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  • 1.
    Carlegrim, E.
    et al.
    Linköping Univ, Dept Sci & Technol ITN.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    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, Skolan för bioteknologi (BIO), Teoretisk kemi.
    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 magnet2008Inngår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 77, nr 5, s. 054420-1-054420-8Artikkel i tidsskrift (Fagfellevurdert)
    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).

  • 2.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    First Principles Studies of Carbon Based Molecular Materials2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The aim of this thesis was to investigate carbon based molecular materials at first principles levels. Special attention has been paid to simulations of X-ray spectroscopies, including near edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron, and X-ray emission spectroscopy, which can provide detailed information about core, occupied and unoccupied molecular orbitals of the systems under investigation. Theoretical calculations have helped to assign fine spectral structures in high resolution NEXAFS spectra of five azabenzenes (pyridine, pyrazine, pyrimidine, pyridazine and s-triazine), and to identify different local chemical environments among them. With the help of NEXAFS, the characters of important chemical bonds that might be responsible for the unique magnetic properties of the tetracyanoethylene compound has been revealed. Calculations have demonstrated that X-ray spectroscopies are powerful tools for isomer identification and structure determination of fullerenes and endohedral metallofullerenes. A joint experimental and theoretical study on metallofullerene Gd@C82 has firmly determined its equilibrium structure, in which the gadolinium atom lies above the hexagon on the C2 axis. It is found that the gadolinium atom could oscillate around its equilibrium position and that its oscillation amplitude increases with increasing temperature.

    In this thesis, several new computational schemes for large-scale systems have been proposed. Parallel implementation of a central insertion scheme (CIS) has been realized, which allows to effectively calculate electronic structures of very large systems, up to 150,000 electrons, at hybrid density functional theory levels. In comparison with traditional computational methods, CIS provides results with the same high accuracy but requires only a fraction of computational time. One of its applications is to calculate electronic structures of nanodiamond clusters varying from 0.76 nm (29 carbons) to 7.3 nm (20,959 carbons) in diameter, which enabled to resolve the long-standing debate about the validity of the quantum confinement model for nanodiamonds. Electronic structures and X-ray spectroscopies of a series of single-walled carbon nanotubes (SWCNTs) with different diameters and lengths have been calculated, which have made it possible to interpret the existing experimental results.

  • 3.
    Gao, Bin
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Jiang, Jun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Liu, Kai
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Wu, Ziyu
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Lu, Wei
    Chinese Acad Sci, Natl Lab Infrared Phys, Shanghai Inst Tech Phys, Beijing.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    An efficient first-principle approach for electronic structures calculations of nanomaterials2008Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, nr 3, s. 434-444Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An efficient parallel implementation has been realized for a recently proposed central insertion scheme (Jiang, Liu, Lu, Luo. J Chem Phys 2006,124,214711; J Chem Phys 2006,125, 149902) that allows to calculate electronic structures of nanomaterials at various density functional theory levels. It has adopted the sparse-matrix format for Fock/Kohn-Sham and overlap matrices, as well as a combination of implicitly restarted Arnoldi methods (IRAM) and spectral transformation for computing selected eigenvalues/eigenvectors. A systematic error analysis and control for the proposed method has been provided based on a strict mathematical basis. The efficiency and applicability of the new implementation have been demonstrated by calculations of electronic structures of two different nanomaterials consisting of one hundred thousand electrons.

  • 4.
    Gao, Bin
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Jiang, Jun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Simulation of electronic structure of nanomaterials by central insertion scheme2009Inngår i: FRONTIERS OF PHYSICS IN CHINA, ISSN 1673-3487, Vol. 4, nr 3, s. 307-314Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An effective central insertion scheme (CIS) that allows to study the electronic structure of nanomaterials at the first principles level is introduced. Taking advantage of advanced numerical methods, such as the implicitly restarted Arnoldi method (IRAM) and spectral transformation, together with efficient parallelization technique, this scheme can provide accurate electronic structures and properties of one-, two-, and three-dimensional nanomaterials with only a fraction of computational time required for conventional quantum chemical calculations. Electronic structures of several nanostructures, such as single-walled carbon nanotubes of sub-100 nm in length, silicon nanoclusters of sub-6.5 nm in diameter and metal doped silicon clusters, calculated at hybrid density functional level are presented.

