identified in the norbornadiene and norbornadienone spectra that indicate effective through-space orbital interactions. The molecular structure of the cis-cis-[4,4,2]propella-3,8-diene-11,12-dione isomer is such that the indirect through-bond or through-space diene orbital interactions are too weak to be assigned by its C1s NEXAFS spectrum.

  • 115.
    Felicissimo, V.C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Guimaraes, F.F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Cesar, A.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Proton transfer mediated by the vibronic coupling in oxygen core ionized states of glyoxalmonoxime studied by infrared-X-ray pump-probe spectroscopy.2006In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 47, p. 12805-12813Article in journal (Refereed)
    Abstract [en]

    The theory of IR-X-ray pump-probe spectroscopy beyond the Born-Oppenheimer approximation is developed and applied to the study of the dynamics of intramolecular proton transfer in glyoxalmonoxime leading to the formation of the tautomer 2-nitrosoethenol. Due to the IR pump pulses the molecule gains sufficient energy to promote a proton to a weakly bound well. A femtosecond X-ray pulse snapshots the wave packet route and, hence, the dynamics of the proton transfer. The glyoxalmonoxime molecule contains two chemically nonequivalent oxygen atoms that possess distinct roles in the hydrogen bond, a hydrogen donor and an acceptor. Core ionizations of these form two intersecting core-ionized states, the vibronic coupling between which along the OH stretching mode partially delocalizes the core hole, resulting in a hopping of the core hole from one site to another. This, in turn, affects the dynamics of the proton transfer in the core-ionized state. The quantum dynamical simulations of X-ray photoelectron spectra of glyoxalmonoxime driven by strong IR pulses demonstrate the general applicability of the technique for studies of intramolecular proton transfer in systems with vibronic coupling.

  • 116.
    Felicissimo, Viviane C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Guimaraes, Freddy Fernandes
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cesar, A.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    The principles of infrared-x-ray pump-probe spectroscopy. Applications on proton transfer in core-ionized water dimers2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 9, article id 094319Article in journal (Refereed)
    Abstract [en]

    In this paper we derive the basic physics underlying infrared-x-ray pump-probe spectroscopy (IR, infrared). Particular features of the spectroscopy are highlighted and discussed, such as dependence on phase of the infrared pulse, duration and delay time of the x-ray pulse, and molecular orientation. Numerical applications are carried out for the water dimer using wave packet techniques. It is shown that core ionization of the donor oxygen of the water dimer results in a drastic change of the potential with the global minimum placed in the proton transfer region. The results of the modeling indicate that IR-x-ray pump-probe spectroscopy can be used to study the dynamics of proton transfer in this core-ionized state, and that, contrary to conventional core level photoelectron spectroscopy, x-ray core-ionization driven by an IR field is a proper method to explore the proton transfer in a system like the water dimer. We observe that the trajectory of the nuclear wave packet in the ground state potential well is strongly affected by the absolute phase of the IR pulse.

  • 117.
    Felicissimo, Viviane
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Minkov, Ivaylo
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Guimaraes, Freddy Fernandes
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cesar, A.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A theoretical study of the role of the hydrogen bond on core ionization of the water dimer2005In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 312, no 1-3, p. 311-318Article in journal (Refereed)
    Abstract [en]

    Motivated by the interest in using X-ray spectra for probing of hydrogen bonded networks we developed a quantum model for simulations of the electronic-vibrational profile of the X-ray core photoelectron spectrum of the water dimer. It is found that the potential surfaces of the donor and acceptor O1s core-ionized states of this system display a qualitative difference. Large gradients of the potential in the core ionized state along some intermolecular coordinates combined with small vibrational frequencies breaks down completely the harmonic approximation. The band profiles are therefore treated using a quasi-continuum approximation. The weak hydrogen bonding and the drastic change of water dimer potential under core ionization is responsible for the anomalously strong vibrational broadening: 0.4 eV for the acceptor band and 0.6 eV for the donor band. The core ionization of the donor oxygen is accompanied by proton transfer which should be observable in X-ray fluorescence or Auger spectra.

  • 118. Feng, Yanli
    et al.
    Zhang, Qiong
    Tan, Wenjuan
    Zhang, Deqing
    Tu, Yaoquan
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tian, He
    A supramolecular photoswitch constructed by intermolecular hydrogen bond between BTEPy and TTF-COOH2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 455, no 4-6, p. 256-260Article in journal (Refereed)
    Abstract [en]

    A novel supramolecular photoswitch containing bisthienylethene- pyridine (BTEPy) and carboxyl attached tetrathiafluvalene (TTF-COOH) was constructed via intermolecular hydrogen bond. FT-IR spectra, XPS characterizations, H-1 NMR and theoretical calculation were carried out to verify the formation of the intermolecular hydrogen bond. The supramolecular self-assemblies BTEPy 2TTF show good photo-chromic properties. A molecular switch with UV/vis light as inputs and electrochemical signals as outputs was obtained.

