Role of the somersault rearrangement in the oxidation step for flavin monooxygenases (FMO). A comparison between FMO and conventional xenobiotic oxidation with hydroperoxides

Model quantum mechanical calculations presented for C-4a-flavin hydroperoxide (FlHOOH) at the B3LYP/6-311+G(d,p) level suggest a new mechanism for flavoprotein monooxygenase (FMO) oxidation involving a concerted homolytic O-O bond cleavage in concert with hydroxyl radical transfer from the flavin hydroperoxide rather than an S(N)2-like displacement by the substrate on the C-4a-hydroperoxide OOH group. Homolytic O-O bond cleavage in a somersault-like rearrangement of hydroperoxide C-4a-flavinhydroperoxide (1) (FLHO-OH → FLHO···HO) produces an internally hydrogen-bonded HO(?) radical intermediate with a classical activation barrier of 27.0 kcal/mol. Model hydroperoxide 1 is used to describe the transition state for the key oxidation step in the paradigm aromatic hydroxylase, p-hydroxybenzoate hydroxylase (PHBH). A comparison of the electron distribution in the transition structures for the PHBH hydroxylation of p-hydroxybenzoic acid (ΔE(?) = 23.0 kcal/mol) with that of oxidation of trimethylamine (ΔE(?) = 22.3 kcal/mol) and dimethyl sulfide (ΔE? = 14.1 kcal/mol) also suggests a mechanism involving a somersault mechanism in concert with transfer of an HO(?) radical to the nucleophilic heteroatom center with a hydrogen transfer back to the FLH-O residue after the barrier is crossed to produce the final product, FLH-OH. In each case the hydroxylation barrier was less than that of the O-O rearrangement barrier in the absence of a substrate supporting an overall concerted process. All three transition structures bear a resemblance to the TS for the comparable hydroxylation of isobutane (ΔE(?) = 29.2 kcal/mol) and for simple Fenton oxidation by aqueous iron(III) hydroperoxides. To our surprise the oxidation of N- and S-nucleophiles with conventional oxidants such as alkyl hydroperoxides and peracids also proceeds by HO(?) radical transfer in a manner quite similar to that for tricyclic hydroperoxide 1. Stabilization of the developing oxyradical produced by somersault rearrangement for concerted enzymatic oxidation with tricyclic hydroperoxide 1 results in a reduced overall activation barrier.     

Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.     

Light-triggered proton and electron transfer in flavin cofactors

The pH dependent behavior of two flavin cofactors, flavin-adenine dinucleotide (FAD) and flavin mononucleotide (FMN), has been characterized using femtosecond transient absorption spectroscopy for the first time. The flavin excited state was characterized in three states of protonation (Fl(-), Fl, and FlH(+)). We found that Fl and Fl(-) exhibit the same excited state absorption but that the lifetime of Fl(-) is much shorter than that of Fl. The transient absorption spectrum of FlH(+) is significantly different from Fl and Fl(-), suggesting that the electronic properties of the flavin chromophore become appreciably modified by protonation. We further studied the excited state protonation of the flavin and found that the protonation sites of the flavin in the ground and excited state are not equivalent. In the case of FAD, its excited state dynamics are controlled by the two conformations it adopts. At low and high pH, FAD adopts an "open" conformation and behaves the same as FMN. In a neutral pH range, FAD undergoes a fast excited state deactivation due to the "stacked" conformer. The transition from stacked to open conformer occurs at pH ～ 3 (because of adenine protonation) and pH ～ 10 (because of flavin deprotonation).     

