Eric A. C. Bushnell

Insights into the catalytic mechanism of coral allene oxide synthase: a dispersion corrected density functional theory study.

In this present work the mechanism by which cAOS catalyzes the formation of allene oxide from its hydroperoxy substrate was computationally investigated by using a DFT-chemical cluster approach. In particular, the effects of dispersion interactions and DFT functional choice (M06, B3LYP, B3LYP*, and BP86), as well as the roles of multistate reactivity and the tyrosyl proximal ligand, were examined. It is observed that the computed relative free energies of stationary points along the overall pathway are sensitive to the choice of DFT functional, while the mechanism obtained is generally not. Large reductions in relative free energies for stationary points along the pathway (compared to the initial reactant complex) of on average 46.3 and 97.3 kJ mol(-1) for the doublet and quartet states, respectively, are observed upon going from the M06 to BP86 functional. From results obtained by using the B3LYP* method, well-tested previously on heme-containing systems, the mechanism of cAOS appears to occur with considerably higher Gibbs free energies than that for the analogous pathway in pAOS, possibly due to the presence of a ligating tyrosyl residue in cAOS. Furthermore, at the IEFPCM-B3LYP*/6-311+G(2df,p)//B3LYP/BS1 level of theory the inclusion of dispersion effects leads to the suggestion that the overall mechanism of cAOS could occur without the need for spin inversion.

Assessment of several DFT functionals in calculation of the reduction potentials for Ni-, Pd-, and Pt-bis-ethylene-1,2-dithiolene and -diselenolene complexes.

We performed an assessment of 10 common DFT functionals to determine their suitability for calculating the reduction potentials of the ([M(S2C2H2)2](0)/[M(S2C2H2)2](1-)), ([M(Se2C2H2)2](0)/[M(Se2C2H2)2](1-)), ([M(S2C2H2)2](1-)/[M(S2C2H2)2](2-)), and ([M(Se2C2H2)2](1-)/[M(Se2C2H2)2](2-)) redox couples (M = Ni, Pd, and Pt). Overall it was found that the M06 functional leads to the best agreement with the gold standard CCSD(T) method with an average difference of only +0.07 V and a RMS of 0.07 V in calculated reduction potentials. The variability in calculated reduction potentials between the various DFT functionals arise, in part, from the multireference character of these systems, which was determined by the T1 diagnostic values. Thus, the bisdiselenolene complexes show similar multireference character as the bisdithiolene complexes, which were previously shown to have such character. In particular, for the Ni-, Pd-, and Pt-bisdiselenolene complexes the average T1 values are 0.05, 0.03, and 0.02, respectively. For the CCSD(T) calculations the similarities in the reduction potentials between analogous bisdithiolene and bisdiselenolene redox couples, which appear to be independent of the metal, is a result of the noninnocence of the dithiolene and diselenolene ligands. Thus, the reduction potential is more dependent on the ligand than the metal.

The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen‐III decarboxylase

In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen‐III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen‐III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate‐limiting step was found to be the initial proton transfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various active site residues as well as several other functional groups.

Model Iron–Oxo Species and the Oxidation of Imidazole: Insights into the Mechanism of OvoA and EgtB?

A density functional theory cluster and first-principles quantum and statistical mechanics approach have been used to investigate the ability of iron-oxygen intermediates to oxidize a histidine cosubstrate, which may then allow for the possible formation of 2- and 5-histidylcysteine sulfoxide, respectively. Namely, the ability of ferric superoxo (Fe(III)O(2)(•-)), Fe(IV)═O, and ferrous peroxysulfur (Fe(III)OOS) complexes to oxidize the imidazole of histidine via an electron transfer (ET) or a proton-coupled electron transfer (PCET) was considered. While the high-valent mononuclear Fe(IV)═O species is generally considered the ultimate biooxidant, the free energies for its reduction (via ET or PCET) suggest that it is unable to directly oxidize histidines imidazole. Instead, only the ferrous peroxysulfur complexes are sufficiently powerful enough oxidants to generate a histidyl-derived radical via a PCET process. Furthermore, while this process preferably forms a HisN(δ)(-H)(•) radical, several such oxidants are also suggested to be capable of generating the higher-energy HisC(δ)(-H)(•) and HisC(ε)(-H)(•) radicals. Importantly, the present results suggest that formation of the sulfoxide-containing products (seen in both OvoA and EgtB) is a consequence of the reduction of a powerful Fe(III)OOS oxidant via a PCET.

A molecular dynamics examination on mutation-induced catalase activity in coral allene oxide synthase.

