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  • 1.
    Ahlquist, Mårten S. G.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Iridium catalyzed hydrogenation of CO2 under basic conditions-Mechanistic insight from theory2010In: Journal of Molecular Catalysis A: Chemical, ISSN 1381-1169, E-ISSN 1873-314X, Vol. 324, no 1-2, 3-8 p.Article in journal (Refereed)
    Abstract [en]

    The iridium(III) catalyzed hydrogenation of carbon dioxide under basic conditions was studied with density functional theory. It was found that the insertion of CO2 into an Ir-H bond proceeds via a two-step mechanism. The rate-limiting step was calculated to be the regeneration of the iridium(III) trihydride intermediate, and the overall barrier for the reaction was calculated to 26.1 kcal mol(-1). The formation of the iridium trihydride proceeds via formation of a cationic Ir(H)(2)(H-2) complex at which the base abstracts a proton from the dihydrogen ligand. (C) 2010 Elsevier B.V. All rights reserved.

  • 2.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Liao, Rong-zhen
    Chen, Shu-feng
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fang, Wei-Hai
    Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 44, 14096-14102 p.Article in journal (Refereed)
    Abstract [en]

    The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.

  • 3.
    Ai, Yuejie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Chen, Shufeng
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fang, Weihai
    Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase2010In: Journal of Physical Chemisty Letters, ISSN 1948-7185, Vol. 1, 743-747 p.Article in journal (Refereed)
    Abstract [en]

    The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this letter that the often used model system, a lumiflavin (7,8-dimethy-10-methyl-isoalloxazine), can not correctly describe geometrical and electronic structures of FADHin DNA photolyase. The intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is found to play a significant role in controlling photochemical properties of FADHin DNA photolyase

  • 4.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cui, Gang-Long
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fang, Wei-Hai
    Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 6, 064302- p.Article in journal (Refereed)
    Abstract [en]

    2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized (1)pi pi(*) excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3464485]

  • 5.
    Alfredsson, Y.
    et al.
    Department of Physics, Uppsala University.
    Brena, Barbara
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Nilson, K.
    Department of Physics, Uppsala University.
    Åhlund, J.
    Department of Physics, Uppsala University.
    Kjeldgaard, L.
    MAX-lab, University of Lund.
    Nyberg, Mats
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Mårtensson, N.
    Department of Physics, Uppsala University.
    Sandell, A.
    Department of Physics, Uppsala University.
    Puglia, C.
    Department of Physics, Uppsala University.
    Siegbahn, H.
    Department of Physics, Uppsala University.
    Electronic structure of a vapor-deposited metal-free phthalocyanine thin film2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 21Article in journal (Refereed)
    Abstract [en]

    The electronic structure of a vapor-sublimated thin film of metal-free phthalocyanine (H2Pc) is studied experimentally and theoretically. An atom-specific picture of the occupied and unoccupied electronic states is obtained using x-ray-absorption spectroscopy (XAS), core- and valence-level x-ray photoelectron spectroscopy (XPS), and density-functional theory (DFT) calculations. The DFT calculations allow for an identification of the contributions from individual nitrogen atoms to the experimental N1s XAS and valence XPS spectra. This comprehensive study of metal-free phthalocyanine is relevant for the application of such molecules in molecular electronics and provides a solid foundation for identifying modifications in the electronic structure induced by various substituent groups.

  • 6. Amira, S.
    et al.
    Spangberg, D.
    Hermansson, Kersti
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Distorted five-fold coordination of Cu2+ (aq) from a Car-Parrinello molecular dynamics simulation2005In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 7, no 15, 2874-2880 p.Article in journal (Refereed)
    Abstract [en]

    The solvation shell structure and dynamics of a single Cu2+ ion in a periodic box with 32 water molecules under ambient conditions has been investigated using Car-Parrinello molecular dynamics simulations in a time-window of 18 ps. Five-fold coordination with four equidistant equatorial water molecules at 2.00 angstrom and one axial water molecule at 2.45 angstrom from the Cu2+ ion is found. A hole without water molecules is found on the opposite side of the axial water. The ion-water bonding character for the equatorial water molecules is different from that of the axial water molecules, as shown by a localized orbital analysis of the electronic structure. Moreover, the calculated OD stretching vibrational band for the equatorial water molecules lies ca. 175 cm(-1) below the axial-water band, in good agreement with experimental data. The equatorial-water band lies below, and the axial-water band above, the pure liquid D2O band, also in agreement with experimental data.