  • 119. Ferrighi, Lara
    et al.
    Frediani, Luca
    Cappelli, Chiara
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Helgaker, Trygve
    Ruud, Kenneth
    Density-functional-theory study of the electric-field-induced second harmonic generation (EFISHG) of push-pull phenylpolyenes in solution2006In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 425, no 4-6, p. 5593-5603Article in journal (Refereed)
    Abstract [en]

    Density-functional theory and the polarizable continuum model have been used to calculate the electric-field-induced second harmonic generation of a series of push-pull phenylpolyenes in chloroform solution. The calculations have been performed using both the Becke 3-parameter Lee-Yang-Parr functional and the recently developed Coulomb-attenuated method functional. Solvation has been investigated by examining the effects of the reaction field, non-equilibrium solvation, geometry relaxation, and cavity field. The inclusion of solvent effects leads to significantly better agreement with experimental observations.

  • 120.
    Frecus, Bogdan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    EPR spin Hamiltonian parameters of encapsulated spin-labels: impact of the hydrogen bonding topology2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 7, p. 2427-2434Article in journal (Refereed)
    Abstract [en]

    Encapsulation of spin-labels into "host'' compounds, like cucurbit[n]urils or cyclodextrins, in solutions has profound effects on the EPR spin Hamiltonian parameters of the spin-labels. In this work we study the microscopic origin of the EPR spin Hamiltonian parameters of spin-labels enclosed in hydrophobic cavities. We focus on the dependence of the EPR properties of encapsulated spin-labels on the hydrogen bonding topologies that occur upon encapsulation, and quantize various contributions to these parameters according to specific hydrogen bonding patterns. The obtained results provide refined insight into the role of the hydrogen bonding induced encapsulation shifts of EPR spin Hamiltonian parameters in solvated "spin-label@host compound'' complexes.

  • 121.
    Frecus, Bogdan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    π –stacking effects on the EPR parameters of a prototypical DNA spin label2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 25, p. 10466-10471Article in journal (Refereed)
    Abstract [en]

    The character and value of spin labels for probing environments like double-stranded DNA depends on the degree of changeof the spin Hamiltonian parameters of the spin label induced by the environment. Herein we provide a systematic theoreticalinvestigation of this issue, based on a density functional theory method applied to a spin labeled DNA model system, focusingon the dependence of the EPR properties of the spin label on the π stacking and hydrogen bonding that occur upon incorporatingthe spin label into selected base pair inside DNA. It is found that the EPR spin Hamiltonian parameters of the spin label is onlynegligibly affected by its incorporation into DNA, when compared to the its free form. This result gives theoretical ground forthe common empirical assumption regarding the behaviour of spin Hamiltonian parameters made in EPR based measurementsof distance between spin labels incorporated into DNA.

  • 122. Frediani, L.
    et al.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Two-photon absorption in solution by means of time-dependent density-functional theory and the polarizable continuum model2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 24Article in journal (Refereed)
    Abstract [en]

    We present the first study of two-photon absorption (TPA) of solvated molecules based on direct evaluation of TPA cross sections from the quadratic response of time-dependent perturbations. A set of prototypical two-photon (TP) chromophores has been selected and analyzed: a pure pi system (t-stilbene) and its substituted homologs obtained employing a donor (D) and an acceptor (A) group to probe the solvent effects along the series pi, D-pi-D, A-pi-D, and A-pi-A. For the selected systems we have calculated the TPA cross sections in different environments by means of the polarizable continuum model. The data have been analyzed to evaluate how the structural and environmental parameters contribute to the final two-photon absorption cross section. These include molecular structure, geometry relaxation in solution, polarity, and refractive index of the solvent. The performances of the three common functionals SVWN, BLYP, and B3LYP have been compared. The results show a significant solvent dependence of the TPA cross section and an unusual trend when passing from cyclohexane to water. The data have also been rationalized in terms of the main orbital excitations leading to the transitions. Finally, trends along the series have been described and comparison with experiments and previous calculations has been drawn.

