Does Cob(II)alamin act as a conductor in coenzyme B12 dependent mutases?
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Free Radicals↗
Biomedical subjects
Kazunari Yoshizawa
Publications and source records attributed to Kazunari Yoshizawa.
Conversion of methane to methanol at the mononuclear and dinuclear copper sites of particulate methane monooxygenase (pMMO): a DFT and QM/MM study.
Methane hydroxylation at the mononuclear and dinuclear copper sites of pMMO is discussed using quantum mechanical and QM/MM calculations. Possible mechanisms are proposed with respect to the formation of reactive copper-oxo and how they activate methane. Dioxygen is incorporated into the Cu(I) species to give a Cu(II)-superoxo species, followed by an H-atom transfer from a tyrosine residue near the monocopper active site. A resultant Cu(II)-hydroperoxo species is next transformed into a Cu(III)-oxo species and a water molecule by the abstraction of an H-atom from another tyrosine residue. This process is accessible in energy under physiological conditions. Dioxygen is also incorporated into the dicopper site to form a (mu-eta(2):eta(2)-peroxo)dicopper species, which is then transformed into a bis(mu-oxo)dicopper species. The formation of this species is more favorable in energy than that of the monocopper-oxo species. The reactivity of the Cu(III)-oxo species is sufficient for the conversion of methane to methanol if it is formed in the protein environment. Since the sigma orbital localized in the Cu-O bond region is singly occupied in the triplet state, this orbital plays a role in the homolytic cleavage of a C-H bond of methane. The reactivity of the bis(mu-oxo)dicopper species is also sufficient for the conversion of methane to methanol. The mixed-valent bis(mu-oxo)Cu(II)Cu(III) species is reactive to methane because the amplitude of the sigma singly occupied MO localized on the bridging oxo moieties plays an essential role in C-H activation.
Binding Sites↗
Catalytic mechanism of dopamine beta-monooxygenase mediated by Cu(III)-oxo.
Mechanisms of dopamine hydroxylation by the Cu(II)-superoxo species and the Cu(III)-oxo species of dopamine beta-monooxygenase (DBM) are discussed using QM/MM calculations for a whole-enzyme model of 4700 atoms. A calculated activation barrier for the hydrogen-atom abstraction by the Cu(II)-superoxo species is 23.1 kcal/mol, while that of the Cu(III)-oxo, which can be viewed as Cu(II)-O*, is 5.4 kcal/mol. Energies of the optimized radical intermediate in the superoxo- and oxo-mediated pathways are 18.4 and -14.2 kcal/mol, relative to the corresponding reactant complexes, respectively. These results demonstrate that the Cu(III)-oxo species can better mediate dopamine hydroxylation in the protein environment of DBM. The side chains of three amino acid residues (His415, His417, and Met490) coordinate to the Cu(B) atom, one of the copper sites in the catalytic core that plays a role for the catalytic function. The hydrogen-bonding network between dopamine and the three amino acid residues (Glu268, Glu369, and Tyr494) plays an essential role in substrate binding and the stereospecific hydroxylation of dopamine to norepinephrine. The dopamine hydroxylation by the Cu(III)-oxo species is a downhill and lower-barrier process toward the product direction with the aid of the protein environment of DBM. This enzyme is likely to use the high reactivity of the Cu(III)-oxo species to activate the benzylic C-H bond of dopamine; the enzymatic reaction can be explained by the so-called oxygen rebound mechanism.
Animals↗
How axial ligands control the reactivity of high-valent iron(IV)-oxo porphyrin pi-cation radicals in alkane hydroxylation: a computational study.
The push effect of anionic axial ligands of high-valent iron(IV)-oxo porphyrin pi-cation radicals, (Porp)(+.)Fe(IV)(O)(X) (X=OH(-), AcO(-), Cl(-), and CF(3)SO(3)(-)), in alkane hydroxylation is investigated by B3LYP DFT calculations. The electron-donating ability of anionic axial ligands influences the activation energy for the alkane hydroxylation by the iron(IV)-oxo intermediates and the Fe-O bond distance of the iron-oxo species in transition state.