  • 7. Amira, S.
    et al.
    Spangberg, D.
    Hermansson, Kersti
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    OD vibrations and hydration structure in an Al3+(aq) solution from a Car-Parrinello molecular-dynamics simulation2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 124, no 10Article in journal (Refereed)
    Abstract [en]

    The optimized geometry, energetics, and vibrational properties of Al(D2O)(n)(3+) clusters, with n=1,2,4, and 6, have been studied using plane waves, different local basis sets, different methodologies [density-functional theory, MP2, CCSD(T)], and different functionals (BLYP, PBE). Moreover, Car-Parrinello molecular-dynamics (MD) simulations using the BLYP functional, plane waves, and the Vanderbilt ultrasoft pseudopotentials have been performed for an aqueous Al3+ solution with 1 ion and 32 D2O molecules in a periodic box at room temperature, studied for 10 ps. The cluster calculations were performed to pinpoint possible shortcomings of the electronic structure description used in the Car-Parinello MD (CPMD) simulation. For the clusters, the hydration structure and interaction energies calculated with the 'BLYP/plane-wave' approach agree well with high-level ab initio methods but the exchange-correlation functional introduces errors in the OD stretching frequencies (both in the absolute values and in the ion-induced shifts). For the aqueous solution, the CPMD simulation yields structural properties in good agreement with experimental data. The CPMD-simulated OD stretching vibrational band for the first-shell water molecules around Al3+ is strongly downshifted by the influence of the ion and is compared with experimental data from the literature. To make such a comparison meaningful, the influences of a number of systematic effects have been addressed, such as the exchange-correlation functional, the fictitious electron mass, anharmonicity effects, and the small box size in the simulation. Each of these factors (except the last one) is found to affect the OD frequency by 100 cm(-1) or more. The final corrected frequencies agree with experiment within similar to 30 cm(-1) for bulk water but are too little downshifted for the first-shell Al3+(aq) water molecules (by similar to 200 cm(-1)).

  • 8. Amira, S.
    et al.
    Spangberg, D.
    Zelin, V.
    Probst, M.
    Hermansson, Kersti
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Car-Parrinello molecular dynamics simulation of Fe3+(aq)2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 29, 14235-14242 p.Article in journal (Refereed)
    Abstract [en]

    The optimized geometry and energetic properties of Fe(D2O)(n)(3+) clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fell ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell(...)second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.

  • 9. Andersson, E.
    et al.
    Niskanen, Johannes
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hedin, L.
    Eland, J. H. D.
    Linusson, P.
    Karlsson, L.
    Rubensson, J. -E
    Carravetta, V.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Feifel, R.
    Core-valence double photoionization of the CS2 molecule2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 9, 094305- p.Article in journal (Refereed)
    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.

  • 10. Andersson, E.
    et al.
    Stenrup, Michael
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Eland, J.H.D.
    Hedin, L.
    Berglund, M.
    Karlsson, L.
    Larson, Åsa
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rubensson, Jan Erik
    Feifel, Raimund
    Single-photon core-valence double ionization of molecular oxygen2008In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 78, no 2, 023409- p.Article in journal (Refereed)
    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.