  • 123. Frediani, L.
    et al.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ferrighi, L.
    Ruud, K.
    Second-harmonic generation of solvated molecules using multiconfigurational self-consistent-field quadratic response theory and the polarizable continuum model2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 14Article in journal (Refereed)
    Abstract [en]

    We present the first implementation of the quadratic response function for multiconfigurational self-consistent-field wave functions of solvated molecules described by a polarizable continuum model employing a molecule-shaped cavity. We apply the methodology to the first hyperpolarizability beta and, in particular, the second-harmonic generation process for a series of conjugated push-pull oligomers, as well as for para-nitroaniline. The effect of solvation on the dispersion of the hyperpolarizability and the change in the hyperpolarizability for increasing chain length of the oligomers in vacuum and in solution is considered. The effect of a correlated description is analyzed by comparing the Hartree-Fock hyperpolarizabilities to the multiconfigurational self-consistent-field hyperpolarizabilities. The effect of geometry relaxation in the solvent on the properties of the solvated molecules are also investigated.

  • 124. Friedlein, R.
    et al.
    Sorensen, S. L.
    Baev, Alexander
    KTH, Superseded Departments, Biotechnology.
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Birgerson, J.
    Crispin, A.
    de Jong, M. P.
    Osikowicz, W.
    Murphy, C.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Salaneck, W. R.
    Role of electronic localization and charge-vibrational coupling in resonant photoelectron spectra of polymers: Application to poly(para-phenylenevinylene)2004In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 69, no 12Article in journal (Refereed)
    Abstract [en]

    A combination of x-ray absorption and resonant photoemission (RPE) spectroscopy has been used to study the electronic structure of the one-dimensional conjugated polymer poly (para-phenylenevinylene) in nonordered (as prepared) thin films. The dispersion of RPE features for the decay to localized and delocalized bands are qualitatively different. A theory for band dispersion of RPE in polymers is given, showing the important roles of electronic state localization and vibrational (phonon) excitations for the character of the dispersion.

  • 125.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Berglind, Eilert
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics.
    Thylén, Lars
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Optical transmission and waveguiding by excitonic quantum dot lattices2006In: Journal of the Optical Society of America. B, Optical physics, ISSN 0740-3224, E-ISSN 1520-8540, Vol. 23, no 11, p. 2441-2447Article in journal (Refereed)
    Abstract [en]

    Metal-dielectric-metal configurations of optical waveguides have a very high laterally packaging density at the cost of high optical loss. Photonic crystals based on refractive-index-modulation materials have been used in optics, e.g., two materials having different refractive indices form a well-defined Bragg refraction mirror. Such a waveguide has lower loss but also lower packaging density. From the outset of these two notions, we propose a photonic-crystal device based on the exciton-polariton effect in a three-dimensional array of semiconductor quantum dots (QDs) for ultradense optical planar circuit applications. Excitons are first photogenerated in the QDs by the incident electromagnetic field, the exciton-polariton effect in the QD photonic crystal then induces an extra optical dispersion in QDs. The high contrast ratio between the optical dispersions of the QDs and the background therefore creates clear photonic bandgaps. By carefully designing the QD size and the QD lattice structure, perfect electromagnetic field reflection can be obtained at a specific wavelength in the lossless case, thus providing the fundamental basis for ultradense optical waveguide applications.

  • 126.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Han, Tiantian
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Dynamic analysis of multiple-photon optical processes in semiconductor quantum dots2006In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 18, no 39, p. 9071-9082Article in journal (Refereed)
    Abstract [en]

    Semiconductor quantum dots (QDs) have been gaining much attention because of their outstanding properties for multiple-photon microscopy applications. By solving nonperturbatively the time-dependent Schrodinger equation, it has been shown that the large number of energy states densely compacted in both the conduction and valence bands of the QD greatly enhance the inter-band and intra-band optical couplings between two energy states induced by multiple photons from ultra-fast and ultra-intense lasers. The multiphoton absorption processes are further enhanced by many energy relaxation processes in commonly used semiconductors, which are generally represented by the relaxation energy in the order of tens of meV. Numerical calculation of multiphoton processes in QDs agrees with experimental demonstration. After proper designing, QDs can be activated by infrared radiation to emit radiation in the visible optical regime (up-conversion) for bioimaging applications.

  • 127.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Han, Tiantian
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Multiphoton excitation of quantum dots by ultrashort and ultraintense laser pulses2006In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 88, no 22, p. 221114-1-221114-3Article in journal (Refereed)
    Abstract [en]

    Multiphoton optical processes in semiconductor quantum dots (QDs) excited by ultrafast (femtosecond) and ultraintense (GW/cm(2)) lasers are considered as the ultimate tags for cellular bioimaging. By solving the time-dependent Schrodinger equation unperturbatively, experimentally observed strong multiphoton excitation is reproduced when optical transitions among all confined states and a few hundred more extended states are taken into account. Model calculations indicate a significant excitation of a CdS QD of 3.7 nm in radius by a 100 fs laser pulse with a 10 GW/cm(2) peak optical power. The excitation rate is almost constant between 1300 and 560 nm, a useful region for bioimaging.

