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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 Systems2006Inngår i: Concepts and Models in Bioinorganic Chemistry / [ed] H.-B. Kraatz and N. Metzler-Nolte, Weinheim: Wiley-VCH , 2006, s. 63-88Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 2. Bengtson, Charlotta
    et al.
    Ahlkvist, Mikaela
    Ekeroth, William
    Nilsen-Moe, Astrid
    Proos Vedin, Nathalie
    Rodiouchkina, Katerina
    Ye, Sofie
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Uppsala University.
    Kursutveckling i partnerskap mellan lärare och studenter2018Inngår i: Pedagogiska utmaningar i en dynamisk samtid: Universitetspedagogisk utvecklingskonferens 12 oktober 2017 / [ed] Amelie Hössjer, Maria Magnusson och Peter Reinholdsson, Uppsala: Uppsala universitet, 2018, s. 38-51Konferansepaper (Fagfellevurdert)
  • 3. Bengtson, Charlotta
    et al.
    Ahlkvist, Mikaela
    Ekeroth, William
    Nilsen-Moe, Astrid
    Proos Vedin, Nathalie
    Rodiouchkina, Katerina
    Ye, Sofie
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Uppsala University.
    Kursutveckling i partnerskap mellan lärare och studenter2018Konferansepaper (Annet vitenskapelig)
    Abstract [sv]

    En kurs på grundutbildningsnivå har omformats i partnerskap mellan studenter och lärare vilket lett till mer omfattande förändringar än motsvarande lärarledd process.(Bengtson et al., 2017) Den nya kursen har getts två gånger och resultatet blev avsevärt bättre betyg på kursvärderingarna och viss förbättring av examensresultateten jämfört med tidigare år. Fokus på presentationen är att diskutera lärdomar och utmaningar för att genomföra lyckade partnerskap i kursutveckling. Målet med projektet var att göra om en fysikkurs på kandidatprogrammet i kemi som studenterna uppfattade som svår och med bristande koppling till deras utbildning i kemi. I den första delen av projektet hördes studentens röst genom intervjuer kring kursens roll i utbildningsprogrammet. Intervjuerna gav inspiration till fortsatt arbete med högre grad av studentmedverkan. I den andra delen av projektet bildades därför en utvecklingsgrupp bestående av sex studenter och två lärare för att utveckla kursplan och läromedel i partnerskap (Mihans et al., 2008). Partnerskap kan leda till ökad motivation och självförtroende hos studenterna och att de tar större ansvar för sitt lärande (Bovill et al., 2011). Samtidigt drar lärarna nytta av att se inlärningsprocessen från studentens perspektiv (Cook-Sather, 2014). Hela gruppen träffades en gång i veckan under sju veckor. Dessutom bildades fyra separata arbetsgrupper som tog fram nytt kursmaterial. Samtliga beslut om förändringar togs genom omröstningar i hela gruppen där allas röster vägde lika. Lärarna kunde behålla ansvaret för kursens kvalitet genom att bestämma vilka förslag som var tillräckligt bra för omröstning, men det blev aldrig aktuellt eftersom det nya materialet höll genomgående hög kvalitet. Bland de genomförda förändringarna var nya seminarier för ökad begreppsmässig förståelse, omformning av alla föreläsningar med mer aktivt studentdeltagande, samt byte av kurslitteratur. Projektet har krävt betydande resurser från både lärare och studenter och med tanke på arbetsinsatsen passar liknande projekt bäst för att periodvis genomföra större förändringar i en kurs. Studenterna arvoderades för de timmar de lagt ned på kursutveckling och projektet finansierades med bidrag från en pedagogisk fond.  Viktiga framgångsfaktorer var deltagande av studenter att rekrytera till projektet, finansiellt stöd från fakulteten, tidigt urval av konkreta utvecklingsuppgifter samt att låta gruppens medlemmar själva välja vad de ville utveckla utifrån deras egen kompetens. En rekommendation är att dela in utvecklingsprocessen i flera steg och öka partnerskap över tid för att hitta balans mellan behovet av vägledning och studenternas frihet att utveckla på egen hand. Nästa steg är att tillsammans med en ny studentgrupp fokuserat arbeta med att förbättra examinationsformerna. Samarbetet mellan lärare och studenter ledde till en djupare förståelse för varandras roller i en akademisk utbildningsmiljö och gav studenterna inspiration att arbeta med förbättring även i andra delar av utbildningen.

