Change search
Refine search result
1234567 1 - 50 of 380
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Ai, Yuejie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cui, Ganglong
    Beijing Normal University.
    Fang, Qiu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fang, Weihai
    Beijing Normal University.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Exploring concerted effects of base pairing and stacking on the excited-state nature of DNA oligonucleotides by DFT and TD-DFT studies2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 10, p. 2366-2377Article in journal (Refereed)
    Abstract [en]

    We have taken (dA)5, (dT)5, and (dA)5•(dT)5 as model systems to study concerted effects of base pairing and stacking on excited-state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFTmethods. The spectroscopic states are determined to be of a partial A →A charge transfernature in the A•T oligonucleotides. The T → T charge-transfer transitionsproduce dark states, which are hidden in the energy region of the steady-stateabsorption spectra. This is different from the previous assignment that the T → Tcharge-transfer transition is responsible for a shoulder at the red side of the first strongabsorption band. The A →T charge-transfer states were predicted to have relativelyhigh energies in the A•T oligonucleotides. The present calculations predict that the T→A charge-transfer states are not involved in the spectra and excited-state dynamics ofthe A•T oligonucleotides. In addition, the influence of base pairing and stacking on thenature of the 1nΠ* and 1ΠΠ* states are discussed in detail.

  • 2. Ai, Yuejie
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ji, Yongfei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Song, Wei-Guo
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hydrophobicity and Hydrophilicity Balance Determines Shape Selectivity of Suzuki Coupling Reactions Inside Pd@meso-SiO2 Nanoreactor2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 19, p. 10244-10251Article in journal (Refereed)
    Abstract [en]

    Molecular sorting and catalysis directed by shape selectivity have been extensively applied in porous extended frameworks for a low-carbon, predictable, renewable component of modern industry. A comprehensive understanding of the underlying recognition mechanism toward different shapes is unfortunately still missing, owing to the lack of structural and dynamic information under operating conditions. We demonstrate here that such difficulties can be overcome by state-of-the-art molecular dynamics simulations which provide atomistic details that are not accessible experimentally, as exemplified by our interpretation for the experimentally observed aggregation induced shape selectivity for Suzuki C-C coupling reaction catalyzed by Pd particles in mesoporous silica. It is found that both aggregation ability and aggregating pattern of the reactants play the decisive role in controlling the shape selectivity, which are in turn determined by the balance between the hydrophobicity and hydrophilicity of the reactants, or in other words, by the balance between the noncovalent hydrogen bonding interaction and van der Waals forces. A general rule that allows prediction of the shape selectivity of a reactant has been proposed and verified against experiments. We show that molecular modeling is a powerful tool for rational design of new mesoporous systems and for the control of catalytic reactions that are important for the petrochemical industry.

  • 3.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liao, Rongzhen
    Stockholm University.
    Chen, Shilu
    Beijing Institute of Technology.
    Hua, Wei-Jie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fang, Wei-Hai
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 37, p. 10976-10982Article in journal (Refereed)
    Abstract [en]

    Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.

  • 4.
    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, p. 14096-14102Article 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.

  • 5.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liao, Rong-Zhen
    Fang, Wei-Hai
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore2012In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, no 38, p. 13409-13414Article in journal (Refereed)
    Abstract [en]

    We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.

  • 6.
    Ai, Yuejie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liao, Rongzhen
    Stockholm University.
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fang, Weihai
    Beijing Normal University.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Intrinsic property of flavin mononucleotide controls its optical spectra in three redox states2011In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, no 16, p. 2899-2902Article in journal (Refereed)
  • 7.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein2013In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, no 9-11, p. 1316-1321Article in journal (Refereed)
    Abstract [en]

    Two-photon absorption spectra of green fluorescent proteins (GFPs) often show a blue-shift band compared to their conventional one-photon absorption spectra, which is an intriguing feature that has not been well understood. We present here a systematic study on one- and two-photon spectra of GFP chromophore by means of the density functional response theory and complete active space self-consistent field (CASSCF) methods. It shows that the popular density functional fails to provide correct vibrational progression for the spectra. The non-Condon vibronic coupling, through the localised intrinsic vibrational modes of the chromophore, is responsible for the blue-shift in the TPA spectra. The cis to trans isomerisation can be identified in high-resolution TPA spectra. Our calculations demonstrate that the high level ab initio multiconfigurational CASSCF method, rather than the conventional density functional theory is required for investigating the essential excited-state properties of the GFP chromophore.

