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  • 101.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Electronic structure investigations of transition metal complexes through X-ray spectroscopy2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Catalysts based on the first-row (3d) transition metals are commonly seen in chemical and biological reactions. To understand the role of the transition metal in the catalyst, the element specific technique core level spectroscopy is used to probe the electronic structure and geometric properties centered around the metal site. Different types of X-ray spectra can be applied to probe the metal 3d character orbitals involved in reactions, which make it possible to identify and characterize the reactive sites of samples in different forms. A detailed interpretation and understanding of the different X-ray spectra requires a unified method which can be used to model different types of X-ray spectra, e.g., soft and hard X-rays. In this thesis, theoretical investigations of the electronic structures of 3d transition metal complexes through X-ray spectroscopy are presented. The restricted active space method (RAS) is used to successfully reproduce different types of X-ray spectra by including all important spectral effects: multiplet structures, spin-orbit coupling, charge-transfer excitations, ligand field splitting and 3d-4p orbital hybridization. Different prototypes of molecules are adopted to test the applicability of the RAS theory.

    The metal L edge X-ray absorption (XAS) spectra of low spin complexes [Fe(CN)6]n and [Fe(P)(ImH)2]n in ferrous and ferric oxidation state are discussed. The RAS calculations on iron L edge spectra of these comparing complexes have been performed to fingerprint the oxidation states of metal ion, and different ligand environments. The Fe(P) system has several low-lying spin states in the ground state, which is used as a model to identify unknown species by their spectroscopic fingerprints through RAS spectra simulations. To pave the route of understanding the electronic structure of oxygen evolution complex of Mn4CaO5 cluster, the MnII(acac)2 and MnIII(acac)3 are adopted as prototypical Mn-complexes. The 3d partial fluorescence yield-XAS are employed on the Mn L-edge in solution. Combining experiments and RAS calculations, primary questions related to the oxidation state and spin state are discussed.

    The first application to simulate the metal K pre-edge XAS of mono-iron complexes and iron dimer using RAS method beyond the electric dipole is completed by implementing the approximate origin independent calculations for the intensities. The K pre-edge spectrum of centrosymmetric complex [FeCl6]n– ferrous state is discussed as s and a donor model systems. The intensity of the K pre-edge increases significantly if the centrosymmetric environment is broken, e:g:, when going from a six-coordinate to the four-coordinate site in [FeCl4]n. Distortions from centrosymmetry allow for 3d-4p orbital hybridization, which gives rise to electric dipole-allowed transitions in the K pre-edge region. In order to deliver ample electronic structure details with high resolution in the hard X-ray energy range, the two-photon 1s2p resonant inelastic X-ray scattering process is employed. Upon the above successful applications of one-photon iron L edge and K pre-edge spectra, the RAS method is extended to simulate and interpret the 1s2p resonant inelastic X-ray scattering spectra of [Fe(CN)6]n in ferrous and ferric oxidation states. The RAS applications on X-ray simulations are not restricted to the presented spectra in the thesis, it can be applied to the photon process of interest by including the corresponding core and valence orbitals of the sample.

    List of papers
    1. Restricted active space calculations of L-edge X-ray absorption spectra: From molecular orbitals to multiplet states
    Open this publication in new window or tab >>Restricted active space calculations of L-edge X-ray absorption spectra: From molecular orbitals to multiplet states
    Show others...
    2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 141, no 12, article id 124116Article in journal (Refereed) Published
    Abstract [en]

    The metal L-edge (2p -> 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d(5)) model systems with well-known electronic structure, viz., atomic Fe3+, high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)(6)](3-) that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-236075 (URN)10.1063/1.4896373 (DOI)000342844100021 ()25273421 (PubMedID)
    Note

    Correction in: Journal of Chemical Physics, vol. 141, issue 4, article number: 149905, DOI: 10.1063/1.4908043 ISI: 000349847000064

    Available from: 2014-11-12 Created: 2014-11-12 Last updated: 2017-12-05Bibliographically approved
    2. Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra
    Open this publication in new window or tab >>Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra
    Show others...
    2016 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 5, p. 477-486Article in journal (Refereed) Published
    Abstract [en]

    The restricted active-space (RAS) approach can accurately simulate metal L-edge X-ray absorption spectra of first-row transition metal complexes without the use of any fitting parameters. These characteristics provide a unique capability to identify unknown chemical species and to analyze their electronic structure. To find the best balance between cost and accuracy, the sensitivity of the simulated spectra with respect to the method variables has been tested for two models, [FeCl6](3-) and [Fe(CN)(6)](3-). For these systems, the reference calculations give deviations, when compared with experiment, of 1 eV in peak positions, 30% for the relative intensity of major peaks, and 50% for minor peaks. When compared with these deviations, the simulated spectra are sensitive to the number of final states, the inclusion of dynamical correlation, and the ionization potential electron affinity shift, in addition to the selection of the active space. The spectra are less sensitive to the quality of the basis set and even a double- basis gives reasonable results. The inclusion of dynamical correlation through second-order perturbation theory can be done efficiently using the state-specific formalism without correlating the core orbitals. Although these observations are not directly transferable to other systems, they can, together with a cost analysis, aid in the design of RAS models and help to extend the use of this powerful approach to a wider range of transition metal systems.