Conformational dynamics of the isoalloxazine in substrate-free p-hydroxybenzoate hydroxylase: single-molecule studies

p-Hydroxybenzoate hydroxylase (PHBH) is a homodimeric enzyme in which each subunit noncovalently binds one molecule of FAD in the active site. PHBH is a model system for how flavoenzymes regulate reactions with oxygen. We report single-molecule fluorescence studies of PHBH in the absence of substrate that provide data consistent with the hypothesis that a critical step in substrate binding is the movement of the isoalloxazine between an "in" conformation and a more exposed or "open" conformation. The isoalloxazine is observed to move between these conformations in the absence of substrate. Studies with the Y222A mutant form of PHBH suggest that the exposed conformation is fluorescent while the in-conformation is quenched. Finally, we note that many of the single-molecule-fluorescence trajectories reveal a conformational heterogeneity, with populations of the enzyme characterized by either fast or slow switching between the in- and open-conformations. Our data also allow us to hypothesize a model in which one flavin in the dimer inhibits the motion of the other.     

Substrate oxidation by copper-dioxygen adducts: mechanistic considerations

A series of copper-dioxygen adducts [{Cu(II)(MePY2)(R)}(2)(O(2))](B(C(6)F(5))(4))(2) (1(R)()), systematically varying in their electronic properties via ligand pyridyl donor substituents (R = H, MeO, and Me(2)N), oxidize a variety of substrates with varying C-H or O-H bond dissociation enthalpies. Detailed mechanistic studies have been carried out, including investigation of 1(R)() thermodynamic redox properties, 1(R)() tetrahydrofuran (THF) and N,N'-dimethylaniline (DMA) oxidation kinetics (including analyses of substrate dicopper binding equilibria), and application of mechanistic probes (N-cyclopropyl-N-methylaniline (CMA) and (p-methoxyphenyl)-2,2-dimethylpropanol (MDP)), which can distinguish if proton-coupled electron-transfer (PCET) processes proceed through concerted electron-transfer proton-transfer (ETPT) or consecutive electron-transfer proton-transfer (ET/PT) pathways. The results are consistent with those of previous complementary studies; at low thermodynamic driving force for substrate oxidation, an ET/PT is operable, but once ET (i.e., substrate one-electron oxidation) becomes prohibitively uphill, the ETPT pathway occurs. Possible differences in coordination structures about 1(Me)()()2(N)()/1(MeO)() compared to those of 1(H)() are also used to rationalize some of the observations.     

Aerobic oxidation of 2,3,6-trimethylphenol to trimethyl-1,4-benzoquinone with copper(II) chloride as catalyst in ionic liquid and structure of the active species

TMQ is an important precursor in industrial vitamin E synthesis. We report a "green chemistry approach" with respect to the highly selective and environmentally friendly oxidation of 2,3,6-trimethylphenol (TMP) to trimethyl-1,4-benzoquinone (TMQ) with molecular oxygen as oxidant and a copper catalyst immobilized in a molten salt. n-Butanol as co-solvent has a positive effect on the activity and selectivity. The structurally characterized catalyst, a 1-n-butyl-3-methylimidazolium oxotetracuprat, is formed in situ via hydrolysis of CuCl2 in the presence of imidazolium chloride. We propose a mechanism of oxidative phenolate activation at a [Cu4(mu4-O)]6+ core as electronically coupled electron acceptor, formation of a copper-bound phenolate radical anion, spin delocalization into the aromatic ring, and attack by triplet oxygen at the para position. Attack of Cu(I) as reduction equivalent at the peroxy radical, proton-mediated elimination of a copper(II)-hydroxo species, will either substitute a copper(I) site in the reduced oxo cluster or take up an electron from the reduced mixed valent cluster [Cu4(mu4-O)]6+ to regenerate the oxidized cluster as the active electron acceptor.     

Kinetic study of the electron-transfer oxidation of the phenolate anion of a vitamin E model by molecular oxygen generating superoxide anion in an aprotic medium

Electron-transfer reduction of molecular oxygen (O2) by the phenolate anion (1-) of a vitamin E model, 2,2,5,7,8-pentamethylchroman-6-ol (1H), occurred to produce superoxide anion, which could be directly detected by a low-temperature EPR measurement. The rate of electron transfer from 1- to O2 was relatively slow, since this process is energetically unfavourable. The one-electron oxidation potential of 1- determined by cyclic voltammetric measurements is sufficiently negative to reduce 2,2-bis(4-tert-octylphenyl)-1-picrylhydrazyl radical (DOPPH*) to the corresponding one-electron reduced anion, DOPPH-, suggesting that 1- can also act as an efficient radical scavenger.     