Coral allene oxide synthase (cAOS) catalyzes the formation of allene oxides from fatty acid hydroperoxides. Interestingly, its active site differs from that of catalase by only a single residue yet is incapable of catalase activity. That is, it is unable to catalyze the decomposition of hydrogen peroxide to molecular oxygen and water. However, the single active-site mutation T66V allows cAOS to exhibit catalase activity. We have performed a series of molecular dynamics (MD) simulations in order to gain insights into the differences in substrate (8R-hydroperoxyeicosatetraenoic) and H2O2 active site binding between wild-type cAOS and the T66V mutant cAOS. It is observed that in wild-type cAOS the active site Thr66 residue consistently forms a strong hydrogen-bonding interaction with H2O2 (catalase substrate) and, importantly, with the aid of His67 helps to pull H2O2 away from the heme Fe center. In contrast, in the T66V-cAOS mutant the H2O2 is much closer to the hemes Fe center and now forms a consistent Fe···O2H2 interaction. In addition, the His67···H2O2 distance shortens considerably, increasing the likelihood of a Cpd I intermediate and hence exhibiting catalase activity.

A Density Functional Theory Investigation into the Binding of the Antioxidants Ergothioneine and Ovothiol to Copper.

The ability of hybrid, nonhybrid and meta-GGA density functional theory (DFT) based methods (B3LYP, BP86, M06 and M06L) to provide reliable structures and thermochemical properties of biochemically important Cu(I)/(II)···ESH (ergothioneine) and ···OSH (ovothiol) has been assessed. For all functionals considered, convergence in the optimized structures and Cu(I)/(II)···S/N bond lengths is only obtained using the 6-311+G(2df,p) basis set or larger, with the nonhybrid DFT method BP86 appearing, in general, to provide the most reliable structures. The reduction potentials associated with the reduction of Cu(II) to Cu(I) when complexed with either OSH and ESH were also determined. The implications for their ability to thus help protect against Cu-mediated oxidative damage are discussed. Importantly, the binding of OSH and ESH with Cu ions disfavors Cu(I)/Cu(II) recycling by increasing the reduction potential for the Cu(II) to Cu(I) reduction and as a result, inhibits the potential oxidative damage caused by such Cu ions.

Computational Insights into the Mechanism of Porphobilinogen Synthase

Porphobilinogen synthase (PBGS) is a key enzyme in heme biosynthesis that catalyzes the formation of porphobilinogen (PBG) from two 5-aminolevulinic acid (5-ALA) molecules via formation of intersubstrate C-N and C-C bonds. The active site consists of several invariant residues, including two lysyl residues (Lys210 and Lys263; yeast numbering) that bind the two substrate moieties as Schiff bases. Based on experimental studies, various reaction mechanisms have been proposed for this enzyme that generally can be classified according to whether the intersubstrate C-C or C-N bond is formed first. However, the detailed catalytic mechanism of PBGS remains unclear. In the present study, we have employed density functional theory methods in combination with chemical models of the two key lysyl residues and two substrate moieties in order to investigate various proposed reaction steps and gain insight into the mechanism of PBGS. Importantly, it is found that mechanisms in which the intersubstrate C-N bond is formed first have a rate-limiting barrier (17.5 kcal/mol) that is lower than those in which the intersubstrate C-C bond is formed first (22.8 kcal/mol).

Gaining insight into the chemistry of lipoxygenases: a computational investigation into the catalytic mechanism of (8R)-lipoxygenase

Lipoxygenases (LOXs) are ubiquitous in nature and catalyze a range of life-essential reactions within organisms. In particular they are critical to the formation of eicosanoids, which are critical for normal cell function. However, a number of important questions about the reactivity and mechanism of these enzymes still remain. Specifically, although the initial step in the mechanism of LOXs has been well studied, little is known of subsequent steps. Thus, with use of a quantum mechanical/molecular mechanical approach, the complete catalytic mechanism of (8R)-LOX was investigated. The results have provided a better understanding of the general chemistry of LOXs as a whole. In particular, from comparisons with soybean LOX-1, it appears that the initial proton-coupled electron transfer may be very similar among all LOXs. Furthermore, LOXs appear to undergo multistate reactivity where potential spin inversion of an electron may occur either in the attack of O2 or in the regeneration of the active site. Lastly, it is shown that with the explicit modeling of the environment, the regeneration of the active center likely occurs via the rotation of the intermediate followed by an outer-sphere

The one-electron oxidation of a dithiolate molecule: The importance of chemical intuition

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