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Electronic structure and EPR spectroscopy of biologically relevant radicals

Aided by our recently developed DFT approach for the calculation of electronic g-tensors, we have been able to relate structure, function, and spectroscopic properties of biologically relevant radicals. These studies have in part been motivated by contacts within the high-field EPR priority program of DFG: At high magnetic fields and microwave frequencies, the g-tensor anisotropies of many bioradicals may now be resolved. As these g-tensors are influenced characteristically by interactions with the protein environment,  their quantitative computation is of considerable interest. Here our DFT approach [1] has allowed a new access with unprecedented accuracy.

This was first demonstrated by systematic validation for various semiquinone radical anions in protic frozen solution (modelled by supermolecular complexes) [2]. After minor scaling of the largest tensor component, the approach provides quantitative predictions. Similar accuracy was obtained for semiquinones in three different protein environments of photosynthetic reaction centers [3]. Analyses provided detailed understanding of the influence of the protein-semiquinone interactions on the g-tensors. An application study with particularly far-reaching consequences dealt with EPR data of so-called reconstituted reaction centers of photosystem I (PS-I), in which smaller quinones had been introduced into the active site. We could show [4] that the g-tensor data in these systems may be rationalized by a reorientation of the semiquinone upon one-electron reduction. The system changes from the crystallographically confirmed Πi-stacking between the quinone and a nearby tryptophan residue to a T-stacking, that is a hydrogen bond of the N-H function of the tryptophan with the Π-system of the semiquinone. This has fundamental consequences for the mechanistic understanding of electron transfer in PS-I [4]. The novel Π-stacking to semiquinone invites furthermore to extensive considerations for other quinone/semiquinone redox pairs in biology. We have started to design intramolecular model systems that should allow a direct observation of the postulated reorientation upon reduction [5]. A recent application of semiquinone g-tensor (and hyperfine tensor) calculations has been to the elucidation of the hydrogen-bonding environment of the semiquinone in the QH binding site of quinole oxidase in the bacterial respiratory chain [6]. In contrast to previous suggestions, a two-sided hydrogen-bonding environment has been established for this site by comparison of computed and experimental EPR parameters [6]. Subsequent EPR-based claims that this radical is actually in a neutral, protonated state, do not agree with computed 13C hyperfine tensors [7]. While most of these calculations used static cluster calculations to model the system and its direct environment, more detailed studies of semiquinone EPR parameters have meanwhile been carried out, that included dynamical and solvent effects in aqueous solution by ab initio molecular dynamics simulations.

We have furthermore studied biologically relevant tyrosyl radicals [1,8]. Particular attention was given to the modified tyrosine identified in the active site of Galactose Oxidase [8]. We could show that the thiolate bridge close to the carbonyl oxygen atom makes a moderate but notable effect on spin-density distribution and g-tensor. This settles a literature controversy. Interesting results have also been obtained for glycyl radicals [9,10]. Based on a detailed study for N-acetyl-glycyl radical in a single-crystal environment, for which detailed structural data were available [9], DFT methodology has been calibrated in detail, and the inherent errors could be estimated. Subsequent application to glycyl radicals in protein environment allowed far-reaching insights [10]. In particular, we have suggested that the glycyl radicals in different protein sites may differ in their conformation [10]. Dynamical and environmental effects on the g-tensor have been studied for the radiation-induced glycyl radical in a glycine single crystal [11].

Further applications and collaborations with experimentalists include structure elucidation for radicals related to ribonucleotide reductase [12,13]. Our computer code has also been used by other authors to study nitroxide spin labels and chlorophyll radical cations. g-Tensor calculations of organic radicals are a relatively recent, exciting development, and we see considerable further potential for various applications on bioradicals. The current state of the field has been reviewed critically [14].

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References

[1] Density-Functional Calculations of Electronic g-Tensors Using Spin-Orbit Pseudopotentials and/or Mean-Field All-Electron Spin-Orbit Operators O. L. Malkina, J. Vaara, B. Schimmelpfennig, M. L. Munzarová, V. G. Malkin, M. Kaupp J. Am. Chem. Soc. 2000, 122, 9206-9218.
Calculation of Electronic g-Tensors for Transition Metal Complexes Using Hybrid Density Functionals and Atomic Meanfield Spin-Orbit Operators M. Kaupp, R. Reviakine, O. L. Malkina, A. Arbuznikov, B. Schimmelpfennig, V. G. Malkin J. Comput. Chem. 2002, 23, 794-803.