     

    Bengtson, C., Ahlkvist, M., Ekeroth, W., Nilsen-Moe, A., Proos Vedin, N., Rodiuchkina, K., Ye, S. & Lundberg, M. 2017. Working as Partners: Course Development by a Student–Teacher Team. International Journal for the Scholarship of Teaching and Learning, 11, 6.

    Bovill, C., Bulley, C. J. & Morss, K. 2011. Engaging and empowering first-year students through curriculum design: perspectives from the literature. Teaching in Higher Education, 16, 197-209.

    Cook-Sather, A. 2014. Multiplying perspectives and improving practice: what can happen when undergraduate students collaborate with college faculty to explore teaching and learning. Instructional Science, 42, 31-46.

    Mihans, I., Richard, J., Long, D. T. & Felten, P. 2008. Power and expertise: Student-faculty collaboration in course design and the scholarship of teaching and learning. International Journal for the Scholarship of Teaching and Learning, 2, 16.

     

  • 4.
    Bengtson, Charlotta
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Ahlkvist, Mikaela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström.
    Ekeroth, William
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström.
    Nilsen-Moe, Astrid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi.
    Proos Vedin, Nathalie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström.
    Rodiuchkina, Katerina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström.
    Ye, Sofie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Working as Partners: Course Development by a Student–Teacher Team2017Inngår i: International Journal for the Scholarship of Teaching & Learning, ISSN 1931-4744, E-ISSN 1931-4744, Vol. 11, nr 2, artikkel-id Article 6Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 5.
    Bengtson, Charlotta
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Studentmedverkan i utvecklingen av kursen ”Fysik för kemister”2016Inngår i: För pedagogisk utveckling tillsammans: Lärare och studenter som medskapare av utbildningen / [ed] Katarina Andreasen och Maria Magnusson, Uppsala: Uppsala universitet, 2016, s. 20-26Konferansepaper (Annet vitenskapelig)
    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.

  • 6.
    Blachucki, W.
    et al.
    Polish Acad Sci, Inst Phys Chem, PL-01224 Warsaw, Poland.
    Kayser, Y.
    Phys Tech Bundesanstalt, D-10587 Berlin, Germany.
    Czapla-Masztafiak, J.
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Guo, Meiyuan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Juranic, P.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Kavcic, M.
    Jozef Stefan Inst, SI-1000 Ljubljana, Slovenia.
    Källman, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Knopp, G.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Milne, C.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Rehanek, J.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Sá, Jacinto
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi. Polish Acad Sci, Inst Phys Chem, PL-01224 Warsaw, Poland.
    Szlachetko, J.
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Inception of electronic damage of matter by photon-driven post-ionization mechanisms2019Inngår i: Structural Dynamics, ISSN 2329-7778, Vol. 6, nr 2, artikkel-id 024901Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    "Probe-before-destroy" methodology permitted diffraction and imaging measurements of intact specimens using ultrabright but highly destructive X-ray free-electron laser (XFEL) pulses. The methodology takes advantage of XFEL pulses ultrashort duration to outrun the destructive nature of the X-rays. Atomic movement, generally on the order of >50 fs, regulates the maximum pulse duration for intact specimen measurements. In this contribution, we report the electronic structure damage of a molecule with ultrashort X-ray pulses under preservation of the atoms' positions. A detailed investigation of the X-ray induced processes revealed that X-ray absorption events in the solvent produce a significant number of solvated electrons within attosecond and femtosecond timescales that are capable of coulombic interactions with the probed molecules. The presented findings show a strong influence on the experimental spectra coming from ionization of the probed atoms' surroundings leading to electronic structure modification much faster than direct absorption of photons. This work calls for consideration of this phenomenon in cases focused on samples embedded in, e.g., solutions or in matrices, which in fact concerns most of the experimental studies.

  • 7. 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.2008Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, nr 39, s. 12880-12881Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 8.
    Delcey, Mickael G
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Sörensen, Lasse Kragh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Vacher, Morgane
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Couto, Rafael Carvalho
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions2019Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, nr 19, s. 1789-1799Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X-ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low-lying electronic states offers an efficient way to reach single and double-core-hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single- and two-photon spectroscopies.

