A proton-shuttle mechanism mediated by the porphyrin in benzene hydroxylation by cytochrome p450 enzymes

Benzene hydroxylation is a fundamental process in chemical catalysis. In nature, this reaction is catalyzed by the enzyme cytochrome P450 via oxygen transfer in a still debated mechanism of considerable complexity. The paper uses hybrid density functional calculations to elucidate the mechanisms by which benzene is converted to phenol, benzene oxide, and ketone, by the active species of the enzyme, the high-valent iron-oxo porphyrin species. The effects of the protein polarity and hydrogen-bonding donation to the active species are mimicked, as before (Ogliaro, F.; Cohen, S.; de Visser, S. P.; Shaik, S. J. Am. Chem. Soc. 2000, 122, 12892-12893). It is verified that the reaction does not proceed either by hydrogen abstraction or by initial electron transfer (Ortiz de Montellano, P. R. In Cytochrome P450: Structure, Mechanism and Biochemistry, 2nd ed.; Ortiz de Montellano, P. R., Ed.; Plenum Press: New York, 1995; Chapter 8, pp 245-303). In accord with the latest experimental conclusions, the theoretical calculations show that the reactivity is an interplay of electrophilic and radicalar pathways, which involve an initial attack on the pi-system of the benzene to produce sigma-complexes (Korzekwa, K. R.; Swinney, D. C.; Trager, W. T. Biochemistry 1989, 28, 9019-9027). The dominant reaction channel is electrophilic and proceeds via the cationic sigma-complex,( 2)3, that involves an internal ion pair made from a cationic benzene moiety and an anionic iron porphyrin. The minor channel proceeds by intermediacy of the radical sigma-complex, (2)2, in which the benzene moiety is radicalar and the iron-porphyrin moiety is neutral. Ring closure in these intermediates produces the benzene oxide product ((2)4), which does not rearrange to phenol ((2)7) or cyclohexenone ((2)6). While such a rearrangement can occur post-enzymatically under physiological conditions by acid catalysis, the computations reveal a novel mechanism whereby the active species of the enzyme catalyzes directly the production of phenol and cyclohexenone. This enzymatic mechanism involves proton shuttles mediated by the porphyrin ring through the N-protonated intermediate, (2)5, which relays the proton either to the oxygen atom to form phenol ((2)7) or to the ortho-carbon atom to produce cyclohexenone product ((2)6). The formation of the phenol via this proton-shuttle mechanism will be competitive with the nonenzymatic conversion of benzene oxide to phenol by external acid catalysis. With the assumption that (2)5 is not fully thermalized, this novel mechanism would account also for the observation that there is a partial skeletal retention of the original hydrogen of the activated C-H bond, due to migration of the hydrogen from the site of hydroxylation to the adjacent carbon (so-called "NIH shift" (Jerina, D. M.; Daly, J. W. Science 1974, 185, 573-582)). Thus, in general, the computationally discovered mechanism of a porphyrin proton shuttle suggests thatthere is an enzymatic pathway that converts benzene directly to a phenol and ketone, in addition to nonenzymatic production of these species by conversion of arene oxide to phenol and ketone. The potential generality of protonated porphyrin intermediates in P450 chemistry is discussed in the light of the H/D exchange observed during some olefin epoxidation reactions (Groves, J. T.; Avaria-Neisser, G. E.; Fish, K. M.; Imachi, M.; Kuczkowski, R. J. Am. Chem. Soc. 1986, 108, 3837-3838) and the general observation of heme alkylation products (Kunze, K. L.; Mangold, B. L. K.; Wheeler, C.; Beilan, H. S.; Ortiz de Montellano, P. R. J. Biol. Chem. 1983, 258, 4202-4207). The competition, similarities, and differences between benzene oxidation viz. olefin epoxidation and alkanyl C-H hydroxylation are discussed, and comparison is made with relevant experimental and computational data. The dominance of low-spin reactivity in benzene hydroxylation viz. two-state reactivity (Shaik, S.; de Visser, S. P.; Ogliaro, F.; Schwarz, H.; Schr?der, D. Curr. Opin. Chem. Biol. 2002, 6, 556-567) in olefin epoxidation and alkane hydroxylation is traced to the loss of benzene resonance energy during the bond activation step.     