Thermal and photochemical rearrangement of bicyclo[3.1.0]hex-3-en-2-one to the ketonic tautomer of phenol. Computational evidence for the formation of a diradical rather than a zwitterionic intermediate

The ground state (S(0)) and lowest-energy triplet state (T(1)) potential energy surfaces (PESs) concerning the thermal and photochemical rearrangement of bicyclo[3.1.0]hex-3-en-2-one (8) to the ketonic tautomer of phenol (11) have been extensively explored using ab initio CASSCF and CASPT2 calculations with several basis sets. State T(1) is predicted to be a triplet pipi lying 66.5 kcal/mol above the energy of the S(0) state. On the S(0) PES, the rearrangement of 8 to 11 is predicted to occur via a two-step mechanism where the internal cyclopropane C-C bond is broken first through a high energy transition structure (TS1-S(0)()), leading to a singlet intermediate (10-S(0)()) lying 25.0 kcal/mol above the ground state of 8. Subsequently, this intermediate undergoes a 1,2-hydrogen shift to yield 11 by surmounting an energy barrier of only 2.7 kcal/mol at 0 K. The rate-determining step of the global rearrangement is the opening of the three-membered ring in 8, which involves an energy barrier of 41.2 kcal/mol at 0 K. This high energy barrier is consistent with the fact that the thermal rearrangement of umbellulone to thymol is carried out by heating at 280 degrees C. Regarding the photochemical rearangement, our results suggest that the most efficient route from the T(1) state of 8 to ground state 11 is the essentially barrierless cleavage of the internal cyclopropane C-C bond followed by radiationless decay to the S(0) state PES via intersystem crossing (ISC) at a crossing point (S(0)()/T(1)()-1) located at almost the same geometry as TS1-S(0)(), leading to the formation of 10-S(0)() and the subsequent low-barrier 1,2-hydrogen shift. The computed small spin-orbit coupling between the T(1) and S(0) PESs at S(0)()/T(1)()-1 (1.2 cm(-)(1)) suggests that the ISC between these PESs is the rate-determining step of the photochemical rearrangement 8 --> 11. Finally, computational evidence indicates that singlet intermediate 10-S(0)() should not be drawn as a zwitterion, but rather as a diradical having a polarized C=O bond.     

Anionic cyclizations of aromatic ester dithioacetals with facially biased α,β-unsaturated ketones

Cyclopent-2-enones bearing a plane-nonsymmetric oxygen function on C-4 reacted efficiently with anions derived from aromatic ester dithioacetals to provide annulated products in a highly diastereoselective fashion. Whereas the anion of a dimethoxy aromatic ester dithiolane more rapidly reacted by an alternative intramolecular pathway, the anion of the corresponding aromatic ester dithiane was suitable for the intermolecular cyclization.     

Fluorescent boron bis(phenolate) with association response to chloride and dissociation response to fluoride

Addition of chloride ions to boron bis(phenolate) 5 in dichloromethane solution produces a selective fluorescence decrease. The fluorescence change is believed to be caused by associative hydrogen bonding between the chloride ion and two boronic acid groups. While addition of fluoride ions to bis(phenolate) 5 generates a purple colorimetric response, the colorimetric response is caused by fluoride induced B-O bond cleavage and air oxidation of the phenolate anion formed by this dissociation.     