  • 11. Aziz, Emad F.
    et al.
    Grasjo, Johan
    Forsberg, Johan
    Andersson, Egil
    Soderstrom, Johan
    Duda, Laurent
    Zhang, Wenhua
    Yang, Jinglong
    Eisebitt, Stefan
    Bergstrom, Christel
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nordgren, Joseph
    Eberhardt, Wolfgang
    Rubensson, Jan-Erik
    Photoinduced formation of N-2 molecules in ammonium compounds2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 39, 9662-9669 p.Article in journal (Refereed)
    Abstract [en]

    Via fluorescence yield (FY) and resonant inelastic scattering spectroscopy in the soft X-ray range we find that soft X-rays induce formation of N-2 molecules in solid NH4Cl and in related compounds. The nitrogen molecules form weak bonds in NH4Cl, so that a substantial fraction of the molecules remains in the sample. From measurements of the FY as a function of exposure and temperature, the rates for the photochemical processes are estimated. At elevated temperatures (363 K), several nitrogen atoms are removed from the sample per incoming photon. At lower temperatures (233 K), the rate is reduced to around 0.02 nitrogen atoms for each incoming photon. Virtually all these atoms form N-2 molecules which are bound in the sample. The generality and implications of these results are briefly discussed.

  • 12. Baev, A.
    et al.
    Kimberg, Viktor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Polyutov, Sergey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Bi-directional description of amplified spontaneous emission induced by three-photon absorption2005In: Journal of the Optical Society of America. B, Optical physics, ISSN 0740-3224, E-ISSN 1520-8540, Vol. 22, no 2, 385-393 p.Article in journal (Refereed)
    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, School of Biotechnology (BIO), Theoretical Chemistry.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Quantum-classical modeling of nonlinear pulse propagation in a dissolved two-photon active chromophore2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 11, 5379-5385 p.Article in journal (Refereed)
    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.
    Welinde, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Light-matter interaction of strong laser pulses in the micro-, nano-, and picosecond regimes2007In: Hybrid functional materials for optical applications, Materials Research Society, 2007, 12-29 p.Conference paper (Refereed)
    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.

  • 15. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A quantum mechanical - Electrodynamical approach to nonlinear properties: Application to optical power limiting with platinum-organic compounds2007In: Journal of nonlinear optical physics and materials, ISSN 0218-8635, Vol. 16, no 2, 157-169 p.Article in journal (Refereed)
    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, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Light-matter interaction of strong laser pulses in the micro-, nano-, and picosecond regimes2007In: Materials Research Society Symposium Proceedings, 2007, 12-29 p.Conference paper (Refereed)
    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.
    Norman, Patrick
    Henriksson, Johan
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Theoretical Simulations of clamping levels in optical power limiting2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 42, 20912-20916 p.Article in journal (Refereed)
    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.

  • 18. Baev, Alexander
    et al.
    Welinder, Pontus
    Erlandsson, Robert
    Henriksson, Johan
    Norman, Patrick
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A quantum mechanical - Electrodynamical approach to nonlinear properties: Application to optical power limiting with platinum-organic compounds2007In: Journal of nonlinear optical physics and materials, ISSN 0218-8635, Vol. 16, no 2, 157-169 p.Article in journal (Refereed)
    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.

  • 19.
    Balamurugan, Kanagasabai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Multistep Modeling Strategy To Improve the Binding Affinity Prediction of PET Tracers to A beta(42): Case Study with Styrylbenzoxazole Derivatives2016In: ACS CHEMICAL NEUROSCIENCE, ISSN 1948-7193, Vol. 7, no 12, 1698-1705 p.Article in journal (Refereed)
    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.

  • 20. Baryshnikov, G. V.
    et al.
    Minaev, B. F.
    Minaeva, V. A.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 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 dyes2010In: Journal of Structural Chemistry, ISSN 0022-4766, E-ISSN 1573-8779, Vol. 51, no 5, 817-823 p.Article in journal (Refereed)
    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.