  • 8.
    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, p. 743-747Article 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

  • 9.
    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, p. 064302-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]

  • 10.
    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.

  • 11. Augustsson, A.
    et al.
    Kashtanov, Stepan
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Chang, C.L.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Rubensson, J.-E.
    Nordgren, J.
    Conformations and core-excitation dynamics liquid water.Manuscript (preprint) (Other academic)
  • 12. 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, p. 9662-9669Article 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.

  • 13. Baev, A.
    et al.
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Macak, P.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    General theory for pulse propagation in two-photon active media2002In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 117, no 13, p. 6214-6220Article in journal (Refereed)
    Abstract [en]

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

  • 14. Bassan, A.
    et al.
    Nyberg, M.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Identifying isomers of C-78 by means of x-ray spectroscopy2002In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 65, no 16Article in journal (Refereed)
    Abstract [en]

    X-ray photoelectron and absorption spectra of C-78 isomers have been generated using density functional theory with inclusion of the full core-hole potentials. Strong isomer dependence has been found in absorption, but not in the photoelectron spectra. C-78 isomers can be thought to be formed by inserting 18 carbon atoms into an opened C-60. We have shown how the different local arrangements of these 18 carbon atoms are responsible for the significant isomer dependence observed. Our calculated spectra are in excellent agreement with the experimental counterparts.

  • 15. Birgerson, J.
    et al.
    Keil, M.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Svensson, S.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Salaneck, W. R.
    A study of the electronic structure of ethylenedioxythiophene in gas phase using NEXAFS and quantum chemical calculations2004In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 392, no 1-3, p. 100-104Article in journal (Refereed)
    Abstract [en]

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

  • 16.
    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, p. 61-68Article 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.

  • 17.
    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, p. 213-224Article 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.

  • 18.
    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, p. 10320-10328Article 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.

  • 19.
    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, p. 1725-1732Article 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.

  • 20.
    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)
  • 21.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Erratum to: Basis set dependence of solute-solvent interaction energy of benzene in waterA HF/DFT study (vol 29, pg 1725, 2008)2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 3, p. 354-354Article in journal (Refereed)
  • 22. Bora, D. K.
    et al.
    Cheng, X.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Lawrence Berkeley National Laboratory, United States; University of Science and Technology of China, China.
    Kapilashrami, M.
    Glans, P. A.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.
    Guo, J. -H
    Influence of crystal structure, ligand environment and morphology on Co L-edge XAS spectral characteristics in cobalt compounds2015In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, p. 1450-1458Article in journal (Refereed)
    Abstract [en]

    The electronic structure of a material plays an important role in its functionality for different applications which can be probed using synchrotron-based spectroscopy techniques. Here, various cobalt-based compounds, differing in crystal structure, ligands surrounding the central metal ion and morphology, have been studied by soft X-ray absorption spectroscopy (XAS) at the Co L-edge in order to measure the effect of these parameters on the electronic structure. A careful qualitative analysis of the spectral branching ratio and relative intensities of the L 3 and L 2 peaks provide useful insight into the electronic properties of compounds such as CoO/Co(OH)2, CoCl2.6H2O/CoF2.4H2O, CoCl2/CoF2, Co3O4 (bulk/nano/micro). For further detailed analysis of the XAS spectra, quantitative analysis has been performed by fitting the spectral profile with simulated spectra for a number of cobalt compounds using crystal field atomic multiplet calculations.