Self-assemblies of new rigid angular ligands and metal centers toward the rational construction and modification of novel coordination polymer networks

Self-assemblies of rigid angular ligands with 120 degrees molecular angle and metal centers have been investigated with the aim of achieving the rational construction and modification of coordination polymer structures. The reactions of Co(NCS)(2) with 1,3-bis(trans-4-styrylpyridyl)benzene (L(1)()), 2,6-bis(trans-4-styrylpyridyl)pyridine (L(2)()), 1,3-bis(trans-4-styrylpyrimidyl)benzene (L(3)()), and 1,3-bis(trans-4-styrylquinoly)benzene (L(4)()) afford complexes [Co(L(1)())(2)(NCS)(2)]( infinity ) (1), [Co(L(2)())(2)(NCS)(2)]( infinity ) (2), Co(L(3)())(2)(NCS)(2)(CH(3)OH)(2) (3), and [Co(L(4)())(NCS)(2)]( infinity ) (4), respectively. The resulting complexes exhibit open framework, stairlike hydrogen-bonded chain and single-stranded helical coil structures, which are controlled by the variation of the geometry around the coordination site in ligands. Moreover, the coordination of L(1)() and L(2)() to Mn(hfac)(2) (hfac = 1,1,1,5,5,5-hexafluoroacetylacetonate) yields single-stranded helical coordination polymers of [Mn(L(1)())(hfac)(2)]( infinity ) (5) and [Mn(L(2)())(hfac)(2)]( infinity ) (6), respectively.     

Dicyclobuta[de,ij]naphthalene and dicyclopenta[cd,gh]pentalene: a theoretical study

The structures, energetics, and aromatic character of dicyclobuta[de,ij]naphthalene, 1, dicyclopenta[cd,gh]pentalene, 2, dihydrodicyclobuta[de,ij]naphthalene, 3, and dihydrocyclopenta[cd,gh]pentalene, 4, have been examined at the B3LYP/6-311++G//B3LYP/6-31G level of theory. All molecules are bowl-shaped, and the pentalene isomers, 2 and 4, are most stable. A comparison with other C(12)H(6) and C(12)H(8) isomers indicates that 2 is approximately 25 kcal/mol less stable than 1,5,9-tridehydro[12]annulene and 4 is approximately 100 kcal/mol higher in energy than acenaphthylene, both of which are synthetically accessible. The transition state structure for bowl-to-bowl inversion of 1 is planar (D(2)(h)()) and lies 30.9 kcal/mol higher in energy than the ground state; the transition state for inversion of 2 is C(2)(h)() and lies 46.6 kcal/mol higher in energy. Symmetry considerations, bond length alternations, and NICS values (a magnetic criterion) all indicate that the ground states of 1, 3, and 4 are very aromatic; however, HOMA values (a measure of bond delocalization) indicate that 3S and 4S are aromatic but that 1S is less so. NICS values for the ground state of 2 strongly indicate aromaticity; however, bond localization, symmetry, and HOMA values argue otherwise.     

Diels–Alder reactions of 5,6‐dihydrothiazolo[3,2‐d][1,4,2]diazaphospholes: A DFT investigation

The density functional theory level (B3LYP/6‐311G**) computations of the Diels–Alder (DA) reactions of 5,6‐dihydrothiazolo[3,2‐d][1,4,2]‐diazaphospholes with 1,3‐butadiene and with isoprene confirm pericyclic mechanism via asynchronous transition states. The aromatic character of the transition states is established by negative nucleus independent chemical shift (NICS) values falling in the range from −14 to −16. Integration of the dienophilic >CP functionality in the 6π aromatic azaphosphole ring raises the activation energy barrier (B3LYP/6‐311++G**//B3LYP/6‐311G**) compared to that for the DA reaction of the acyclic phosphaethene, but it is lower than the activation energy barrier for the DA reaction of the corresponding 10π aromatic system, thiazolo[3,2‐d][1,4,2]diazaphospholes. The experimentally observed stereo‐ and regioselectivities in the reactions can be accounted on the basis of secondary molecular orbital (SMO) interactions detected in the respective transition structures. The attachment of an electron‐withdrawing group to the dienophilic moiety enhances both stereo‐ and regio‐ selectivities which agree well with the experimental values. Solvent (toluene) effect studied with polarizable continuum model (PCM) indicates that the stereo‐ and regioselectivities are not affected by the solvent. © 2006 Wiley Periodicals, Inc. Heteroatom Chem 17:402–410, 2006; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20196     