  • 128.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Han, Tiantian
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Lin, L.
    Institute of Modern Optics, Nankai University.
    Chen, P.
    Institute of Modern Optics, Nankai University.
    Liu, Y.
    Institute of Modern Optics, Nankai University.
    Tang, G.-Q.
    Institute of Modern Optics, Nankai University.
    Wu, J.
    National Lab. for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences.
    Yue, Y.
    National Lab. for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences.
    Dai, N.
    National Lab. for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences.
    Design of semiconductor CdSe core ZnS/CdS multishell quantum dots for multiphoton applications2007In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 90, no 17, p. 173102-1-173102-3Article in journal (Refereed)
    Abstract [en]

    Optical properties of colloidal II-VI semiconductor CdSe cores with ZnS and CdS multishell quantum dots (QDs) have been studied by experimental characterization and theoretical analysis. Due to the large number of energy states densely compacted in both conduction and valence bands of the quantum dots, strong interband and intraband optical couplings are induced by the multiphoton excitation, implicating an efficient fluorescence of such II-VI-based core-multishell CdSe QDs. This fact in combination with the advantage of the size tolerance of II-VI QDs with respect to the narrow fluorescence bandwidth make these systems excellent candidates for applications using fluorescence induced by multiphoton excitation.

  • 129.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hellström, Staffan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nonlinear optical properties of quantum dots: Excitons in nanostructures2009In: Journal of nonlinear optical physics and materials, ISSN 0218-8635, Vol. 18, no 2, p. 195-226Article, review/survey (Refereed)
    Abstract [en]

    We review the concepts of excitons and excitonic polaritons, their nonlinear optical properties in nanostructures and their applications within integrated electronics and optoelectronics. Various theoretical aspects of excitons and excitonic polaritons are introduced, followed by a summary of their experimental and application-specific development in nanostructures at the electronic and photonic engineering levels. A number of technical applications are highlighted.

  • 130.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Multiple-photon spectrum of CdS semiconductor quantum dot for bioimaging2006In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 515, no 2, p. 842-845Article in journal (Refereed)
    Abstract [en]

    We study the dynamic processes of multiple-photon absorption and emission in a semiconductor quantum dot. By the non-perturbative time-dependent Schrodinger equation, it is shown that electrons in the quantum dot can be optically excited from the valence band to the conduction band via multiphoton processes, leaving holes in the valence band. The radiative recombination of the conduction-band electrons with the valence-band holes results in optical emission of a single photon having an energy which is larger than the input photon energy, resulting in the high-photon-energy luminescence from the quantum dot activated by low-energy photons to emit radiation in the visible optical regime for bioimaging application.

  • 131.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Thylén, Lars
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    A lossless negative dielectric constant from quantum dot exciton polaritons2008In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 8, no 5, p. 1551-1555Article in journal (Refereed)
    Abstract [en]

    Prospects for a lossless negative dielectric constant material for optical devices are studied. Simulations show that with sufficient gain, a mixture of two semiconductor quantum dots (QDs) can produce an effective dielectric constant that is lossless and negative. This permits, in concept, arbitrarily small scaling of the optical mode volume, a major goal in the field of nanophotonics. The proposed implementation of a lossless negative dielectric constant material based on colloidal QDs opens a tractable path.

  • 132.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zeng, Yong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Berglind, Eilert
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics.
    Thylén, Lars
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Nanoscale excitonic-plasmonic optical waveguiding by metal-coated quantum dots2006In: Proceedings of International Symposium on Biophotonics, Nanophotonics and Metamaterials, 2006, p. 426-431Conference paper (Refereed)
    Abstract [en]

    A three-dimensional metal-coated semiconductor-quantum-dot (QD) nanoscale lattice structure is designed for optical waveguiding. It is based on three notions: i) Excitons are first photogenerated in the QDs by the incident electromagnetic field which is the optical wave to be guided: ii) The exciton-polariton effect in the QD structure induces an extra optical dispersion in the QDs: iii) The high contrast ratio between the optical dispersions of the QDs and the background material creates clear photonic bandgaps. By carefully designing the QD size and the QD lattice structure, perfect electromagnetic field reflection can be obtained for the incident wave in the lossless case, thus providing the fundamental basis of QDs for optical waveguide applications. Metal coating at the QD surface generates a surface plasmon spatially confined in the QD so that the exciton generation becomes enhanced for a better dielectric modulation.

