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  • 1. Bassan, Arianna
    et al.
    Borowski, Thomasz
    Lundberg, Marcus
    Department of Physics, Stockholm University, AlbaNova University Center.
    Siegbahn, Per E.M.
    Theoretical Modeling of Redox Processes in Enzymes and Biomimetic Systems2006In: Concepts and Models in Bioinorganic Chemistry / [ed] H.-B. Kraatz and N. Metzler-Nolte, Weinheim: Wiley-VCH , 2006, p. 63-88Chapter in book (Other academic)
  • 2.
    Bengtson, Charlotta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ahlkvist, Mikaela
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Ekeroth, William
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Nilsen-Moe, Astrid
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Proos Vedin, Nathalie
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Rodiuchkina, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Ye, Sofie
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Working as Partners: Course Development by a Student–Teacher Team2017In: International Journal for the Scholarship of Teaching & Learning, ISSN 1931-4744, E-ISSN 1931-4744, Vol. 11, no 2, article id Article 6Article in journal (Refereed)
    Abstract [en]

    A first-year undergraduate course at Uppsala University has been redesigned in a process exploring differentlevels of student participation. In the first part of the project, the student voice was heard through interviewsfocusing on the role of the course in the degree program. In the second part, a student-teacher team wasformed to develop course curriculum and teaching material in partnership. Among the implemented changeswere new seminars focusing on conceptual understanding, redesign of all lectures to include active studentparticipation, and a change of the course literature. The redesigned course significantly increased studentsatisfaction compared to previous years. Important success factors were involvement of the studentorganization to promote the project, institutional support, early selection of concrete development tasks, andallowing team members to choose what they wanted to develop according to their own expertise.

  • 3.
    Bengtson, Charlotta
    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.
    Studentmedverkan i utvecklingen av kursen ”Fysik för kemister”2016In: För pedagogisk utveckling tillsammans: Lärare och studenter som medskapare av utbildningen / [ed] Katarina Andreasen och Maria Magnusson, Uppsala: Uppsala universitet, 2016, p. 20-26Conference paper (Other academic)
    Abstract [sv]

    Vi utforskar olika nivåer av studentmedverkan i utvecklingen av kursen ’Fysik för kemister’ på kandidatprogrammet i kemi vid Uppsala universitet. Målet med kursen är att ge alla studenter, även de med en självupplevt svag fysikbakgrund, en god grund för framtida studier i kemi. För att nå dit vill vi bjuda in en bred grupp av studenter att bli medskapare av en bättre kurs. Projektets första steg var att intervjua sex studenter i olika steg av utbildningen, fyra kvinnor och två män. Två av studenterna har redan läst hela kandidatutbildningen och har ett unikt perspektiv över vilken nytta de har haft av kursen i sin utbildning, samt vilka kunskaper de egentligen hade behövt. Resultaten från intervjuerna har använts för att skriva en ny kursplan samt att utveckla nya former av studentaktiv undervisning. Nästa steg, som fortfarande pågår, är att öka deltagandenivån genom att arbeta i en kursutvecklingsgrupp, bestående av sex studenter från olika årskurser samt två lärare.

  • 4. Chung, L. W.
    et al.
    Hayashi, S.
    Lundberg, Marcus
    Kyoto University.
    Nakatsu, T.
    Kato, H.
    Morokuma, K.
    Mechanism of efficient firefly bioluminescence via adiabatic transition state and seam of sloped conical intersection.2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 39, p. 12880-12881Article in journal (Refereed)
    Abstract [en]

    Firefly emission is a well-known efficient bioluminescence. However, the mystery of the efficient thermal generation of electronic excited states in firefly still remains unsolved, particularly at the atomic and molecular levels. We performed SA-CASSCF(12,12)/6-31G* and CASPT2(12,12)/6-31G*//SA-CASSCF(12,12)/6-31G* calculations to elucidate the reaction mechanism of bioluminescence from the firefly dioxetanone in the gas phase. Adiabatic transition state (TS) for the O-O bond cleavage and the minimum energy conical intersection (MECI) were located and characterized. The unique topology of MECI featuring a seam of a sloped conical intersection for the firefly dioxetanone, which was uncovered for the first time, emerges along the reaction pathway to provide a widely extended channel to diabatically access the excited-state from the ground state.

  • 5.
    Farahani, Pooria
    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.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ab initio quantum mechanical calculation of the reaction probability for the Cl- + PH2Cl -> ClPH2 + Cl- reaction2013In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 134-140Article in journal (Refereed)
    Abstract [en]

    The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2ClClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

  • 6.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Lundberg, Marcus
    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.
    Roca-Sanjuan, Daniel
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 28, p. 18653-18664Article in journal (Refereed)
    Abstract [en]

    Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio-and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light - chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference multiconfigurational quantum chemistry methods and accurate reaction-path computational strategies were used to determine the reaction coordinate of three successive processes: decomposition of the dioxetane moiety, non-adiabatic energy transfer from the ground to the excited state, and finally non-radiative decay of the 1,3-butadiene group. With the present study, we open a new area of research within computational photochemistry to study chemically-induced excited-state chemistry that is difficult to tackle experimentally due to the short-lived character of the species involved in the process. The findings shall be of relevance to unveil "dark'' photochemistry mechanisms, which might operate in biological systems under conditions of lack of light. These mechanisms might allow reactions that are typical of photo-induced phenomena.

  • 7.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Maeda, Satoshi
    Hokkaido Univ, Dept Chem, Fac Sci, Kita Ku, Sapporo, Hokkaido 0600810, Japan.
    Fancisco, Joseph S.
    Purdue Univ, Dept Chem, W Lafayette, IN 47907 USA.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Mechanisms for the Breakdown of Halomethanes through Reactions with Ground-State Cyano Radicals2015In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 16, no 1, p. 181-190Article in journal (Refereed)
    Abstract [en]

    One route to break down halomethanes is through reactions with radical species. The capability of the artificial force-induced reaction algorithm to efficiently explore a large number of radical reaction pathways has been illustrated for reactions between haloalkanes (CX3Y; X=H, F; Y=Cl, Br) and ground-state (2Σ+) cyano radicals (CN). For CH3Cl+CN, 71 stationary points in eight different pathways have been located and, in agreement with experiment, the highest rate constant (108 s−1 M−1 at 298 K) is obtained for hydrogen abstraction. For CH3Br, the rate constants for hydrogen and halogen abstraction are similar (109 s−1 M−1), whereas replacing hydrogen with fluorine eliminates the hydrogen-abstraction route and decreases the rate constants for halogen abstraction by 2–3 orders of magnitude. The detailed mapping of stationary points allows accurate calculations of product distributions, and the encouraging rate constants should motivate future studies with other radicals.

  • 8.
    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.

  • 9.
    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.

  • 10.
    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.

  • 11. 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.
    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.