    Keywords
    transition metals; X-ray absorption spectroscopy; multiconfigurational wavefunction; spin-orbit coupling; charge transfer
    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-276263 (URN)10.1002/jcc.24237 (DOI)000369176900002 ()26502979 (PubMedID)
    Funder
    Swedish National Infrastructure for Computing (SNIC), s00112-267 liu-2012-00060-46Carl Tryggers foundation Marcus and Amalia Wallenberg FoundationSwedish Research Council
    Available from: 2016-02-10 Created: 2016-02-10 Last updated: 2017-11-30Bibliographically approved
    3. Fingerprinting electronic structures of heme using theoretical modeling of L-edge X-ray absorption spectra
    Open this publication in new window or tab >>Fingerprinting electronic structures of heme using theoretical modeling of L-edge X-ray absorption spectra
    (English)Manuscript (preprint) (Other academic)
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-327409 (URN)
    Available from: 2017-08-10 Created: 2017-08-10 Last updated: 2017-08-16
    4. Probing the oxidation state: A case study of Mn II (acac) 2 and Mn III (acac) 3 on how charge and spin densities determine Mn L-edge X-ray absorption energies
    Open this publication in new window or tab >>Probing the oxidation state: A case study of Mn II (acac) 2 and Mn III (acac) 3 on how charge and spin densities determine Mn L-edge X-ray absorption energies
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-327410 (URN)
    Available from: 2017-08-10 Created: 2017-08-10 Last updated: 2017-08-16
    5. Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method
    Open this publication in new window or tab >>Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method
    Show others...
    2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 4, p. 3250-3259Article in journal (Refereed) Published
    Abstract [en]

    The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d-4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6](n-), [FeCl4](n-), and [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4](2-/1-), the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems.

    National Category
    Theoretical Chemistry
    Research subject
    Chemistry with specialization in Quantum Chemistry
    Identifiers
    urn:nbn:se:uu:diva-243571 (URN)10.1039/c5cp07487h (DOI)000369506000108 ()26742851 (PubMedID)
    Funder
    Marcus and Amalia Wallenberg FoundationSwedish Research CouncilCarl Tryggers foundation Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish National Infrastructure for Computing (SNIC), snic2013-1-317Swedish National Infrastructure for Computing (SNIC), snic2014-5-36
    Available from: 2015-02-10 Created: 2015-02-10 Last updated: 2018-08-13Bibliographically approved
    6. Applications to metal K pre-edges of transitionmetal dimers illustrate the approximate origin independence for the intensities in the length representation
    Open this publication in new window or tab >>Applications to metal K pre-edges of transitionmetal dimers illustrate the approximate origin independence for the intensities in the length representation
    2017 (English)In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 1-2, p. 174-189Article in journal (Refereed) Published
    Abstract [en]

    X-ray absorption spectroscopy (XAS) in the metal K pre-edge is a standard probe of electronic and geometric structure of transition metal complexes. Simulating the K pre-edge spectra requires contributions beyond the electric dipole, but if that term is non-zero, the second-order terms, e. g. electric quadrupoles, are no longer origin-independent. In the velocity representation, complete origin independence can be achieved by including all terms to the same order in the oscillator strength. Here, we implement that approach in the length representation and use it for restricted active space (RAS) simulations of metal K pre-edges of iron monomers and dimers. Complete origin independence is not achieved and the size of the remaining errors depends on the electric dipole oscillator strength and its ratio in length and velocity representations. The error in the origin independence is in the ANO basis sets two orders of magnitude smaller than the value of the individual contributions. For systemswith strong electric dipole contributions, the errors are not significant within 3 angstrom from a metal centre, far enough to handlemany multi-metal systems. Furthermore, we discuss the convergence of the multipole expansion, the possibility to assign spectral contributions, and the origin of negative absorption intensities. [GRAPHICS]

    Place, publisher, year, edition, pages
    TAYLOR & FRANCIS LTD, 2017
    Keywords
    Multiconfigurational wavefunction, oscillator strengths, quadrupole intensities, properties, X-ray spectroscopy
    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-319774 (URN)10.1080/00268976.2016.1225993 (DOI)000396794700015 ()
    Funder
    Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish Research Council, 2012-3910 2012-3924
    Available from: 2017-04-12 Created: 2017-04-12 Last updated: 2018-08-14Bibliographically approved
    7. Molecular orbital simulations of metal 1s2p resonant inelastic X-ray scattering
    Open this publication in new window or tab >>Molecular orbital simulations of metal 1s2p resonant inelastic X-ray scattering
    Show others...
    2016 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 29, p. 5848-5855Article in journal (Refereed) Published
    Abstract [en]

    For first-row transition metals, high-resolution 3d electronic structure information can be obtained using resonant inelastic X-ray scattering (RIXS). In the hard X-ray region, a K pre-edge (1s -> 3d) excitation can be followed by monitoring the dipole-allowed K alpha (2p -> 1s) or K beta (3p -> 1s) emission, processes labeled 1s2p or 1s3p RIXS. Here the restricted active space (RAS) approach, which is a molecular orbital method, is used for the first time to study hard X-ray RIXS processes. This is achieved by including the two sets of core orbitals in different partitions of the active space. Transition intensities are calculated using both first- and second-order expansions of the wave vector, including, but not limited to, electric dipoles and quadrupoles. The accuracy of the approach is tested for 1s2p RIXS of iron hexacyanides [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. RAS simulations accurately describe the multiplet structures and the role of 2p and 3d spin-orbit coupling on energies and selection rules. Compared to experiment, relative energies of the two [Fe(CN)(6)](3-) resonances deviate by 0.2 eV in both incident energy and energy transfer directions, and multiplet splittings in [Fe(CN)(6)](4-) are reproduced within 0.1 eV. These values are similar to what can be expected for valence excitations. The development opens the modeling of hard X-ray scattering processes for both solution catalysts and enzymatic systems.