  • 133.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Zeng, Yong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Surface-plasmon-assisted electromagnetic field enhancement in semiconductor quantum dots2007In: Applied Physics A: Materials Science & Processing, ISSN 0947-8396, E-ISSN 1432-0630, Vol. 87, no 2, p. 167-169Article in journal (Refereed)
    Abstract [en]

    The temporal development of incident electromagnetic plane waves across semiconductor quantum dots (QDs) is analyzed by the finite-difference time-domain method. By coating the QDs using thin metal films, surface plasmon polaritons (SPPs) can be created. As illustration, our modeling approach is applied to fluorescent multiphoton quantum dots made of cadmium sulphide of particular size (3.7 nm) and energy band gap (2.67 eV). When such a QD is coated by a metal film, a dipole-formed SPP is generated at the external surface of the coated QD by the incident electromagnetic wave with a photon energy of 1.34 eV corresponding to a two-photon process. When the thickness of the metal film is 0.37 nm, the peak intensity of the SPP oscillates through both the thin metal film and the core QD, resulting in an electromagnetic field inside the QD enhanced by a factor of 10, and thus an increased two-photon excitation that can be useful for bioimaging applications. Further increasing the metal film thickness blockades the SPP initially generated at the external surface of the coated QD from penetrating through the metal film, reducing the electromagnetic field inside the QD.

  • 134.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhou, Y. -H
    Su, H.
    Boey, F. Y. C.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Nanyang Technological University, Singapore .
    Reply to "comment on 'impact ionization and auger recombination rates in semiconductor quantum dots'"2010In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 39, p. 16860-16860Article in journal (Refereed)
  • 135.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Zhou, Y. H.
    Su, Haibin
    Boey, F. Y. C.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Impact Ionization and Auger Recombination Rates in Semiconductor Quantum Dots2010In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 9, p. 3743-3747Article in journal (Refereed)
    Abstract [en]

    Impact ionization and Auger recombination in nanoscale spherical quantum dots (QDs) have been Studied theoretically. It is shown that due to the strong quantum confinement of both electrons in the conduction band and holes ill the valence band. impact ionization and Auger recombination energies in these QDs call be oil the order of a few millielectronvolts when various selection rules are fulfilled, which are Much higher than spontaneous radiative emission energies. This explains the experimentally reported high Occurrence rates of the multiple exciton generation (MEG) effect in QDs. However, due to quantum confinement, the energy States are discrete in QDs, especially for low-energy states where the densities of states are low. This implies that only a limited number of high-energy electron states call interact with (i.e., impact ionize) low-energy hole states in QDs having certain values of radii due to the energy conservation requirement. This explains the vastly scattered experimental data and difficulties ill Utilizing the MEG effect in practice.

  • 136.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Optical Properties of Quantum Dot Nano-composite Materials Studied by Solid-State Theory Calculations2012In: Handbook of Computational Chemistry / [ed] J. Leszczynski, Springer Berlin/Heidelberg, 2012, p. 869-899Chapter in book (Refereed)
    Abstract [en]

    This chapter reviews the fundamental concepts of excitons and excitonic polaritons and their extraordinary optical properties in quantum dot nano-composite materials. By starting with the optical excitation of an exciton in the nanostructure we show that the effective dielectric constant of the nanostructure becomes significantly modified due to the exciton generation and recombination, resulting in high positive and negative dielectric constants. We also discuss single exciton generation by multiple photons and multiple exciton generation by single photon. All these nonlinear optical properties of quantum dot nano-composite materials offer novel possibilities and are expected to have deep impact in nanophotonics.

  • 137.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Andersson, J. Y.
    Asplund, C.
    Qiu, Min
    KTH, School of Information and Communication Technology (ICT), Microelectronics and Applied Physics, MAP.
    Thylén, Lars
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics (Closed 20120101).
    Optical reflection from excitonic quantum-dot multilayer structures2008In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 93, no 18, p. 183117-Article in journal (Refereed)
    Abstract [en]

    We study theoretically and experimentally the optical reflection from excitonic quantum-dot (QD) multilayer structures composed of InAs QDs in a GaAs substrate. Quantum mechanical and finite-difference time-domain numerical calculations indicate that the incident radiation in the optical reflectance measurement photoexcites the InAs QDs which then form excitonic dipoles. The excitonic dipole modifies significantly the dielectric constant of the QD, which results in a reflectance peak in the vicinity of the excitonic energy, as observed experimentally.