  • 12.
    Kawatsu, Tsutomu
    et al.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Lundberg, Marcus
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Morokuma, Keiji
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan; Emory Univ, Cherry L Emerson Ctr Sci Computat, Atlanta, GA 30322 USA; Emory Univ, Dept Chem, Atlanta, GA 30322 USA.
    Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 2, p. 390-401Article in journal (Refereed)
    Abstract [en]

    The protein environment can have significant effects on the enzyme catalysis even though the reaction occurs locally at the reaction center. In this paper, we describe an efficient scheme that includes a classical molecular dynamics (MD) free-energy perturbation (FEP) correction to the reaction energy diagram, as a complement to the protein effect obtained from static ONIOM (QM:MM) calculations. The method is applied to eight different reaction steps, from the O2-bound reactant to formation of a high-valent ferryl-oxo intermediate, in the nonheme iron enzyme isopenicillin N synthase (IPNS), for which the QM:MM energy diagram has previously been computed [ Lundberg, M. et al. J. Chem. Theory Comput. 2009, 5, 220 ‚àí 234 ]. This large span of the reaction coordinate is covered by dividing each reaction step into microsteps using a virtual reaction coordinate, thus only requiring ONIOM information about the stationary points themselves. Protein effects are important for C‚àíH bond activation and heterolytic O‚àíO bond cleavage because both these two steps involve charge transfer, and compared to a static QM:MM energies, the dynamics of the protein environment changes the barrier for O‚àíO bond cleavage by several kcal/mol. The origin of the dynamical contribution is analyzed in two terms, the geometrical effect caused by the change in average protein geometry (compared to the optimized geometry) in the room temperature MD simulation with the solvent, and the statistical (entropic) effect resulting from fluctuations in the interactions between the active site and the protein environment. These two effects give significant contributions in different steps of the reaction.

  • 13.
    Kroll, Thomas
    et al.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA; Stanford Univ, SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA.
    Hadt, Ryan G
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Wilson, Samuel A
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Yan, James J.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Weng, Tsu-Chien
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Sokaras, Dimosthenis
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Alonso-Mori, Roberto
    Stanford Univ, SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA.
    Casa, Diego
    Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA.
    Upton, Mary H.
    Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA.
    Hedman, Britt
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Hodgson, Keith O.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA; Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Solomon, Edward I.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA; Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Resonant Inelastic X-ray Scattering on Ferrous and Ferric bis-imidazole Porphyrin and Cytochrome c: Nature and Role of the Axial Methionine-Fe Bond2014In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 136, no 52, p. 18087-18099Article in journal (Refereed)
    Abstract [en]

    Axial Cu–S(Met) bonds in electron transfer (ET) active sites are generally found to lower their reduction potentials. An axial S(Met) bond is also present in cytochrome c (cyt c) and is generally thought to increase the reduction potential. The highly covalent nature of the porphyrin environment in heme proteins precludes using many spectroscopic approaches to directly study the Fe site to experimentally quantify this bond. Alternatively, L-edge X-ray absorption spectroscopy (XAS) enables one to directly focus on the 3d-orbitals in a highly covalent environment and has previously been successfully applied to porphyrin model complexes. However, this technique cannot be extended to metalloproteins in solution. Here, we use metal K-edge XAS to obtain L-edge like data through 1s2p resonance inelastic X-ray scattering (RIXS). It has been applied here to a bis-imidazole porphyrin model complex and cyt c. The RIXS data on the model complex are directly correlated to L-edge XAS data to develop the complementary nature of these two spectroscopic methods. Comparison between the bis-imidazole model complex and cyt c in ferrous and ferric oxidation states show quantitative differences that reflect differences in axial ligand covalency. The data reveal an increased covalency for the S(Met) relative to N(His) axial ligand and a higher degree of covalency for the ferric states relative to the ferrous states. These results are reproduced by DFT calculations, which are used to evaluate the thermodynamics of the Fe–S(Met) bond and its dependence on redox state. These results provide insight into a number of previous chemical and physical results on cyt c.

  • 14.
    Kroll, Thomas
    et al.
    SLAC Natl Accelerator Lab, SSRL, Menlo Pk, CA USA..
    Hadt, Ryan
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.;Argonne Natl Lab, Lemont, IL USA..
    Wilson, Samuel
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA..
    Baker, Michael
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA..
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Yan, James
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA..
    Weng, Tsu-Chien
    SLAC Natl Accelerator Lab, SSRL, Menlo Pk, CA USA..
    Sokaras, Dimosthenis
    SLAC Natl Accelerator Lab, SSRL, Menlo Pk, CA USA..
    Alonso-Mori, Roberto
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA USA..
    Casa, Diego
    Argonne Natl Lab, Lemont, IL USA..
    Upton, Mary
    Argonne Natl Lab, Lemont, IL USA..
    Hedman, Britt
    SLAC Natl Accelerator Lab, SSRL, Menlo Pk, CA USA..
    Hodgson, Keith
    SLAC Natl Accelerator Lab, SSRL, Menlo Pk, CA USA.;Stanford Univ, Dept Chem, Stanford, CA 94305 USA..
    Solomon, Edward
    SLAC Natl Accelerator Lab, SSRL, Menlo Pk, CA USA.;Stanford Univ, Dept Chem, Stanford, CA 94305 USA..
    Insight into the electronic structure of transition metal ion complexes from resonant inelastic X-ray scattering2017In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 254Article in journal (Other academic)
  • 15. Kroll, Thomas
    et al.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Solomon, Edward I.
    X-Ray Absorption and RIXS on Coordination Complexes2016In: X-Ray Absorption and X-Ray Emission Spectroscopy: Theory and Applications, Hoboken: John Wiley & Sons, Ltd , 2016, p. 407-435Chapter in book (Other academic)
  • 16.
    Kubin, Markus
    et al.
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Berlin, Germany.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ekimova, Maria
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Berlin, Germany.
    Baker, Michael L.
    Univ Manchester Harwell, Sch Chem, Oxon, England.
    Kroll, Thomas
    SLAG Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA USA.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Kern, Jan
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA USA.
    Yachandra, Vittal K.
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA USA.
    Yano, Junko
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA USA.
    Nibbering, Erik T. J.
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Berlin, Germany.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Wernet, Philippe
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Berlin, Germany.
    Direct Determination of Absolute Absorption Cross Sections at the L-Edge of Dilute Mn Complexes in Solution Using a Transmission Flatjet2018In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 57, no 9, p. 5449-5462Article in journal (Refereed)
    Abstract [en]

    The 3d transition metals play a pivotal role in many charge transfer processes in catalysis and biology. X-ray absorption spectroscopy at the L-edge of metal sites probes metal 2p–3d excitations, providing key access to their valence electronic structure, which is crucial for understanding these processes. We report L-edge absorption spectra of MnII(acac)2 and MnIII(acac)3 complexes in solution, utilizing a liquid flatjet for X-ray absorption spectroscopy in transmission mode. With this, we derive absolute absorption cross-sections for the L-edge transitions with peak magnitudes as large as 12 and 9 Mb for MnII(acac)2 and MnIII(acac)3, respectively. We provide insight into the electronic structure with ab initio restricted active space calculations of these L-edge transitions, reproducing the experimental spectra with excellent agreement in terms of shapes, relative energies, and relative intensities for the two complexes. Crystal field multiplet theory is used to assign spectral features in terms of the electronic structure. Comparison to charge transfer multiplet calculations reveals the importance of charge transfer in the core-excited final states. On the basis of our experimental observations, we extrapolate the feasibility of 3d transition metal L-edge absorption spectroscopy using the liquid flatjet approach in probing highly dilute biological solution samples and possible extensions to table-top soft X-ray sources.