    National Category
    Theoretical Chemistry
    Research subject
    Chemistry with specialization in Quantum Chemistry
    Identifiers
    urn:nbn:se:uu:diva-302165 (URN)10.1021/acs.jpca.6b05139 (DOI)000380730400008 ()27398775 (PubMedID)
    Funder
    Marcus and Amalia Wallenberg FoundationSwedish Research CouncilKnut and Alice Wallenberg Foundation, KAW-2013.0020
    Available from: 2016-08-31 Created: 2016-08-31 Last updated: 2017-11-21Bibliographically approved
  • 102.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Electronic structures of transition metal complexes-core level spectroscopic investigation2016Licentiate thesis, comprehensive summary (Other academic)
    List of papers
    1. Restricted active space calculations of L-edge X-ray absorption spectra: From molecular orbitals to multiplet states
    Open this publication in new window or tab >>Restricted active space calculations of L-edge X-ray absorption spectra: From molecular orbitals to multiplet states
    Show others...
    2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 141, no 12, article id 124116Article in journal (Refereed) Published
    Abstract [en]

    The metal L-edge (2p -> 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d(5)) model systems with well-known electronic structure, viz., atomic Fe3+, high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)(6)](3-) that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-236075 (URN)10.1063/1.4896373 (DOI)000342844100021 ()25273421 (PubMedID)
    Note

    Correction in: Journal of Chemical Physics, vol. 141, issue 4, article number: 149905, DOI: 10.1063/1.4908043 ISI: 000349847000064

    Available from: 2014-11-12 Created: 2014-11-12 Last updated: 2017-12-05Bibliographically approved
    2. Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra
    Open this publication in new window or tab >>Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra
    Show others...
    2015 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987XArticle in journal (Refereed) Published
    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-272445 (URN)
    Available from: 2016-01-13 Created: 2016-01-13 Last updated: 2017-11-30
    3. Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method
    Open this publication in new window or tab >>Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method
    Show others...
    2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 4, p. 3250-3259Article in journal (Refereed) Published
    Abstract [en]

    The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d-4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6](n-), [FeCl4](n-), and [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4](2-/1-), the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems.

    National Category
    Theoretical Chemistry
    Research subject
    Chemistry with specialization in Quantum Chemistry
    Identifiers
    urn:nbn:se:uu:diva-243571 (URN)10.1039/c5cp07487h (DOI)000369506000108 ()26742851 (PubMedID)
    Funder
    Marcus and Amalia Wallenberg FoundationSwedish Research CouncilCarl Tryggers foundation Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish National Infrastructure for Computing (SNIC), snic2013-1-317Swedish National Infrastructure for Computing (SNIC), snic2014-5-36
    Available from: 2015-02-10 Created: 2015-02-10 Last updated: 2018-08-13Bibliographically approved
    4. Molecular orbital simulations of metal 1s2p resonant inelastic X-ray scattering
    Open this publication in new window or tab >>Molecular orbital simulations of metal 1s2p resonant inelastic X-ray scattering
    Show others...
    2016 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 29, p. 5848-5855Article in journal (Refereed) Published
    Abstract [en]

    For first-row transition metals, high-resolution 3d electronic structure information can be obtained using resonant inelastic X-ray scattering (RIXS). In the hard X-ray region, a K pre-edge (1s -> 3d) excitation can be followed by monitoring the dipole-allowed K alpha (2p -> 1s) or K beta (3p -> 1s) emission, processes labeled 1s2p or 1s3p RIXS. Here the restricted active space (RAS) approach, which is a molecular orbital method, is used for the first time to study hard X-ray RIXS processes. This is achieved by including the two sets of core orbitals in different partitions of the active space. Transition intensities are calculated using both first- and second-order expansions of the wave vector, including, but not limited to, electric dipoles and quadrupoles. The accuracy of the approach is tested for 1s2p RIXS of iron hexacyanides [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. RAS simulations accurately describe the multiplet structures and the role of 2p and 3d spin-orbit coupling on energies and selection rules. Compared to experiment, relative energies of the two [Fe(CN)(6)](3-) resonances deviate by 0.2 eV in both incident energy and energy transfer directions, and multiplet splittings in [Fe(CN)(6)](4-) are reproduced within 0.1 eV. These values are similar to what can be expected for valence excitations. The development opens the modeling of hard X-ray scattering processes for both solution catalysts and enzymatic systems.

    National Category
    Theoretical Chemistry
    Research subject
    Chemistry with specialization in Quantum Chemistry
    Identifiers
    urn:nbn:se:uu:diva-302165 (URN)10.1021/acs.jpca.6b05139 (DOI)000380730400008 ()27398775 (PubMedID)
    Funder
    Marcus and Amalia Wallenberg FoundationSwedish Research CouncilKnut and Alice Wallenberg Foundation, KAW-2013.0020
    Available from: 2016-08-31 Created: 2016-08-31 Last updated: 2017-11-21Bibliographically approved
  • 103.
    Guo, Meiyuan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Erik, Kallman
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pinjari, Rahul V.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. ¶ School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, Maharashtra, India..
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fingerprinting electronic structures of heme using theoretical modeling of L-edge X-ray absorption spectraManuscript (preprint) (Other academic)
  • 104.
    Guo, Meiyuan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Erik, Källman
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sørensen, Lasse Kragh
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA.; Univ Calif Berkeley, Kenneth S Pitzer Ctr Theoret Chem, Dept Chem, Berkeley, CA 94720 USA.
    Pinjari, Rahul V.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, Maharashtra, India..
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Molecular orbital simulations of metal 1s2p resonant inelastic X-ray scattering2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 29, p. 5848-5855Article in journal (Refereed)
    Abstract [en]