  • 21. Bassan, A.
    et al.
    Zou, W. B.
    Reyes, E.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Cordova, A.
    The origin of stereoselectivity in primary amino acid catalyzed intermolecular Aldol reactions2005In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 44, no 43, 7028-7032 p.Article in journal (Refereed)
  • 22. Bast, Radovan
    et al.
    Hesselmann, Andreas
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Helgaker, Trygve
    Saue, Trond
    Static and frequency-dependent dipole-dipole polarizabilities of all closed-shell atoms up to radium: A four-component relativistic DFT study2008In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 9, no 3, 445-453 p.Article in journal (Refereed)
    Abstract [en]

    We test the performance of four-component relativistic density functional theory by calculating the static and frequency-dependent electric dipole-dipole polarizabilities of all (ground-state) closed-shell atoms-up to Ra. We consider 12 nonrelativistic functionals, including three asymptotically, shape-corrected functionals, by using two smooth interpolation schemes introduced by the Baerends group: the gradient-regulated asymptotic connection (GRAC) procedure and the statistical averaging of (model) orbital potentials (SAOP). Basis sets of doubly augmented triple-zeta quality are used. The results are compared to experimental data or to accurate ob initio results. The reference static electric dipole polarizability of palladium has been obtained by finite-field calculations using the coupled-cluster singles, doubles, and perturbative triples method within this work. The best overall performance is obtained using hybrid functionals and their GRAC shape-corrected versions. The performance of SAOP is among the best for nonhybrid functionals for Group 18 atoms but its precision degrades when considering the full set of atoms. In general, we find that conclusions based on results obtained for the rare-gas atoms are not necessarily representative of the complete set of atoms. GRAC cannot be used with effective core potentials since the asymptomatic correction is switched on in the core region.

  • 23. Bolognesi, P.
    et al.
    O'Keeffe, P.
    Feyer, V.
    Plekan, O.
    Prince, K.
    Coreno, M.
    Mattioli, G.
    Amore Bonapasta, A.
    Zhang, Wenhua
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). University of Science and Technology of China, Hefei, China .
    Carravetta, V.
    Ovcharenko, Y.
    Avaldi, L.
    Inner shell excitation, ionization and fragmentation of pyrimidine2010In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 212, 012002- p.Article in journal (Refereed)
    Abstract [en]

    The inner shell excitation and ionisation of pyrimidine have been studied at the carbon K edge by near-edge X ray absorption fine structure (NEXAFS) and X ray photoelectron (XPS) spectroscopies. The theoretical predictions of density functional theory (DFT) provide a satisfactory assignment of the complex spectra of this polyatomic molecule. The fragmentation following the C(1s -1)π* excitation has been investigated by resonant Auger electron-ion coincidence spectroscopy, which allows a site and state selective study.

  • 24. Bondarchuk, Sergey V.
    et al.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Density functional study of ortho-substituted phenyl cations in polar medium and in the gas phase2011In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 389, no 1-3, 68-74 p.Article in journal (Refereed)
    Abstract [en]

    Density functional theory (DFT) calculations of several 2-X-substituted phenyl cations (X = 2-CHO, 2-CH(2)OH, 2-CHS, 2-CH=NH, 2-OCH=NH, 2-SCH=NH, 2-CH=CH-CH=CH(2), 2-CH=CH(2) and 2-NO(2)) have been carried out in the gas phase and in acetonitrile (MeCN) at the B3LYP/6-31G(d,p) level of theory. The stationary point geometry of these aryl cations have been found to be in strong dependency of the medium. In the gas phase, unexpected behavior of considered aryl cations takes place resulting in the rearrangement or ring closure reaction. Such the cyclization reaction is proceeding via the nearby atom of the substituent which appears in relative vicinity (up to similar to 3 angstrom) to the cationic center. Only in the case of 2-NO(2) derivative, the geometry optimization has lead to rearranged quazi-quinoid structure of the cation that, obviously, takes place because of instability of the ring formed. Scan of the potential energy surface (PES) of 2-nitrophenyl cation has displayed no any reaction path leading toward the rearranged structure. Thus, the impossibility of existing of the singlet state of 2-nitrophenyl cation in the gas phase has been offered. The singlet-triplet transition of 2-nitrophenyl cation has been discussed in terms of the spin-orbit coupling (SOC) effects.