  • 17.
    Kubin, Markus
    et al.
    Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ekimova, Maria
    Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Kern, Jan
    Lawrence Berkeley National Laboratory, Berkeley, United States.
    Yachandra, Vittal K.
    Lawrence Berkeley National Laboratory, Berkeley, United States.
    Yano, Junko
    Lawrence Berkeley National Laboratory, Berkeley, United States.
    Nibbering, Erik T. J.
    Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Wernet, Philippe
    Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.
    Cr L-Edge X-ray Absorption Spectroscopy of CrIII(acac)3 in Solution with Measured and Calculated Absolute Absorption Cross Sections2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 29, p. 7375-7384Article in journal (Refereed)
    Abstract [en]

    X-ray absorption spectroscopy at the L-edge of 3d transition metals is widely used for probing the valence electronic structure at the metal site via 2p–3d transitions. Assessing the information contained in L-edge absorption spectra requires systematic comparison of experiment and theory. We here investigate the Cr L-edge absorption spectrum of high-spin chromium acetylacetonate CrIII(acac)3 in solution. Using a transmission flatjet enables determining absolute absorption cross sections and spectra free from X-ray-induced sample damage. We address the challenges of measuring Cr L absorption edges spectrally close to the O K absorption edge of the solvent. We critically assess how experimental absorption cross sections can be used to extract information on the electronic structure of the studied system by comparing our results of this CrIII (3d3) complex to our previous work on L-edge absorption cross sections of MnIII(acac)3 (3d4) and MnII(acac)2 (3d5). Considering our experimental uncertainties, the most insightful experimental observable for this d3(CrIII)–d4(MnIII)–d5(MnII) series is the L-edge branching ratio, and we discuss it in comparison to semiempirical multiplet theory and ab initio restricted active space calculations. We further discuss and analyze trends in integrated absorption cross sections and correlate the spectral shapes with the local electronic structure at the metal sites.

    The full text will be freely available from 2019-06-29 20:42
  • 18.
    Kubin, Markus
    et al.
    Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.
    Kern, Jan
    Lawrence Berkeley National Laboratory, Berkeley, USA.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Mitzner, Rolf
    Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.
    Yachandra, Vittal K.
    Lawrence Berkeley National Laboratory, Berkeley, USA.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Yano, Junko
    Lawrence Berkeley National Laboratory, Berkeley, USA.
    Wernet, Philippe
    Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.
    X-ray-induced sample damage at the Mn L-edge: a case study for soft X-ray spectroscopy of transition metal complexes in solution2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 24, p. 16817-16827Article in journal (Refereed)
    Abstract [en]

    X-ray induced sample damage can impede electronic and structural investigations of radiation-sensitive samples studied with X-rays. Here we quantify dose-dependent sample damage to the prototypical Mn-III(acac)(3) complex in solution and at room temperature for the soft X-ray range, using X-ray absorption spectroscopy at the Mn L-edge. We observe the appearance of a reduced Mn-II species as the X-ray dose is increased. We find a half-damage dose of 1.6 MGy and quantify a spectroscopically tolerable dose on the order of 0.3 MGy (1 Gy = 1 J kg(-1)), where 90% of Mn-III(acac)(3) are intact. Our dose-limit is around one order of magnitude lower than the Henderson limit (half-damage dose of 20 MGy) which is commonly employed for protein crystallography with hard X-rays. It is comparable, however, to the dose-limits obtained for collecting un-damaged Mn K-edge spectra of the photosystem II protein, using hard X-rays. The dose-dependent reduction of Mn-III observed here for solution samples occurs at a dose limit that is two to four orders of magnitude smaller than the dose limits previously reported for soft X-ray spectroscopy of iron samples in the solid phase. We compare our measured to calculated spectra from ab initio restricted active space (RAS) theory and discuss possible mechanisms for the observed dose-dependent damage of Mn-III(acac)(3) in solution. On the basis of our results, we assess the influence of sample damage in other experimental studies with soft X-rays from storage-ring synchrotron radiation sources and X-ray free-electron lasers.

  • 19.
    Kunnus, Kristjan
    et al.
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA..
    Zhang, Wenkai
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA.;Beijing Normal Univ, Dept Phys, Beijing 100875, Peoples R China..
    Delcey, Mickael 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.
    Miedema, Piter S.
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Schreck, Simon
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Quevedo, Wilson
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Schröder, Henning
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Foehlisch, Alexander
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Gaffney, Kelly J.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA..
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Odelius, Michael
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Wernet, Philippe
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Viewing the Valence Electronic Structure of Ferric and Ferrous Hexacyanide in Solution from the Fe and Cyanide Perspectives2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 29, p. 7182-7194Article in journal (Refereed)
    Abstract [en]

    The valence-excited states of ferric and ferrous hexacyanide ions in aqueous solution were mapped by resonant inelastic X-ray scattering (RIXS) at the Fe L-2,L-3 and N K edges. Probing of both the central Fe and the ligand N atoms enabled identification of the metal-and ligand-centered excited states, as well as ligand-to-metal and metal-to-ligand charge-transfer excited states. Ab initio calculations utilizing the RASPT2 method were used to simulate the Fe L-2,L-3-edge RIXS spectra and enabled quantification of the covalencies of both occupied and empty orbitals of pi and sigma symmetry. We found that pi back-donation in the ferric complex is smaller than that in the ferrous complex. This is evidenced by the relative amounts of Fe 3d character in the nominally 2 pi CN- molecular orbital of 7% and 9% in ferric and ferrous hexacyanide, respectively. Utilizing the direct sensitivity of Fe L-3-edge RIXS to the Fe 3d character in the occupied molecular orbitals, we also found that the donation interactions are dominated by sigma bonding. The latter was found to be stronger in the ferric complex, with an Fe 3d contribution to the nominally 5 sigma CN- molecular orbitals of 29% compared to 20% in the ferrous complex. These results are consistent with the notion that a higher charge at the central metal atom increases donation and decreases back-donation.

  • 20.
    Lundberg, Marcus
    Ericsson Mobile Communications.
    Battery operable device with battery state-of-charge indicator2002Patent (Other (popular science, discussion, etc.))
  • 21.
    Lundberg, Marcus
    Stockholms universitet.
    Challenges in Enzyme Catalysis - Photosystem II and Orotidine Decarboxylase: A Density Functional Theory Treatment2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms.

    The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions.

    Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.