    For first-row transition metals, high-resolution 3d electronic structure information can be obtained using resonant inelastic X-ray scattering (RIXS). In the hard X-ray region, a K pre-edge (1s -> 3d) excitation can be followed by monitoring the dipole-allowed K alpha (2p -> 1s) or K beta (3p -> 1s) emission, processes labeled 1s2p or 1s3p RIXS. Here the restricted active space (RAS) approach, which is a molecular orbital method, is used for the first time to study hard X-ray RIXS processes. This is achieved by including the two sets of core orbitals in different partitions of the active space. Transition intensities are calculated using both first- and second-order expansions of the wave vector, including, but not limited to, electric dipoles and quadrupoles. The accuracy of the approach is tested for 1s2p RIXS of iron hexacyanides [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. RAS simulations accurately describe the multiplet structures and the role of 2p and 3d spin-orbit coupling on energies and selection rules. Compared to experiment, relative energies of the two [Fe(CN)(6)](3-) resonances deviate by 0.2 eV in both incident energy and energy transfer directions, and multiplet splittings in [Fe(CN)(6)](4-) are reproduced within 0.1 eV. These values are similar to what can be expected for valence excitations. The development opens the modeling of hard X-ray scattering processes for both solution catalysts and enzymatic systems.

  • 105.
    Guo, Meiyuan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Southwest Univ, Dept Chem & Chem Engn, Chongqing, Peoples R China.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pinjari, Rahul V.
    Swami Ramanand Teerth Marathwada Univ, Sch Chem Sci, Nanded, Maharashtra, India.
    Couto, Rafael Carvalho
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sörensen, Lasse Kragh
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pierloot, Kristine
    Univ Leuven, Dept Chem, Heverlee, Belgium.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Siena, Dept Biotechnol Chem & Pharm, Siena, Italy.
    Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 1, p. 477-489Article in journal (Refereed)
    Abstract [en]

    The capability of the multiconfigurational restricted active space approach to identify electronic structure from spectral fingerprints is explored by applying it to iron L-edge X-ray absorption spectroscopy (XAS) of three heme systems that represent the limiting descriptions of iron in the Fe-O-2 bond, ferrous and ferric [Fe(P)(ImH)(2)](0/1+) (P = porphine, ImH = imidazole), and Fe-II(P). The level of agreement between experimental and simulated spectral shapes is calculated using the cosine similarity, which gives a quantitative and unbiased assignment. Further dimensions in fingerprinting are obtained from the L-edge branching ratio, the integrated absorption intensity, and the edge position. The results show how accurate ab initio simulations of metal L-edge XAS can complement calculations of relative energies to identify unknown species in chemical reactions.

  • 106.
    Guo, Meiyuan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    S. Miedema, Piter
    L2,3-edge 3d-Partial-fluorescence yield x-ray absorption as a sensitive probe of a distorted symmetryManuscript (preprint) (Other academic)
  • 107.
    Guo, Meiyuan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sörensen, Lasse Kragh
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pinjari, Rahul V.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 4, p. 3250-3259Article in journal (Refereed)
    Abstract [en]

    The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d-4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6](n-), [FeCl4](n-), and [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4](2-/1-), the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems.

  • 108.
    Gürkan, Nilhan
    et al.
    Department of Industrial Engineering, Gediz University, Menemen-Izmir, Turkey.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Realization of a holonomic quantum computer in a chain of three-level systems2015In: Physics Letters A, ISSN 0375-9601, E-ISSN 1873-2429, Vol. 379, no 47-48, p. 3050-3053Article in journal (Refereed)
    Abstract [en]

    Holonomic quantum computation is the idea to use non-Abelian geometric phases to implement universal quantum gates that are robust to fluctuations in control parameters. Here, we propose a compact design for a holonomic quantum computer based on coupled three-level systems. The scheme does not require adiabatic evolution and can be implemented in arrays of atoms or ions trapped in tailored standing wave potentials. 

  • 109.
    Hast, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Hanke, Michael
    Royal Inst Technol, KTH, Dept Math, Sch Engn Sci, Stockholm, Sweden.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Swedish eScience Education – a Graduate School in eScience2015In: Proc. 11th International Conference on e-Science, IEEE Computer Society, 2015, p. 31-35Conference paper (Refereed)
    Abstract [en]

    Swedish eScience Education (SeSE) is a national graduate school in eScience in Sweden. It comes from the collaboration between two major research initiatives in eScience and the school has turned out to be very successful. It has made it possible for students at different universities to get access to education that is not normally available at their home universities. With SeSE they get access to education by the top experts within their respective field. We argue why such graduate school is important and how it is different from training offered by many HPC centres in Europe. Furthermore, examples of courses and their structure is discussed as well as lessons learned from SeSE and its two predecessors in Sweden.