  • 138.
    Fu, Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kowalewski, Jacob
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Wu, J.
    Yue, Y.
    Dai, N.
    Thylén, Lars
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics. KTH, School of Information and Communication Technology (ICT), Centres, Kista Photonics Research Center, KPRC.
    Radiative and nonradiative recombination of photoexcited excitons in multi-shell-coated CdSe/CdS/ZnS quantum dots2009In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 86, no 3, p. 37003-Article in journal (Refereed)
    Abstract [en]

    Colloidal quantum dots (QDs) have been widely studied for nanophotonics and bioimaging applications for which the lifetime of their fluorescence is of critical importance. We report experimental and theoretical characterizations of dynamic optical properties of multi-shell-coated CdSe/CdS/ZnS QDs. Quantum-mechanical studies of fundamental optical excitations and Monte Carlo simulations of energy relaxation mechanisms indicate that the excitonic states are densely compacted in the QDs and are easily photoexcited by the laser pulse in the presence of nonradiative electron-phonon interactions. For spherical QDs, the decay time of spontaneous radiative emission of individual photoexcited excitonic states with zero angular momenta is found to be only tens of picoseconds. In our multi-shell QDs, high-energy excitonic states of nonzero angular momenta have to go through a number of nonradiative electron-phonon interaction steps in order to relax to zero-angular-momentum excitonic states for radiative emission, resulting in an effective fluorescence peak at about 2 ns in the photoncount-time relationship. This explains the measured long average fluorescence lifetime of 3.6 ns. Such a long lifetime facilitates the applications of colloidal QDs in areas such as QD-based solar cells, bioimaging and metamaterials.

  • 139.
    Gao, Bin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wu, ZiYu
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chirality and diameter dependent x-ray absorption of single walled carbon nanotubes2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, no 3, p. 034704-1-034704-7Article in journal (Refereed)
    Abstract [en]

    The lack of good understanding on the electronic structure of individual carbon nanotubes severely limited the applications of carbon nanotubes. By employing density functional theory in combination with the equivalent core hole approximation, we are able to provide near edge x-ray absorption fine structure (NEXAFS) spectra of all possible single walled carbon nanotubes (SWCNTs) with diameters below 1.45 nm. It is shown that the pi(*) absorption edges in NEXAFS spectra of SWCNTs are converged already at the length of 3 nm, while a good description of the full spectra can only be obtained after 7 nm. A recent high resolution experimental spectrum of a bundle of SWCNTs with diameters 1.37 +/- 0.08 nm has been successfully assigned by the calculations. Noticeable chirality and diameter dependence have been identified for the simulated NEXAFS spectra. The collection of calculated spectra serves as a useful reference for experimental identification of individual carbon nanotubes.

  • 140.
    Gao, Li
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sun, Xianqiang
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Eriksson, Leif A.
    Modification of the anticancer drug tamoxifen to avoid CYP2D6 polymorphism2013In: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 91, no 9, p. 916-924Article in journal (Refereed)
    Abstract [en]

    The prodrug tamoxifen (TAM) is the most widely used drug to treat breast cancer, and is metabolised to the active 4-hydroxy derivatives dominantly by hepatic CYP2D6. However, the application to patients with different polymorphic CYP2D6 has been under debate, because the efficacy of TAM is suspected to be suppressed in patients who have diminished CYP2D6 activity, resulting in inadequate active metabolites. We here propose modified structures, such as 4-methylTAM, which is highly possible to be activated by CYP3A, the most abundant CYP isoforms in the liver, whereby the genetic polymorphism of CYP2D6 is avoided. The diversity of CYP catalyzed metabolic paths for TAM and its derivatives are studied by quantum chemistry calculations on the reaction energies of the initial H atom abstraction steps. The ability of forming DNA adducts is compared through the formation enthalpy of the carbocation intermediate. The results suggest that the modified structures are safe with regard to forming DNA adducts and may be used as prodrugs in a wide range of patients, due to CYP3A, rather than CYP2D6, mediated activation.

  • 141.
    Gao, Li
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Eriksson, Leif A.
    Characterization of Agonist Binding to His524 in the Estrogen Receptor alpha Ligand Binding Domain2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 16, p. 4823-4830Article in journal (Refereed)
    Abstract [en]

    The bioactivities of the natural steroidal estrogen 17 beta-estradiol (E-2), the synthetic estrogen diethylstilbestrol (DES), and the phytoestrogen genistein (GEN) are intimately associated with their binding to the estrogen receptor alpha ligand binding domain (ER alpha LBD) and accordingly allostery. Molecular modeling techniques have been performed on agonists in complex with the LBD, focusing on the pivotal role of His524 modeled as the epsilon-tautomer and the protonated form (depending on pH). It is found that E-2 binds to the active LBD with the aid of Leu525, showing existing stable patterns of an H-binding network with Glu419 via His524 in all models. The main difference seen in the effect is that the full agonists E-2 and DES have higher binding energies to the protonated His524 than the partial agonists GEN and Way-169916 (W), which is in line with noted experimental transcriptional activities. In conclusion, the study demonstrates that the phytoestrogen GEN interacts differently with the LBD than what E-2 and DES do, which explains the observed signaling differences.