  • 22.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Studenter som undervisar lär sig på djupet2014In: I stort och smått– med studenten i fokus / [ed] Gunnlaugsson, Geir, Uppsala, 2014, p. 231-239Conference paper (Refereed)
  • 23.
    Lundberg, Marcus
    Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan..
    Understanding Cross-Boundary Events in ONIOM QM:QM' Calculations2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 4, p. 406-415Article in journal (Refereed)
    Abstract [en]

    QM:QM' models, where QM' is a fast molecular orbital method, offers advantages over standard quantum mechanics: molecular mechanics (QM:MM) models, especially in the description of charge transfer and mutual polarization between layers. The ONIOM QM:QM' scheme also allows for reactions across the layer boundary, but the understanding of these events is limited. To explain the factors that affect cross-boundary events, a set of proton transfer processes, including the acylation reaction in serine protease, have been investigated. For reactions inside out, that is, when a group breaks a bond in the high layer and forms a new bond with a group in the low layer, QM' methods that are overbinding relative to the QM method, for example, Hartree-Fock versus B3LYP, can severely overestimate the exothermicity of the reaction. This might lead to artificial reactivity across the QM:QM' boundary, a phenomenon called model escape. The accuracy for reactions that occur outside in, that is, when a group in the low layer forms a new bond with the high layer, is mainly determined by the QM' calculation. Cross-boundary reactions should generally be avoided in the present ONIOM scheme. Fortunately, a better understanding of these events makes it easy to design stable ONIOM QM:QM' models, for example, by choosing a proper model system. Importantly, an accurate description of cross-boundary reactions would open up possibilities to simulate chemical reactions without a priori limiting the reactivity in the design of the computational model. Challenges to implement a simulation scheme (ONIOM-XR) that can automatically handle chemical reactions between different layers are briefly discussed.

  • 24.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University.
    Blomberg, M. R. A.
    Siegbahn, P. E. M.
    Modeling water exchange on monomeric and dimeric Mn centers2003In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 110, no 3, p. 130-143Article in journal (Refereed)
    Abstract [en]

    Water exchange on Mn centers in proteins has been modeled with density functional theory using the B3LYP functional. The reaction barrier for dissociative water exchange on [Mn-IV(H2O)(2)(OH)(4)] is only 9.6 kcal mol(-1), corresponding to a rate of 6 x 10(5) s(-1). It has also been investigated how modifications of the model complex change the exchange rate. Three cases of water exchange on Mn dimers have been modeled. The reaction barrier for dissociative exchange of a terminal water ligand on [(H2O)(2)(OH)(2)Mn-IV(mu-O)(2)Mn-IV(H2O)(2) (OH)(2)] is 8.6 kcal mol(-1), while the bridging oxo group exchange with a ring-opening mechanism has a barrier of 19.2 kcal mol(-1). These results are intended for interpretations of measurements of water exchange for the oxygen evolving complex of photosystem II. Finally, a tautomerization mechanism for exchange of a terminal oxyl radical has been modeled for the synthetic 02 catalyst [(terpy)(H2O)Mn-IV(mu-O)(2)Mn-IV(O.)(terpy)](3+) (terpy=2,2':6,2"-terpyridine). The calculated reaction barrier is 14.7 kcal mol(-1).

  • 25.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University.
    Blomberg, Margareta R. A.
    Siegbahn, Per E. M.
    Density functional models of the mechanism for decarboxylation in orotidine decarboxylase2002In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 8, no 4, p. 119-130Article in journal (Refereed)
    Abstract [en]

    The mechanism of orotidine 5-monophosphate decarboxylase (ODCase) has been modeled using hybrid Density Functional Theory (B3LYP functional). The main goal of the present study was to investigate if much larger quantum chemical models of the active site than previously used could shed new light on the mechanism. The models used include the five conserved amino acids expected to be the most important ones for catalysis. One result of this model is that a mechanism involving a direct cleavage of the C-C bond followed by a protonation of C6 by Lys93 appears unlikely, with a barrier for decarboxylation 20 kcal mol(-1) too high. Additional effects like electrostatic stress and ground-state destabilization have been estimated to have only a minor influence on the reaction barrier. The conclusion from the calculations is that the negative charge developing on the substrate during decarboxylation must be stabilized by a protonation of the carbonyl O2 of the substrate. For this mechanism, the addition of the catalytic amino acids decreases the reaction barrier by 25 kcal mol(-1), but full agreement with experimental results has still not been reached. Further modifications of this mechanism are discussed.

  • 26.
    Lundberg, Marcus
    et al.
    Stockholm University.
    Blomberg, Margareta R. A.
    Siegbahn, Per E. M.
    Developing active site models of ODCase: from large quantum models to a QM/MM approach2004In: Topics in current chemistry, ISSN 0340-1022, E-ISSN 1436-5049, Vol. 238, p. 79-112Article in journal (Refereed)
    Abstract [en]

    The catalytic mechanism of orotidine monophosphate decarboxylase (ODCase) has been modeled using density functional theory with the B3LYP functional. Barriers for three different mechanisms have been calculated using large QM and QM/MM models. A concerted protonation mechanism where TS stabilization is provided only by the positive Lys93 has a high barrier around 35 kcal/mol. QM/MM calculations confirm the results obtained using QM models. For a base protonation mechanism, 02 protonation gives a barrier for decarboxylation of 26 kcal/mol. Extensions to this QM model indicate that the cost of protonation may be inderestimated and the support for the base protonation mechanism is uncertain. An initial QM/MM investigation of a stepwise mechanism, where water molecules seem to play an important role for TS stabilization, gives the most promising results with an estimated barrier of 22 kcal/mol.

  • 27.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm University, AlbaNova University Center.
    Blomberg, Margareta R. A.
    Siegbahn, Per E. M.
    Oxyl radical required for O-O bond formation in synthetic Mn-catalyst2004In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 43, no 1, p. 264-274Article in journal (Refereed)
    Abstract [en]

    DFT calculations using the B3LYP functional support the suggestion that the [(terpy)(H2O)Mn-IV(mu-O)(2)Mn-III(H2O)-(terpy)](3+) (terpy=2,2':6,2"-terpyridine) complex functions as a synthetic O-2 catalyst. The calculated barrier for O-O bond formation with water is 23 kcal/mol. In this complex, as well as in models of the oxygen evolving complex in PSII, the active species is a Mn-IV-oxyl radical. From comparisons with inactive Mn-V-oxo complexes, it is proposed that radical formation is actually a requirement for O-2 formation activity in Mn-complexes.