  • 23.
    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, p. 184316-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.

  • 24.
    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)
  • 25.
    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, p. 244305-1-244305-4Article 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.

  • 26.
    Brena, Barbara
    et al.
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Electronic structures of azafullerene C48N122003In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 119, no 14, p. 7139-7144Article in journal (Refereed)
    Abstract [en]

    Two recently proposed low-energy azafullerene C48N12 isomers have been theoretically characterized using x-ray spectroscopies. The x-ray photoelectron spectroscopy, the near-edge absorption fine structure, the x-ray emission spectroscopy, and the ultraviolet photoelectron spectroscopy for both isomers have been predicted at the gradient-corrected density functional theory level. These spectroscopies together give a comprehensive insight of the electronic structure on the core, valence, and unoccupied orbitals. They have also provided a convincing way for identifying the isomer structures.

  • 27.
    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, p. 1578-1581Article 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.

  • 28.
    Brena, Barbara
    et al.
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Nyberg, Mats
    KTH, Superseded Departments, Biotechnology.
    Puglia, C.
    et al.,
    Equivalent core-hole time-dependent density functional theory calculations of carbon 1s shake-up states of phthalocyanine2004In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 70, no 19, p. 195214-Article in journal (Refereed)
    Abstract [en]

    The shake-up transition energies of the carbon 1s photoelectron spectrum of metal-free phthalocyanine (H2Pc) have been calculated by means of time-dependent density functional theory, for which an equivalent core approximation is adopted. Model calculations for the C 1s shake-up states of benzene are in excellent agreement with the latest experimental results. The complex C 1s shake-up structures associated with the aromatic and pyrrole carbons in the phthalocyanine are computed, as well as their ionization potentials. They allow us to determine the origin of the anomalous intensity ratio between the pyrrole and benzene carbons in a high resolution C 1s photoelectron spectrum measured for a H2Pc film, as due to a benzene-related shake-up contribution, hidden under the pyrrole main intensity feature.

  • 29.
    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, p. 7907-7914Article 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.

  • 30.
    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, p. 11018-11022Article 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.

  • 31.
    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, p. 6674-+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.

  • 32.
    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, p. 350-355Article 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.

  • 33.
    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)
  • 34.
    Cao, Hui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ma, Jing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Statistical Behavior of Electrochemical Single Molecular Field Effect Transistor2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126Article in journal (Refereed)
  • 35.
    Cao, Hui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ma, Jing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Time-Dependent Current Through Molecular Junctions: Analysis in State SpaceManuscript (preprint) (Other academic)
  • 36.
    Cao, Hui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ma, Jing
    Yi, Luo
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Conductance Oscillation in Dithiolated Oligoacene JunctionsIn: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648XArticle in journal (Refereed)
  • 37.
    Cao, Xinrui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fu, Qiang
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Catalytic activity of Pd-doped Cu nanoparticles for hydrogenation as a single-atom-alloy catalyst2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 18, p. 8367-8375Article in journal (Refereed)
    Abstract [en]

    The single atom alloy of extended surfaces is known to provide remarkably enhanced catalytic performance toward heterogeneous hydrogenation. Here we demonstrate from first principles calculations that this approach can be extended to nanostructures, such as bimetallic nanoparticles. The catalytic properties of the single-Pd-doped Cu-55 nanoparticles have been systemically examined for H-2 dissociation as well as H atom adsorption and diffusion, following the concept of single atom alloy. It is found that doping a single Pd atom at the edge site of the Cu-55 shell can considerably reduce the activation energy of H-2 dissociation, while the single Pd atom doped at the top site or in the inner layers is much less effective. The H atom adsorption on Cu-55 is slightly stronger than that on the Cu(111) surface; however, a larger nanoparticle that contains 147 atoms could effectively recover the weak binding of the H atoms. We have also investigated the H atom diffusion on the 55-atom nanoparticle and found that spillover of the produced H atoms could be a feasible process due to the low diffusion barriers. Our results have demonstrated that facile H-2 dissociation and weak H atom adsorption could be combined at the nanoscale. Moreover, the effects of doping one more Pd atom on the H-2 dissociation and H atom adsorption have also been investigated. We have found that both the doping Pd atoms in the most stable configuration could independently exhibit their catalytic activity, behaving as two single-atom-alloy catalysts.