  • 25.
    Bondesson, Laban
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Microscopic Interpretations of Drug Solubility2007Doctoral thesis, comprehensive summary (Other scientific)
  • 26.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Frediani, Luca
    Department of Chemistry, University of Tromsø, Norway.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Mennucci, Bendetta
    Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Italy.
    Solvation of N3- at the water surface: the Polarizable Continuum Model approach2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 23, 11361-11368 p.Article in journal (Refereed)
    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.

  • 27.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hugosson, H. W.
    Calculations of the cavitation volumes and partial molar volumes of drugs in waterManuscript (preprint) (Other academic)
  • 28.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Mikkelsen, Kurt V.
    Department of Chemistry, University of Copenhagen.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Garberg, Per
    Biovitrum AB, Stockholm.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Density functional theory calculations of hydrogen bonding energies of drug molecules2006In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 776, no 1-3, 61-68 p.Article in journal (Refereed)
    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.

  • 29.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Mikkelsen, Kurt V.
    Department of Chemistry, University of Copenhagen.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Garberg, Per
    Biovitrum AB, Stockholm.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hydrogen bonding effects on infrared and Raman spectra of drug molecules2007In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 66, no 2, 213-224 p.Article in journal (Refereed)
    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.

  • 30.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A linear scaling study of solvent-solute interaction energy of drug molecules in aqua solution2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 34, 10320-10328 p.Article in journal (Refereed)
    Abstract [en]

    Solvent-solute interaction energies for three well-known drug molecules in water solution are computed at the Hartree-Fock and B3LYP density functional theory levels using a linear scaling technique, which allows one to explicitly include in the model water molecules up to 14 A away from the solute molecule. The dependence of calculated interaction energies on the amount of included solvent has been examined. It is found that it is necessary to account for water molecules within an 8 A radius around the drug molecule to reach the saturated solvent interaction level. Effects of electron correlation and basis set on solvent-solute interaction energies are discussed.

  • 31.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Basis set dependence of solute-solvent interaction energy of benzene in water: a HF/DFT study2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 11, 1725-1732 p.Article in journal (Refereed)
    Abstract [en]

    Solute-solvent interaction energies for the benzene molecule dissolved in water are computed using Hartree-Fock and B3LYP density functional theories. Explicit solvent molecules up to 14-angstrom away from the dissolved benzene molecule are included in the calculation of interaction energies. Both basis set dependence and basis Set Superposition errors are carefully examined. It is found that the use of a larger basis set for the region near the solute together with a smaller basis set for the outer region gives results very close to what would have been obtained if the larger basis set had been used for the whole system. It is also shown that a correction for the basis Set superposition error is a necessary component in this kind of calculations. With this correction, results obtained with different tested basis sets converge to within 1 kcal/mol.

  • 32.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Basis set dependence of solvent-solute interaction energy of benzene in water: a linear scaling ab initio studyArticle in journal (Refereed)
  • 33. Bouchet, Aude
    et al.
    Brotin, Thierry
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cavagnat, Dominique
    Buffeteau, Thierry
    Conformational Effects Induced by Guest Encapsulation in an Enantiopure Water-Soluble Cryptophane2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 5, 1372-1383 p.Article in journal (Refereed)
    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.

  • 34. Bratkovsky, Alexander
    et al.
    Ponizovskaya, Ekaterina
    Wang, Shih-Yuan
    Holmström, Petter
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics.
    Thylén, Lars
    KTH, School of Information and Communication Technology (ICT), Optics and Photonics.
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    A metal-wire/quantum-dot composite metamaterial with negative epsilon and compensated optical loss2008In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 93, no 19, 193106- p.Article in journal (Refereed)
    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.