  • 110.
    Head-Gordon, Martin
    et al.
    Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    A celebration of the Swedish school2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, p. 1993-1994Article in journal (Other academic)
  • 111.
    Heijkenskjöld, Filip
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Edvardsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Astrophysics.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aktiva studenter gör demonstrationsexperiment (2)2017Conference paper (Other academic)
    Abstract [sv]

    Aktiva studenter gör demonstrationsexperiment

    Filip Heijkenskjöld, Institutionen för fysik och astronomi avd. Fysikens didaktik

    Bengt Edvardsson, Institutionen för fysik och astronomi, avd. Astronomi

    Marcus Lundberg, Institutionen för kemi - Ångström, Teoretisk kemi

    Sammanfattning

    Projektet avser att aktivera studenterna och gör dem till deltagande aktörer i föreläsningarna genom att ge studenterna ansvar för att designa sina egna experiment som kan visa på centrala begrepp inom fysiken. Studenterna får använda ett mätverktyg (IOLab) för att enkelt kunna experimentera och samla in data. För information om IOLab se http://www.iolab.science

    Vi låter studenterna i kursen 1KB302, Fysik för kemister, ta ansvar för en del av undervisningen. De väljer själva ut vad de vill illustrera med experiment. Studenterna bidrar med var sitt ca 5 minuter långt demonstrationsexperiment och deltar i en efterföljande diskussion på 10 minuter. Efter godkänd insats får de en tentamensdel godkänd. Detta ökar studenternas engagemang och även kopplingen till andra kurser som studeras inom programmen.

  • 112.
    Heijkenskjöld, Filip
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Edvardsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Astrophysics.
    Marcus, Lundberg
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aktiva studenter gör demonstrationsexperiment (1)2017Conference paper (Other academic)
    Abstract [sv]

    Aktiva studenter gör demonstrationsexperiment

    Filip Heijkenskjöld, Institutionen för fysik och astronomi avd. Fysikens didaktik

    Bengt Edvardsson, Institutionen för fysik och astronomi, avd. Astronomi

    Marcus Lundberg, Institutionen för kemi - Ångström, Teoretisk kemi

    Sammanfattning

    Projektet avser att aktivera studenterna och gör dem till deltagande aktörer i föreläsningarna genom att ge studenterna ansvar för att designa sina egna experiment som kan visa på centrala begrepp inom fysiken. Studenterna får använda ett mätverktyg (IOLab) för att enkelt kunna experimentera och samla in data. För information om IOLab se http://www.iolab.science

    Vi låter studenterna i kursen 1KB302, Fysik för kemister, ta ansvar för en del av undervisningen. De väljer själva ut vad de vill illustrera med experiment. Studenterna bidrar med var sitt ca 5 minuter långt demonstrationsexperiment och deltar i en efterföljande diskussion på 10 minuter. Efter godkänd insats får de en tentamensdel godkänd. Detta ökar studenternas engagemang och även kopplingen till andra kurser som studeras inom programmen.

  • 113.
    Hoffmann, Inga
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Hamberg, Mats
    Karolinska institutet.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Oliw, Ernst H.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Novel insights into cyclooxygenases, linoleate diol synthases, and lipoxygenases from deuterium kinetic isotope effects and oxidation of substrate analogs2012In: Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids, ISSN 1388-1981, E-ISSN 1879-2618, Vol. 1821, no 12, p. 1508-1517Article in journal (Refereed)
    Abstract [en]

    Cyclooxygenases (COX) and 8R-dioxygenase (8R-DOX) activities of linoleate diol synthases (LDS) are homologous heme-dependent enzymes that oxygenate fatty acids by a tyrosyl radical-mediated hydrogen abstraction and antarafacial insertion of O2. Soybean lipoxygenase-1 (sLOX-1) contains non-heme iron and oxidizes 18:2n-6 with a large deuterium kinetic isotope effect (D-KIE). The aim of the present work was to obtain further mechanistic insight into the action of these enzymes by using a series of n-6 and n-9 fatty acids and by analysis of D-KIE. COX-1 oxidized C20 and C18 fatty acids in the following order of rates: 20:2n-6 > 20:1n-6 > 20:3n-9 > 20:1n-9 and 18:3n-3 ≥ 18:2n-6 > 18:1n-6. 18:2n-6 and its geometrical isomer (9E,12Z)18:2 were both mainly oxygenated at C-9 by COX-1, but the 9Z,12E isomer was mostly oxygenated at C-13. A cis-configured double bond in the n-6 position therefore seems important for substrate positioning. 8R-DOX oxidized (9Z,12E)18:2 at C-8 in analogy with 18:2n-6, but the 9E,12Z isomer was only subject to hydrogen abstraction at C-11 and oxygen insertion at C-9 by 8R-DOX of 5,8-LDS. sLOX-1 and 13R-MnLOX oxidized [11S-2H]18:2n-6 with similar D-KIE (~53), which implies that the catalytic metals did not alter the D-KIE. Oxygenation of 18:2n-6 by COX-1 and COX-2 took place with a D-KIE of 3-5 as probed by incubations of [11,11-2H2]- and [11S-2H]18:2n-6. In contrast, the more energetically demanding hydrogen abstractions of the allylic carbons of 20:1n-6 by COX-1 and 18:1n-9 by 8R-DOX were both accompanied by large D-KIE (>20).

  • 114.
    Hoffmann, Mark
    et al.
    Univ North Dakota, Grand Forks, ND 58202 USA..
    Brändas, Erkki
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Preface2018In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 118, no 1, article id e25517Article in journal (Other academic)
  • 115.
    Hotokka, Matti
    et al.
    Åbo Akademi, Finland.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Maruani, Jean
    UPMC & CNRS.
    Delgado-Barrio, Gerardo
    CSIC, Spain.
    Advances in Quantum Methods and Applications in Chemistry, Physics,and Biology: Progress in Theoretical Chemistry and Physics B 272013Book (Refereed)
    Abstract [en]

    This volume collects 20 selected papers from the scientific contributions presented at the Seventeenth International Workshop on Quantum Systems in Chemistry and Physics (and Biology), QSCP-XVII, which was organized by Prof. Matti Hotokka at Åbo Akademi University, Turku, Finland, from August 19 to 25, 2012. Over 120 scientists from 27 countries attended this meeting. Participants of the QSCP-XVII workshop discussed the state of the art, new trends and future evolution of methods in molecular quantum mechanics, as well as their applications to a wide variety of problems in chemistry, physics, and biology.