  • 38.
    Cao, Xinrui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ji, Yongfei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hu, Wei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Department of Chemical Physics, University of Science and Technology of ChinaHefei, China.
    Duan, Sai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Department of Chemical Physics, University of Science and Technology of ChinaHefei, China .
    Feasible Catalytic Strategy for Writing Conductive Nanoribbons on a Single-Layer Graphene Fluoride2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 39, p. 22643-22648Article in journal (Refereed)
    Abstract [en]

    An accessible method for local reduction of graphene fluoride catalyzed by the Pt-coated nanotip with the assistance of a mixture of hydrogen and ethylene atmosphere is proposed and fully explored theoretically. Detailed mechanisms and roles of hydrogen and ethylene molecules in the cyclic reduction is discussed based on extensive first-principles calculations. It is demonstrated that the proposed cyclic reduction strategy is energetically favorable. This new strategy can be effectively applied in scanning probe lithography to fabricate electronic circuits at the nanoscale on graphene fluoride under mild conditions.

  • 39.
    Cao, Xinrui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ji, Yongfei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.
    Dehydrogenation of Propane to Propylene by a Pd/Cu Single-Atom Catalyst: Insight from First-Principles Calculations2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 2, p. 1016-1023Article in journal (Refereed)
    Abstract [en]

    The catalytic properties of the single-Pd-doped Cu55 nanoparticle toward propane dehydrogenation have been systemically investigated by first-principles calculations, and the possible reaction mechanisms and effects of the single and multiple Pd doping on the catalytic activity have been discussed. Calculations reveal that the low-energy catalytic conversion of propane to propylene by the Pd/Cu single-atom catalyst comprises the initial crucial C–H bond breaking at either the methyl or methylene group, the facile diffusion of detached H atoms on the Cu surface, and the subsequent C–H bond dissociation activation of the adsorbed propyl species. The single-Pd-doped Cu55 nanoparticle shows remarkable activity toward C–H bond activation, and the presence of relatively inactive Cu surface is beneficial for the coupling and desorption of detached H atoms and can reduce side reactions such as deep dehydrogenation and C–C bond breaking. The single-Pd-doped Cu55 cluster bears good balance between the maximum use of the noble metal and the activity, and it may serve as a promising single-atom catalyst toward selective dehydrogenation of propane.

  • 40.
    Cao, Xinrui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Study of the Electronic and Optical Properties of Hybrid Triangular (BN)(x)C-y Foams2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 38, p. 22181-22187Article in journal (Refereed)
    Abstract [en]

    The triangular foam is a newly designed 3D network structure only containing sp(2) bonding. The triangular carbon foam and its boron nitride analogue are predicted to be metallic and semiconducting, respectively (Chem. Commun. 2011, 47 (15), 4406-4408). Here a series of hybrid 3D network models from the BN- and C-doping of both carbon and BN foams have been designed. These newly designed hybrid (BN)(x)C-y foams are predicted to have comparable stability with their undoped crystalline networks, and the conversion between metallic and semiconducting behavior can be achieved by different doping patterns. Furthermore, these hybrid network structures have strong absorption in a wide range of UV region and relatively weak absorption in the visible-light range, and they should be quite promising for the design of electronic and optical devices.

