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  • 1. 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, p. 012002-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.

  • 2.
    Li, Zhenyu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhang, Wenhua
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO).
    Yang, Jinlong
    Hou, Jian Guo
    How Graphene is Cut upon Oxidation?2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 18, p. 6320-6321Article in journal (Refereed)
    Abstract [en]

    Our first principles calculations reveal that an oxidative cut of graphene is realized by forming epoxy and then carbonyl pairs. Direct formation of a carbonyl pair to tear graphene up from an edge position is not favorable in energy. This atomic picture is valuable for developing effective means of graphene manipulation. The proposed epoxy pairs may be related to some long puzzling experimental observations on graphene oxide.

  • 3. Monti, Susanna
    et al.
    Carravetta, Vincenzo
    Zhang, Wenhua
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Yang, Jinlong
    Effects due to interadsorbate interactions on the dipeptide/TiO2 surface binding mechanism investigated by molecular dynamics simulations2007In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 111, no 21, p. 7765-7771Article in journal (Refereed)
    Abstract [en]

    Classical molecular dynamics simulations, supported by ab initio periodic calculations, were carried out to investigate peptide adsorption mechanisms onto a rutile (110) TiO2 layer in the presence of water molecules. Different binding modes, comprising multiple coordination to the titanium atoms, of several conformers, simultaneously adsorbed upon the surface, were analyzed in detail. In agreement with experimental and theoretical findings, peptide carbonyl oxygens and nitrogens were found to be possible coordination atoms. Local effects were responsible of adsorption and desorption events and intermolecular interactions induced conformational changes and reorientations of the molecules with respect to the surface that produced both strongly and weakly adsorbed species.

  • 4.
    Zhang, Wenhua
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    First Principles Studies on Chemical and Electronic Structures of Adsorbates2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, we focus on theoretical study of adsorbates on metal and oxide surfaces that are important for surface chemistry and catalysis. Based on first principles calculations, the adsorption ofCO, NO, NO2, C4H6S2, C22H27SH and other molecules or radicals on nobel metal surfaces (gold and silver) are investigated. Also, NO oxidation on oxygen pre-covered Au(111)surface and CO oxidation on water-oxygen covered Au(111)surface aretheoretically studied. A new mechanism of water-enhanced COoxidation is proposed. As for oxide surfaces, we first investigatethe geometric, electronic and magnetic structures of FeO ultrathin film on Pt(111) surface. The experimentally observed scanning tunneling microscopy images are well reproduced for the first timewith our model. The adsorption and dissociation of water on rutileTiO2(110) surface are investigated by quantum molecular dynamics.By theoretical X-ray photoemission spectroscopy (XPS) calculations,the surface species are properly assigned. The same strategy has applied to the study of the phase transition of water covered reconstructed anatase TiO2(001) surface, from which two different phases are theoretically identified. The structure of graphene oxideis also studied by comparing experimental and theoretical XPS spectra. Based on the novel structures identified, a new cutmechanism of graphene oxide is proposed.

  • 5.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Carravetta, Vincenzo
    Li, Zhenyu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Yang, Jinlong
    Oxidation states of graphene: Insights from computational spectroscopy2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, no 24Article in journal (Refereed)
    Abstract [en]

    When it is oxidized, graphite can be easily exfoliated forming graphene oxide (GO). GO is a critical intermediate for massive production of graphene, and it is also an important material with various application potentials. With many different oxidation species randomly distributed on the basal plane, GO has a complicated nonstoichiometric atomic structure that is still not well understood in spite of intensive studies involving many experimental techniques. Controversies often exist in experimental data interpretation. We report here a first principles study on binding energy of carbon 1s orbital in GO. The calculated results can be well used to interpret experimental x-ray photoelectron spectroscopy (XPS) data and provide a unified spectral assignment. Based on the first principles understanding of XPS, a GO structure model containing new oxidation species epoxy pair and epoxy-hydroxy pair is proposed. Our results demonstrate that first principles computational spectroscopy provides a powerful means to investigate GO structure.

  • 6.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Carravetta, Vincenzo
    Monti, Susanna
    Interaction of biomolecular systems with titanium-based materials: computational investigations2009In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 123, no 3-4, p. 299-309Article in journal (Refereed)
    Abstract [en]

    Ab initio calculations and molecular dynamics simulations were performed to investigate the adsorption mode of various oligopeptides on titanium dioxide surfaces and to characterize their conformational behavior upon adsorption. The models were progressively improved obtaining a description compatible with the experimental observations.