Ti/SiO_2催化H_2O_2氧化苯甲醇制苯甲醛反应机理的理论研究

采用密度泛函理论B3LYP方法研究了非贵金属Ti催化H2O2氧化苯甲醇为苯甲醛的反应机理.考察了6条可能的反应途径,优化得到了各个途径的过渡态和中间体结构,计算了气相和液相中的反应势垒.结果表明,无催化剂时,H2O2氧化苯甲醇的反应途径具有非常高的反应势垒,反应不能进行;以Ti/SiO2为催化剂时,标题反应在乙腈溶液中的反应势垒为123.8kJ/mol,反应可在约353K下发生.结果还表明,标题反应在极性较大的溶剂中有较高的反应势垒,而在气相或者极性较小的溶剂中的反应势垒较低.     

Interactions in single wall carbon nanotubes/pyrene/porphyrin nanohybrids

This work provides an in-depth look at a range of physicochemical aspects of (i) single wall carbon nanotubes (SWNT), (ii) pyrene derivatives (pyrene(+)), (iii) porphyrin derivatives (ZnP(8)()(-)() and H(2)()P(8)()(-)()), (iv) poly(sodium 4-styrenesulfonate), and (v) their combinations. Implicit in their supramolecular combinations is the hierarchical integration of SWNT (as electron acceptors), together with ZnP(8)()(-)() or H(2)()P(8)()(-)() (as electron donors), in an aqueous environment mediated through pyrene(+). This supramolecular approach yields novel electron donor-acceptor nanohybrids (SWNT/pyrene(+)/ZnP(8)()(-)() or SWNT/pyrene(+)/H(2)()P(8)()(-)()). In particular, we report on electrochemical and photophysical investigations that as a whole suggest sizeable and appreciable interactions between the individual components. The key step to form SWNT/pyrene(+)()/ZnP(8)()(-)() or SWNT/pyrene(+)()/H(2)()P(8)()(-)() hybrids is pi-pi interactions between SWNT and pyrene(+), for which we have developed for the first time a sensitive marker. The marker is the monomeric pyrene fluorescence, which although quenched is (i) only present in SWNT/pyrene(+) and (ii) completely lacking in just pyrene(+). Electrostatic interactions help to immobilize ZnP(8)()(-)() or H(2)()P(8)()(-)() onto SWNT/pyrene(+) to yield the final electron donor-acceptor nanohybrids. A series of photochemical experiments confirm that long-lived radical ion pairs are formed as a product of a rapid excited-state deactivation of ZnP(8)()(-)() or H(2)()P(8)()(-)(). This formation is fully rationalized on the basis of the properties of the individual moieties. Additional modeling shows that the data are likely to be relevant to the SWNTs present in the sample, which possess wider diameters.     

Density functional theory study of the reaction mechanism and energetics of the reduction of hydrogen peroxide by ebselen, ebselen diselenide, and ebselen selenol

Density functional theory calculations at the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31G(d,p) level have been performed to elucidate the mechanism and reaction energetics for the reduction of hydrogen peroxide by ebselen, ebselen diselenide, ebselen selenol, and their sulfur analogues. The effects of solvation have been included with the CPCM model, and in the case of the selenol anion reaction, diffuse functions were used on heavy atoms for the geometry optimizations and thermochemical calculations. The topology of the electron density in each system was investigated using the quantum theory of atoms in molecules, and a detailed interpretation of the electronic charge and population data as well as the atomic energies is presented. Reaction free energy barriers for the oxidation of ebselen, ebselen diselenide, and ebselen selenol are 36.8, 38.4, and 32.5 kcal/mol, respectively, in good qualitative agreement with experiment. It is demonstrated that the oxidized selenium atom is significantly destabilized in all cases and that the exothermicity of the reactions is attributed to the peroxide oxygen atoms via reduction. The lower barrier to oxidation exhibited by the selenol is largely due to entropic effects in the reactant complex.     

