Timothy Lovell

Density functional methods applied to metalloenzymes

Abstract Density functional calculations for structures, spin states, redox energetics and reaction pathways are presented for some selected metalloenzymes. The specific enzymes examined are: (1) Fe and Mn superoxide dismutase for redox energetics and the role of second shell residues; (2) galactose oxidase (Cu enzyme) and (3) glyoxalase I (Zn enzyme) for reaction pathways, mechanisms, intermediates, and transition states (reaction barriers); (4) iron-oxo dimer enzymes methane monooxygenase and ribonucleotide reductase for characterizing the oxidized and reduced forms in terms of structures and protonation states, and for a proposed structure for the high-valent intermediate Q in MMO. The interaction of the active site with the surrounding protein environment is also explored in a number of cases either by using expanded quantum mechanically treated clusters, or by using electrostatic/dielectric representations of the protein–solvent environment.

Density functional studies of the ground- and excited-state potential-energy curves of stilbene cis - trans isomerization

Using spin-unrestricted density functional theory (the VWN Becke-Perdew potential), including broken-symmetry and spin-projection methods, we have obtained the potential-energy curves as a function of the central torsional angle of stilbene in the ground (S0), the first excited triplet (T1), the first excited singlet (S1), and the doubly excited singlet (S2) states. The thermal trans-->cis isomerization of stilbene passes through a diradical broken-symmetry electronic structure around the twisted conformation (90 degrees central torsional angle) in the ground state. Our calculations support the proposed triplet mechanism for sensitized cis [symbol: see text] trans photoisomerization and the nonadiabatic singlet mechanism proposed by Orlandi and Siebrand. On the T1 potential-energy curve, the rotation of the C=C bond for both trans- and cis-stilbene will lead stilbene to the twisted conformation, from which the twisted stilbene will decay to the ground-state surface that is nearly isoenergetic with the T1 surface and has diradical electronic structure in the twisted region. On the S1 potential-energy curve, the energy increases in the direction from trans- to the twisted stilbene, and crosses with the neutral doubly excited S2 potential-energy curve, which has a minimum at the twisted structure and is lower in energy than the zwitterionic doubly excited state. The twisted stilbene around the energy minimum of the neutral doubly excited S2-state will decay onto the ground-state surface from where the rotation of the C=C bond leads the twisted stilbene to either the trans or cis configuration and the isomerization of stilbene is then completed. Similar studies have also been performed on a stilbene derivative with a substituent group, NHCOCH3.

Dft calculations of 57Fe mössbauer isomer shifts and quadrupole splittings for iron complexes in polar dielectric media : Applications to methane monooxygenase and ribonucleotide reductase

To predict the isomer shifts of Fe complexes in different oxidation and spin states more accurately, we have performed linear regression between the measured isomer shifts (δexp) and DFT (PW91 potential with all‐electron triple‐ζ plus polarization basis sets) calculated electron densities at Fe nuclei [ρ(0)] for the Fe2+,2.5+ and Fe2.5+,3+,3.5+,4+ complexes separately. The geometries and electronic structures of all complexes in the training sets are optimized within the conductor like screening (COSMO) solvation model. Based on the linear correlation equation δexp = α[ρ(0) − 11884.0] + C, the best fitting for 17 Fe2+,2.5+ complexes (totally 31 Fe sites) yields α = −0.405 ± 0.042 and C = 0.735 ± 0.047 mm s−1. The correlation coefficient is r = −0.876 with a standard deviation of SD = 0.075 mm s−1. In contrast, the linear fitting for 19 Fe2.5+,3+,3.5+,4+ complexes (totally 30 Fe sites) yields α = −0.393 ± 0.030 and C = 0.435 ± 0.014 mm s−1, with the correlation coefficient r = −0.929 and a standard deviation SD = 0.077 mm s−1. We provide a physical rationale for separating the Fe2+,2.5+ fit from the Fe2.5+,3+,3.5+,4+ fit, which also is clearly justified on a statistical empirical basis. Quadrupole splittings have also been calculated for these systems. The correlation between the calculated (ΔEQ(cal)) and experimental (ΔEQ(exp)) quadrupole splittings based on |ΔEQ(exp)| = A |ΔEQ(cal)| + B yields slope A, which is almost the ideal value 1.0 (A = 1.002 ± 0.030) and intercept B almost zero (B = 0.033 ± 0.068 mm s−1). Further calculations on the reduced diferrous and oxidized diferric active sites of class‐I ribonucleotide reductase (RNR) and the hydroxylase component of methane monooxygenase (MMOH), and on a mixed‐valent [(tpb)Fe3+(μ‐O)(μ‐CH3CO2)Fe4+(Me3[9]aneN3)]2+ (S = 3/2) complex and its corresponding diferric state have been performed. Calculated results are in very good agreement with the experimental data.

FeMo cofactor of nitrogenase: energetics and local interactions in the protein environment.

Abstract. A combined broken-symmetry density functional and continuum electrostatics approach has been applied to the iron-molybdenum center (FeMoco) of nitrogenase to evaluate the energetic effects of the local amino acid environment for several spin alignments of FeMoco. The protein environment preferentially stabilizes certain spin coupling patterns. The lowest energy spin alignment pattern in the protein displays calculated properties that match the experimental data better than any of the alternative possibilities. The total interaction energy of the protein with FeMoco has been evaluated and the contribution of each amino acid residue has been broken down into sidechain and backbone components. Arginine, lysine, aspartate and glutamate sidechains exert the largest electrostatic influence on FeMoco; specific residues are highlighted and their interaction with FeMoco discussed in the context of the available X-ray data from Azotobactervinelandii (Av). Observed data for the MN(resting state)→MOX(one-electron oxidized state) and MN→MR(one-electron reduced state) or MI(alternative one-electron reduced state) redox couples are compared with those calculated for Av. The calculated redox potentials are fairly insensitive to the spin state of the oxidized or reduced states and the predicted qualitative trend of a more negative redox potential for the more reduced MN→MR or MI couple is in accord with the available redox data. These calculations represent a first step towards the development of a microscopic model of electron and proton transfer events at the nitrogenase active site.

Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase; comparisons with methane monooxygenase.

Abstract. A combined broken symmetry density functional and electrostatics approach has been used to examine the active sites of the resting (RNRox) and reduced (RNRred) forms of class I type ribonucleotide reductase in the protein and solvent environment. Active site cluster geometries and Heisenberg J values are discussed in the context of the available protein data. The total electrostatic interaction energy in the protein comprises a large reaction field component and a much smaller protein field term, the former suggesting strong dielectric polarization between the cluster and protein-solvent dielectrics; the latter is indicative of a very weak link to the protein environment. Decomposition of the protein field term elucidates the major electrostatic interactions between amino acid residues in the RNR R2 local environment and the active site cluster, enabling an energetic comparison of structurally equivalent residues with a related diiron protein, methane monooxygenase.