  • 9.
    Esmieu, Charlene
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik. CNRS, LCC, 205 Route Narbonne,BP 44099, F-31077 Toulouse 4, France.
    Guo, Meiyuan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Redman, Holly J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Berggren, Gustav
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Synthesis of a miniaturized [FeFe] hydrogenase model system2019Inngår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 48, nr 7, s. 2280-2284Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The reaction occurring during artificial maturation of [FeFe] hydrogenase has been recreated using molecular systems. The formation of a miniaturized [FeFe] hydrogenase model system, generated through the combination of a [4Fe4S] cluster binding oligopeptide and an organometallic Fe complex, has been monitored by a range of spectroscopic techniques. A structure of the final assembly is suggested based on EPR and FTIR spectroscopy in combination with DFT calculations. The capacity of this novel H-cluster model to catalyze H-2 production in aqueous media at mild potentials is verified in chemical assays.

  • 10.
    Farahani, Pooria
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Karlsson, Hans O.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Ab initio quantum mechanical calculation of the reaction probability for the Cl- + PH2Cl -> ClPH2 + Cl- reaction2013Inngår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, s. 134-140Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 11.
    Farahani, Pooria
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 dioxetane2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 28, s. 18653-18664Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 12.
    Farahani, Pooria
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Mechanisms for the Breakdown of Halomethanes through Reactions with Ground-State Cyano Radicals2015Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 16, nr 1, s. 181-190Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 13.
    Fernández Galván, Ignacio
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Vacher, Morgane
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Alavi, Ali
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Angeli, Celestino
    Univ Ferrara, Dipartimento Sci Chim & Farmaceut, Via Luigi Borsari 46, I-44121 Ferrara, Italy.
    Aquilante, Francesco
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.
    Bao, Jie J.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Bokarev, Sergey I.
    Univ Rostock, Inst Phys, Albert Einstein Str 23-24, D-18059 Rostock, Germany.
    Bogdanov, Nikolay A.
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Carlson, Rebecca K.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Chibotaru, Liviu F.
    Univ Leuven, Theory Nanomat Grp, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
    Creutzberg, Joel
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden;Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Dattani, Nike
    Harvard Smithsonian Ctr Astrophys, 60 Garden St, Cambridge, MA 02138 USA.
    Delcey, Mickael G
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Dong, Sijia S.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Dreuw, Andreas
    Heidelberg Univ, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205 A, D-69120 Heidelberg, Germany.
    Freitag, Leon
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Manuel Frutos, Luis
    Univ Alcala De Henares, Dept Quim Analit Quim Fis & Ingn Quim, E-28871 Madrid, Spain;Univ Alcala De Henares, Inst Invest Quim Andres M del Rio, E-28871 Madrid, Spain.
    Gagliardi, Laura
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Gendron, Frederic
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.
    Giussani, Angelo
    UCL, Dept Chem, 20 Gordon St, London WC1H 0AJ, England;Univ Valencia, Inst Ciencia Mol, Apartado 22085, ES-46071 Valencia, Spain.
    Gonzalez, Leticia
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Grell, Gilbert
    Univ Rostock, Inst Phys, Albert Einstein Str 23-24, D-18059 Rostock, Germany.
    Guo, Meiyuan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Hoyer, Chad E.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Johansson, Marcus
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Keller, Sebastian
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Knecht, Stefan
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Kovacevic, Goran
    Rudjer Boskovic Inst, Div Mat Phys, POB 180,Bijenicka 54, HR-10002 Zagreb, Croatia.
    Källman, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Li Manni, Giovanni
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Ma, Yingjin
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Mai, Sebastian
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Malhado, Joao Pedro
    Imperial Coll London, Dept Chem, London SW7 2AZ, England.
    Malmqvist, Per Ake
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Marquetand, Philipp
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Mewes, Stefanie A.
    Heidelberg Univ, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205 A, D-69120 Heidelberg, Germany;Massey Univ Albany, Ctr Theoret Chem & Phys, NZLAS, Private Bag 102904, Auckland 0632, New Zealand.
    Norell, Jesper
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden.
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via A Moro 2, I-53100 Siena, Italy;Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA;Univ Strasbourg, CNRS, USIAS, F-67034 Strasbourg, France;Univ Strasbourg, CNRS, Inst Phys & Chim Mat Strasbourg, F-67034 Strasbourg, France.
    Oppel, Markus
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Phung, Quan Manh
    Pierloot, Kristine
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
    Plasser, Felix
    Loughborough Univ, Dept Chem, Loughborough LE11 3TU, Leics, England.
    Reiher, Markus
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Sand, Andrew M.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Schapiro, Igor
    Hebrew Univ Jerusalem, Inst Chem, Jerusalem, Israel.
    Sharma, Prachi
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Stein, Christopher J.
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Sörensen, Lasse Kragh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Truhlar, Donald G.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Ugandi, Mihkel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Ungur, Liviu
    Natl Univ Singapore, Dept Chem, Singapore 117543, Singapore.
    Valentini, Alessio
    Res Unit MolSys, Theoret Phys Chem, Allee 6 Aout 11, B-4000 Liege, Belgium.
    Vancoillie, Steven
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Veryazov, Valera
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Weser, Oskar
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Wesolowski, Tomasz A.
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Widmark, Per-Olof
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Wouters, Sebastian
    Brantsandpatents, Pauline van Pottelsberghelaan 24, B-9051 Sint Denijs Westrem, Belgium.
    Zech, Alexander
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Zobel, J. Patrick
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi. Uppsala Center for Computational Chemistry (UC3), Uppsala University, P.O. Box 596, SE-751 24 Uppsala, Sweden.
    OpenMolcas: From Source Code to Insight2019Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, nr 11, s. 5925-5964Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.

