Patrick J. O'Malley

Density functional studies of free radicals: accurate geometry and hyperfine coupling prediction for semiquinone anions

Abstract Density functional calculations utilising the B3LYP functional are used to calculate geometries together with 1 H, 13 C and 17 O isotropic coupling constants for p-benzosemiquinone, durosemiquinone and plastosemiquinone anion radicals. Comparison of results obtained with experimental determinations indicates excellent agreement between theory and experiment.

Mechanistic aspects of hydrogen abstraction for phenolic antioxidants. Electronic structure and topological electron density analysis

Density functional calculations using the B3LYP functional are used to provide insight into the hydrogen abstraction mechanism of phenolic antioxidants. The energy profiles for 13 ortho, meta, para and di-methyl substituted phenols with hydroperoxyl radical have been determined. An excellent correlation between the enthalpy (DeltaH) and activation energy (DeltaEa) was found, obeying the Evans-Polanyi rule. The effects of hydrogen bonding on DeltaEa are also discussed. Electron donating groups at the ortho and para positions are able to lower the activation energy for hydrogen abstraction. The highly electron withdrawing fluoro substituent increases the activation energies relative to phenol at the meta position but not at the para position. The electron density is studied using the atoms in molecules (AIM) approach. Atomic and bond properties are extracted to describe the hydrogen atom abstraction mechanism. It is found that on going from reactants to transition state, the hydrogen atom experiences a loss in volume, electronic population and dipole moment. These features suggest that the phenol hydroperoxyl reactions proceed according to a proton coupled electron transfer (PCET) as opposed to a hydrogen atom transfer (HAT) mechanism.

Hydrogen bonding and spin density distribution in the QB semiquinone of bacterial reaction centers and comparison with the QA site

In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q(B) function and comparisons with the Q(A) site are discussed.

The mechanism of alkane activation over zeolite Brønsted acid sites. A density-functional study

Abstract Semi-empirical and density-functional molecular orbital methods are used to investigate the mechanism of monomolecular cracking of n -butane over Bronsted acid sites. Both techniques show the reaction proceeds via protolytic attack at the centre of CC bonds and not at the carbon atoms themselves, as has been previously suggested. The carbonium ion is also shown to collapse to an alkane/alkene and not an alkane/alkoxide as has been recently proposed.

Density functional studies of the carbonium ion species CH+5, C2H+7 and C3H+9

Abstract The carbonium ion structures Ch+5, C2H+7 and C3H+9 were investigated using Hartree—Fock, post Hartree—Fock (MP2) and density functional methods (DFT). Reaction energetics calculated by DFT methods show good agreement with experimental data and are comparable with correlated levels of HF theory. The more economical nature of DFT calculations should permit the study of larger systems such as those encountered in the initial stages of petroleum cracking.

A density functional study of the effect of reduction on the geometry and electron affinity of hydrogen bonded 1,4-benzoquinone. Implications for quinone reduction and protonation in photosynthetic reaction centres

Abstract Hybrid density functional studies using the B3LYP functional show that the two electron reduction of 1,4-benzoquinone (BQ) to the dianion (BQ2−) via the semiquinone radical anion (BQ−) form is accompanied by a gradual change in the internal geometry of the quinone from quinonoid to benzenoid form. The hydrogen bonds formed to neighbouring proton donors are progressively shortened. These changes contribute to the ultimate transfer of the hydrogen bonded protons from the hydrogen bonded proton donors leading to the formation of the quinol form. The reduced forms are progressively stabilised relative to the oxidised from with increasing hydrogen bonding interactions. Similar changes can be expected to play a crucial role in the reduction and protonation of the Qb site of photosynthetic reaction centres in bacteria and higher plants.