  • 116. Häse, Florian
    et al.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aspuru-Guzik, Alan
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    How machine learning can assist the interpretation of ab initio molecular dynamics simulations and conceptual understanding of chemistry2019In: Chemical Science, ISSN 2041-6520, Vol. 10, no 8, p. 2298-2307Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations are often key to the understanding of the mechanism, rate and yield of chemical reactions. One current challenge is the in-depth analysis of the large amount of data produced by the simulations, in order to produce valuable insight and general trends. In the present study, we propose to employ recent machine learning analysis tools to extract relevant information from simulation data without a priori knowledge on chemical reactions. This is demonstrated by training machine learning models to predict directly a specific outcome quantity of ab initio molecular dynamics simulations - the timescale of the decomposition of 1,2-dioxetane. The machine learning models accurately reproduce the dissociation time of the compound. Keeping the aim of gaining physical insight, it is demonstrated that, in order to make accurate predictions, the models evidence empirical rules that are, today, part of the common chemical knowledge. This opens the way for conceptual breakthroughs in chemistry where machine analysis would provide a source of inspiration to humans.

  • 117. Jay, Raphael M.
    et al.
    Norell, Jesper
    Eckert, Sebastian
    Hantschmann, Markus
    Beye, Martin
    Kennedy, Brian
    Quevedo, Wilson
    Schlotter, William F.
    Dakovski, Georgi L.
    Minitti, Michael P.
    Hoffmann, Matthias C.
    Mitra, Ankush
    Moeller, Stefan P.
    Nordlund, Dennis
    Zhang, Wenkai
    Liang, Huiyang W.
    Kunnus, Kristian
    Kubicek, Katharina
    Techert, Simone A.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Department of Biotechnology, Chemistry and Pharmacy, Universita ̀ di Siena, Siena, Italy.
    Wernet, Philippe
    Gaffney, Kelly
    Odelius, Michael
    Foehlisch, Alexander
    Disentangling Transient Charge Density and Metal-Ligand Covalency in Photoexcited Ferricyanide with Femtosecond Resonant Inelastic Soft X-ray Scattering2018In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 9, no 12, p. 3538-3543Article in journal (Refereed)
    Abstract [en]

    Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal-ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. pi-Back-donation is found to be mainly determined by the metal site occupation, whereas the ligand hole instead influences sigma-donation. Our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes.

  • 118.
    Jay, Raphael
    et al.
    Univ Potsdam, Potsdam, Germany.
    Norell, Jesper
    Stockholm Univ, Dept Phys, Stockholm, Sweden.
    Kunnus, Kristjan
    Stanford Univ, PULSE Inst, Menlo Pk, CA USA.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Gaffney, Kelly
    Stanford Univ, SLAC Natl Accelerator Lab, Palo Alto, CA 94304 USA.
    Wernet, Philippe
    Helmholtz Zentrum Berlin, Berlin, Germany.
    Odelius, Michael
    Stockholm Univ, Dept Phys, Stockholm, Sweden.
    Foehlisch, Alexander
    Univ Potsdam, Potsdam, Germany;Helmholtz Zentrum Berlin, Berlin, Germany.
    Dynamcis of local charge densities and metal-ligand covalency in iron complexes from femtosecond resonant inelastic soft X-ray scattering2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 256Article in journal (Other academic)
  • 119.
    Jayasinghe-Arachchige, Vindi M.
    et al.
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Hu, Qiaoyu
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Sharma, Gaurav
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Paul, Thomas J.
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Quinonero, David
    Univ Illes Balears, Dept Chem, Palma de Mallorca, Spain.
    Parac-Vogt, Tatjana N.
    Katholieke Univ Leuven, Dept Chem, B-3001 Leuven, Belgium.
    Prabhakar, Rajeev
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Hydrolysis of Chemically Distinct Sites of Human Serum Albumin by Polyoxometalate: A Hybrid QM/MM (ONIOM) Study2019In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, no 1, p. 51-61Article in journal (Refereed)
    Abstract [en]

    In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH) (PW11O39)](4-)(ZrK) have been investigated using the hybrid two-layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392-Glu393 site of HSA is predicted to occur in the rate-limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392-Glu393, Ala257-Asp258, Lys313-Asp314, and Arg114-Leu115) for the hydrolysis of all four sites of HSA. (C) 2018 Wiley Periodicals, Inc.

  • 120.
    Jenkins, Andrew J.
    et al.
    University of Washington, Seattle, Washington, USA.
    Spinlove, K. Eryn
    University College London, London, United Kingdom.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Worth, Graham A.
    University College London, London, United Kingdom.
    Robb, Michael A.
    Imperial College London, London, England.
    The Ehrenfest method with fully quantum nuclear motion (Qu-Eh): Application to charge migration in radical cations2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 149, no 9, article id 094108Article in journal (Refereed)
    Abstract [en]

    An algorithm is described for quantum dynamics where an Ehrenfest potential is combined with fully quantum nuclear motion (Quantum-Ehrenfest, Qu-Eh). The method is related to the single-set variational multi-configuration Gaussian approach (vMCG) but has the advantage that only a single quantum chemistry computation is required at each time step since there is only a single time-dependent potential surface. Also shown is the close relationship to the “exact factorization method.” The quantum Ehrenfest method is compared with vMCG for study of electron dynamics in a modified bismethylene-adamantane cation system. Illustrative examples of electron-nuclear dynamics are presented for a distorted allene system and for HCCI+ where one has a degenerate Π system.