  • 14.
    Giussani, Angelo
    et al.
    Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia, Spain.
    Farahani, Pooria
    KTH Royal Inst Technol, Dept Theoret Chem & Biol, Sch Engn Sci Chem Biotechnol & Hlth CBH, S-10691 Stockholm, Sweden.
    Martinez-Muñoz, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Roca-Sanjuan, Daniel
    Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia, Spain.
    Molecular Basis of the Chemiluminescence Mechanism of Luminol2019Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 25, nr 20, s. 5202-5213Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.

  • 15.
    Guo, Meiyuan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Erik, Källman
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Sørensen, Lasse Kragh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Delcey, Mickaël G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. 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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, Maharashtra, India..
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Molecular orbital simulations of metal 1s2p resonant inelastic X-ray scattering2016Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, nr 29, s. 5848-5855Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 16.
    Guo, Meiyuan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Southwest Univ, Dept Chem & Chem Engn, Chongqing, Peoples R China.
    Källman, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Pinjari, Rahul V.
    Swami Ramanand Teerth Marathwada Univ, Sch Chem Sci, Nanded, Maharashtra, India.
    Couto, Rafael Carvalho
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Sörensen, Lasse Kragh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Pierloot, Kristine
    Univ Leuven, Dept Chem, Heverlee, Belgium.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Univ Siena, Dept Biotechnol Chem & Pharm, Siena, Italy.
    Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra2019Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, nr 1, s. 477-489Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 17.
    Guo, Meiyuan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Sörensen, Lasse Kragh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Delcey, Mickaël G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Pinjari, Rahul V.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method2016Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 4, s. 3250-3259Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 18.
    Heijkenskjöld, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Fysikundervisningens didaktik.
    Edvardsson, Bengt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Teoretisk astrofysik.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Aktiva studenter gör demonstrationsexperiment (2)2017Konferansepaper (Annet vitenskapelig)
    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.