  • 35.
    Brena, Barbara
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    First principles modeling of soft X-ray spectroscopy of complex systems2005Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The electronic structures of complex systems have been studied by theoretical calculations of soft x-ray spectroscopies like x-ray photoelectron spectroscopy, near edge x-ray absorption fine structure, and x-ray emission spectroscopies. A new approach based on time dependent density functional theory has been developed for the calculation of shake-up satellites associated with photoelectron spectra. This method has been applied to the phthalocyanine molecule, describing in detail its electronic structure, and revealing the origin of controversial experimental features. It is illustrated in this thesis that the theoretical intepretation plays a fundamental role in the full understanding of experimental spectra of large and complex molecular systems. Soft x-ray spectroscopies and valence band photoelectron spectroscopies have proved to be powerful tools for isomer identification, in the study of newly synthesized fullerene molecules, the azafullerene C48N12 and the C50Cl10 molecule, as well as for the determination of the conformational changes in the polymeric chain of poly(ethylene oxide). The dynamics of the core excitation process, revealed by the vibrational fine structure of the absorption resonances, has been studied by means of density functional and transition state theory approaches.

  • 36.
    Brena, Barbara
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Carniato, S.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Functional and basis set dependence of K-edge shake-up spectra of molecules2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 18, 184316- p.Article in journal (Refereed)
    Abstract [en]

    A straightforward approach for computing the K -edge shake-up spectra of molecules based on equivalent core-hole linear response theory at both Hartree-Fock and density functional theory levels is proposed. Benchmark calculations have been performed to explore its sensitivity to different types of functionals and basis sets for the carbon 1s shake-up spectra of benzene and metal-free phthalocyanine (H2 Pc). A very good agreement with previous theoretical and experimental works for the benzene molecule has been obtained for all the functionals and basis sets tested. Electron correlation is found to be essential for a good description of the H2 Pc system, whose experimental C 1s shake-up spectrum is best reproduced by the hybrid density functional.

  • 37.
    Brena, Barbara
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Carniato, Stéphane
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Electronic and geometrical structures of the N1s-13(pi) excited states in the N2O moleculeManuscript (preprint) (Other academic)
  • 38.
    Brena, Barbara
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Characterization of the electronic structure of C50Cl10 by means of soft x-ray spectroscopies2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 24, 244305-1-244305-4 p.Article in journal (Refereed)
    Abstract [en]

    The electronic structure of the last synthesized fullerene molecule, the C50Cl10, has been characterized by theoretical simulation of x-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, and near-edge x-ray-absorption fine structure. All the calculations were performed at the gradient-corrected and hybrid density-functional theory levels. The combination of these techniques provides detailed information about the valence band and the unoccupied molecular orbitals, as well as about the carbon core orbitals.

  • 39.
    Brena, Barbara
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Time-dependent DFT calculations of core electron shake-up states of metal-(free)-phthalocyanines2006In: Radiation Physics and Chemistry, ISSN 0969-806X, E-ISSN 1879-0895, Vol. 75, no 11, 1578-1581 p.Article in journal (Refereed)
    Abstract [en]

    We have introduced a new approach for the calculation of the shake-up structures of molecular photoelectron spectra, based on the combination of time-dependent density functional theory (TD-DFT) and equivalent core hole (or Z + 1) approximation. The method, suitable for large molecules, has been applied to compute the complex shake-up states associated with the carbon Is X-ray photoelectron spectroscopy (XPS) of metal-free and nickel phthalocyanines (H2Pc and NiPc, respectively). A similar satellite profile emerges for both molecules.

  • 40.
    Brena, Barbara
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Nordlund, D
    Odelius, M
    Ogasawara, H
    Nilsson, A
    Pettersson, L G M
    Ultrafast molecular dissociation of water in ice2004In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 93, no 14, 148302- p.Article in journal (Refereed)
    Abstract [en]

    Using x-ray emission and photoemission spectroscopies to measure the occupied valence levels in a thin crystalline ice film, we resolve the ionization-induced dissociation of water in ice on a femtosecond time scale. Isotope substitution confirms proton transfer during the core-hole lifetime in spite of the nonresonant excitation. Through ab initio molecular dynamics on the core-ionized state, the dissociation and spectrum evolution are followed at femtosecond intervals. The theoretical simulations confirm the experimental analysis and allow for a detailed study of the dissociative reaction path.