  • 28.
    Lundberg, Marcus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Borowski, Tomasz
    Polish Acad Sci, Jerzy Haber Inst Catalysis & Surface Chem, PL-30239 Krakow, Poland.
    Oxoferryl species in mononuclear non-heme iron enzymes: biosynthesis, properties and reactivity from a theoretical perspective2013In: Coordination chemistry reviews, ISSN 0010-8545, E-ISSN 1873-3840, Vol. 257, no 1, p. 277-289Article, review/survey (Refereed)
    Abstract [en]

    Mononuclear non-heme iron enzymes perform a wide range of chemical reactions. Still, the catalytic mechanisms are usually remarkably similar, with formation of a key oxoferryl (Fe(IV)=O) intermediate through two well-defined steps. First, two-electron reduction of dioxygen occurs to form a peroxo species, followed by O-O bond cleavage. Even though the peroxo species have different chemical character in various enzyme families, the analogies between different enzymes in the group make it an excellent base for investigating factors that control metal-enzyme catalysis. We have used density-functional theory to model the complete chemical reaction mechanisms of several enzymes, e.g., for aromatic and aliphatic hydroxylation, chlorination, and oxidative ring-closure. Reactivity of the Fe(IV)=O species is discussed with focus on electronic and steric factors determining the preferred reaction path. Various spin states are compared, as well as the two reaction channels that stem from involvement of different frontier molecular orbitals of Fe(IV)=O. Further, the two distinctive species of Fe(IV)=O, revealed by Mossbauer spectroscopy, and possibly relevant for specificity of aliphatic chlorination, can be identified. The stability of the modeling results have been analyzed using a range of approaches, from active-site models to multi-scale models that include classical free-energy contributions. Large effects from an explicit treatment of the protein matrix (similar to 10 kcal/mol) can be observed for O-2 binding, electron-transfer and product release.

  • 29.
    Lundberg, Marcus
    et al.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Kawatsu, T.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Vreven, T.
    Gaussian Inc, Wallingford, CT 06492 USA.
    Frisch, M. J.
    Gaussian Inc, Wallingford, CT 06492 USA.
    Morokuma, K.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Transition States in a Protein Environment: ONIOM QM:MM Modeling of Isopenicillin N Synthesis2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 1, p. 222-234Article in journal (Refereed)
    Abstract [en]

    To highlight the role of the protein in metal enzyme catalysis, we optimize ONIOM QM:MM transition states and intermediates for the full reaction of the nonheme iron enzyme isopenicillin N synthase (IPNS). Optimizations of transition states in large protein systems are possible using our new geometry optimizer with quadratic coupling between the QM and MM regions [Vreven, T. et al. MoL Phys. 2006, 104, 701-704]. To highlight the effect of the metal center, results from the protein model are compared to results from an active site model containing only the metal center and coordinating residues [Lundberg, M. et al. Biochemistry 2008, 47, 1031-10421. The analysis suggests that the main catalytic effect comes from the metal center, while the protein controls the reactivity to achieve high product specificity. As an example, hydrophobic residues align the valine substrate radical in a favorable conformation for thiazolicline ring closure and contribute to product selectivity and high stereospecificity. A low-barrier pathway for P-lactam formation is found where the proton required for heterolytic O-O bond cleavage comes directly from the valine N-H group of the substrate. The alternative mechanism, where the proton in 0-0 bond cleavage initially comes from an iron water ligand, can be disfavored by the electrostatic interactions with the surrounding protein. Explicit protein effects on transition states are typically 1-6 kcal/mol in the present enzyme and can be understood by considering whether the transition state involves large movements of the substrate as well as whether it involves electron transfer.

  • 30.
    Lundberg, Marcus
    et al.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Kroll, Thomas
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    DeBeer, Serena
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Bergmann, Uwe
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Wilson, Samuel A.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Glatzel, Pieter
    ESRF, F-38043 Grenoble 9, France.
    Nordlund, Dennis
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Hedman, Britt
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Hodgson, Keith Owen
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA; Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Solomon, Edward I.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA; Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Metal-ligand Covalency of Iron Complexes from High-Resolution Resonant Inelastic X-ray Scattering2013In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, no 45, p. 17121-17134Article in journal (Refereed)
    Abstract [en]

    Data from Kα resonant inelastic X-ray scattering (RIXS) have been used to extract electronic structure information, i.e., the covalency of metal–ligand bonds, for four iron complexes using an experimentally based theoretical model. Kα RIXS involves resonant 1s→3d excitation and detection of the 2p→1s (Kα) emission. This two-photon process reaches similar final states as single-photon L-edge (2p→3d) X-ray absorption spectroscopy (XAS), but involves only hard X-rays and can therefore be used to get high-resolution L-edge-like spectra for metal proteins, solution catalysts and their intermediates. To analyze the information content of Kα RIXS spectra, data have been collected for four characteristic σ-donor and π-back-donation complexes: ferrous tacn [FeII(tacn)2]Br2, ferrocyanide [FeII(CN)6]K4, ferric tacn [FeIII(tacn)2]Br3 and ferricyanide [FeIII(CN)6]K3. From these spectra metal–ligand covalencies can be extracted using a charge-transfer multiplet model, without previous information from the L-edge XAS experiment. A direct comparison of L-edge XAS and Kα RIXS spectra show that the latter reaches additional final states, e.g., when exciting into the eg (σ*) orbitals, and the splitting between final states of different symmetry provides an extra dimension that makes Kα RIXS a more sensitive probe of σ-bonding. Another key difference between L-edge XAS and Kα RIXS is the π-back-bonding features in ferro- and ferricyanide that are significantly more intense in L-edge XAS compared to Kα RIXS. This shows that two methods are complementary in assigning electronic structure. The Kα RIXS approach can thus be used as a stand-alone method, in combination with L-edge XAS for strongly covalent systems that are difficult to probe by UV/vis spectroscopy, or as an extension to conventional absorption spectroscopy for a wide range of transition metal enzymes and catalysts.

  • 31.
    Lundberg, Marcus
    et al.
    Kyoto University.
    Morokuma, Keiji
    Determining Transition States in Bioinorganic Reactions2009In: Computational Inorganic and Bioinorganic Chemistry / [ed] E.I. Solomon, R.B. King, and R.A. Scott, Hoboken: John Wiley & Sons, Ltd , 2009, p. 17-31Chapter in book (Other academic)
  • 32.
    Lundberg, Marcus
    et al.
    Fukui Institute for Fundamental Chemistry, Kyoto University.
    Morokuma, Keiji
    Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan, Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 .
    Protein environment facilitates O-2 binding in non-heme iron enzyme: An insight from ONIOM calculations on isopenicillin N synthase (IPNS)2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 31, p. 9380-9389Article in journal (Refereed)
    Abstract [en]

    Binding of dioxygen to a non-heme enzyme has been modeled using the ONIOM combined quantum mechanical/molecular mechanical (QM/MM) method. For the present system, isopenicillin N synthase (IPNS), binding of dioxygen is stabilized by 8-10 kcal/mol for a QM:MM (B3LYP:Amber) protein model compared to a quantum mechanical model of the active site only. In the protein system, the free energy change of O-2 binding is close to zero. Two major factors consistently stabilize O-2 binding. The first effect, evaluated at the QM level, originates from a change in coordination geometry of the iron center. The active-site model artificially favors the deoxy state (O-2 not bound) because it allows too-large rearrangements of the five-coordinate iron site. This error is corrected when the protein is included. The corresponding effect on binding energies is 3-6 kcal/mol, depending on the coordination mode of O-2 (side-on or end-on). The second major factor that stabilizes O-2 binding is van der Waals interactions between dioxygen and the surrounding enzyme. These interactions, 3-4 kcal/mol at the MM level, are neglected in models that include only the active site. Polarization of the active site by surrounding amino acids does not have a significant effect on the binding energy in the present system.