  • 19. 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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Department of Biotechnology, Chemistry and Pharmacy, Universita ̀ di Siena, Siena, Italy.
    Wernet, Philippe
    Gaffney, Kelly
    Odelius, Michael
    Foehlisch, Alexander
    Disentangling Transient Charge Density and Metal-Ligand Covalency in Photoexcited Ferricyanide with Femtosecond Resonant Inelastic Soft X-ray Scattering2018Inngår i: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 9, nr 12, s. 3538-3543Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 20.
    Jay, Raphael
    et al.
    Univ Potsdam, Potsdam, Germany.
    Norell, Jesper
    Stockholm Univ, Dept Phys, Stockholm, Sweden.
    Kunnus, Kristjan
    Stanford Univ, PULSE Inst, Menlo Pk, CA USA.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Gaffney, Kelly
    Stanford Univ, SLAC Natl Accelerator Lab, Palo Alto, CA 94304 USA.
    Wernet, Philippe
    Helmholtz Zentrum Berlin, Berlin, Germany.
    Odelius, Michael
    Stockholm Univ, Dept Phys, Stockholm, Sweden.
    Foehlisch, Alexander
    Univ Potsdam, Potsdam, Germany;Helmholtz Zentrum Berlin, Berlin, Germany.
    Dynamcis of local charge densities and metal-ligand covalency in iron complexes from femtosecond resonant inelastic soft X-ray scattering2018Inngår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 256Artikkel i tidsskrift (Annet vitenskapelig)
  • 21.
    Jayasinghe-Arachchige, Vindi M.
    et al.
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Hu, Qiaoyu
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Sharma, Gaurav
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Paul, Thomas J.
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Quinonero, David
    Univ Illes Balears, Dept Chem, Palma de Mallorca, Spain.
    Parac-Vogt, Tatjana N.
    Katholieke Univ Leuven, Dept Chem, B-3001 Leuven, Belgium.
    Prabhakar, Rajeev
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Hydrolysis of Chemically Distinct Sites of Human Serum Albumin by Polyoxometalate: A Hybrid QM/MM (ONIOM) Study2019Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, nr 1, s. 51-61Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 22.
    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)2011Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, nr 2, s. 390-401Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 23.
    Kayser, Yves
    et al.
    Phys Tech Bundesanstalt, Abbestr 2-12, D-10587 Berlin, Germany;Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Milne, Chris
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Juranic, Pavle
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Sala, Leonardo
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Czapla-Masztafiak, Joanna
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Follath, Rolf
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Kavcic, Matjaz
    Inst Jozef Stefan, Jamova 39, Ljubljana 1000, Slovenia.
    Knopp, Gregor
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Rehanek, Jens
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland;Adv Accelerator Technol AG, CH-5234 Villigen, Switzerland.
    Blachucki, Wojciech
    Polish Acad Sci, Inst Phys Chem, PL-01224 Warsaw, Poland.
    Delcey, Mickael G
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Tyrala, Krzysztof
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Zhu, Diling
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Alonso-Mori, Roberto
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Abela, Rafael
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Sá, Jacinto
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi. Polish Acad Sci, Inst Phys Chem, PL-01224 Warsaw, Poland.
    Szlachetkc, Jakub
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses2019Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, artikkel-id 4761Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved.

  • 24.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. 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 Bond2014Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 136, nr 52, s. 18087-18099Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 25.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 scattering2017Inngår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 254Artikkel i tidsskrift (Annet vitenskapelig)
  • 26. Kroll, Thomas
    et al.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Solomon, Edward I.
    X-Ray Absorption and RIXS on Coordination Complexes2016Inngår i: X-Ray Absorption and X-Ray Emission Spectroscopy: Theory and Applications, Chichester: John Wiley & Sons, Ltd , 2016, s. 407-435Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 27.
    Kubin, Markus
    et al.
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Berlin, Germany.
    Guo, Meiyuan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 Flatjet2018Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 57, nr 9, s. 5449-5462Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 28.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Ekimova, Maria
    Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany.
    Källman, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 Sections2018Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, nr 29, s. 7375-7384Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 29. Kubin, Markus
    et al.
    Guo, Meiyuan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Kroll, Thomas
    Lächel, Heike
    Källman, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Baker, Michael L.
    Mitzner, Rolf
    Gul, Sheraz
    Kern, Jan
    Föhlisch, Alexander
    Erko, Alexei
    Bergmann, Uwe
    Yachandra, Vittal
    Yano, Junko
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Wernet, Philippe
    Probing the oxidation state of transition metal complexes: a case study on how charge and spin densities determine Mn L-edge X-ray absorption energies2018Inngår i: Chem. Sci., Vol. 9, nr 33, s. 6813-6829Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Transition metals in inorganic systems and metalloproteins can occur in different oxidation states, which makes them ideal redox-active catalysts. To gain a mechanistic understanding of the catalytic reactions, knowledge of the oxidation state of the active metals, ideally in operando, is therefore critical. L-edge X-ray absorption spectroscopy (XAS) is a powerful technique that is frequently used to infer the oxidation state via a distinct blue shift of L-edge absorption energies with increasing oxidation state. A unified description accounting for quantum-chemical notions whereupon oxidation does not occur locally on the metal but on the whole molecule and the basic understanding that L-edge XAS probes the electronic structure locally at the metal has been missing to date. Here we quantify how charge and spin densities change at the metal and throughout the molecule for both redox and core-excitation processes. We explain the origin of the L-edge XAS shift between the high-spin complexes MnII(acac)2 and MnIII(acac)3 as representative model systems and use ab initio theory to uncouple effects of oxidation-state changes from geometric effects. The shift reflects an increased electron affinity of MnIII in the core-excited states compared to the ground state due to a contraction of the Mn 3d shell upon core-excitation with accompanied changes in the classical Coulomb interactions. This new picture quantifies how the metal-centered core hole probes changes in formal oxidation state and encloses and substantiates earlier explanations. The approach is broadly applicable to mechanistic studies of redox-catalytic reactions in molecular systems where charge and spin localization/delocalization determine reaction pathways.