  • 121.
    Johansson, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Entanglement and Quantum Computation from a Geometric and Topological Perspective2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis we investigate geometric and topological structures in the context of entanglement and quantum computation.

    A parallel transport condition is introduced in the context of Franson interferometry based on the maximization of two-particle coincidence intensity. The dependence on correlations is investigated and it is found that the holonomy group is in general non-Abelian, but Abelian for uncorrelated systems. It is found that this framework contains a parallel transport condition developed by Levay in the case of two-qubit systems undergoing local SU(2) evolutions.

    Global phase factors of topological origin, resulting from cyclic local SU(2) evolution, called topological phases, are investigated in the context of multi-qubit systems. These phases originate from the topological structure of the local SU(2)-orbits and are an attribute of most entangled multi-qubit systems. The relation between topological phases and SLOCC-invariant polynomials is discussed. A general method to find the values of the topological phases in an n-qubit system is described.

    A non-adiabatic generalization of holonomic quantum computation is developed in which high-speed universal quantum gates can be realized by using non-Abelian geometric phases. It is shown how a set of non-adiabatic holonomic one- and two-qubit gates can be implemented by utilizing transitions in a generic three-level Λ configuration. The robustness of the proposed scheme to different sources of error is investigated through numerical simulation. It is found that the gates can be made robust to a variety of errors if the operation time of the gate can be made sufficiently short. This scheme opens up for universal holonomic quantum computation on qubits characterized by short coherence times.

    List of papers
    1. Correlation-induced non-Abelian quantum holonomies
    Open this publication in new window or tab >>Correlation-induced non-Abelian quantum holonomies
    Show others...
    2011 (English)In: Journal of Physics A: Mathematical and General, ISSN 0305-4470, E-ISSN 1361-6447, Vol. 44, no 14, p. 145301-Article in journal (Refereed) Published
    Abstract [en]

    In the context of two-particle interferometry, we construct a parallel transport condition that is based on the maximization of coincidence intensity with respect to local unitary operations on one of the subsystems. The dependence on correlation is investigated and it is found that the holonomy group is generally non-Abelian, but Abelian for uncorrelated systems. It is found that our framework contains the Lévay geometric phase (2004 J. Phys. A: Math. Gen. 37 1821) in the case of two-qubit systems undergoing local SU(2) evolutions.

    Keywords
    Quantum holonomy, quantum correlations, quantum interferometry
    National Category
    Physical Sciences
    Research subject
    Physics
    Identifiers
    urn:nbn:se:uu:diva-148641 (URN)10.1088/1751-8113/44/14/145301 (DOI)000288597500011 ()
    Note
    Also in IOP Select, http://Select.iop.org. Additional address (E. Sjöqvist): Centre for Quantum Technologies, NUS, Singapore. Additional address (M. S. Williamson): Erwin Schrödinger International Institute for Mathematical Physics, Wien, AustriaAvailable from: 2011-03-09 Created: 2011-03-09 Last updated: 2017-12-11Bibliographically approved
    2. Topological phases and multiqubit entanglement
    Open this publication in new window or tab >>Topological phases and multiqubit entanglement
    Show others...
    2012 (English)In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 85, no 3, p. 032112-1-032112-11Article in journal (Refereed) Published
    Abstract [en]

    Global phase factors of topological origin, resulting from cyclic local $\rm{SU}$ evolution, called topological phases, were first described in [Phys. Rev. Lett. {\bf 90}, 230403 (2003)], in the case of entangled qubit pairs. In this paper we investigate topological phases in multi-qubit systems as the result of cyclic local $\rm{SU(2)}$ evolution. These phases originate from the topological structure of the local $\rm{SU(2)}$-orbits and are an attribute of most entangled multi-qubit systems. We discuss the relation between topological phases and SLOCC-invariant polynomials and give examples where topological phases appear. A general method to find the values of the topological phases in an $n$-qubit system is described and a complete list of these phases for up to seven qubits is given.

    Keywords
    Topological phase, multipartite entanglement, quantum information
    National Category
    Other Physics Topics
    Research subject
    Physics
    Identifiers
    urn:nbn:se:uu:diva-169141 (URN)10.1103/PhysRevA.85.032112 (DOI)000301333700003 ()
    Funder
    Swedish Research Council
    Note

    Additional address (E. Sjöqvist): Centre for Quantum Technologies, NUS, Singapore

    Available from: 2012-02-23 Created: 2012-02-23 Last updated: 2017-12-07Bibliographically approved
    3. Non-Adiabatic Holonomic Quantum Computation
    Open this publication in new window or tab >>Non-Adiabatic Holonomic Quantum Computation
    Show others...
    2012 (English)In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 14, article id 103035Article in journal (Refereed) Published
    Abstract [en]

    We develop a non-adiabatic generalization of holonomic quantum computation in which high-speed universal quantum gates can be realized using non-Abelian geometric phases. We show how a set of non-adiabatic holonomic one- and two-qubit gates can be implemented by utilizing optical transitions in a generic three-level Λ configuration. Our scheme opens up the possibility of realizing universal holonomic quantum computation on qubits characterized by short coherence time.