  • 41.
    Carlegrim, E.
    et al.
    Linköping Univ, Dept Sci & Technol ITN.
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kanciurzewska, A.
    Linköping Univ, Dept Sci & Technol ITN.
    de Jong, M. P.
    Linköping Univ, Dept Phys Chem & Biol IFM.
    Wu, Z.
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fahlman, M.
    Linköping Univ, Dept Sci & Technol ITN.
    Near-edge x-ray absorption studies of Na-doped tetracyanoethylene films: A model system for the V(TCNE)x room-temperature molecular magnet2008In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 77, no 5, p. 054420-1-054420-8Article in journal (Refereed)
    Abstract [en]

    V(TCNE)(x), with TCNE=tetracyanoethylene and x similar to 2, is an organic-based molecular magnet with potential to be used in spintronic devices. With the aim of shedding light on the unoccupied frontier electronic structure of V(TCNE)(x) we have studied pristine TCNE and sodium-intercalated TCNE by near edge x-ray absorption fine structure (NEXAFS) spectroscopy as well as with theoretical calculations. Sodium-intercalated TCNE was used as a model system of the more complex V(TCNE)(x) and both experimental and theoretical results of the model compound have been used to interpret the NEXAFS spectra of V(TCNE)(x). By comparing the experimental and theoretical C K-edge of pristine TCNE, the contributions from the various carbon species (cyano and vinyl) could be disentangled. Upon fully sodium intercalation, TCNE is n doped with one electron per molecule and the features in the C and N K-edge spectra of pristine TCNE undergo strong modification caused by partially filling the TCNE lowest unoccupied molecular orbital (LUMO). When comparing the C and N K-edge NEXAFS spectra of fully sodium-doped TCNE with V(TCNE)(x), the spectra are similar except for broadening of the features which originates from structural disorder of the V(TCNE)(x) films. The combined results from the model system and V(TCNE)(x) suggest that the lowest unoccupied molecular orbital with density on the nitrogen atoms in V(TCNE)(x) has no significant hybridization with vanadium and is similar to the so-called singly occupied molecular orbital of the TCNE anion. This suggests that the LUMO of V(TCNE)(x) is TCNE- or vanadiumlike, in contrast to the frontier occupied electronic structure where the highest occupied molecular orbital is a hybridization between V(3d) and cyano carbons. The completely different nature of the unoccupied and occupied frontier electronic structure of the material will most likely affect both charge injection and transport properties of a spintronic device featuring V(TCNE)(x).

  • 42. Carniato, S.
    et al.
    Dufour, G.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    Ab initio study of the Cu 2p and 3s core-level XPS spectra of copper phthalocyanine2002In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 66, no 4Article in journal (Refereed)
    Abstract [en]

    The x-ray photoelectron spectra (XPS) of copper tetraazaporphyrin (CuTAP), used as a model of copper phthalocyanine(CuPc) are studied by theoretical simulations. The nature of the main and satellite features observed in the XPS Cu 2p and Cu 3s photoelectron spectra are discussed based on the results of the charge-transfer (CT) model and of ab initio calculations in the sudden approximation limit. It is shown that the two descriptions of the core level final states can be derived from the two types of approaches. The final-state wave functions given by the CT model are described in a shakedown scenario. This process produces a well-screened final 2p(5)3d(10)(L) under bar configuration ((L) under bar denotes a ligand hole) on the Cu atom together with the core hole, resulting in the main spectral peak. On the other hand, the process where the outer electron stays on the ligand corresponds to the satellite with a poorly-screened 2p(5)3d(9) character. The ab initio calculations, performed on an isolated copper tetraazaporphyrin molecule at the Hartree-Fock (HF) level, the multi-configuration self-consistent field level, and the hybrid density-functional-theory levels show that the core hole final states (satellite/main peak) can be attributed to valence-valence transitions. We show that a correct intensity distribution of the different features, including the so-called white line and the satellite structures, can be obtained when the electronic relaxation and correlation and the overlap between the ground-state and final-state Slater determinants are explicitly taken into account. It is found that the nature of the main peak is strongly depending on the Ligand-to-Metal charge transfer, on the exchange interaction and on the core-hole-3d-hole interaction energies.