Density functional calculated 13C and 17O hyperfine couplings for the ubisemiquinone anion radical in an alcohol solvent model and in a model of the Qa binding site of Rb sphaeroides

Abstract Hybrid density functional calculations are used to calculate the spin density distribution and the 17 O and 13 C hyperfine coupling constants for the ubisemiquinone anion radical in model complexes simulating the radicals environment in alcohol solvents and in the Q a binding site of Rb sphaeroides . Good agreement is observed between the alcohol solvent model calculated couplings and experimental determinations. For the Q a site model, best agreement is observed for a Q a site model containing a positively charged imidazole hydrogen bonding interaction at the O4 atom of the semiquinone. This may suggest that the asymmetry observed for the Q a site of Rb sphaeroides is due to strong hydrogen bonding by the O4 oxygen atom of the semiquinone to an imidazole carrying a partial positive charge. The obvious candidate to fulfil this role in the reaction centre is the HIS M219 ligand of an Fe(II) complex.

1H, 13C and 17O principal hyperfine tensor determination for the p-benzosemiquinone anion radical using hybrid density functional methods

Abstract The 1 H, 13 C and 17 O hyperfine coupling tensors for the p-benzosemiquinone anion radical have been directly calculated using hybrid density functional methods. Excellent agreement between experimentally determined tensor values and theoretically calculated ones are reported. Proton tensors for solvent hydrogen bonding interactions with an alcohol solvent are also well reproduced.

A density functional study of the effect of orientation of hydrogen bond donation on the hyperfine couplings of benzosemiquinones: relevance to semiquinone–protein hydrogen bonding interactions in vivo

Abstract The B3LYP hybrid density functional method has been used to investigate the effect of hydrogen bond orientation on spin densities and hyperfine couplings for the p -benzosemiquinone anion radical. Out-of-plane hydrogen bonding leads to a redistribution of spin density from the semiquinone carbonyl oxygen atom on to the oxygen atom of the hydrogen bonding water molecule. This leads principally to a significant anisotropic 17 O hyperfine coupling for the water oxygen and a negative isotropic hyperfine coupling for the 1 H hydrogen bond donor atom. The implications of these findings for the interpretation of EPR and ENDOR spectra of in vivo semiquinones are discussed.

Interactions of intermediate semiquinone with surrounding protein residues at the QH site of wild-type and D75H mutant cytochrome bo 3 from Escherichia coli

Selective (15)N isotope labeling of the cytochrome bo(3) ubiquinol oxidase from Escherichia coli with auxotrophs was used to characterize the hyperfine couplings with the side-chain nitrogens from residues R71, H98, and Q101 and peptide nitrogens from residues R71 and H98 around the semiquinone (SQ) at the high-affinity Q(H) site. The two-dimensional ESEEM (HYSCORE) data have directly identified N(ε) of R71 as an H-bond donor carrying the largest amount of unpaired spin density. In addition, weaker hyperfine couplings with the side-chain nitrogens from all residues around the SQ were determined. These hyperfine couplings reflect a distribution of the unpaired spin density over the protein in the SQ state of the Q(H) site and the strength of interaction with different residues. The approach was extended to the virtually inactive D75H mutant, where the intermediate SQ is also stabilized. We found that N(ε) of a histidine residue, presumably H75, carries most of the unpaired spin density instead of N(ε) of R71, as in wild-type bo(3). However, the detailed characterization of the weakly coupled (15)N atoms from selective labeling of R71 and Q101 in D75H was precluded by overlap of the (15)N lines with the much stronger ~1.6 MHz line from the quadrupole triplet of the strongly coupled (14)N(ε) atom of H75. Therefore, a reverse labeling approach, in which the enzyme was uniformly labeled except for selected amino acid types, was applied to probe the contribution of R71 and Q101 to the (15)N signals. Such labeling has shown only weak coupling with all nitrogens of R71 and Q101. We utilize density functional theory-based calculations to model the available information about (1)H, (15)N, and (13)C hyperfine couplings for the Q(H) site and to describe the protein-substrate interactions in both enzymes. In particular, we identify the factors responsible for the asymmetric distribution of the unpaired spin density and ponder the significance of this asymmetry to the quinones electron transfer function.