  • 7.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Carravetta, Vincenzo
    Plekan, Oksana
    Feyer, Vitaliy
    Richter, Robert
    Coreno, Marcello
    Prince, Kevin C.
    Electronic structure of aromatic amino acids studied by soft x-ray spectroscopy2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, no 3, p. 035103-Article in journal (Refereed)
    Abstract [en]

    The electronic structure of phenylalanine, tyrosine, tryptophan, and 3-methylindole in the gas phase was investigated by x-ray photoemission spectroscopy (XPS) and near edge x-ray absorption fine structure (NEXAFS) spectroscopy at the C, N, and O K-edges. The XPS spectra have been calculated for the four principal conformers of each amino acid, and the spectra weighted by the Boltzmann population ratios calculated from published free energies. Instead of the single peaks expected from the stoichiometry of the compounds, the N 1s core level spectra of phenylalanine and tryptophan show features indicating that more than one conformer is present. The calculations reproduce the experimental features. The C and O 1s spectra do not show evident effects due to conformational isomerism. The calculations predict that such effects are small for carbon, and for oxygen it appears that only broadening occurs. The carbon K-edge NEXAFS spectra of these aromatic amino acids are similar to the published data of the corresponding molecules in the solid state, but show more structure due to the higher resolution in the present study. The N K-edge spectra of tryptophan and 3-methylindole differ from phenylalanine and tyrosine, as the first two both contain a nitrogen atom located in a pyrrole ring. The nitrogen K-edge NEXAFS spectra of aromatic amino acids do not show any measurable effects due to conformational isomerism, in contrast to the photoemission results. Calculations support this result and show that variations of the vertical excitation energies of different conformers are small, and cannot be resolved in the present experiment. The O NEXAFS spectra of these three aromatic compounds are very similar to other, simpler amino acids, which have been studied previously.

  • 8.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Yang, Jinlong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Caravetta, V.
    Wu, Z.
    Electronic structure of [121]tetramantane-6-thiol on gold and silver surfaces2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 054705Article in journal (Refereed)
    Abstract [en]

    The mechanism for electron photoemission of [121]tetramantane and its functionalized compound [121]tetramantane-6-thiol adsorbed on different noble metal surfaces has been investigated by density functional theory calculations. It is found that good chemical bonding between molecules and metal surfaces is a helpful but not a necessary condition for electron photoemission. A lower work function and weaker hybridization between the molecule and the metal could lead to much more efficient electron photoemission. It is observed that, neglecting final state effect, a simple ground state picture cannot result in negative electron affinity for the systems under investigation. Calculations have shown that by exciting an electron in the lowest unoccupied molecular orbital, the highest singly occupied molecular orbital of the molecule can be shifted above the vacuum level, resulting in negative electron affinity and emission of the accumulated electrons.

  • 9.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Li, Zhenyu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Theoretical Study of X-ray PhotoemissionSpectra of Graphene OxideManuscript (Other academic)
    Abstract [en]

    Chemical structure of graphene oxide is complicated by the presence of many different oxidation species. We report here a density functional theory study on binding energy of carbon 1s at different oxidation environments on a graphene oxide sheet. It is shown that the calculated results can be wellused to interpret experimental X-ray photoemission spectra of different research groups and provide united spectral assignments. New species that are important for understanding cut mechanisms of graphene oxide have been identified.

  • 10.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Li, Zhenyu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Yang, A
    A first-principles study of NO adsorption and oxidation on Au(111) surface2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 13, p. 134708-Article in journal (Refereed)
    Abstract [en]

    Density functional theory and slab models are employed to study NO molecule adsorption and reaction on clean and atomic oxygen precovered Au(111) surfaces. While clean Au(111) surface is catalytically inert and can only weakly adsorb NO, an atomic oxygen precovered Au(111) surface is found to be very active to NO. On the clean surface, NO prefers to bond at the onefold on-top surface site with a tilted geometry. On 0.33 ML (monolayer) oxygen precovered surface NO reacts with chemisorbed oxygen to form chemisorbed NO2 by conquering a small energy barrier about 0.18 eV, and the desorption energy of NO 2 is 0.64 eV. On 1.0 ML oxygen coverage surface, no barrier is found while NO reacts with precovered oxygen. The desorption energy of NO2 is 0.03 eV. The desorption of NO2 is the rate determining step on both surfaces and the overall reaction barriers are 0.64 and 0.03 eV, respectively. The activation energies depend on the initial coverage of oxygen, which compare favorably with experiments on Au surface with different oxygen coverages.