    Keywords
    Quantum computation, geometric phase, quantum gates
    National Category
    Physical Sciences Atom and Molecular Physics and Optics
    Research subject
    Physics
    Identifiers
    urn:nbn:se:uu:diva-157181 (URN)10.1088/1367-2630/14/10/103035 (DOI)000310439000001 ()
    Note

    Additional address (E. Sjöqvist): Centre for Quantum Technologies, NUS, Singapore.

    Available from: 2011-08-18 Created: 2011-08-18 Last updated: 2017-12-08Bibliographically approved
    4.
    The record could not be found. The reason may be that the record is no longer available or you may have typed in a wrong id in the address field.
  • 122.
    Johansson, Markus
    et al.
    Centre for Quantum Technologies, NUS, Singapore.
    Ericsson, Marie
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Osterloh, Andreas
    Fakultät für Physik, Universität Duisburg-Essen, Germany.
    Classification scheme of pure multipartite states based on topological phases2014In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 89, no 1, p. 012320-Article in journal (Refereed)
    Abstract [en]

    We investigate the connection between the concept of a-balancedness introduced in [Phys. Rev A. 85, 032112 (2012)] and polynomial local SU invariants and the appearance of topological phases respectively. It is found that different types of a-balancedness correspond to different types of local SU invariants analogously to how different types of balancedness as defined in [New J. Phys. 12, 075025 (2010)] correspond to different types of local SL invariants. These different types of SU invariants distinguish between states exhibiting different topological phases. In the case of three qubits the different kinds of topological phases are fully distinguished by the three-tangle together with one more invariant. Using this we present a qualitative classification scheme based on balancedness of a state. While balancedness and local SL invariants of bidegree $(2n,0)$ classify the SL-semistable states [New J. Phys. 12, 075025 (2010), Phys. Rev. A 83, 052330 (2011)], a-balancedness and local SU invariants of bidegree (2n-m,m) gives a more fine grained classification. In this scheme the a-balanced states form a bridge from the genuine entanglement of balanced states, invariant under the SL-group, towards the entanglement of unbalanced states characterized by U invariants of bidegree (n,n). As a by-product we obtain generalizations to the W-state, states that are entangled, but contain only globally distributed entanglement of parts of the system.

  • 123.
    Johansson, Markus
    et al.
    Centre for Quantum Technologies, NUS, Singapore.
    Khoury, Antonio
    Instituto de Fisica, Universidade Federal Fluminense, Rio de Janeiro, Brazil.
    Singh, Kuldip
    Centre for Quantum Technologies, NUS, Singapore.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Three-qubit topological phase on entangled photon pairs2013In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 87, no 4, p. 042112-Article in journal (Refereed)
    Abstract [en]

    We propose an experiment to observe the topological phases associated with cyclic evolutions, generated by local SU(2) operations, on three-qubit entangled states prepared on different degrees of freedom of entangled photon pairs. The topological phases reveal the nontrivial topological structure of the local SU(2) orbits. We describe how to prepare states showing different topological phases, and discuss their relation to entanglement. In particular, the presence of a π/2 phase shift is a signature of genuine tripartite entanglement in the sense that it does not exist for two-qubit systems. 

  • 124.
    Johnstone, Erik V.
    et al.
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA.;Univ Sheffield, Dept Mat Sci & Engn, Sheffield S1 3JD, S Yorkshire, England..
    Poineau, Frederic
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA..
    Todorova, Tanya K.
    UPMC, CNRS, Coll France, Lab Chim Proc Biol,UMR 8229, 11 Pl Marcelin Berthelot, F-75231 Paris 05, France..
    Forster, Paul M.
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA..
    Sørensen, Lasse K.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Czerwinski, Kenneth R.
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA..
    Sattelberger, Alfred P.
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA.;Argonne Natl Lab, Argonne, IL 60439 USA..
    Molecular and Electronic Structure of Re2Br4(PMe3)(4)2016In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 55, no 14, p. 7111-7116Article in journal (Refereed)
    Abstract [en]

    The dinuclear rhenium(II) complex Re2Br4(PMe3)(4) was prepared from the reduction of [Re2Br8](2-) with (n-Bu4N)BH4 in the presence of PMe3 in propanol. The complex was characterized by single-crystal X-ray diffraction (SCXRD) and UV-visible spectroscopy. It crystallizes in the monoclinic C2/c space group and is isostructural with its molybdenum and technetium analogues. The Re-Re distance (2.2521(3) angstrom) is slightly longer than the one in Re2Cl4(PMe3)(4) (2.247(1) angstrom). The molecular and electronic structure of Re2X4(PMe3)(4) (X = Cl, Br) were studied by multiconfigurational quantum chemical methods. The computed ground-state geometry is in excellent agreement with the experimental structure determined by SCXRD. The calculated total bond order (2.75) is consistent with the presence of an electron-rich triple bond and is similar to the one found for Re2Cl4(PMe3)(4). The electronic absorption spectrum of Re2Br4(PMe3)(4) was recorded in benzene and shows a series of low-intensity bands in the range 10 000-26 000 cm(-1). The absorption bands were assigned based on calculations of the excitation energies with the multireference wave functions followed by second-order perturbation theory using the CASSCF/CASPT2 method. Calculations predict that the lowest energy band corresponds to the delta* -> sigma* transition, while the next higher energy bands were attributed to the delta* -> pi*, delta -> sigma*, and delta -> pi* transitions.

  • 125.
    Jorner, Kjell