[2] Density Functional Calculations of Electronic g-Tensors for Semiquinone Radical Anions. The Role of Hydrogen Bonding and Substituent Effects M. Kaupp, C. Remenyi, J. Vaara, O. L. Malkina, V. G. Malkin J. Am. Chem. Soc. 2002, 124, 2709-2722.

[3] Electronic g-Tensors of Semiquinones in Photosynthetic Reaction Centers. A Density Functional Study S. Kacprzak, M. Kaupp J. Phys. Chem. B 2004, 108, 2464-2469.

[4] The Function of Photosystem I. Quantum Chemical Insight into the Role of Tryptophan-Quinone Interactions M. Kaupp Biochemistry 2002, 41, 2895-2900.


[5] Molecular Mechanical Devices Based on Quinone-Pyrrole and Quinone-Indole Dyads. A Computational Study S. Kacprzak, M. Kaupp J.Phys. Chem. B 2006, 110, 8158-8165.

[6] Protein-Cofactor Interactions and EPR Parameters for the QH Quinol Binding Site of Quinol Oxidase. A Density Functional Study S. Kacprzak, M. Kaupp, F. MacMillan J. Am. Chem. Soc. 2006, 128, 5659-5671.

[7] Elucidating mechanisms in haem copper oxidases: The high-affinity QH binding site in quinol oxidase as studied by DONUT-HYSCORE spectroscopy and DFT  F. MacMillan, S. Kacprzak, P. Hellwig, H. Michel, M. Kaupp J. Chem. Soc., Faraday Trans. 2010, 148, 315-344.

[8] g-Tensor and Spin Density of the Modified Tyrosyl Radical in Galactose Oxidase. A Density Functional StudyM. Kaupp, T. Gress, R. Reviakine, O. L. Malkina, V. G. Malkin J. Phys. Chem. B 2003, 107, 331-337.

[9] Understanding the EPR Parameters of Glycine-Derived Radicals. The Case of N-Acetylglycyl in the N-Acetylglycine Single-Crystal Environment S. Kacprzak, R. Reviakine, M. Kaupp J. Phys. Chem. B 2007, 111, 811-819.

[10] Understanding the EPR Parameters of Protein-Bound Glycyl Radicals S. Kacprzak, R. Reviakine, M. Kaupp J. Phys. Chem. B 2007, 111, 820-831.

[11] Cluster or periodic, static or dynamic – the challenge of calculating the g tensor of the solid-state glycine radical E. Pauwels, J. Asher, M. Kaupp, M. Waroquier Phys. Chem. Chem. Phys. 2011, 13, 18638-18646.

[12] Structure of the nitrogen-centered radical formed during inactivation of E. coli ribonucleotide reductase by 2'-azido-2'-deoxyuridine-5'-diphosphate: trapping of the 3'-ketonucleotide J. Fritscher, J. Antonic, S. Wnuk, G. Bar, J. H. Robblee, S. Kacprzak, M. Kaupp, R. G. Griffin, M. Bennati, J. Stubbe J. Am. Chem. Soc. 2005, 127, 7729-7738.

[13] Structure of the nucleotide radical formed during reaction of CDP/TTP with the E441Q-α2β2 of E. coli ribonucleotide reductase H. Zipse, E. Artin, S. Wnuk, G. J. S. Lohman, D. Martino, R. G. Griffin, S. Kacprzak, M. Kaupp, B. Hoffman, M. Bennati, J. Stubbe, N. Lees J. Am. Chem. Soc. 2009, 131, 200-211.

[14] Ab initio and Density Functional Calculations of Electronic g-Tensors for Organic Radicals M. Kaupp in: EPR Spectroscopy of Free Radicals in Solids. Trends in Methods and Applications (Eds. A. Lund, M. Shiotani) Kluwer, Dordrecht, 2003 (1st edition), 2012 (2nd edition).

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Chair

Prof. Dr. M. Kaupp
Theoretical Chemistry
Quantum Chemistry
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