  • 11.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Li, Zhenyu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Yang, J.
    Density Functional Study on the Mechanism of CO Oxidation with Activated Water on O/Au(111) Surface2009In: Chinese Science Bulletin, ISSN 1001-6538, E-ISSN 1861-9541, Vol. 54, no 11, p. 1973-1977Article in journal (Refereed)
    Abstract [en]

    With density functional theory, the mechanism of water-enhanced CO oxidation on oxygen pre-covered Au (111) surface is theoretically studied. First, water is activated by the pre-covered oxygen atom and dissociates to OHads group. Then, OHads reacts with COads to form chemisorbed HOCOads. Finally, with the aid of water, HOCO ads dissociates to CO2. The whole process can be described as 1/2H2O ads + H2Oads + 1/2O ads + COads → H3Oads + CO 2, gas. One CO2 is formed with only 1/2 pre-covered oxygen atom. That is why more CO2 is observed when water is present on oxygen pre-covered Au (111) surface. Activation energy of each elementary step is low enough to allow the reaction to proceed at low temperature

  • 12.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Li, Zhenyu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Yang, Jinlong
    First Principles Study on the Geometric and Electronic Structures of the FeO/Pt(111) Surface2009In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, no 19, p. 8302-8305Article in journal (Refereed)
    Abstract [en]

    The geometric, electronic, and magnetic properties of the FeO monolayer on a Pt(111) surface are investigated by first principles calculations. Generally, antiferromagnetic (AFM) structures are more stable than that of the ferromagnetic one. On the basis of a specific AFM structure, the long puzzling scanning tunneling microscopy (STM) experimental observations can be well explained. In this AFM model, the Fe-O layer distance at the fee region is larger than the hcp region, in contrast to previous theoretical results. The STM images at the field-emission regime are explained by local surface potential.

  • 13.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    First-Principles Study on Different BDT-gold Contact StructuresManuscript (Other academic)
    Abstract [en]

    Density functional theory calculations have been carried out for a benzene-1,4-dithiol (BDT)molecule adsorbed on a perfect Au (111) surface, a gold nanowire of 1 nm in diameter and alsosurface supported gold cluster (point). It is indicated that a BDT molecule prefers to adsorbon irregular surface sites. The Simulated S K-edge x-ray absorption spectra (XAS) and ultra-violet photoemission spectra (UPS) are presented. The predicted XAS spectra show that x-rayspectroscopy could be a powerful method to study the structure of molecule-metal contact.

  • 14.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Theoretical study on phase transition of watercovered anatase TiO2 (001) surfaceManuscript (Other academic)
    Abstract [en]

    With the (4x1) ADM structural model proposed by Lazzeri and Selloni, the behavior of wateron reconstructed anatase TiO2 (001) surface is studied by quantum molecular dynamics simulationsand an interpretation of the x-ray photoemission spectra, recently collected for such systems, with different water coverage, is provided. The spectrum of the low coverage phase is assigned to oxygencore ionization of only acceptor hydrogen bonded hydroxyl species, while the spectrum of the highcoverage phase is due to contributions from both donor and acceptor hydrogen bonded hydrox-yls. The experimental spectral evolution with temperature and dosing is also well interpreted bytheoretical simulations.

  • 15.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Caravetta, V.
    Monti, Susanna
    Yang, Jinlong
    Quantum molecular dynamics study of water onTiO2(110) surface2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 064703Article in journal (Refereed)
    Abstract [en]

    The adsorption of water on perfect TiO2(110) surface is studied by quantum molecular dynamics simulation adopting a periodic model formed by five water molecules on a (5 x 1) surface unit cell of a five layer slab of TiO2. The total simulation time is 3.2 ps. At about 1.3 ps, one water molecule dissociates with the help of other adsorbed waters and surface bridging oxygens. During the remaining 1.9 ps, the waters and OH groups vibrate, but no more dissociation or recombination is observed. By comparing recent experimental O1s photoemission (x-ray photoelectron spectroscopy) spectra of H2O/TiO2(110) to the computed spectrum of the adsorbate in the configurations supplied by the molecular dynamics simulation, the observed peaks can be attributed to different oxygen species. The proposed assignment of the main spectral features supports the occurrence of partial water dissociation (similar to 20%) also on a perfect TiO2 surface.

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