  • 142.
    Gao, Li
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Eriksson, Leif A.
    Modification of the anticancerdrug tamoxifen to avoid CYP2D6 polymorphismManuscript (preprint) (Other academic)
  • 143.
    Gavrilyuk, Sergey
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Liu, Ji-Cai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Kamada, Kenji
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Optical limiting for microsecond pulses2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 5, article id 054114Article in journal (Refereed)
    Abstract [en]

    We present a dynamical theory of nonlinear absorption and propagation of laser pulses with duration in the microsecond time domain. The general theory is applied to fullerene C-60 because of its good optical limiting properties, namely, a rather low ground state absorption and a strong triplet-triplet absorption. It is shown that sequential absorption involving strong triplet-triplet transitions is the major mechanism of nonlinear absorption. The intrinsic hierarchy of time scales makes an adiabatic solution of the coupled rate equations valid, which therefore can be reduced to a single dynamical equation for the ground state population. The slow evolution of this population is defined by an effective rate of population transfer to the triplet state and by the pulse duration. The propagation effect plays an important role in the optical power limiting performance. The intensity of the field as well as the population of the triplet state decreases during the pulse propagation, and a weakened nonlinear sequential two-photon absorption is followed by a linear one-photon absorption which gradually becomes the dominating process. The competition between these qualitatively different processes depends on the field intensity, the length of the absorber, and the concentration. The pulse propagation is studied by solving numerically the two-dimensional paraxial field equation together with the effective rate equation for the ground state population.

  • 144.
    Gavrilyuk, Sergey
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Polyutov, Sergey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jha, Prakash Chandra
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Many-photon dynamics of photobleaching2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, p. 11961-11975Article in journal (Refereed)
    Abstract [en]

    A detailed dynamical theory of photobleaching by periodical sequences of laser pulses is presented. The theory is used for interpretation of recent experiments with pyrylium salts. Our simulations are based on first-principles simulations of photoabsorption cross-sections and on empirical rate constants. Two competitive channels of photobleaching, namely, photobleaching from the lowest excited singlet and triplet states and from higher excited states, are found to explain different intensity dependences of the photobleaching rates in different samples. The process includes two-photon excitation from the ground state to the first or second excited singlet states and one-photon excitation from the first singlet or triplet states to higher excited states. The fluorescence follows double-exponential dynamics with two characteristic times. The first and the shorter one is the equilibrium settling time between the ground and the lowest triplet states. The second characteristic time, the time of photobleaching, is responsible for the long-term dynamics. The effective rate of photobleaching from the first excited singlet and lowest triplet states depends differently on the irradiance in comparison with the photobleaching in higher states. The first channel is characterized by a quadratic intensity dependence in contrast to the second channel that shows a cubic dependence. The competition between these photobleaching channels is very sensitive to the rate constants as well as to the repetition rate, the pulse duration, and the peak intensity. The double-exponential decay of the fluorescence is explained by the spatial inhomogeneity C of the light beam. The findings in this work are discussed in terms of the possibility of using many-photon-induced photobleaching for new three-dimensional read-write devices.

  • 145.
    Gavrilyuk, Sergey
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Sun, Yuping
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Levin, S.
    St Petersburg Universitet.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Recoil splitting of x-ray-induced optical fluorescence2010In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 81, no 3, article id 035401Article in journal (Refereed)
    Abstract [en]

    We show that the anisotropy of the recoil velocity distribution of x-ray-ionized atoms or molecules leads to observable splittings in subsequent optical fluorescence or absorption when the polarization vector of the x rays is parallel to the momentum of the fluorescent photons. The order of the magnitude of the recoil-induced splitting is about 10 mu eV, which can be observed using Fourier or laser-absorption spectroscopic techniques.