  • 43. Carniato, S.
    et al.
    Ilakovac, V.
    Gallet, J. J.
    Kukk, E.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hybrid density-functional theory calculations of near-edge x-ray absorption fine-structure spectra: Applications on benzonitrile in gas phase2005In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 71, no 2Article in journal (Refereed)
    Abstract [en]

    The experimental N(1s) near-edge x-ray-absorption fine-structure spectrum of the benzonitrile molecule in the gas phase shows well separated double peaks with different vibrational profiles. Hybrid density-functional theory calculations reveal that such a separation is a result of the conjugation effect on the nitrogen 2p orbitals and the double spectral peaks can be assigned as the N(1s)-pi* out-of-plane and in-plane resonances. The vibrational profiles have been analyzed using a combined transition state theory and linear coupling model. Each profile consists of two different vibrational progressions corresponding to stretching modes and a broad continuum of bending excited states. The use of transition state theory allows identifying the dynamics of the N 1s core excitation. It is found that upon core excitations the C-N bond of the benzonitrile molecule can go from initial linear to final bent structures through different paths. The calculated spectrum is in excellent agreement with experiment.

  • 44. Carniato, S.
    et al.
    Ilakovac, V.
    Gallet, J. J.
    Kukk, E.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Multidimensional transition-state theory calculations for nuclear dynamics of core-excited molecules2004In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 70, no 3Article in journal (Refereed)
    Abstract [en]

    We have extended the transition-state theory to describe the dynamics of core hole excitation. This allows us to interpret the abnormally bland near-edge x-ray absorption fine structure spectrum of the gas phase benzonitrile molecule at the N 1s edge. We have brought to light different paths for the two most intensive resonances, going from the linear to the bent structure. The profile of each resonance consists of two different vibrational progressions corresponding to stretching modes and a broad continuum of bending excited states.

  • 45. Carniato, S.
    et al.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Role of differential correlation energy in core ionization of pyrrole and pyridine2005In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 142, no 2, p. 163-171Article in journal (Refereed)
    Abstract [en]

    DeltaHartree-Fock (DeltaHF) and DeltaKohn-Sham (DeltaKS) orbital theories are used to calculate C(1s) and N(1s) core electron binding energies and chemical shifts of pyrrole and pyridine molecules. As a result, combination of DeltaKS and B3LYP functional appears as a very promising approach for the determination of the core excitation/ionization energies. For the carbon series in pyridine, electronic correlation is essential in correctly predicting the relative shifts among carbon atoms. A strong dynamical differential correlation energy for carbon and nitrogen has been revealed and can be related to the large magnitude of electronic transfer from ligands to the core ionized site.

  • 46. Carniato, S.
    et al.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Theoretical study of the near-edge Cu L x-ray absorption spectrum of copper phthalocyanine2001In: Physical Review B Condensed Matter, ISSN 0163-1829, E-ISSN 1095-3795, Vol. 6308, no 8Article in journal (Refereed)
    Abstract [en]

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

  • 47. Carniato, Stéphane
    et al.
    Taïeb, Richard
    Kukk, Edwin
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Brena, Barbara
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    N-K near edge x-ray absorption fine structures of acetonitrile in gas phase2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 21, p. 214301-Article in journal (Refereed)
    Abstract [en]

     The dynamic processes of N(1s) core-hole excitation in gas-phase CH3CN molecule have been studied at both Hartree-Fock and hybrid density-functional theory levels. The vibrational structure is analyzed for fully optimized core-excited states. Frank-Condon factors are obtained using the linear coupling model for various potential surfaces. It is found that the vibrational profile of the N-K absorption can be largely described by a summation of two vibrational progressions: a structure-rich profile of nu((CN)) stretching mode and a large envelope of congestioned vibrational levels related to the strong (-C-CN) terminal bending bond. Excellent agreement between theoretical and experimental spectra is obtained.