  • 5.
    Gao, Bin
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Jiang, Jun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Wu, ZiYu
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Energy gaps, electronic structures, and x-ray spectroscopies of finite semiconductor single-walled carbon nanotubes2008Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, nr 8, s. 084707-1-084707-8Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We report hybrid density functional theory calculations for electronic structures of hydrogen-terminated finite single-walled carbon nanotubes (6,5) and (8,3) up to 100 nm in length. Gap states that are mainly arisen from the hydrogen-terminated edges have been found in (8,3) tubes, but their contributions to the density of states become invisible when the tube is longer than 10 nm. The electronic structures of (6,5) and (8,3) tubes are found to be converged around 20 nm. The calculated band-gap energies of 100 nm long nanotubes are in good agreement with experimental results. The valence band structures of (6,5), (8,3), as well as (5,5) tubes are also investigated by means of ultraviolet photoelectron spectra (UPS), x-ray emission spectroscopy (XES), and the resonant inelastic x-ray scattering (RIXS) spectra theoretically. The UPS, XES and RIXS spectra become converged already at 10 nm. The length-dependent oscillation behavior is found in the RIXS spectra of (5,5) tubes, indicating that the RIXS spectra may be used to determine the size and length of metallic nanotubes. Furthermore, the chiral dependence observed in the simulated RIXS spectra suggests that RIXS spectra could be a useful technique for the determination of chirality of carbon nanotubes.

  • 6.
    Gao, Bin
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Liu, Lei
    Institute of High Energy Physics, Chinese Academy of Sciences, Beijing.
    Wang, ChunRu
    Institute of Chemistry, Chinese Academy of Sciences, Beijing.
    Wu, ZiYu
    Institute of High Energy Physics, Chinese Academy of Sciences, Beijing.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Spectral identification of fullerene C82 isomers2007Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, nr 16, s. 164314-1-164314-8Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ultraviolet photoelectron spectra (UPS) of C-82 isomers have been calculated using hybrid density functional theory in combination with the Gelius model [Proceedings of the International Conference on Electron spectroscopy, edited by D. A. Shirley (North-Holland, Amsterdam, 1972), p. 311; J. Electron Spectrosc. Relat. Phenom. 5, 985 (1974)]. The calculated UPS spectra are found to be isomer dependent and in good agreement with the experimental counterparts. Near-edge x-ray absorption fine structure (NEXAFS), x-ray photoelectron spectroscopy (XPS), x-ray emission spectroscopy, and the resonant inelastic x-ray scattering (RIXS) spectra of three important isomers [3(C-2), 6(C-s), and 9(C-2v)] have also been simulated. Strong isomer dependence has also been found for NEXAFS, XPS, and RIXS spectra.

  • 7.
    Gao, Bin
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Wu, ZiYu
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    A density functional theory study of shake-up satellites in photoemission of carbon fullerenes and nanotubes2008Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, nr 23, s. 234704-1-234704-7Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Carbon 1s shake-up spectra of fullerenes C-60, C-70, and C-82 and single-walled carbon nanotubes (SWCNTs) of (5,5), (6,5), and (7,6) have been investigated by using equivalent core hole Kohn-Sham density functional theory approach, in which only one-electron transition between molecular orbitals within core-hole potential is considered. The calculated spectra are generally in good agreement with results of equivalent core-hole time-dependent density functional theory calculations and available experiments, and reliable assignments for the complicated shake-up spectra of such large systems are provided. Calculations have also been performed for endohedral metallofullerene Gd@C-82 to demonstrate the possible use of shake-up processes to identify the charge transfer between the metal ion and the carbon cage. It is found that the exciton binding energy of all systems under investigation is around 0.5 eV.