  • 33.
    Lundberg, Marcus
    et al.
    Kyoto University.
    Morokuma, Keiji
    The ONIOM Method and its Applications to Enzymatic Reactions2009In: Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications / [ed] T.-S. Lee and D.M. York, Springer Verlag , 2009Chapter in book (Other academic)
  • 34.
    Lundberg, Marcus
    et al.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Nishimoto, Y.
    Nagoya Univ, Grad Sch Sci, Dept Chem, Chikusa Ku, Nagoya, Aichi 4648601, Japan.
    Irle, S.
    Nagoya Univ, Grad Sch Sci, Dept Chem, Chikusa Ku, Nagoya, Aichi 4648601, Japan.
    Delocalization errors in a hubbard-€like model: Consequences for density-€functional tight-€binding calculations of molecular systems2012In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, no 6, p. 1701-1711Article in journal (Refereed)
    Abstract [en]

    It has previously been shown that self-consistent-charge density-functional tight-binding (SCC-DFTB) suffers from a self-interaction error that leads to artificial stabilization of delocalized states. The effects of the error are similar to those appearing for many density functionals. In SCC-DFTB, the delocalization error is inherently related to the use of a Hubbard-like term to describe on-site charge interactions. The mathematical simplicity of this Hubbard-like term makes it easy to estimate if a complex system is subject to artificial stabilization of delocalized states and to quantitatively predict the delocalization error in the system energy at large fragment separation. The error is directly proportional to the on-site charge interaction term but decreases as the fragments become more asymmetric. The difference in orbital energies required to eliminate the delocalization error becomes equal to the Hubbard-like parameter of the fragment with the highest electron affinity. However, in most cases, the localized state will be favored by spin polarization, fragment repulsion, solvent effects, and large reorganization energies, in analogy to density functional theory, from which SCC-DFTB is derived. The presented analysis gives an early indication whether the standard approach is suitable, or if a different method is required to correct the delocalization error. In addition to cationic dimers, we discuss the effects of the delocalization error for asymmetric systems, bond dissociation of neutral molecules, and the description of mixed valence transition metal systems, exemplified by the enzyme cytochrome oxidase.

  • 35.
    Lundberg, Marcus
    et al.
    Fukui Institute for Fundamental Chemistry, Kyoto University.
    Sasakura, Y.
    Fukui Institute for Fundamental Chemistry, Kyoto University.
    Zheng, G. S.
    Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta..
    Morokuma, K.
    Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan; Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta. .
    Case Studies of ONIOM(DFT:DFTB) and ONIOM(DFT:DFTB:MM) for Enzymes and Enzyme Mimics2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 4, p. 1413-1427Article in journal (Refereed)
    Abstract [en]

    The replacement of standard molecular mechanics force fields by inexpensive molecular orbital (QM') methods in multiscale models has many advantages, e.g., a more straightforward description of mutual polarization and charge transfer between layers. The ONIOM(QM:QM') scheme with mechanical embedding can combine any two methods without prior parametrization or significant coding effort. In this scheme, the environmental effect is evaluated fully at the QM' level, and the accuracy therefore depends on how well the low-level QM' method describes the changes in electron density of the reacting region. To examine the applicability of the QM:QM' approach, we perform case studies with density-functional tight-binding (DFTB) as the low-level QM' method in two-layer ONIOM(B3LYP/6-31G(d):DFTB) models. The investigated systems include simple amino acid models one nonheme iron enzyme mimic, and the enzymatic reactions of Zn-beta-lactamase and trypsin. For the last example, we also illustrate the use of a three-layer ONIOM(B3LYP/6-31G(d):D::TB:Amber96) model. The ONIOM extension, compared to the QM calculation for the small model system, improves the relative energies, but high accuracy (deviations below 1 kcal/mol) is not achieved even with relatively large QM models. Polarization effects are fairly well described using DFTB, but in some cases QM and QM' methods converge to different electronk: states. We discuss when the QM:QM' approach is appropriate and the possibilities of estimating the quality of the ONIOM extension without having to make explicit benchmarks of the entire system.

  • 36.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm University, AlbaNova University Center.
    Siegbahn, P. E. M.
    Theoretical investigations of structure and mechanism of the oxygen-evolving complex in PSII2004In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 6, no 20, p. 4772-4780Article in journal (Refereed)
    Abstract [en]

    Hybrid density functional theory has been used to study a proposed Mn3Ca-Mn cubane-like structure for the oxygen-evolving complex in photosystem II. A refined analysis of the structure is made regarding the position of the heavy atoms, the oxidation states of the manganese centers and the protonation states of the ligands. After finding the most stable S-2 structure, S-0 --> S-1 and S-1 --> S-2 transitions are proposed. Further, proposals for the higher S state transitions, S-2 --> S-3 and S-3 --> S-4 have been investigated, using the O-H bond dissociation energy as a probe. With an intact cubane-like structure, oxidation to a high valent Mn-oxo species has so far not been found to be energetically feasible. Instead, tentative proposals of the S-2 --> S-3 transition involving structural rearrangements are made.

  • 37.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm University, AlbaNova University Center.
    Siegbahn, Per E. M.
    Agreement between experiment and hybrid DFT calculations for O-H bond dissociation enthalpies in manganese complexes2005In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 26, no 7, p. 661-667Article in journal (Refereed)
    Abstract [en]

    Information on the accuracy of DFT functionals for redox reactions in transition metal systems is rather limited. To analyze the performance of some popular functionals for redox reactions in manganese systems, calculated O-H bond dissociation enthalpies for Mn-ligands in six different complexes are compared to experimental results. In this benchmark, B3LYP performs well with a mean absolute error of 3.0 kcal/mol. B98 gives similar results to B3LYP (error of 3.8 kcal/mol). B3LYP* gives lower O-H bond strengths than B3LYP and has a mean error of 5.0 kcal/tnol. Compared to B98 and B3LYP, B3LYP* has an error trend for the manganese ligands that is more similar to the error for a free water molecule. The nonhybrid functional BLYP consistently and significantly underestimates the O-H bond strengths by approximately 20 kcal/mol. HCTH407 has a rather large mean error of 9.4 kcal/mol and shows no consistent trend. The results support the use of hybrid functionals and the present computational method for large model systems containing manganese. An example is the oxygen evolving complex in photosystem 11 where hybrid functionals predict the appearance of a Mn(IV)-oxyl radical before the O-O bond formation step.

  • 38.
    Lundberg, Marcus
    et al.
    Department of Physics, AlbaNova University Center, Stockholm University.
    Siegbahn, Per E. M.
    Minimum energy spin crossings for an O–O bond formation reaction2005In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 401, no 4-6, p. 347-351Article in journal (Refereed)
    Abstract [en]

    The O-O bond formation reaction in the synthetic O-2, formation catalyst, [(terpy)((HO)-O-2)Mn-IV(mu-O)(2)Mn-III(H2O)(terpy)](3+) (terpy=2,2':6,2"-terpyridine), goes through a transition between two spin surfaces. Using DFT with the B3LYP functional. three different minimum energy crossing points have been located for this redox reaction. The system is predicted to perform the spin crossing close to (+0.1 kcal/mol) the low-spin MnIII-OOH product and this transition does not significantly affect the kinetics. The location of spin crossings in this system is relevant for discussions of O-O bond formation in the oxygen evolving complex of photosystem II.

