Can a single oxidant with two spin states masquerade as two different oxidants? A study of the sulfoxidation mechanism by cytochrome p450

Density functional calculations were performed on the sulfoxidation reaction by a model compound I (Cpd I) of cytochrome P450. By contrast to previous alkane hydroxylation studies, which exhibit a dominant low-spin (LS) pathway, the sulfoxidation follows a dominant high-spin (HS) reaction. Thus, competing hydroxylation and sulfoxidation processes as observed for instance by Jones et al. (Volz, T. J.; Rock, D. A.; Jones, J. P. J. Am. Chem. Soc. 2002, 124, 9724) are the result of a two-state reactivity scenario, whereby the hydroxylation originates from the LS pathway and the sulfoxidation from the HS pathway. In this manner, two spin states of a single oxidant (Cpd I) can be disguised as two different oxidants. The calculations rule out the possibility that a second oxidant (the ferric peroxide, Cpd 0 species) interferes in the observed results of Jones et al.     

New features in the catalytic cycle of cytochrome P450 during the formation of compound I from compound 0

Density functional theory (DFT) is applied to the dark section of the catalytic cycle of the enzyme cytochrome P450, namely, the formation of the active species, Compound I (Cpd I), from the ferric-hydroperoxide species (Cpd 0) by a protonation-assisted mechanism. The chosen 96-atom model includes the key functionalities deduced from experiment: Asp(251), Thr(252), Glu(366), and the water channels that relay the protons. The DFT model calculations show that (a) Cpd I is not formed spontaneously from Cpd 0 by direct protonation, nor is the process very exothermic. The process is virtually thermoneutral and involves a significant barrier such that formation of Cpd I is not facile on this route. (b) Along the protonation pathway, there exists an intermediate, a protonated Cpd 0, which is a potent oxidant since it is a ferric complex of water oxide. Preliminary quantum mechanical/molecular mechanical calculations confirm that Cpd 0 and Cpd I are of similar energy for the chosen model and that protonated Cpd 0 may exist as an unstable intermediate. The paper also addresses the essential role of Thr(252) as a hydrogen-bond acceptor (in accord with mutation studies of the OH group to OMe).     

Relaxation dynamics in glycerol-water mixtures: I. Glycerol-rich mixtures

We discuss the relaxation dynamics of glycerol-water mixtures, as studied by dielectric spectroscopy in the frequency range from 1 Hz to 250 MHz and at temperatures between 173 and 323 K. The experimental results obtained for the glycerol-rich mixtures suggest that the main dielectric relaxation process, as well as the so-called high-frequency "excess wing" (EW) and dc conductivity, follow the same temperature dependence. This result indicates that all of these processes are induced by the same molecular origin. A new phenomenological function is proposed to describe the whole dielectric spectrum in the covered frequency range, and some possible mechanisms of dielectric behaviors through the dc conductivity, the main relaxation process, and the EW are discussed.     

The Menshutkin Reaction in the Gas Phase and in Aqueous Solution: A Valence Bond Study

The recently developed (L. Song, W. Wu, Q. Zhang, S. Shaik, J. Phys. Chem. A 2004 , 108, 6017–6024) valence bond method coupled to a polarized continuum model (VBPCM) is applied to the Menshutkin reaction, NH₃+CH₃Cl→CH₃NH₃⁺+Cl^?, in the gas phase and in aqueous solution. The computed barriers and reaction energies at the level of the breathing orbital VB method (P. C. Hiberty, J. P. Flament, E. Noizet, Chem. Phys. Lett. 1992 , 189, 259), BOVB and VBPCM//BOVB, are comparable to CCSD(T) and CCSD(T)//PCM results and to experimental values in solution. The gas‐phase reaction is endothermic and leads to an ion‐pair complex via a late transition state. By contrast, the reaction in the aqueous phase is exothermic and leads to separate solvated ions as reaction products, via an early transition state. The VB calculations provide also the reactivity parameters needed to apply the valence bond state correlation diagram method, VBSCD (S. Shaik, A. Shurki, Angew. Chem. Int. Ed. 1999 , 38, 586). It is shown that the reactivity parameters along with their semiempirical derivations provide together a satisfactory qualitative and quantitative account of the barriers.     

Dynamic mechanism of photochemical induction of turing superlattices in the chlorine dioxide-iodine-malonic acid reaction-diffusion system

We study the mechanism of development of superlattice Turing structures from photochemically generated hexagonal patterns of spots with wavelengths several times larger than the characteristic wavelength of the Turing patterns that spontaneously develop in the nonilluminated system. Comparison of the experiment with numerical simulations shows that interaction of the photochemical periodic forcing with the Turing instability results in generation of multiple resonant triplets of wave vectors, which are harmonics of the external forcing. Some of these harmonics are situated within the Turing instability band and are therefore able to maintain their amplitude as the system evolves and after illumination ceases, while photochemically generated harmonics outside the Turing band tend to decay.     

Active species of horseradish peroxidase (HRP) and cytochrome P450: two electronic chameleons

The active site of HRP Compound I (Cpd I) is modeled using hybrid density functional theory (UB3LYP). The effects of neighboring amino acids and of environmental polarity are included. The low-lying states have porphyrin radical cationic species (Por(*)(+)). However, since the Por(*)(+) species is a very good electron acceptor, other species, which can be either the ligand or side chain amino acid residues, may participate in electron donation to the Por(*)(+) moiety, thereby making Cpd I behave like a chemical chameleon. Thus, this behavior that was noted before for Cpd I of P450 is apparently much more wide ranging than initially appreciated. Since chemical chameleonic behavior property was found to be expressed not only in the properties of Cpd I itself, but also in its reactivity, the roots of this phenomenon are generalized. A comparative discussion of Cpd I species follows for the enzymes HRP, CcP, APX, CAT (catalase), and P450.     

How does product isotope effect prove the operation of a two-state "rebound" mechanism in C-H hydroxylation by cytochrome P450?

C-H hydroxylation is a fundamental process. In Nature it is catalyzed by the enzyme cytochrome P450, in a still-debated mechanism that poses a major intellectual challenge for both experiment and theory; currently, the opinions keep swaying between the original single-state rebound mechanism, a two-oxidant mechanism (where ferric peroxide participates as a second oxidant, in addition to the primary active species, the high-valent iron-oxo species), and two-state reactivity (TSR) mechanism (where two spin states are involved). Recent product isotope effect (PIE) measurements for the trans-2-phenyl-methyl cyclopropane probe (1), led Newcomb and co-workers (Newcomb, M.; Aebisher, D.; Shen, R.; Esala, R.; Chandrasena, P.; Hollenberg, P.; Coon, M. J. J. Am. Chem. Soc. 2003, 125, 6064-6065) to rule out TSR in favor of the two-oxidant scenario, since the direction of the PIE was at odds with the one predicted from calculations on methane hydroxylation. The present report describes a density functional theoretical study of C-H hydroxylation of the Newcomb probe, 1, leading to rearranged (3) and unrearranged (2) products. Our study shows that the reaction occurs via TSR in which the high-spin pathway gives dominant rearranged products, whereas the low-spin pathway favors unrearranged products. The calculated PIE(2/3) values based on TSR are found to be in excellent agreement with the experimental data of Newcomb and co-workers. This match between experiment and theory makes a strong case that the reaction occurs via TSR mechanism.