Alkanes↗
Nonradical mechanism for methane hydroxylation by iron-oxo complexes.
A nonradical mechanism for methane hydroxylation by the bare FeO+ complex, Fe-ZSM-5 zeolite, and soluble methane monooxygenase is proposed from quantum chemical calculations. This mechanism is applicable when a metal-oxo species is coordinatively unsaturated. Direct interaction between methane and a metal active center can form a weakly bound methane complex in the initial stages of this reaction. Subsequent C-H bond cleavage to form an intermediate with an HO-Fe-CH3 moiety in a nonradical manner and recombination of the resultant OH and CH3 ligands take place at a metal active center to form a final methanol complex. Thus, this is a nonradical, two-step reaction. The fact that methyl radical is 10-20 kcal/mol less stable than secondary and tertiary carbon radicals and benzyl radicals leads us to propose this mechanism.
Journal Article↗
End-cap effects on vibrational structures of finite-length carbon nanotubes.
Vibrational structures of C60-related finite-length nanotubes, C(40+20n) and C(42+18n) (1 < or = n < or = 4), in which n is, respectively, the number of cyclic cis- and trans-polyene chains inserted between fullerene hemispheres, are analyzed from density functional theory (DFT) calculations. To illuminate the end-cap effects on their vibrational structures, the corresponding tubes terminated by H atoms C(20n)H20 and C(18n)H18 (1 < or = n < or = 5) are also investigated. DFT calculations show a broad range of vibrational frequencies for the finite-size nanotubes: high-frequency modes (1100-1600 cm(-1)) containing oscillations along tangential directions (tangential modes), medium-frequency modes (700-850 cm(-1)) whose oscillations are located on the edges or end caps, and low-frequency modes (300-600 cm(-1)) involving oscillations along the radial directions (radial modes). Broadening of the calculated frequencies is due to the number of nodes in the standing waves of normal modes in the finite-size tubes. In the capped tubes, calculated vibrational frequencies are insensitive to the number of chains (n), whereas in the uncapped tubes, most vibrational frequencies change significantly with an increase in tube length. The discrepancy in the size dependency is reasonably understood by their C-C bonding networks; the capped tubes have similar bond-length alternation patterns within the polyene chains irrespective of n, whereas the uncapped tubes have various bond-deformation patterns. Thus, DFT calculations illuminate that the edge effects have strong impacts on the vibrational frequencies in the finite-size nanotubes.
Models, Chemical↗
Water-assisted oxo mechanism for heme metabolism.
A mechanism of heme metabolism by heme oxygenase (HO) is discussed from B3LYP density functional theory calculations. The concerted OH group attack to the alpha-carbon by the iron-hydroperoxo species is investigated using a model with full protoporphyrin IX to confirm our previous conclusion that this species does not have sufficient oxidizing power for heme oxidation (J. Am. Chem. Soc. 2004, 126, 3672). Calculated activation energies and structures of the intermediates and transition state for this process remain unchanged from those for a small model with porphine in the previous study, which shows that the inclusion of the side chain of the porphyrin ring is not essential in describing the OH group transfer. The activation barrier for a direct oxo attack to the alpha-carbon by an iron-oxo model is calculated to be 49.8 kcal/mol, the barrier height of which looks very high for the enzymatic reaction under physiological conditions. This large activation energy is due to a highly bent porphyrin structure in the transition state. However, a bridging water molecule plays an important role in reducing the porphyrin distortion in the transition state, resulting in a remarkable decrease of the activation barrier to 13.9 kcal/mol. A whole-enzyme model with about 4000 atoms is constructed to elucidate functions of the protein environment in this enzymatic reaction using QM/MM calculations. The key water molecule is fixed in the protein environment to ensure the low-barrier and regioselective heme oxidation. A water-assisted oxo mechanism of heme oxidation by heme oxygenase is proposed from these calculational results.
Heme↗
Quantum transport effects in copper(II) phthalocyanine sandwiched between gold nanoelectrodes.