  • 8.
    Gao, Bin
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Wu, ZiYu
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Chirality and diameter dependent x-ray absorption of single walled carbon nanotubes2009Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, nr 3, s. 034704-1-034704-7Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 9.
    Han, Tiantian
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Jiang, Jun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Fu, Ying
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Quantum chemistry study of energy band structures of GaAs nano clustersManuskript (Annet vitenskapelig)
  • 10.
    Hua, Weijie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Li, Shuhua
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    X-ray absorption spectra of graphene from first-principles simulations2010Inngår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 82, nr 15, s. 155433-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Near edge x-ray absorption fine-structure spectra of graphenes are calculated using hybrid density-functional theory with the equivalent core hole approximation, aiming to resolve the ongoing debate on the interpretation of corresponding experimental spectra. Effects of size, stacking, edges, and defects on the spectra have been analyzed in detail for both C 1s-pi* and C 1s-sigma* transitions. The infinite graphene sheet has been modeled by graphene nanoribbons of different size. The size dependence and convergence of the spectra have been revealed. It is found that the pi-pi interaction between layers have mainly effects on the C 1s-pi* transitions in two different energy regions. The stacking effect smears out the double-peaks structure of the first main pi* peak around 285 eV and results in blueshift of the second pi* structure by almost 2 eV. The calculations show that the pi spectrum of hydrogen saturated edge carbons is redshifted with respect to the central ones and that a new weak sigma* peak around 288 eV appears. The presence of defects can also introduce new spectral features in both pi and sigma regions.

  • 11.
    Hua, Weijie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Yamane, Hiroyuki
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Jiang, Jun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Li, Shuhua
    Kato, Hiroyuki S.
    Kawai, Maki
    Hatsui, Takaki
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Kosugi, Nobuhiro
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Systematic Study of Soft X-ray Spectra of Poly(Dg)center dot Poly(Dc) and Poly(Da)center dot Poly(Dt) DNA Duplexes2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 20, s. 7016-7021Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and resonant inelastic X-ray scattering applied to poly(dG)center dot poly(dC) and poly(dA)center dot poly(dT) DNA duplexes. We have derived several conclusions on the nature of these X-ray spectra: the stacking of pairs has very little influence on the spectra; the spectra of a DNA composed of mixed Watson-Crick base pairs are well reproduced by linear combinations of GC and AT base pairs involved; the amine and imine nitrogens show noticeable differences as building blocks in the absorption, emission, and resonant emission spectra. The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed.

  • 12.
    Jiang, Jun
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Han, Tiantian
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Fu, Ying
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Ab initio study of energy band structures of GaAs nanoclusters2009Inngår i: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 94, nr 9Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Electronic states and optical transitions of hydrogen terminated GaAs nanoclusters up to 16.9 nm in diameter were studied using a large-scale quantum chemistry approach called central insertion scheme by which the quantum confinement effect is shown to quantitatively agree with experimental results. The ab initio study further reveals that the effective mass of the conduction-band electron (valence-band hole) in the GaAs nanocluster is larger (smaller) than the bulk material value.

  • 13.
    Jiang, Jun
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Sun, Lian
    Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Han, Tiantian
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Wu, Ziyu
    Institute of High Energy Physics, Chinese Academy of Sciences, Beijing.
    Lu, Wei
    National Lab for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences.
    Yang, Jinlong
    Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    A magic structural factor in hydrogen-terminated nanodiamond clustersInngår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114Artikkel i tidsskrift (Annet vitenskapelig)
  • 14.
    Liu, Lei
    et al.
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Chu, Wangsheng
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Chen, Dongliang
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Hu, Tiandou
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Wang, Chunru
    Chinese Acad Sci, Inst Chem, Beijing.
    Dunsch, Lothar
    Leibniz Institute for Solid State and Materials Research (IFW), Dresden.
    Marcelli, Augusto
    Laboratori Nazionali di Frascati, Istituto Nazionale di Fisica Nucleare.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Wu, Ziyu
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    The structural determination of endohedral metallofullerene Gd@C-82 by XANES2008Inngår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, nr 4, s. 474-476Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although the Gd ion in Gd@C-82 has been shown to lie above the C-C bond on the C-2 axis as an anomalous structure from the MEM/Rietveld analysis, the present XANES study reveals that it lies above the hexagon on the C-2 axis as a normal structure, and Gd oscillates around its equilibrium position with an amplitude increasing with temperature increase.

  • 15.
    Vall Llosera, Gemma
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Kivimaeki, A.
    Coreno, M.
    Ruiz, J. Alvarez
    de Simone, M.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Rachlew, Elisabeth
    KTH, Skolan för teknikvetenskap (SCI), Fysik.
    The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase (vol 128, 044316, 2008)2009Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, nr 16Artikkel i tidsskrift (Fagfellevurdert)
  • 16.
    Vall-llosera, Gemma
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Atom- och molekylfysik.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Kivimäki, A.
    CNR-INFM, Laboratorio Nazionale TASC, Trieste.
    Coreno, M.
    CNR-IMIP, Montelibretti, Rome.
    Álvarez Ruiz, Jesús
    CSIC, Inst Quim Fis Rocasolano, Dept Quim Laser, Madrid.
    de Simone, M.
    CNR-INFM, Laboratorio Nazionale TASC, Trieste.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Rachlew, Elisabeth
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Atom- och molekylfysik.
    The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase2008Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, nr 4, s. 044316-1-044316-12Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with pi* symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are assigned to transitions to valence/Rydberg orbitals with mixed pi*/sigma* character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to sigma* orbitals. Calculating the experimental and theoretical Delta(pi) term values at both edges, we observe that they are almost the same within +/- 1 eV as expected for isoelectronic bonded pairs. The term values of the pi* and sigma* resonances are discussed in terms of the total Z number of the atoms participating in the bond.

  • 17. Yu, Meijuan
    et al.
    Yang, Feifei
    Chu, Wangsheng
    Wang, Yu
    Zhao, Haifeng
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Zhao, Wei
    Sun, Jianping
    Wu, Fangming
    Zhang, Xiaowei
    Shi, Yunyu
    Wu, Ziyu
    3D local structure around Zn in Kti11p as a representative Zn-(Cys)4 motif as obtained by MXAN2008Inngår i: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 374, nr 1, s. 28-32Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Zinc is an important component of many proteins that play key roles in transcription, translation, and catalysis. Kti11p, DESR1, both belonging to a protein family characterized by a CSL zinc finger domain, and the co-catalytic zinc-protein PML containing a Zn2+ binding domain called RING or C3HC4 finger are all structurally determined by NMR although the zinc sites are silent to this spectroscopical method. The comparison of X-ray absorption near-edge spectroscopy (XANES) data for the three proteins demonstrates that fingerprints effect is a reliable method for a primary characterization of ligand species. Ab initio full MS Calculations performed by MAN are applied to obtain chemical and stereo structural information around the Zn ion in Kti11p. For the first time this high-spatial resolution technique confirms the formation of a stable Zn tetrahedral configuration with four sulfur ligands, and returns extremely accurate bond angle information between ligands.

  • 18.
    Zhang, Igor Ying
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Jiang, Jun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Xu, Xin
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    The RRS-PBC Method: Bridge Finite Cluster to Crystalline Bulk SolidInngår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448Artikkel i tidsskrift (Annet vitenskapelig)
  • 19.
    Zhang, Wenhua
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Yang, Jinlong
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Caravetta, V.
    Wu, Z.
    Electronic structure of [121]tetramantane-6-thiol on gold and silver surfaces2009Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, nr 054705Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 20. Zhong, Jun
    et al.
    Guo, Jinghua
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Chiou, Jau-Wern
    Li, Jiong
    Chu, Wangsheng
    Pong, Way-Faung
    Chang, Chinglin
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Wu, Ziyu
    Understanding the scattering mechanism of single-walled carbon nanotube based gas sensors2010Inngår i: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 48, nr 7, s. 1970-1976Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the interaction between gas molecules with single-walled carbon nanotube (SWCNT) we show that as a result of collisions the gas scattering contributes with an important background signal and should be considered in SWCNT-based gas sensors. Experimental evidence of the collision-induced tube wall deformation is demonstrated using in situ X-ray absorption near-edge structure spectroscopy. Results support the occurrence of the scattering process and show how gas collisions may affect the electronic structure of SWCNTs.

  • 21. Zhong, Jun
    et al.
    Song, Li
    Meng, Jie
    Gao, Bin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Chu, Wangsheng
    Xu, Haiyan
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Guo, Jinghua
    Marcelli, Augusto
    Xie, Sishen
    Wu, Ziyu
    Bio-nano interaction of proteins adsorbed on single-walled carbon nanotubes2009Inngår i: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 47, nr 4, s. 967-973Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We applied X-ray absorption near edge structure (XANES) spectroscopy to investigate the adsorption of proteins onto single-walled carbon nanotubes (SWCNTs). Specific XANES spectral features such as peptide C=O bonds in proteins were recognized and found to be affected by the corresponding aromatic structure of SWCNTs. Experimental data combined with first-principle calculation of the investigated nano-complex allow the understanding of adsorption mechanism and reveal that an interface interaction occurs leading to precise structural distortions of proteins. The study also demonstrates that XANES is a powerful tool to characterize structural details of proteins at the interface of complex systems.

1 - 21 of 21
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