  • 30.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Källman, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 solution2018Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, nr 24, s. 16817-16827Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 31.
    Kunnus, Kristjan
    et al.
    Stanford Univ, PULSE Inst, Menlo Pk, CA USA.
    Harlang, Tobias
    Lund Univ, Lund, Sweden.
    Kjaer, Kasper Skov
    Stanford Univ, PULSE Inst, Menlo Pk, CA USA;Lund Univ, Lund, Sweden.
    Vacher, Morgane
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Vanko, Gyorgy
    Wigner Res Ctr Phys, Budapest, Hungary.
    Haldrup, Kristoffer
    Tech Univ Denmark, Lyngby, Denmark.
    van Driel, Tim
    Reinhard, Marco
    Stanford Univ, PULSE Inst, Menlo Pk, CA USA.
    Hartsock, Robert
    Stanford Univ, PULSE Inst, Menlo Pk, CA USA.
    Biasin, Elisa
    Stanford Univ, PULSE Inst, Menlo Pk, CA USA;Tech Univ Denmark, Lyngby, Denmark.
    Nielsen, Martin
    Tech Univ Denmark, Lyngby, Denmark.
    Sundstrom, Villy
    Lund Univ, Lund, Sweden.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Warnmark, Kenneth
    Lund Univ, Lund, Sweden.
    Gaffney, Kelly
    Stanford Univ, SLAC Natl Accelerator Lab, Palo Alto, CA 94304 USA.
    Coherent structural dynamics observed with femtosecond Fe K alpha and K beta X-ray emission spectroscopies2018Inngår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 256Artikkel i tidsskrift (Annet vitenskapelig)
  • 32.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Pinjari, Rahul V.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 Perspectives2016Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, nr 29, s. 7182-7194Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 33.
    Liu, Tianfei
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi.
    Guo, Meiyuan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Orthaber, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Lomoth, Reiner
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Ott, Sascha
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Hammarström, Leif
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi.
    Accelerating proton-coupled electron transfer of metal hydrides in catalyst model reactions2018Inngår i: Nature Chemistry, ISSN 1755-4330, E-ISSN 1755-4349, Vol. 10, nr 8, s. 881-887Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Metal hydrides are key intermediates in catalytic proton reduction and dihydrogen oxidation. There is currently much interest in appending proton relays near the metal centre to accelerate catalysis by proton-coupled electron transfer (PCET). However, the elementary PCET steps and the role of the proton relays are still poorly understood, and direct kinetic studies of these processes are scarce. Here, we report a series of tungsten hydride complexes as proxy catalysts, with covalently attached pyridyl groups as proton acceptors. The rate of their PCET reaction with external oxidants is increased by several orders of magnitude compared to that of the analogous systems with external pyridine on account of facilitated proton transfer. Moreover, the mechanism of the PCET reaction is altered by the appended bases. A unique feature is that the reaction can be tuned to follow three distinct PCET mechanisms-electron-first, proton-first or a concerted reaction-with very different sensitivities to oxidant and base strength. Such knowledge is crucial for rational improvements of solar fuel catalysts.

  • 34.
    Lundberg, Marcus
    Ericsson Mobile Communications.
    Battery operable device with battery state-of-charge indicator2002Patent (Annet (populærvitenskap, debatt, mm))
  • 35.
    Lundberg, Marcus
    Stockholms universitet.
    Challenges in Enzyme Catalysis - Photosystem II and Orotidine Decarboxylase: A Density Functional Theory Treatment2005Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

  • 36.
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Studenter som undervisar lär sig på djupet2014Inngår i: I stort och smått– med studenten i fokus / [ed] Gunnlaugsson, Geir, Uppsala, 2014, s. 231-239Konferansepaper (Fagfellevurdert)
  • 37.
    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' Calculations2012Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, nr 4, s. 406-415Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 38.
    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 centers2003Inngår i: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 110, nr 3, s. 130-143Artikkel i tidsskrift (Fagfellevurdert)
    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).

  • 39.
    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 decarboxylase2002Inngår i: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 8, nr 4, s. 119-130Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 40.
    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 approach2004Inngår i: Topics in current chemistry, ISSN 0340-1022, E-ISSN 1436-5049, Vol. 238, s. 79-112Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 41.
    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-catalyst2004Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 43, nr 1, s. 264-274Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 42.
    Lundberg, Marcus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    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 perspective2013Inngår i: Coordination chemistry reviews, ISSN 0010-8545, E-ISSN 1873-3840, Vol. 257, nr 1, s. 277-289Artikkel, forskningsoversikt (Fagfellevurdert)
    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.

  • 43.
    Lundberg, Marcus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Uppsala University.
    Delcey, Mickael G
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Multiconfigurational Approach to X-ray Spectroscopy of Transition Metal Complexes2019Inngår i: Transition Metals in Coordination Environments: Computational chemistry and catalysis viewpoints / [ed] Ewa Broclawik; Tomasz Borowski; Mariusz Radoń, Springer, 2019Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Close correlation between theoretical modeling and experimental spectroscopy allows for identification of the electronic and geometric structure of a system through its spectral fingerprint. This is can be used to verify mechanistic proposals and is a valuable complement to calculations of reaction mechanisms using the total energy as the main criterion. For transition metal systems, X-ray spectroscopy offers a unique probe because the core-excitation energies are element specific, which makes it possible to focus on the catalytic metal. The core hole is atom-centered and sensitive to the local changes in the electronic structure, making it useful for redox active catalysts. The possibility to do time-resolved experiments also allows for rapid detection of metastable intermediates. Reliable fingerprinting requires a theoretical model that is accurate enough to distinguish between different species and multiconfigurational wavefunction approaches have recently been extended to model a number of X-ray processes of transition metal complexes. Compared to ground-state calculations, modeling of X-ray spectra is complicated by the presence of the core hole, which typically leads to multiple open shells and large effects of spin–orbit coupling. This chapter describes how these effects can be accounted for with a multiconfigurational approach and outline the basic principles and performance. It is also shown how a detailed analysis of experimental spectra can be used to extract additional information about the electronic structure.

  • 44.
    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 Synthesis2009Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, nr 1, s. 222-234Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 45.
    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 Scattering2013Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, nr 45, s. 17121-17134Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 46.
    Lundberg, Marcus
    et al.
    Kyoto University.
    Morokuma, Keiji
    Determining Transition States in Bioinorganic Reactions2009Inngår i: Computational Inorganic and Bioinorganic Chemistry / [ed] E.I. Solomon, R.B. King, and R.A. Scott, Hoboken: John Wiley & Sons, Ltd , 2009, s. 17-31Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 47.
    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)2007Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, nr 31, s. 9380-9389Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 48.
    Lundberg, Marcus
    et al.
    Kyoto University.
    Morokuma, Keiji
    The ONIOM Method and its Applications to Enzymatic Reactions2009Inngår i: Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications / [ed] T.-S. Lee and D.M. York, Springer Verlag , 2009Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 49.
    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 systems2012Inngår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, nr 6, s. 1701-1711Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 50.
    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 Mimics2010Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, nr 4, s. 1413-1427Artikkel i tidsskrift (Fagfellevurdert)
    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.

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