  • 41.
    Brena, Barbara
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Zhuang, G. V.
    Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley.
    Augustsson, A.
    Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley.
    Liu, G.
    Environmental Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley.
    Nordgren, J.
    Department of Physics, Uppsala University.
    Guo, J. H.
    Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley.
    Ross, P. N.
    Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Conformation dependence of electronic structures of poly(ethylene oxide)2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 16, 7907-7914 p.Article in journal (Refereed)
    Abstract [en]

    The electronic structure of pure poly(ethylene oxide) (PEO) for four different polymeric chain conformations has been studied by Hartree-Fock (HF) and density functional theory (DFT) through the analysis of their valence band photoelectron spectroscopy (VB-PES), X-ray emission spectroscopy (XES), and resonant inelastic X-ray scattering (RIXS). It is shown that the valence band of PEO presents specific conformation dependence, which can be used as a fingerprint of the polymeric structures. The calculated spectra have been compared with experimental results for PEO powder.

  • 42.
    Brinne Roos, Johanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Electron Recombination with Small Molecular Ions2007Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    In this thesis I have theoretically studied electron recombination processes with small molecular ions.

    In these kind of processes resonant states are involved. To calculate the potential energy for these states as a function of internuclear distance, structure calculations and scattering calculations have to be performed.

    So far I have been studying the ion-pair formation with in electron recombination with H3+. The cross section for this process has been calculated using different kind of models, both a time dependent quantum mechanical and a semiclassical.

    I have also studied the direct process of dissociative recombination of HF+. To calculate the total cross section for this process, we have performed wave packet propagation on thirty resonant states and summed up the individual cross sections for these states.

    The cross sections for both these processes have a similar appearance to those measured experimentally in the ion storage ring CRYRING in Stockholm.

  • 43.
    Brinne Roos, Johanna
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Larson, Åsa
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Orel, Ann E.
    A direct, local model of dissociative recombination of HF+2009In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 192Article in journal (Refereed)
    Abstract [en]

    The direct mechanism of dissociative recombination of HF+ have been studied by propagating wave packets on 30 resonant states. The relevant electronic states have been calculated ab initio with electron scattering calculations and multireference configuration interaction calculations. We obtain a qualitative good agreement with experiments for energies in the range from 0.04 eV to 10 eV. Some of the structures in the experimental cross section can be explained by the direct capture and dissociation along the resonant states. To fully describe the measured cross section, the electronic couplings between the neutral states cannot be neglected.

  • 44. Böhlin, J.
    et al.
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Stafström, S.
    Effect of dynamic disorder on charge transport along a pentacene chain2011In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 83, no 8, 085209- p.Article in journal (Refereed)
    Abstract [en]

    The lattice equation of motion and a numerical solution of the time-dependent Schrodinger equation provide us with amicroscopic picture of charge transport in highly ordered molecular crystals. We have chosen the pentacene single crystal as a model system, and we study charge transport as a function of phonon-mode time-dependent fluctuations in the intermolecular electron transfer integral. For comparison, we include similar fluctuations also in the intramolecular potentials. The variance in these energy quantities is closely related to the temperature of the system. The pentacene system is shown to be very sensitive to fluctuation in the intermolecular transfer integral, revealing a transition from adiabatic to nonadiabatic polaron transport for increasing temperatures. The extension of the polaron at temperatures above 200 K is limited by the electron localization length rather than the interplay between the electron transfer integral and the electron-phonon coupling strength.

  • 45.
    Cao, Hui
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Dynamic Effects on Electron Transport in Molecular Electronic Devices2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    HTML clipboardIn this thesis, dynamic effects on electron transport in molecular electronic devices are presented. Special attention is paid to the dynamics of atomic motions of bridged molecules, thermal motions of surrounding solvents, and many-body electron correlations in molecular junctions.