  • 48. Chen, Lan
    et al.
    Hu, Zhenpeng
    Zhao, Aidi
    Wang, Bing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Yang, Jinlong
    Hou, J. G.
    Mechanism for negative differential resistance in molecular electronic devices: Local orbital symmetry matching2007In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 99, no 14Article in journal (Refereed)
    Abstract [en]

    A new mechanism for negative differential resistance (NDR) originating from local orbital symmetry matching between an electrode and a molecule in a single molecular electronic device is proposed and demonstrated by a joint experimental and theoretical scanning tunneling microscope study of a cobalt phthalocyanines (CoPc) molecule on a gold substrate. For two different metal tips used, Ni and W, NDR occurs only with Ni tips and shows no dependence on the geometrical shape of the tip. Calculations reveal that such a behavior is a result of local orbital symmetry matching between the Ni tip and Co atom.

  • 49.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Role of the 3(ππ*) state in photolysis of lumisantonin: insight from ab initio studies2011In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 26, p. 7815-7822Article in journal (Refereed)
    Abstract [en]

    The CASSCF and CASPT2 methodologies have been used to explore the potential energy surfaces of lumisantonin in the ground and low-lying triplet states along the photoisomerization pathways. Calculations indicate that the (n pi*) state is the accessible low-lying singlet state with a notable oscillator strength under an excitation wavelength of 320 nm and that it can effectively decay to the (3)(pi pi*) state through intersystem crossing in the region of minimum surface crossings with a notable spin-orbital coupling constant. The 3(pi pi*) state, derived from the promotion of an electron from the pi-type orbital mixed with the sigma orbital localized on the C-C bond in the three-membered alkyl ring to the pi* orbital of conjugation carbon atoms, plays a critical role in C-C bond cleavage. Based on the different C-C bond rupture patterns, the reaction pathways can be divided into paths A and B. Photolysis along path A arising from C1-C5 bond rupture is favorable because of the dynamic and thermodynamic preferences on the triplet excited-state PES. Path B is derived from the cleavage of the C5-C6 bond, leading first to a relatively stable species, compared to intermediate A-INT formed on the ground state PES. path B is relatively facile for the pyrolytic reaction. The present results provide a basis to interpret the experimental observations.

  • 50.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Theoretical studies on the mechanism of α-santonin photo-induced rearrangement2012In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 13, no 1, p. 353-362Article in journal (Refereed)
    Abstract [en]

    α-Santonin is the first organic compound observed to feature a photoinduced rearrangement and is now known to undergo a series of photochemical processes under UV irradiation. On the basis of the considerable interest of this system as a prototype, and of the yet limited insights reached for the basic photo mechanisms, we calculate the high-level electronic structures and explore the potential energy surfaces (PES) of α-santonin in the ground and lowest-lying excited states, their couplings, and the possible photoinduced isomerization pathways. The calculations identify the low-lying singlet excited state 1(nπ*) accessible under light irradiation, which decays to the low-energy 3(ππ*) state through an intersystem crossing in the Franck–Condon region to initiate the photoinduced rearrangement. The initial reaction from the C3C5 bond coupling, which takes place on the 3(ππ*) state potential energy surface, leads to a three-membered alkyl-ring compound intermediate state INT. The following photochemical reactions have the possibility to arise from two distinct CC bond cleavages, C4C5 and C3C4, denoted as path A and path B. Path A is favored both dynamically on the excited-state PES and thermodynamically on the ground-state PES in vacuo. Experiments show that it also becomes the dominant photoinduced rearrangement process in the crystal, which can be explained by considering the requirement for less space and the stacking effect under the confined environment. Path B is dynamical advantaged both on the ground- and excited-state PESs in a weak polar solvent, such as dioxane. Once the biradical intermediate B-INT is accessible on the ground-state PES, the formation of the product B-P is almost barrier free.

1234567 1 - 50 of 380
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf