Dr. Ragnar Björnsson - Computational Chemistry

Dr. Ragnar Björnsson
Head of Group Computational Chemistry
Department Inorganic Spectroscopy

Vita

B.Sc.University of Iceland (2006)
M.Sc.University of Iceland (2008)
Ph.D. University of St Andrews, UK (2012)
PostdocMPI CEC (2012-2014)
Research assistant professorUniversity of Iceland (2014-2018)
Group leaderMPI CEC (since 2018)

Publications

Download: Publications list (.pdf)

2019

  • Barclay, M.; Bjornsson, R.; Cipriani, M.; Terfort, A.; Fairbrother, H.; Ingólfsson, O. (2019) The role of the dihedral angle and excited cation states in ionization and dissociation of mono-halogenated biphenyls; a combined experimental and theoretical coupled cluster study. Phys. Chem. Chem. Phys., 21, 4556-4567.
  • Thorhallsson, A. Th.; Bjornsson, R. (2019), Computational mechanistic study of [MoFe3S4] cubanes for catalytic reduction of nitrogenase substrates. Inorg. Chem. 58, 1886-1894.
  • Sterling, C. M.; Bjornsson, R. (2019) A Multi-Step Explicit Solvation Protocol for Calculation of Redox Potentials. J. Chem. Theory Comput., 15, 52-67.

 

2018

  • Benediktsson, B.; Thorhallsson, A. T.; Bjornsson, R., (2018) QM/MM calculations reveal a bridging hydroxo group in a vanadium nitrogenase crystal structure. Chem. Comm., 54, 7310-7313.
  • P, R. K. T.; Weirich, P.; Hrachowina, L.; Hanefeld, M.; Bjornsson, R.; Hrodmarsson, H. R.; Barth, S.; Fairbrother, D. H.; Huth, M.; Ingólfsson, O. Beilstein (2018) Electron interactions with the heteronuclear carbonyl precursor H2FeRu3(CO)13 and comparison with HFeCo3(CO)12: from fundamental gas phase and surface science studies to focused electron beam induced deposition. J. Nanotechnol., 9, 555–579.
  • Thorman, R. M.; Unlu, I.; Johnson, K. R.; Bjornsson, R., McElwee-White, L.; Fairbrother, H.; Ingólfsson, O. (2018) Low energy electron-induced decomposition of (η5-Cp)Fe(CO)2Mn(CO)5, a potential bimetallic precursor for focused electron beam induced deposition of alloy structures. Phys. Chem. Chem. Phys., 20, 5644-5656.
  • Abbehausen, C.; Ferraz de Paiva, R. E.; Bjornsson, R., Quintana Gomes, S.; Du, Z.; Corbi, P. P.; Lima, F. A.; Farrell, N. (2018) X‐ray Absorption Spectroscopy Combined with Time-Dependent Density Functional Theory Elucidates Differential Substitution Pathways of Au(I) and Au(III) with Zinc Fingers. Inorg. Chem., 57, 218-230.

 

2017

  • Benediktsson, B.; Bjornsson, R. (2017) QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site. Inorg. Chem., 56, 13417-13429. Free e-print Link 
  • Ómarsson, B.; Bjornsson, R., Ingolfsson, O. (2017) Proton Shuttling and Reactions Paths in Dissociative Electron Attachment to Ortho- and Para-Tetrafluorohydroquinone, an Experimental and Theoretical Study. J. Phys. Chem. A, 121, 5580-5585.
  • Kumar T. P., R.; Bjornsson, R., Barth, S.; Ingólfsson, O. (2017) Formation and decay of negative ion states up to 11 eV above the ionization energy of the nanofabrication precursor HFeCo3(CO)12. Chem. Sci., 8, 5949-5952. Hot article for June!
  • Rees, J. A.; Bjornsson, R.; Kowalska, J. K.; Lima, F. A.; Schlesier, J.; Sippel, D.; Weyhermüller, T.; Einsle, O.; Kovacs, J. A.; DeBeer, S. (31) Comparative Electronic Structures of Nitrogenase FeMoco and FeVco. Dalton Trans., 46, 2445-2455.
  • Bjornsson, R.;Neese, F.; DeBeer, S. (2017) Revisiting the Mössbauer isomer shifts of the FeMoco cluster of nitrogenase and the cofactor charge. Inorg. Chem., 56, 1470-1477.
  • Belyakov, A. V.; Sigolaev, Y. F.; Shlykov, S. A.; Wallevik, S. Ó.; Jonsdottir, N.R.; Jonsdottir, S.; Kvaran, Á.; Bjornsson, R.; Arnason, I. (2017) Conformational properties of 1-cyano-1-silacyclohexane, C5H10SiHCN: gas electron diffraction, low-temperature NMR and quantum chemical calculations. J. Mol. Struct., 1132, 149-156.

 

2016

  • Sigurdardóttir, B. K.; Kvaran, A.; Bjornsson, R.; Arnason, I. (2016) Dissociative Photoionization of 1-Halogenated Silacyclohexanes: Silicon Traps the Halogen. J. Phys. Chem A., 120, 9188-9197.
  • Ólafsson, S. N.; Bjornsson, R.; Helgason, Ö.; Jonsdottir, S.; Suman, S. G. (2016) Coordination geometry determination of stannane compounds with phosphinoyldithioformate ligands using multinuclear NMR, Sn Mössbauer and DFT methods. J. Organomet. Chem., 825-826, 125-138.
  • Thorman, R. M.; Bjornsson, R.; Ingólfsson, O. (2016) Computational study of dissociative electron attachment to π-allyl ruthenium (II) tricarbonyl bromide. Eur. Phys. J. D, 70, 164. 
  • Kumar T P, R.; Barth, S.; Bjornsson, R.; Ingólfsson, O. (2016) Structure and energetics in dissociative electron attachment to HFeCo3(CO)12. Eur. Phys. J. D, 70, 163.
  • Kowalska, J. K.; Hahn, A. W.; Albers, A.; Schiewer, C. E.; Bjornsson, R., Lima, F. A.; Meyer, F.; DeBeer, S. (2016) X-ray Absorption and Emission Spectroscopic Studies of [L2Fe2S2]n Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron–Sulfur Clusters. Inorg. Chem., 55, 4485-4497. 

 

2015

  • Rees, J. A.; Bjornsson, R.; Schlesier, J.; Sippel, D.; Einsle, O.; DeBeer, S. (2015) The Fe-V Cofactor of Vanadium Nitrogenase Contains an Interstitial Carbon. Atomm Angew. Chem. Int. Edit., 54, 13249-13252. 
  • Bjornsson, R.; Neese, F.; Schrock, R. R.; Einsle, O.; DeBeer, S. (2015) The discovery of Mo(III) in FeMoco: reuniting enzyme and model chemistry. J. Biol. Inorg. Chem., 20, 447-460. (invited review article)
  • Bjornsson, R.; Delgado, M.; Lima, F. A.; Einsle, O.; Neese, F.; DeBeer, S. (2015) Molybdenum L-edges of molybdenum-dependendent nitrogenase. ZAAC, 641, 65-71. 
  • Masters, S.; Robertson, H.; Wann, D.; Hölbling, M.; Hassler, K.; Bjornsson, R.; Wallevik, S. Ó.; Arnason, I. (2015) Molecular Structure of 1,2-bis(trifluoromethyl)-1,1,2,2-tetramethyldisilane in the Gas, Liquid and Solid Phases – Unusual Conformational Changes Between Phases. J. Phys. Chem. A, 119, 1600-1618.
  • Belyakov, V.; Sigolaev, Y.; Shlykov, S. A.; Wallevik, S. Ó.; Jonsdottir, N. R.; Bjornsson, R.; Jonsdottir, S.; Kvaran, Á.; Kern, T.; Hassler, K.; Arnason, I. (2015) Conformational properties of 1-tert-butyl-1-silacyclohexane, C5H10SiH(t-Bu): gas-phase electron diffraction, temperature-dependent Raman spectroscopy and quantum chemical calculations. Struct Chem., 26, 445-453.

 

2014

  • Cormanich, R. A.; Durie, A.; Bjornsson, R.; Rittner, R.; O'Hagan, D.; Bühl, M. (2014) Density Functional Study of Interactions between Fluorinated Cyclohexanes and Arenes. Helvetica Chimica Acta, 97, 797-807.
  • Bjornsson, R.; Lima, F. A.; Weyhermüller, T.; Spatzal, T.; Einsle, O.; Bill, E.; Neese F.; DeBeer, S. (2014) Identification of a spin-coupled Mo(III) in the Nitrogenase Iron-Molybdenum Cofactor. Chemical Science, 5, 3096-3103.

 

2013

  • Lima, F. A.; Bjornsson, R.; Weyhermuller, T.; Chandrasekaran, P.; Glatzel, P.; Neese F.; DeBeer, S. (2013) High-Resolution Molybdenum K-edge X-ray Absorption Spectroscopy analyzed with Time-Dependent Density Functional Theory. Phys. Chem. Chem. Phys, 15, 20911-20920.
  • Wallevik, S. Ó.; Bjornsson, R.; Kvaran, Á.; Jonsdottir, S.; Arnason, I.; Belyakov, A. V.; Baskakov, A. A.; Kern T.; Hassler, K. (2013) Conformational Properties of Halogenated-1-Silacyclohexanes, C5H10SiHX (X = Cl, Br, I): Gas Electron Diffraction, Low-Temperature NMR, Temperature-Dependent Raman Spectroscopy, and Quantum Chemical Calculations.
    Organometallics, 32, 6996-7005.
  • Jonsdottir, N. R.; Kvaran, Á.; Jonsdottir, S.; Arnason, I.; Bjornsson, R., (2013) Conformational Properties of 1-Methyl-1-Germacyclohexane: Low-Temperature NMR and Quantum Chemical Calculations. Struct. Chem.201324, 769-774.
  • Bjornsson, R.; Bühl, M. (2013) Electric field gradients of transition metal complexes: Basis set uncontraction and scalar relativistic effects. Chem. Phys. Lett.559, 112-116.


2012

  • Kern, T.; Hölbling, M.; Dzambaski, A.; Flock, M.; Hassler, K.; Wallevik, S. Ó.; Arnason I.; Bjornsson, R. (2012) Conformational Energies of Silacyclohexanes C5H10SiHMe, C5H10SiH(CF3) and C5H10SiCl(SiCl3) from Variable Temperature Raman Spectra. J. Raman Spect.43, 1337-1342. 
  • Bjornsson R.; Bühl, M. (2012) Modelling Molecular Crystals by QM/MM: Self-Consistent Electrostatic Embedding for Geometry Optimizations and Molecular Property Calculations in the Solid. J. Chem. Theory Comput.8, 498-508.
  • Cao, J.; Bjornsson, R.; Bühl, M.; Thiel W.; van Mourik T. (2012) Modelling zwitterions in solution: 3-fluoro-γ-aminobutyric acid (3F-GABA). Chem. Eur. J.18, 184-195.
  • Tacke, R.; Bertermann, R.; Burschka, C.; Dörrich, S.; Fischer, M.; Müller, B.; Meyerhans, G.; Schepmann, D.; Wünsch, B.; Arnason I.; Bjornsson, R. (2012) High-Affinity, Selective Sigma Ligands of the 1,2,3,4-Tetrahydro-1,4'-silaspiro[naphthalene-1,4'-piperidine] Type: Syntheses, Structures, and Pharmacological Properties. Chem. Med. Chem.7, 523-532.



2011

  • Arnason, I ; Gudnason, P. I; Bjornsson, R.; Oberhammer, H. (2011) Gas Phase Structures, Energetics, and Potential Energy Surfaces of Disilacyclohexanes. J. Phys. Chem. A115, 10000-10008.
  • Bjornsson, R.; Früchtl, H.; Bühl, M. (2011) 51V NMR parameters of VOCl3: Static and dynamic density functional study from the gas phase to the bulk. Phys. Chem. Chem. Phys.13, 619-627.

 

2010

  • Hagan, R. M.; Bjornsson, R.; McMahon, S. A.; Schomburg, B.; Braithwaite, V.; Bühl, M.; Naismith J. H.; Schwarz-Linek, U. (2010) NMR and Theoretical Analysis of a Spontaneously Formed Lys-Asp Isopeptide Bond. Angew. Chem. Int. Ed., 45, 8421-8425.
  • Bjornsson R.; Bühl, M. (2010) Electric Field Gradients of Transition Metal Complexes from Density Functional Theory: Assessment of Functionals, Geometries and Basis sets.
    Dalton. T.39, 5319-5324.
  • Wallevik, S. O.; Bjornsson, R.; Kvaran, A.; Jonsdottir, S.; Girichev, G. V.; Giricheva, N. I.; Hassler K.; Arnason, I. (2010) Conformational properties of 1-fluoro-1-methyl-silacyclohexane and 1-methyl-1-trifluoromethyl-1-silacyclohexane: GED, NMR, Raman, and QC calculations. J. Mol. Struct., 209-219.
  • Bodi, A.; Bjornsson R.; Arnason I. (2010) A phenomenological relationship between molecular geometry change and conformational energy change. J. Mol. Struct. 2010978, 14-19. 
  • Wallevik, S. O.; Bjornsson, R.; Kvaran, A.; Jonsdottir, S.; Arnason, I.; Belyakov, A. V.; Baskakov, A. A.; Hassler K.; Oberhammer, H. (2010) Conformational Properties of 1-Silyl-1-Silacyclohexane, C5H10SiHSiH3: GED, NMR, Raman, and QC Calculations. J. Phys. Chem. A114, 2127-2135.


2009

  • Bjornsson, R.; Arnason, I. (2009) Conformational properties of six-membered heterocycles: accurate relative energy differences with DFT, the importance of dispersion interactions and silicon substitution effects. Phys. Chem. Chem. Phys.11, 8689-8697.

Group members

PhD students

  • Albert Thor Thorhallson

Computational Chemistry

Understanding Biological Nitrogen Reduction

Despite intense research for the last decades, the mechanism for biological nitrogen reduction remains elusive. Only recently was the identity of the interstitial atom of the FeMo cofactor (FeMoco) clarified but many questions remain about the electronic structure of the cofactor and its connection to substrate interaction and catalysis.

In a joint experimental-theoretical study [1] the molybdenum ion in FeMoco was reassigned as Mo(III) rather than the common Mo(IV) assignment that has been in the literature since the 1980s. Using Mo XAS spectroscopy of MoFe protein and selected model compounds, combined with TDDFT-calculated spectra and analysis of the electronic structure using broken-symmetry DFT we were able to assign the molybdenum ion as a d3 Mo(III). Furthermore theoretical calculations revealed Mo in an unusual non-Hund configuration, apparently arising due to strong spin-coupling to the Fe atoms in an unusual (and currently not completely understood). A Mo XAS L-edge study further supported the Mo(III) oxidation state [2]. A computational study revisiting the Mössbauer properties of FeMoco demonstrated conclusively the charge of the cofactor as [MoFe7S9C]1- [3].

Crucial to this recent research into the FeMoco cofactor has been the comparioson of the complex cofactor to heterometallic model compounds. A recent review on molecular and electronic structure aspects of FeMoco highlights the molecular and electronic similarity of FeMoco to synthetic cubanes by Holm et al. and Coucouvanis et al. [4].

Going beyond cluster models, we now employ hybrid QM/MM approaches where a large part of the MoFe protein is described, removing the need for artificial constraints on amino acids near the cofactor. In a study on MoFe protein we demonstrated that unprecedented agreement between broken-symmetry DFT calculations and the crystal structure can be obtained. Not only could the charge of FeMoco be confirmed as [MoFe7S9C]1-, but via comparison of metal-metal distances and an understanding of the electronic structure we made a case for the cofactor predominantly populating a specific electronic state, described via a broken-symmetry solution labelled BS7-235, where Fe ions 2, 3 and 5 are "spin-down" [5], see Figure 1.

Additionally vanadium nitrogenase is being studied in our group, and recently Fe XES experiments and calculations were together able to demonstrate the presence of a carbide in FeVco [6]. Furthermore Fe XAS experiments and calculations revealed a more reduced Fe component of FeVco compared to FeMoco, despite the same spin state of both cofactors [7]. This can be explained by the heterometal substitution of a d3 Mo(III) ion for a d2 V(III) ion requiring a 1-electron reduced Fe part of FeVco compared to FeMoco.

An unusual crystal structure of VFe protein recently showed a light-atom ligand replacing a sulfide bridge on FeVco, under turnover conditions (Sippel et al. Science, 359, 1484-1489). The ligand was proposed as either NH or OH based on the crystallographic analysis. Via our QM/MM approach we could demonstrate conclusively that the ligand is an OH group, likely derived from a water molecule as shown in Figure 2 [8].

Many mysteries remain about nitrogenase such as the site of N2 binding, the nature of FeMoco/FeVco redox states and the mechanism of N2 reduction and associated H2 evolution. These questions are currently being explored by computations in our group, together with experimental efforts going on in the department.

QM/MM methods for solution and solid phases

Environmental effects have important effects on the molecular or electronic structure of molecular systems and usually some account of the solution or solid environment is necessary in calculations. Some molecular species are only stable in solution (e.g. zwitterions) or the solid phase and the solvent contribution is an integral part of solution properties like redox potentials or pKa values.

Continuum solvation models are typically employed for including solution phase effects. For large biomolecules like proteins the QM/MM approach has been very successful and has e.g. been applied to the nitrogenase enzymes successfully by us (see above), demonstrating considerable improvement in the description of the cofactor over cluster models. For the solution and solid phases, it is often less clear how to apply QM/MM methodology due to questions of availability of forcefield parameters and accounting for adequate sampling.

A QM/MM approach for computing local structure and properties of molecules inside molecular crystals was previously described [9] and was found to satisfactorily describe molecular geometries as well as solid-state NMR properties. We are currently improving the methodology and expanding its use beyond molecular crystals.

Molecular redox potentials in solution are an example of where accounting for solvent effects is crucial. Continuum solvation models suffer from considerable errors in computed potentials, particularly for aqueous solution, likely due to the lack of explicit solvent molecules. Explicit solvation methodology, on the other hand suffers from lack of established methodology. We are currently developing an explicit solvation QM/MM-based protocol for describing redox potentials of molecules in aqueous solution, see Figure 3. The main focus is currently on accuracy and robustness and improvement over continuum models, with the next target to bring the computational cost down. This will be followed by applications to redox chemistry and spectroscopy of molecular inorganic catalysts.

References

[1] Bjornsson, R., Lima, F. A., Spatzal, T., Weyhermueller, T., Glatzel, P., Bill, E., Einsle, O., Neese, F., and DeBeer, S. (2014) Identification of a spin-coupled Mo(III) in the nitrogenase iron-molybdenum cofactor, Chem. Sci., 5, 3096-3103.
[2] Bjornsson, R., Delgado, M., Lima, F. A. , Einsle, O., Neese, F., DeBeer. S. (2015) Molybdenum L-edges of molybdenum-dependendent nitrogenase, ZAAC, 641, 65-71.
[3] Bjornsson, R., Neese, F., DeBeer S., (2017) Revisiting the Mössbauer isomer shifts of the FeMoco cluster of nitrogenase and the cofactor charge, Inorg. Chem., 56, 1470-1477.
[4] Bjornsson, R., Neese, F., Schrock, R. R., Einsle, O., and DeBeer, S. (2015) The discovery of Mo(III) in FeMoco: reuniting enzyme and model chemistry, J. Biol. Inorg. Chem., 20, 447-460.
[5] Benediktsson, B., Bjornsson, R. (2017) QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site, Inorg. Chem., 57, 218-230.
[6] Rees, J. A., Bjornsson, R., Schlesier, J., Sippel, D., Einsle, O., and DeBeer, S. (2015) The Fe-V Cofactor of Vanadium Nitrogenase Contains an Interstitial Carbon Atom, Angew. Chem. Int. Ed. 54, 13249-13252.
[7] Rees, J. A., Bjornsson, R., Kowalska, J. K., Lima, F. A., Schlesier, J., Sippel, D., Weyhermueller, T., Einsle, O., Kovacs, J. A., and DeBeer, S. (2017) Comparative electronic structures of nitrogenase FeMoco and FeVco, Dalton T. 46, 2445-2455.
[8] Benediktsson, B., Thorhallsson, A. Th., Bjornsson, R. (2018) QM/MM calculations reveal a bridging hydroxo group in a vanadium nitrogenase crystal structure, Chem. Comm., DOI: 10.1039/C8CC03793K
[9] Bjornsson, R., Bühl, M. (2012) Modelling Molecular Crystals by QM/MM: Self-Consistent Electrostatic Embedding for Geometry Optimizations and Molecular Property Calculations in the Solid, J. Chem. Theory Comput., 8, 498-508.