    In the framework of single-body Green’s function, the effect of nuclear motions on electron transport in molecular junctions is introduced on the basis of Born-Oppenheimer approximation. Contributions to electron transport from electron-vibration coupling are investigated from the second derivative of current-voltage characteristics, in which each peak is corresponding to a normal mode of the vibration. The inelastic-tunneling spectrum is thus a useful tool in probing the molecular conformations in molecular junctions. By taking account of the many-body interaction between electrons in the scattering region, both time-independent and time-dependent many-body Green’s function formula based on timedependent density functional theory have been developed, in which the concept of state of the system is used to provide insight into the correlation effect on electron transport in molecular devices.

    An effective approach that combines molecular dynamics simulations and first principles calculations has also been developed to study the statistical behavior of electron transport in electro-chemically gated molecular junctions. The effect of thermal motions of polar water molecules on electron transport at different temperatures has been found to be closely related to the temperature-dependent dynamical hydrogen bond network.

  • 46.
    Cao, Hui
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Multi-Scale Modelling of Electron Transport in Molecular Devices2009Licentiate thesis, comprehensive summary (Other academic)
  • 47.
    Cao, Hui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jiang, Jun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ma, Jing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Identification of switching mechanism in molecular junctions by inelastic electron tunneling spectroscopy2008In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 112, no 29, 11018-11022 p.Article in journal (Refereed)
    Abstract [en]

    We present first-principles studies on electron transport properties of Pd-dithiolated oligoaniline-Pd molecular junctions. It is to demonstrate the possibility of using inelastic electron tunneling spectroscopy (IETS) to identify the switching mechanism in the molecular junction. Calculations have successfully reproduced the experimentally observed conductance switching behavior and the corresponding inelastic electron tunneling spectra. It is shown that the conductance switching is induced by conformation changes of the intercalated dithiolated oligoaniline in the junctions rather than oxidation/reduction as proposed earlier. Among three possible isomers, the low and high conductance states are related to two symmetrical structures. The possible involvement of asymmetric structure is discussed. It is revealed that chemical bonds between the terminal S atom and Pd electrodes are quite weak with relatively long bond distances.

  • 48.
    Cao, Hui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jiang, Jun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ma, Jing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Temperature-dependent statistical behavior of single molecular conductance in aqueous solution2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 21, 6674-+ p.Article in journal (Refereed)
    Abstract [en]

    We have combined molecular dynamics simulations with first principles calculations to study electron 4 transport in a single molecule of perylene tetracarboxylic diimide (PTCDI) sandwiched between two gold electrodes with an aqueous electrolyte. This combination has for the first time allowed one to reveal statistical behavior of molecular conductance in solution at different temperatures and to produce conductance histograms that can be directly compared with experiments. Our calculations show that experimentally observed temperature-dependent conductance ran be attributed to the thermal effect on the hydrogen bonding network around the molecule and can be described by the radial distribution of water molecules surrounding the oxygen atom in the PTCDI molecule.

  • 49.
    Cao, Hui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ma, Jing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Field Effects on the Statistical Behavior of the Molecular Conductance in a Single Molecular Junction in Aqueous Solution2010In: NANO RES, ISSN 1998-0124, Vol. 3, no 5, 350-355 p.Article in journal (Refereed)
    Abstract [en]

    We have combined molecular dynamics simulations with first-principles calculations to study electron transport in a single molecular junction of perylene tetracarboxylic diimide (PTCDI) in aqueous solution under external electric gate fields. It is found that the statistics of the molecular conductance are very sensitive to the strength of the electric field. The statistics of the molecular conductance are strongly associated with the thermal fluctuation of the water molecules around the PTCDI molecule. Our simulations reproduce the experimentally observed three orders of magnitude enhancement of the conductance, as well as the temperature dependent conductance, under the electrochemical gates. The effects of the molecular polarization and the dipole rearrangement of the aqueous solution are also discussed.

  • 50.
    Cao, Hui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ma, Jing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Many-Body Interaction Formulism of Electron Transport in Molecular JunctionsManuscript (preprint) (Other academic)
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