  • 39.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm University, AlbaNoVa University Center.
    Siegbahn, Per E. M.
    Optimized spin crossings and transition states for short-range electron transfer in transition metal dimers2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 20, p. 10513-10520Article in journal (Refereed)
    Abstract [en]

    Electron-transfer reactions in eight mixed-valence manganese dimers are studied using B3LYP. One of the dimers is a model of the active site of manganese catalase, while another represents a basic building block of the oxygen-evolving complex in photosystem II. The adiabatic reactions are characterized by fully optimized transition states where the single imaginary frequency represents the electron-transfer coordinate. When there is antiferromagnetic coupling between different high-spin centers, electron transfer must be accompanied by a spin transition. Spin transitions are characterized by minimum-energy crossing points between spin surfaces. Three reaction mechanisms have been investigated. First, a single-step reaction where spin flip is concerted with electron transfer. Second, an initial transition to a center with intermediate spin that can be followed by electron transfer. Third, an initial transition to a ferromagnetic state from which the electron can be transferred adiabatically. The complexes prefer the third route with rate-determining barriers ranging from 5.7 kcal/mol to 17.2 kcal/mol for different complexes. The origins of these differences are discussed in terms of oxidation states and ligand environments. Many DFT functionals overestimate charge-transfer interactions, but for the present complexes, the error should be limited because of short Mn-Mn distances.

  • 40.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm University, AlbaNova University Center.
    Siegbahn, Per E. M.
    Quantifying the effects of the self-interaction error in DFT: When do the delocalized states appear?2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 22, p. 224103-Article in journal (Refereed)
    Abstract [en]

    The self-interaction error in density-functional theory leads to artificial stabilization of delocalized states, most evident in systems with an odd number of electrons. Clear examples are dissociations of carbocation radicals that often give delocalized states at long distances and large errors in computed binding energies. On the other hand, many mixed-valence transition-metal dimers known to exhibit valence trapping are correctly predicted to be localized. To understand the effects of the self-interaction error on these different systems, energy differences between delocalized and localized states are calculated with B3LYP. In the dissociation of radicals into symmetric fragments at infinite distance, this energy difference equals the error of the density-functional treatment. The energy difference decreases with increasing size of the system, from 55 kcal/mol in H-2(+) to 15 kcal/mol for C12H26+. Solvent corrections stabilize the localized state and result in smaller errors. Most reactions are asymmetric and this decreases the effect of the self-interaction error. In many systems, delocalization will not occur if the cost to move the electron from one fragment to the other is 70-80 kcal/mol (3.0-3.5 eV). This estimate refers to a situation where the distance between the fragments is infinite. The limit decreases with decreasing fragment distance. B3LYP calculations on the ferromagnetic state of a Mn(III,IV) dimer predict that the correct localized state is 22 kcal/mol more stable than the incorrect delocalized state. At short metal-metal distances the effect of the self-interaction error is predicted to be small. However, as the distance between the two manganese centers is increased to 7 A, the dimer starts to delocalize and the energy artificially decreases. In the dissociation limit, the error is 10 kcal/mol. This is interpreted as an artifact originating from the self-interaction error. Delocalization is not encountered in many systems due to relatively short metal-metal distances and asymmetric ligand environments. However, some charge-transfer complexes cannot be properly calculated and delocalized states may become a problem in large models of enzyme systems with multiple transition-metal complexes.

  • 41.
    Lundberg, Marcus
    et al.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Siegbahn, Per E. M.
    Stockholm Univ, Dept Phys, Quantum Chem Grp, SE-10691 Stockholm, Sweden.
    Morokuma, Keiji
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    The mechanism for isopenicillin N synthase from density-functional modeling highlights the similarities with other enzymes in the 2-his-1-carboxylate family2008In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 47, no 3, p. 1031-1042Article in journal (Refereed)
    Abstract [en]

    Isopenicillin N synthase (IPNS) catalyzes a key step in the biosynthesis of the important P-lactam antibiotics penicillins and cephalosporins. Density-functional calculations with the B3LYP functional are used to propose a detailed mechanism for this reaction. The results support the general scheme outlined from experimental observations, with formation of a four-membered beta-lactam ring followed by formation of a five-membered thiazolidine ring. However, an alternative mechanism for the heterolytic O-O bond cleavage and beta-lactam ring formation steps is proposed. The former part involves protonation of the distal oxygen by an iron-bound water ligand. This mechanism highlights the strong similarities that exist between IPNS and other enzymes of the 2-histidine-1-carboxylate family, especially pterin-dependent amino acid hydroxylases and alpha-keto acid-dependent dioxygenases. Both activation of the cysteine beta-C-H bond by an iron-bound superoxo radical and activation of the valine beta-C-H bond by a ferryl-oxo species show reaction barriers close to the experimentally measured one. These results are in agreement with kinetic isotope experiments that suggest both C-H bond activation steps to be partially rate limiting. The ring formation sequence is determined by the relative strengths of the two C-H bonds. Only the ferryl-oxo intermediate is capable of activating the stronger valine beta-C-H bond.

  • 42.
    Nishimoto, Yoshio
    et al.
    Nagoya Univ, Dept Chem, Nagoya, Aichi 4648602, Japan; Nagoya Univ, Res Ctr Mat Sci, Nagoya, Aichi 4648602, Japan.
    Yoshikawa, Hirofumi
    Nagoya Univ, Dept Chem, Nagoya, Aichi 4648602, Japan; Nagoya Univ, Res Ctr Mat Sci, Nagoya, Aichi 4648602, Japan.
    Awaga, Kunio
    Nagoya Univ, Dept Chem, Nagoya, Aichi 4648602, Japan; Nagoya Univ, Res Ctr Mat Sci, Nagoya, Aichi 4648602, Japan.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Irle, Stephan
    Nagoya Univ, Dept Chem, Nagoya, Aichi 4648602, Japan; Nagoya Univ, Res Ctr Mat Sci, Nagoya, Aichi 4648602, Japan; Nagoya Univ, Inst Transformat Biomol WPI ITbM, Nagoya, Aichi 4648602, Japan.
    Theoretical investigation of molecular and electronic structure changes of the molecular magnet Mn-12 cluster upon super-reduction2014In: Physica Status Solidi. Rapid Research Letters, ISSN 1862-6254, E-ISSN 1862-6270, Vol. 8, no 6, p. 517-521Article in journal (Refereed)
    Abstract [en]

    Density functional theory calculations on the neutral [Mn-12](0) molecular magnet and super-reduced [Mn-12](8-) cluster were employed to investigate the experimental geometrical changes observed during discharging in a molecular cluster battery. It was found that for relevant low-spin states the eight electrons added in [Mn-12](8-) are mainly added to the outer eight Mn atoms, causing elongation of the bonds between outer Mn and their surrounding O atoms, while the inner Mn-4 cluster is less affected by the reduction. [GRAPHICS] Schematic representation of the spin density of the neutral [Mn-12](0) cluster and its super-reduced state [Mn-12](8-), for which several possible spin states were found.

