Proton-shuffle mechanism of O-O activation for formation of a high-valent oxo-iron species of bleomycin.

Bleomycins (BLMs) can utilize H2O2 to cleave DNA in the presence of ferric ions. DFT calculations were used to study the mechanism of O-O bond cleavage in the low-spin FeIII-hydroperoxo complex of BLM. The following alternative hypotheses were investigated using realistic structural models: (a) heterolytic cleavage of the O-O bond, generating a Compound I (Cpd I) like intermediate, formally BLM-FeV=O; (b) homolytic O-O cleavage, leading to a BLM-FeIV=O species and an OH* radical; and (c) a direct O-O cleavage/H-abstraction mechanism by ABLM.

Characterization of manganese(V)-oxo polyoxometalate intermediates and their properties in oxygen-transfer reactions.

A manganese(III)-substituted polyoxometalate, [alpha2-P2MnIII(L)W17O61]7- (P2W17MnIII), was studied as an oxidation catalyst using iodopentafluorobenzene bis(tifluoroacetate) (F5PhI(TFAc)2) as a monooxygen donor. Pink P2W17MnIII turns green upon addition of F5PhI(TFAc)2. The 19F NMR spectrum of F5PhI(TFAc)2 with excess P2W17MnIII at -50 degrees C showed the formation of an intermediate attributed to P2W17MnIII-F5PhI(TFAc)2 that disappeared upon warming.

On the identity and reactivity patterns of the "second oxidant" of the T252A mutant of cytochrome P450cam in the oxidation of 5-methylenenylcamphor.

Density functional calculations show that in the absence of Compound I, the primary oxidant species of P450, the precursor species, Compound 0 (FeOOH), can effect double bond activation of 5-methylenylcamphor (1). The mechanism is initiated by homolytic cleavage of the O-O bond and formation of an OH radical bound to the Compound II species by hydrogen bonding interactions. Subsequently, the so-formed OH radical can either activate the double bond of 1 or attack the meso position of the heme en route to heme degradation.

A valence bond study of the dioxygen molecule.

The dioxygen molecule has been the subject of valence bond (VB) studies since 1930s, as it was considered as the first "failure" of VB theory. The object of this article is to provide an unambiguous VB interpretation for the nature of chemical bonding of the molecule by means of modern VB computational methods, VBSCF, BOVB, and VBCI. It is shown that though the VBSCF method can not provide quantitative accuracy for the strongly electronegative and electron-delocalized molecule because of the lack of dynamic correlation, it still gives a correct qualitative analysis for wave function of the molecule and provides intuitive insights into chemical bonding.

A survey of recent developments in ab initio valence bond theory.

Starting from the 1980s and onwards, Valence Bond theory has been enjoying renaissance that is characterized by the development of a growing number of ab initio methods, and by many applications to chemical reactivity and to the central paradigms of chemistry. Owing the increase of computational power of modern computers and to significant advances in the methodology, valence bond theory begins to offer a sound and attractive alternative to Molecular Orbital theory. This review aims at summarizing the most important developments of ab initio valence bond methods during the last two or three decades, and is primarily devoted to a description of what the various methods can actually achieve within their specific scopes and limitations.

The Lewis legacy: the chemical bond--a territory and heartland of chemistry.

Is chemistry a science without a territory? I argue that "chemical bonding" has been a traditional chemical territory ever since the chemical community amalgamated in the seventeenth century, and even before. The modern charter of this territory is Gilbert Newton Lewis, who started the "electronic structure revolution in chemistry." As a tribute to Lewis, I describe here three of his key papers from the years 1913, 1916, and 1923, and analyze them.

An efficient proton-coupled electron-transfer process during oxidation of ferulic acid by horseradish peroxidase: coming full cycle.

Quantum mechanics/molecular mechanics calculations were utilized to study the process of oxidation of a native substrate (ferulic acid) by the active species of horseradish peroxidase (Dunford, H. B. Heme Peroxidases; Wiley-VCH: New York, 1999), Compound I and Compound II, and the manner by which the enzyme returns to its resting state.

Catalysts for monooxygenations made from polyoxometalate: an iron(V)-oxo derivative of the Lindqvist anion.

This work uses density functional calculations to design a new high-valent Fe(V)=O catalyst [Mo5O18Fe=O]3-, which is based on the Lindqvist polyoxometalate (Mo6O19(2-)). Because the parent species is stable to oxidative conditions, one may assume that the newly proposed iron-oxo species will be stable, too. The calculated Mössbauer spectroscopic data may be helpful toward an eventual identification of the species.

QM/MM study of mechanisms for compound I formation in the catalytic cycle of cytochrome P450cam.

In the catalytic cycle of cytochrome P450cam, after molecular oxygen binds as a ligand to the heme iron atom to yield a ferrous dioxygen complex, there are fast proton transfers that lead to the formation of the active species, Compound I (Cpd I), which are not well understood because they occur so rapidly. In the present work, the conversion of the ferric hydroperoxo complex (Cpd 0) to Cpd I has been investigated by combined quantum-mechanical/molecular-mechanical (QM/MM) calculations. The residues Asp(251) and Glu(366) are considered as proton sources.

Does substrate oxidation determine the regioselectivity of cyclohexene and propene oxidation by cytochrome p450?

DFT and QM/MM computations of allylic C-H hydroxylation versus C=C epoxidation in cyclohexene and propene by Compound I of P450cam demonstrate that the relative barriers for the oxidative processes themselves are not good predictors of the observed selectivity. However, a kinetic expression previously developed (Kozuch, S.; Shaik, S.