Active anionic zero-valent palladium catalysts: characterization by density functional calculations

This works uses DFT (B3LYP/LACVP*(+)//B3LYP/LACVP* level) to ascertain the existence of the tricoordinate, anionic zero-valent palladium complexes that were postulated as the active species in the catalytic cycles of Pd-catalyzed Heck and cross-coupling reactions. The variety of complexes studied (1 and 2), include [Pd(PR(3))(2)X](-) species, in which R=H, Me, vinyl, and phenyl, and X=Cl, Br, I, AcO, and TFA, as well as bidentate complexes, [Pd[Ph(2)P(CH(2))(n)Ph(2)P]X](-), in which X=Cl, AcO and n=3-6. The study shows that these complexes exist as distinct minima in the gas phase as well as in THF. In addition, it provides geometric features and Pd--X(-) dissociation energies for all these complexes as well as some NMR and IR data, which show a clear distinction in these features between the tri- and dicoordinate Pd(0) species. An orbital interaction model and perturbation theory arguments account for the bonding mechanism and rationalize all the trends in the stability of the Pd--X bond. These trends include the effects of variation of X, R, and the length of the linker in the bidentate ligands.     

Control of carbon nanotube-surface interactions: the role of grafted polymers

We have investigated the interactions between single-walled carbon nanotubes, coated with polymer chains end-grafted to the tubes, and planar surfaces. By proper functionalization of the grafted polymers' free ends, we show how to obtain an attractive interaction that can be used to immobilize the tube at a desired distance from the surface. We demonstrate how the strength and distance of the minimal interaction can be controlled by the proper choice of polymer chain length, surface coverage, and type of functional end-group.     

Relaxation dynamics in glycerol-water mixtures. 2. Mesoscopic feature in water rich mixtures

The relaxation dynamics of water-rich glycerol-water mixtures is studied by broadband dielectric spectroscopy (BDS) at 173-323 K and differential scanning calorimetry (DSC) at 138-313 K. These data indicate the existence of the critical concentration of 40 mol % glycerol. In the studied temperature range for water-rich glycerol mixtures, the two states of water (ice and interfacial water) are observed in addition to water in the mesoscopic 40 mol % glycerol-water domains. The possible kinetics of water exchange between different water states is discussed in order to explain the mechanism of the broad melting behavior observed by DSC.     

Theoretical investigation of C--H hydroxylation by (N4Py)Fe(IV)=O(2+): an oxidant more powerful than P450?

DFT calculations of C-H hydroxylation by a synthetic nonheme oxoiron(IV) oxidant supported by a neutral pentadentate N5 ligand show that this reagent is intrinsically more reactive than compound I of P450. This nonheme iron oxidant is predicted to exhibit stereoselective reactions, strong solvent effect, and involve multistate reactivity with spin-state crossing.     

Theory favors a stepwise mechanism of porphyrin degradation by a ferric hydroperoxide model of the active species of heme oxygenase

The report uses density functional theory to address the mechanism of heme degradation by the enzyme heme oxygenase (HO) using a model ferric hydroperoxide complex. HO is known to trap heme molecules and degrade them to maintain iron homeostasis in the biosystem. The degradation is initiated by complexation of the heme, then formation of the iron-hydroperoxo species, which subsequently oxidizes the meso position of the porphyrin by hydroxylation, thereby enabling eventually the cleavage of the porphyrin ring. Kinetic isotope effect studies indicate that the mechanism is assisted by general acid catalysis, via a chain of water molecules, and that all the events occur in concert. However, previous theoretical treatments indicated that the concerted mechanism has a high barrier, much higher than an alternative mechanism that is initiated by O-O bond homolysis of iron-hydroperoxide. The present contribution studies the stepwise and concerted acid-catalyzed mechanisms using H(3)O(+)(H(2)O)(n)(), n = 0-2. The effect of the acid strength is tested using the H(4)N(+)(H(2)O)(2) cluster and a fully protonated ferric hydroperoxide. All the calculations show that a stepwise mechanism that involves proton relay and O-O homolysis, in the rate-determining step, has a much lower barrier (>10 kcal/mol) than the corresponding fully concerted mechanism. The best fit of the calculated solvent kinetic isotope effect, to the experimental data, is obtained for the H(3)O(+)(H(2)O)(2) cluster. The calculated alpha-deuterium secondary kinetic isotope effect is inverse (0.95-0.98), but much less so than the experimental value (0.7). Possible reasons for this quantitative difference are discussed. Some probes are suggested that may enable experiment to distinguish the stepwise from the concerted mechanism.     