  • 146. Gelmukhanov, F
    et al.
    Privalov, Timofei
    KTH, Superseded Departments, Chemistry.
    Ågren, Hans
    KTH, Superseded Departments, Chemistry.
    Collapse of vibrational structure in spectra of resonant x-ray Raman scattering1997In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 56, no 1, p. 256-264Article in journal (Refereed)
    Abstract [en]

    Extreme narrowing, or collapse, of electron-vibrational bands is predicted as a new phenomenon in resonant radiative and nonradiative x-ray scattering (RXS) spectra. It is shown that in the inelastic scattering case, that is, when the potential surfaces of ground and final slates are different, a considerable narrowing of the vibronic RXS band results from detuning the excitation Photon frequency omega away from the absorption resonance. By fine tuning the frequency, this may under special circumstances also occur in the region of strong photoabsorption. In the case of elastic Rayleigh scattering, that is, when the potential surfaces of ground and final states are identical, the narrowing results in a total collapse to a single resonance by detuning the frequency. The theory predicts how the differencies in vibrational structure of resonant and nonresonant photoemission spectra depends on the excitation frequency. The effect of frequency detuning on complex spectral multilevel structures due to multiplet: and spin-orbit splittings is discussed qualitatively. It is shown that the notion of: duration time for the x-ray scattering process plays a crucial role in the understanding of RXS spectra.

  • 147. Gelmukhanov, F
    et al.
    Privalov, Timofei
    KTH, Superseded Departments, Chemistry.
    Ågren, Hans
    KTH, Superseded Departments, Chemistry.
    Restoration of selection rules in nonadiabatic resonant inelastic x-ray scattering1997In: Journal of Experimental and Theoretical Physics, ISSN 1063-7761, E-ISSN 1090-6509, Vol. 85, no 1, p. 20-26Article in journal (Refereed)
    Abstract [en]

    Recently a new effect in the Raman scattering of x-ray radiation has been predicted theoretically and discovered in experiments, the effect of restoration of the selection rules for the scattering tensor under strong electron-vibrational interaction. We propose a fairly simple model for describing this effect, a model that allows for an exact solution and takes into account the real vibrational structure of the molecule and electron-vibrational interaction.

  • 148. Gel'mukhanov, F
    et al.
    Privalov, Timofei
    KTH, Superseded Departments, Chemistry.
    Ågren, Hans
    KTH, Superseded Departments, Chemistry.
    Soft and hard x-ray Raman scattering by oriented symmetrical molecules: Selection rules, interference, and dephasing mechanisms1998In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 109, no 12, p. 5060-5069Article in journal (Refereed)
    Abstract [en]

    Resonant x-ray Raman scattering in chaotical, partial, and fixed oriented symmetric molecules is analyzed for x-ray photon excitation frequencies in both the soft and the hard x-ray regions. Different dephasing mechanisms and their connection with channel interference and the observation of selection rules are investigated. It is predicted that for harder x-ray energies the scattering cross sections become strongly anisotropic and oscillatory due to channel interference. The orientational dephasing is predicted to be an important coherence-blocking mechanism and can be introduced even by zero-point vibrational or librational motions. The connections between selection rules, symmetry and phase factors of the photon wave function, Bragg conditions and the channel interference show that the selection rules may operate for oriented, surface adsorbed, molecules even in the hard x-ray region. The possibility of using the interference effect for structure determination of adsorbates is discussed.

  • 149.
    Gel'mukhanov, Faris
    et al.
    KTH, Superseded Departments, Biotechnology.
    Baev, A.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Resonant X-ray Raman scattering from dense gases and solutions2001In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 346, no 06-maj, p. 437-442Article in journal (Refereed)
    Abstract [en]

    To complement conventional theory of resonant X-ray Raman scattering (RXS) adapted either for rarefied gases or solids, we propose a theory and corresponding analysis for RXS from dense gases and solutions. We show that the dephasing broadening of the spectral lines due to interaction with buffer or solvent particles qualitatively changes the physics of the X-ray scattering. The dephasing results in an additional, two-step (TS) scattering, contribution to the RXS cross-section, which interferes with the Raman one-step (OS) channel and which shows a nondispersive behaviour, This results in a doubling of the spectral lines by detuning the excitation frequency away from resonance. The theory is demonstrated numerically for RXS of formaldehyde in solution.

  • 150.
    Gel'mukhanov, Faris
    et al.
    KTH, Superseded Departments, Biotechnology.
    Baev, A.
    Macak, P.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Dynamics of two-photon absorption by molecules and solutions2002In: Journal of the Optical Society of America. B, Optical physics, ISSN 0740-3224, E-ISSN 1520-8540, Vol. 19, no 5, p. 937-945Article in journal (Refereed)
    Abstract [en]

    A dynamic density-matrix based theory of two-photon absorption (TPA) of molecules and solutions is presented. The theory highlights the influence of pulse duration, dephasing, and resonant conditions on the final TPA cross section as well as that of saturation, including a hierarchy of saturation intensities. A breakdown of the conventional identification of TPA with coherent one-step TPA is predicted for the long-pulse regime in which incoherent two-step TPA can even dominate the coherent one-step TPA process. The major role of the solvent is to enhance the off-resonant contributions to TPA furnished by collisional dephasing.

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