Identity SN2 reactions X- + CH3X --> XCH3 + X- (X=F, Cl, Br, and I) in vacuum and in aqueous solution: a valence bond study.

The recently developed (L. Song, W. Wu, Q.

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.

Ferromagnetic bonding: high spin copper clusters (n+1)Cu(n); n = 2-14) devoid of electron pairs but possessing strong bonding.

Density functional theoretic studies are performed for the high-spin copper clusters (n)(+1)Cu(n) (n = 2-14), which are devoid of electron pairs shared between atoms, hence no-pair clusters (J. Phys. Chem.

Two-state reactivity in alkane hydroxylation by non-heme iron-oxo complexes.

Density functional theory is used to explore the mechanisms of alkane hydroxylation for four synthetic non-heme iron(IV)-oxo complexes with three target substrates (Kaizer, J.; Klinker, E. J.

Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor.

The hydrogen abstraction reaction of camphor in cytochrome P450(cam) has been investigated in the native enzyme environment by combined quantum mechanical/molecular mechanical (QM/MM) calculations and in the gas phase by density functional calculations. This work has been motivated by contradictory published QM/MM results. In an attempt to pinpoint the origin of these discrepancies, we have systematically studied the factors that may affect the computed barriers, including the QM/MM setup, the optimization procedures, and the choice of QM region, basis set, and protonation states.

Two-state reactivity, electromerism, tautomerism, and "surprise" isomers in the formation of compound II of the enzyme horseradish peroxidase from the principal species, compound I.

QM and QM/MM calculations on Compound II, the enigmatic species in the catalytic cycle of the horseradish peroxidase enzyme, reveal six low-lying isomers. The principal isomer is the triplet oxo-ferryl form (PorFe(IV)=O) that yields the hydroxo-ferryl isomer (PorFe(IV)-OH+). These are the only forms observed in experimental studies.

The Poulos-Kraut mechanism of Compound I formation in horseradish peroxidase: a QM/MM study.

QM/MM calculations are used to elucidate the Poulos-Kraut (Poulos, T. L.; Kraut, J.

Theoretical analysis of the structural and electronic properties of metalloporphyrin pi-cation radicals.

A method for analyzing the A(1u)/A(2u) contents of metalloporphyrin pi-cation radicals is developed and applied to a series of unsubstituted planar metalloporphines (MPs) (M=Cr, Mn, Fe, Co, Ni, Cu, and Zn). The structures and electronic properties of the MPs and their cation radicals were calculated by density functional theory (DFT) and subsequently analyzed. It was found that the MPs with small core sizes have a tendency to form A(1u)-type radicals, while the MPs with large core size have a preference for an A(2u)-type.

Sericea lespedeza hay as a natural deworming agent against gastrointestinal nematode infection in goats.

Infection with gastrointestinal nematodes (GIN), particularly Haemonchus contortus, is the biggest constraint to profitable goat production in the United States (US). Due to widespread prevalence of anthelmintic resistance in goat GIN, alternative, non-chemical control methodologies are needed to increase profitability of small ruminant industries. A study was designed to test the efficacy of a high condensed tannin (CT) legume, sericea lespedeza [SL, Lespedeza cuneata (Dum.

The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM study.

The discrepancies between the published QM/MM studies (Schöneboom, J. C.; Cohen, S.

A combined kinetic-quantum mechanical model for assessment of catalytic cycles: application to cross-coupling and Heck reactions.

The efficiency of catalytic cycles is measured by their turnover frequency (TOF). The degree of TOF control determines which states contribute most to the rate of the cycle, and thus indicates the steps that have the highest impact on the cycle. A kinetic model developed by Christiansen (Christiansen, J.

Barriers of hydrogen abstraction vs halogen exchange: an experimental manifestation of charge-shift bonding.

This paper shows that the differences between the barriers of the halogen exchange reactions, in the H + XH systems, and the hydrogen abstraction reactions, in the X + HX systems (X = F, Cl, Br), measure the covalent-ionic resonance energies of the corresponding X-H bonds. These processes are investigated using CCSD(T) calculations as well as the breathing-orbital valence bond (BOVB) method. Thus, the VB analysis shows that (i) at the level of covalent structures the barriers are the same for the two series and (ii) the higher barriers for halogen exchange processes originate solely from the less efficient mixing of the ionic structures into the respective covalent structures.

A single transition state serves two mechanisms. The branching ratio for CH2O*- + CH3Cl on improved potential energy surfaces.

The reaction of formaldehyde radical anion with methyl chloride, CH2O*- + CH3Cl, is an example in which a single transition state leads to two products: substitution at carbon (Sub(C), CH3CH2O* + Cl-) and electron transfer (ET, CH2O + CH3* + Cl-). The branching ratio for this reaction has been studied by ab initio molecular dynamics (AIMD). The energies of transition states and intermediates were computed at a variety of levels of theory and compared to accurate energetics calculated by the G3 and CBS-QB3 methods.

In silico design of a mutant of cytochrome P450 containing selenocysteine.

A mutant of P450(cam), in which the cysteine ligand was replaced by selenocysteine, was designed theoretically using hybrid QM/MM (quantum mechanical/molecular mechanical) calculations. The calculations of the active species, Se-CpdI (selenocysteine-Compound I), of the mutant enzyme indicate that Se-Cpd I will be formed faster than the wild-type species and be consumed more slowly in C-H hydroxylation. As such, our calculations suggest that Se-Cpd I can be observed unlike the elusive species of the wild-type enzyme (Denisov, I.