The Quadruple Bonding in C2 Reproduces the Properties of the Molecule

Ever since Lewis depicted the triple bond for acetylene, triple bonding has been considered as the highest limit of multiple bonding for main elements. Here we show that C₂ is bonded by a quadruple bond that can be distinctly characterized by valence‐bond (VB) calculations. We demonstrate that the quadruply‐bonded structure determines the key observables of the molecule, and accounts by itself for about 90 % of the molecule's bond dissociation energy, and for its bond lengths and its force constant. The quadruply‐bonded structure is made of two strong π bonds, one strong σ bond and a weaker fourth σ‐type bond, the bond strength of which is estimated as 17–21 kcal mol^?1. Alternative VB structures with double bonds; either two π bonds or one π bond and one σ bond lie at 129.5 and 106.1 kcal mol^?1, respectively, above the quadruply‐bonded structure, and they collapse to the latter structure given freedom to improve their double bonding by dative σ bonding. The usefulness of the quadruply‐bonded model is underscored by “predicting” the properties of the ³ state. C₂’s very high reactivity is rooted in its fourth weak bond. Thus, carbon and first‐row main elements are open to quadruple bonding!     

Quantitatively modeling the equilibrium properties of thiol-decorated gold nanoparticles

We employ a molecular mean-field theory to quantitatively understand the sizes, surfactant surface coverage, and size fluctuations of gold nanocrystals decorated with thiol surfactants of different chain lengths. Our model assumes that surfactant-coated nanoparticles are equilibrium structures. We find that packing constraints experienced by the surfactant tails are less significant for more curved (smaller) particles. This effect enables us to rationalize the experimental observations/deductions that the thiol coverage per unit area increases with decreasing particle size. The reduction of surface coverage with increasing size also explains the fact that size polydispersity increases with increasing nanoparticle size. We find that increasing the length of the surfactants results in larger nanoparticles.     

Transition from traveling to standing waves as a function of frequency in a reaction-diffusion system

The addition of polyethylene glycol to the Belousov-Zhabotinsky reaction increases the frequency of oscillations, which in an extended system causes a transition from traveling to standing waves. A further increase in frequency causes another transition to bulk oscillations. The standing waves are composed of two domains, which oscillate out of phase with a small delay between them, the delay being smaller as the frequency of oscillations is increased.     

Multistate reactivity in styrene epoxidation by compound I of cytochrome p450: mechanisms of products and side products formation

Density functional theoretical calculations are used to elucidate the epoxidation mechanism of styrene with a cytochrome P450 model Compound I, and the formation of side products. The reaction features multistate reactivity (MSR) with different spin states (doublet and quartet) and different electromeric situations having carbon radicals and cations, as well as iron(III) and iron(IV) oxidation states. The mechanisms involve state-specific product formation, as follows: a) The low-spin pathways lead to epoxide formation in effectively concerted mechanisms. b) The high-spin pathways have finite barriers for ring-closure and may have a sufficiently long lifetime to undergo rearrangement and lead to side products. c) The high-spin radical intermediate, (4)2(rad)-IV, has a ring closure barrier as small as the C--C rotation barrier. This intermediate will therefore lose stereochemistry and lead to a mixture of cis and trans epoxides. The barriers for the production of aldehyde and suicidal complexes are too high for this intermediate. d) The high-spin radical intermediate, (4)2(rad)-III, has a substantial ring closure barrier and may survive long enough time to lead to suicidal, phenacetaldehyde and 2-hydroxostyrene side products. e) The phenacetaldehyde and 2-hydroxostyrene products both originate from crossover from the (4)2(rad)-III radical intermediate to the cationic state, (4)2(cat,z(2) ). The process involves an N-protonated porphyrin intermediate that re-shuttles the proton back to the substrate to form either phenacetaldehyde or 2-hydroxostyrene products. This resembles the internally mediated NIH-shift observed during benzene hydroxylation.