Sebastian Sinnecker

QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study.

A detailed study of the influence of the surrounding protein on magnetic and optical spectra of metalloproteins is presented using the quantum‐mechanical/molecular mechanical (QM/MM) approach. The well‐studied type I copper site in plastocyanin in the cupric oxidation state is taken as a test case because its spectroscopic properties have been extensively studied and are well understood. The calculations have been performed using nonrelativistic and scalar relativistic (at the level of the zeroth order regular approximation, ZORA) calculations (B3LYP functional). Linear response theory has been used to calculate first‐ and second‐order properties, namely the EPR g‐tensor, the central metal hyperfine couplings (HFCs), the HFCs of the directly coordinating ligands, as well as superhyperfine couplings (1H, 14N) from remote nuclei, transition energies, and oscillator strengths. Two different model systems have been defined that do not and do include important amino acids from the second coordination sphere, respectively. For comparison, calculations have been carried out in the gas phase and in a dielectric continuum (conductor like screening model, COSMO) with a dielectric constant of four. The best results were obtained at the scalar relativistic ZORA level for the largest model in conjunction with explicit modeling of the protein environment through the QM/MM procedure, which is also considered to be the highest level of theory used in this work. The protein effects beyond the second coordination sphere were found to be quite substantial (up to 30% changes on some properties), and were found to require an explicit treatment of the protein beyond the second coordination sphere. In addition, the embedding water cage was found to have a nonnegligible influence on the calculated spectroscopic data, which is of the same order as the influence of the protein backbone charges. However, while qualitatively satisfactory, the errors in the calculated spectroscopic parameters are still substantial, and can all be traced back to the fact that the linear‐response of the presently available functionals is “too stiff” with respect to the external perturbations at least for the model systems studied here. Ligand field‐based approaches are used to correct for systematic errors in the DFT procedures. As a consequence, we propose a new breakdown of the copper hyperfine interaction into Fermi‐contact, spin‐dipolar and spin‐orbit contributions.

Dimanganese catalase—spectroscopic parameters from broken-symmetry density functional theory of the superoxidized Mn III /Mn IV state

Broken-symmetry density functional theory was used to study the catalytic center of manganese catalase in the superoxidized MnIII/MnIV state. Heisenberg exchange coupling constants, 55Mn and 14N hyperfine coupling constants (hfcs) and nuclear quadrupole splittings, as well as the electronic g tensors were evaluated for different model systems of the active site after complete geometry optimizations in the high-spin and broken-symmetry states. A comparison of the experimental data with the spectroscopic parameters computed for the models with unprotonated and protonatedxa0μ-oxo bridges shows best agreement between theory and experiment for a Mn2(μ-O)2(μ-OAc) core. The calculated Mn–Mn distances and 55Mn hfcs clearly support a dimanganese cluster with unprotonatedxa0μ-oxo bridges in the superoxidized state. Furthermore, it is shown that an interchange of the MnIII and MnIV oxidation states in this trapped valence system leads to specific changes in the molecular and electronic structure of the manganese clusters.

Protein–cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: Effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study

The effect of hydrogen bonding to the primary quinone (Q(A) and Q(*)(-)(A)) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q(A) was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N(delta)-H of His M219 forms a shorter H-bond to Q(A) than the N-H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q(*)(-)(A) in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q(*)(-)(A) are reliable values. From a comparison of the neutral and reduced state of Q(A) it was concluded that the H-bond distances are shortened by approximately 0.17 Angstroms (His M219) and approximately 0.13 Angstroms (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of (2)H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.

Electronic Structure of the Quinone Radical Anion A1˙― of Photosystem I Investigated by Advanced Pulse EPR and ENDOR Techniques

Vitamin K1 (VK1) is an important cofactor of the electron-transfer chain in photosystem I (PS I), referred to as A1. The special properties of this quinone result from its unique interaction(s) with the protein surrounding. In particular, a single H-bond to neutral A1 was identified previously in the X-ray crystal structure of PS I. During light-induced electron transfer in PS I, A1 is transiently reduced to the radical anion A1*-. In this work, we characterized the electron spin density distribution of A1*- with the aim of understanding the influence of the protein surrounding on it. We studied the light-induced spin-polarized radical pair P700*+A1*- and the photoaccumulated radical anion A1*-, using advanced pulse EPR, ENDOR, and TRIPLE techniques at Q-band (34 GHz). Exchange with fully deuterated quinone in the A1 binding site allowed differentiation between proton hyperfine couplings from the quinone and from the protein surrounding. In addition, DFT calculations on a model of the A1 site were performed and provided proton hyperfine couplings that were in close agreement with the ones determined experimentally. This combined approach allowed the assignment of proton hyperfine coupling tensors to molecular positions, thereby yielding a picture of the spin density distribution in A1*-. Comparison with VK1*- in organic solvents (Epel et al. J. Phys. Chem. B 2006, 110, 11549.) leads to the conclusion that the single H-bond present in both the radical pair P700*+A1*- and the photoaccumulated radical anion A1*- is, indeed, the crucial factor that governs the electronic structure of A1*-.

Probing the Electronic Structure of Bacteriochlorophyll Radical Ions – A Theoretical Study of the Effect of Substituents on Hyperfine Parameters

In reaction centers (RCs) of photosynthesis, a light‐induced charge separation takes place creating radical cations and anions of the participating cofactors. In photosynthetic bacteria, different bacteriochlorophylls (BChl) are involved in this process. Information about the electronic structure of the BChl radical cations and anions can be obtained by measuring the electron spin density distribution via the electron–nuclear hyperfine interaction using EPR and ENDOR techniques. In this communication, we report isotropic hyperfine coupling constants (hfcs) of the BChl b and g radical cations and anions, calculated by density functional theory, and compare them with the more common radical ions of BChl a and with available experimental data. The observed differences in the computed hyperfine data are discussed in view of a possible distinction between these species by EPR/ENDOR methods. In addition, 14N nuclear quadrupole coupling constants (nqcs) computed for BChl a, b, g, and also for Chl a in their charge neutral, radical cation and radical anion states are presented. These nqcs are compared with experimental values obtained by ESEEM spectroscopy on several different radical ions.