The electrical transmission of copper(II) phthalocyanine (CuPc) sandwiched between gold nanoelectrodes is studied on the basis of the Green function formalism coupled with the Gaussian-broadening technique. In the Au-CuPc-Au junction, broadened density of states (DOS) of the Au chains is defined as continuous DOS of electrodes to calculate the Green function of the electrodes. Two peaks of the transmission function found in the vicinity of the Fermi level are analyzed in terms of molecular orbitals (MOs). A convenient procedure to analyze MO contribution to a transmission peak is proposed. It is found that (I) symmetry-matched interactions between CuPc and the gold nanoelectrodes are important to the enhancement of the transmission function and (II) the nanoelectrodes have almost no effect on the electronic states of CuPc.
Journal Article↗
Computational exploration of the catalytic mechanism of dopamine beta-monooxygenase: modeling of its mononuclear copper active sites.
Dopamine hydroxylation by the copper-superoxo, -hydroperoxo, and -oxo species of dopamine beta-monooxygenase (DBM) is investigated using theoretical calculations to identify the active species in its reaction and to reveal the key functions of the surrounding amino acid residues in substrate binding. A 3D model of rat DBM is constructed by homology modeling using the crystal structure of peptidylglycine alpha-hydroxylating monooxygenase (PHM) with a high sequence identity of 30% as a template. In the constructed 3D model, the CuA site in domain 1 is coordinated by three histidine residues, His265, His266, and His336, while the CuB site in domain 2 is coordinated by two histidine residues, His415 and His417, and by a methionine residue, Met490. The three Glu268, Glu369, and Tyr494 residues are suggested to play an important role in the substrate binding at the active site of DBM to enable the stereospecific hydrogen-atom abstraction. Quantum mechanical/molecular mechanical (QM/MM) calculations are performed to determine the structure of the copper-superoxo, -hydroperoxo, and -oxo species in the whole-enzyme model with about 4700 atoms. The reactivity of the three oxidants is evaluated in terms of density-functional-theory calculations with small models extracted from the QM region of the whole-enzyme model.
Amino Acid Sequence↗
Participation of multioxidants in the pH dependence of the reactivity of ferrate(VI).
Alcohol oxidation by ferrate (FeO(4)(2)(-)) in water is investigated from B3LYP density functional theory calculations in the framework of polarizable continuum model. The oxidizing power of three species, nonprotonated, monoprotonated, and diprotonated ferrates, was evaluated. The LUMO energy levels of nonprotonated and monoprotonated ferrates are greatly reduced by solvent effects, and as a result the oxidizing power of these two species is increased enough to effectively mediate a hydrogen-atom abstraction from the C-H and O-H bonds of methanol. The oxidizing power of these oxidants increases in the order nonprotonated ferrate < monoprotonated ferrate < diprotonated ferrate. The reaction pathway is initiated by C-H bond activation, followed by the formation of a hydroxymethyl radical intermediate or an organometallic intermediate with an Fe-C bond. Kinetic aspects of this reaction are analyzed from calculated energy profiles and experimentally known pK(a) values. The pH dependence of this reaction in water is explained well in terms of a multioxidant scheme.
Journal Article↗
Catalytic roles of active-site amino acid residues of coenzyme B12-dependent diol dehydratase: protonation state of histidine and pull effect of glutamate.
The hydrogen abstraction and the OH migration processes catalyzed by diol dehydratase are discussed by means of a quantum mechanical/molecular mechanical method. To evaluate the push effect of His143 and the pull effect of Glu170, we considered three kinds of whole-enzyme model, the protonated and two unprotonated His143 models. A calculated activation energy for the hydrogen abstraction by the adenosyl radical is 15.6 (13.6) kcal/mol in the protonated (unprotonated) His143 model. QM/MM calculational results show that the mechanism of the OH migration is significantly changed by the protonation of His143. In the protonated His143 model, the OH group migration triggered by the full proton donation from the imidazolium to the migrating OH group occurs by a stepwise OH abstraction/re-addition process in which the water production reduces the barrier for the C-O bond cleavage. On the other hand, the OH migration in the unprotonated His143 model proceeds in a concerted manner, as we previously proposed using a simple model including only K+ ion and substrate. The latter mechanism seems to be kinetically more favorable from the calculated energy profiles and is consistent with experimental results. The activation barrier of the OH group migration step is only 1.6 kcal/mol reduced by the hydrogen-bonding interaction between the O2 of the substrate and unprotonated His143. Thus, it is predicted that His143 is not protonated, and therefore the main active-site amino acid residue that lowers the energy of the transition state for the OH group migration is determined to be Glu170.