  • 43.
    Norell, Jesper
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.
    Jay, Raphael M.
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 32, D-14476 Potsdam, Germany.
    Hantschmann, Markus
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.
    Eckert, Sebastian
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 32, D-14476 Potsdam, Germany;Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Gaffney, Kelly J.
    Stanford Univ, SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA;SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Wernet, Philippe
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Siena, Dept Biotechnol Chem & Pharm, Via A Moro 2, I-53100 Siena, Italy.
    Foehlisch, Alexander
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 32, D-14476 Potsdam, Germany;Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.
    Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 10, p. 7243-7253Article in journal (Refereed)
    Abstract [en]

    We describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L-3-edge RIXS in the ferricyanide complex Fe(CN)(6)(3-), we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject the presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.

  • 44.
    Pinjari, Rahul V.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Swami Ramanand Teerth Marathwada Univ, Sch Chem Sci, Nanded 431606, Maharashtra, India.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 5, p. 477-486Article in journal (Refereed)
    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.

  • 45.
    Pinjari, Rahul V.
    et al.
    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.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Restricted active space calculations of L-edge X-ray absorption spectra: From molecular orbitals to multiplet states2014In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 141, no 12, article id 124116Article in journal (Refereed)
    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.

  • 46.
    Roca-Sanjuan, Daniel
    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.
    Mazziotti, D. A.
    Univ Chicago, James Franck Inst, Dept Chem, Chicago, IL 60637 USA.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Comment on "€œDensity functional theory study of 1,2-€dioxetanone decomposition in condensed phase€"2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 26, p. 2124-2126Article in journal (Refereed)
    Abstract [en]

    In the preceding paper results are presented, which are in serious conflict with state-of-the-art ab initio method. Based on these new results the authors propose a new explanation of the reason for the preferential production of a phosphorescent state. Here we show that these controversial results are flawed, since the model use exclude biradical electron structures.

  • 47.
    Sauri, Vicenta
    et al.
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Gobbo, João P.
    Univ Sao Paulo, Inst Quim, BR-05508900 Sao Paulo, Brazil;USP Consortium Photochem Technol, NAPPhotoTech, BR-05508900 Sao Paulo, Brazil.
    Serrano-Pérez, Juan J.
    Univ London Imperial Coll Sci Technol & Med, Dept Chem, London SW7 2AZ, England.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Coto, Pedro B.
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain; Univ Erlangen Nurnberg, Inst Theoret Phys, D-91058 Erlangen, Germany; Univ Alcala de Henares, Dept Quim Fis, E-28871 Alcala De Henares, Spain.
    Serrano-Andrés, Luis
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Borin, Antonio C.
    Univ Sao Paulo, Inst Quim, BR-05508900 Sao Paulo, Brazil;USP Consortium Photochem Technol, NAPPhotoTech, BR-05508900 Sao Paulo, Brazil.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Merchán, Manuela
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Roca-Sanjuán, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Proton/Hydrogen Transfer Mechanisms in the Guanine-€“Cytosine Base Pair: Photostability and Tautomerism2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 1, p. 481-496Article in journal (Refereed)
    Abstract [en]

    Proton/hydrogen-transfer processes have been broadly studied in the past 50 years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine–cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo, and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair, and a new contribution to tautomerism is provided. The C-based imino-oxo and imino-enol GC tautomers, which can be generated during the UV irradiation of the Watson–Crick base pair, have analogous radiationless energy-decay channels to those of the canonical base pair. In addition, the C-based imino-enol GC tautomer is thermally less stable. A study of the GC base pair is carried out subsequently taking into account the DNA surroundings in the biological environment. The most important stationary points are computed using the quantum mechanics/molecular mechanics (QM/MM) approach, suggesting a similar scenario for the proton/hydrogen-transfer phenomena in vacuo and in DNA. Finally, the static model is complemented by ab initio dynamic simulations, which show that vibrations at the hydrogen bonds can indeed originate hydrogen-transfer processes in the GC base pair. The relevance of the present findings for the rationalization of the preservation of the genetic code and mutagenesis is discussed.

  • 48. Siegbahn, P. E. M.
    et al.
    Lundberg, Marcus
    Department of Physics, Stockholm University, AlbaNova University Center.
    Hydroxide instead of bicarbonate in the structure of the oxygen evolving complex2006In: Journal of Inorganic Biochemistry, ISSN 0162-0134, E-ISSN 1873-3344, Vol. 100, no 5-6, p. 1035-1040Article in journal (Refereed)
    Abstract [en]

    The energy diagram for the catalytic cycle of dioxygen evolution in photosystem II has been recomputed using a slightly different model than the one used previously, since the results showed an erroneous trend in the critical region from S-2 to S-3. By replacing the bicarbonate ligand, which was bridging between calcium and the outer manganese, by a hydroxide a significant improvement of the energy diagram is obtained. Most notably, the S-2 to S-3 transition is now exergonic as it should be. However, for the S-2 state an artificial constraint is needed on the hydrogen bonding, indicating that there is still some problem with the model used. This hydroxide model was used to study the effects of replacing calcium with strontium, magnesium and cadmium. The computed results reproduce the results observed experimentally that magnesium and cadmium suppress water oxidation and that strontium slows it down. For both magnesium and cadmium the process stops already at S-2.

  • 49. Siegbahn, Per E. M.
    et al.
    Lundberg, Marcus
    Stockholm University.
    The mechanism for dioxygen formation in PSII studied by quantum chemical methods2005In: Photochemical and Photobiological Sciences, ISSN 1474-905X, E-ISSN 1474-9092, Vol. 4, no 12, p. 1035-1043Article in journal (Refereed)
    Abstract [en]

    The availability of an X-ray structure for PSII including the water-oxidizing cluster, where the metal atoms and the amino acids are assigned, has opened up new possibilities to study the mechanism for dioxygen formation. In the present paper the main results of an ongoing hybrid DFT study are presented. The model used follows the structure suggested by the X-ray analysis as closely as possible. After nearly one thousand optimizations of different structures, each one with about 70 atoms, the main features of a water oxidizing mechanism start to emerge. The key intermediate is an oxyl radical state in S,, stabilized by a weak trans effect to a bridging oxo in the cube. To reach this radical state a structural rearrangement appears necessary, in which one additional bridging oxo is formed between the dangling manganese and a manganese in the cube. The calculated energetics is reasonable but still not fully consistent with a correct mechanism. It is suggested that some part of the structure is not correct, probably the presence of the bicarbonate.

  • 50. Stawström, CO
    et al.
    Beskow, B
    Ericson, M
    Frenckner, K
    Nilsson, L
    Lundberg, Marcus
    KTH, Royal Institute of Technology.
    Teknologernas arbetstid, KTH1997Report (Other academic)
12 1 - 50 of 57
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