Besides N(2), What Is the Most Stable Molecule Composed Only of Nitrogen Atoms?

Polynitrogen molecules have been studied systematically at high levels of ab initio and density functional theory (DFT). Besides N(2), the thermodynamically most stable N(n)() molecules, located with the help of a newly developed energy increment system, are all based on pentazole units. The geometric, energetic, and magnetic criteria establish pentazole (2) and its anion (3) to be as aromatic as their isoelectronic analogues, e.g., furan, pyrrole, and the cyclopentadienyl anion. The bond lengths in 2 and 3 are equalized; both have large aromatic stabilization energies (ASE) and also substantial magnetic susceptibility exaltations (Lambda). The C(s)() symmetric azidopentazole (14), a candidate for experimental investigation, is the lowest energy N(8) isomer but is still 196.7 kcal/mol higher in energy than four N(2) molecules. Octaazapentalene (12) with 10 pi electrons also is aromatic. The D(2)(d)() symmetric bispentazole (21) is the lowest energy N(10) minimum but is 260 kcal/mol higher in energy than five N(2) molecules. For strain-free molecules, the average deviation is +/-2.6 kcal/mol between the DFT energies and those based on the increment scheme. The increment scheme also provides estimates of the strain energies of polynitrogen compounds, e.g., tetraazatetrahedrane (8, 48.2 kcal/mol), octaazacubane (11, 192.6 kcal/mol), and N(20) (27, 294.6 kcal/mol), and is useful in searching for new high-energy-high-density materials.     

Ab initio study of the atmospheric oxidation of CS2.

The reactions of OH with CS2, OCS, and 3SO and of 3O2 with CS2, SCSOH, and HOSO have been studied by optimizing minima and transition states with B3LYP/6-31+G(d) and carrying out higher-level ab initio calculations on fixed geometries. The combined calculations provide valuable insight into the mechanism for the atmospheric oxidation of CS2. The initial step is the formation of the SCSOH complex (1) which readily adds molecular oxygen to form the SC(OO)SOH complex (8). A key step is the oxygen atom transfer to the sulfur bearing the hydroxyl group which leads directly to OCS plus HOSO. The HOSO + 3O2 reaction has a near zero calculated activation barrier so generation of O2H + SO2 should proceed readily in the atmosphere.     

Electronically Mediated Selectivity in Ring Opening of 1-Azirines. The 3-X Mode: Convenient Route to 3-Oxazolines

The mild base-promoted reaction of methyl 2-phenyl-1-azirine-3-acetate (1) with aldehydes and acetone provides a new and simple route to the 3-oxazolines 5, which are formed in good yields by the electrophilic trapping of an imino anion produced by C-N bond cleavage in the 1-azirine enolate intermediate 6. Chloranil oxidation of 5 containing an aromatic substituent at C-2 affords oxazoles 7, while reaction of 5 containing an aliphatic group at C-2 produces 5-methylene-3-oxazolines 8 and 5-spiro-2-oxazolines 9 in addition to 7.     

Spectroscopic and electronic structure studies of phenolate Cu(II) complexes: phenolate ring orientation and activation related to cofactor biogenesis

A combination of spectroscopies and DFT calculations have been used to define the electronic structures of two crystallographically defined Cu(II)-phenolate complexes. These complexes differ in the orientation of the phenolate ring which results in different bonding interactions of the phenolate donor orbitals with the Cu(II), which are reflected in the very different spectroscopic properties of the two complexes. These differences in electronic structures lead to significant differences in DFT calculated reactivities with oxygen. These calculations suggest that oxygen activation via a Cu(I) phenoxyl ligand-to-metal charge transfer complex is highly endergonic (>50 kcal/mol), hence an unlikely pathway. Rather, the two-electron oxidation of the phenolate forming a bridging Cu(II) peroxoquinone complex is more favorable (11.3 kcal/mol). The role of the oxidized metal in mediating this two-electron oxidation of the coordinated phenolate and its relevance to the biogenesis of the covalently bound topa quinone in amine oxidase are discussed.