Binding Sites↗
Oscillation of conductance in molecular junctions of carbon ladder compounds.
The electrical conductances of dithiolates of polyacene (PA(n)DTs) and polyphenanthrene (PPh(n)DTs), which are typical carbon ladder compounds, are calculated by means of the Landauer formulation combined with density functional theory, where n is the number of benzene rings involved. Surface Green function used in the Landauer formulation is calculated with the Slater-Koster parameters. Attention is turned to the wire-length dependence of the conductances of PA(n)DTs and PPh(n)DTs. The damping of conductance of PA(n)DTs is much smaller than that of PPh(n)DTs because of the small HOMO-LUMO gaps of PA(n)DTs. PA(n)DTs are thus good molecular wires for nanosized electronic devices. Conductance oscillation is found for both molecular wires when n is less than 7. The electrical conductance is enhanced in PA(n)DTs with even-numbered benzene rings, whereas it is enhanced in PPh(n)DTs with odd-numbered benzene rings. The observed conductance oscillation of PA(n)DTs and PPh(n)DTs is due to the oscillation of orbital energy and electron population. Other pi-conjugated oligomers (polyacetylene-DT, oligo(thiophene)-DT, oligo(meso-meso-linked zinc(II) porphyrin-butadiynylene)-DT, oligo(p-phenylethynylene)-DT, and oligo(p-phenylene)-DT) are also studied. In contrast to PA(n)DTs and PPh(n)DTs, the five molecular wires show ordinary exponential decays of conductance.
Journal Article↗
Highly versatile organostibine mediators for living radical polymerization.
A new versatile method for conducting living radical polymerization has been developed in which organostibines induce consecutive group-transfer radical reactions with alkenes. The method has been successfully applied, for the first time, to the controlled polymerization of both conjugated and unconjugated vinyl monomers, and the desired polymers with predetermined molecular weight and low polydispersity index were obtained in excellent yields. This characteristic feature of this method is exemplified in the first synthesis of block copolymers composed of conjugated and unconjugated monomers, which would be of great importance as functional smart organic nanomaterials.
Journal Article↗
Green's function formalism coupled with Gaussian broadening of discrete states for quantum transport: application to atomic and molecular wires.
A Green's function formalism incorporating broadened density of states (DOS) is proposed for the calculation of electrical conductance. In cluster-molecule-cluster systems, broadened DOS of the clusters are defined as continuous DOS of electrodes and used to calculate Green's function of electrodes. This approach combined with density functional theory is applied to the electrical transmission of gold atomic wires and molecular wires consisting of benzene-1,4-dithiolate, benzene-1,4-dimethanethiolate, 4,4(')-bipyridine, hexane dithiolate, and octane dithiolate. The B3LYP, B3PW91, MPW1PW91, SVWN, and BPW91 functionals with the LANL2DZ, CEP, and SDD basis sets are employed in the calculation of conductance. The width parameter was successfully determined to reproduce the quantum unit of conductance 2e(2)/h in gold atomic wires. The combination of the B3LYP hybrid functional and the CEP-31G basis set is excellent in reproducing measured conductances of molecular wires by Tao et al. [Science 301, 1221 (2003); J. Am. Chem. Soc. 125, 16164 (2003); Nano Lett. 4, 267 (2004)].
Journal Article↗
How heme metabolism occurs in heme oxygenase: computational study of oxygen-donation ability of the oxo and hydroperoxo species.
We report a density functional theory study on the heme metabolism in heme oxygenase using iron-hydroperoxo and -oxo models. The activation energies for heme oxidation at the alpha-carbon by the iron-hydroperoxo and -oxo species are calculated to be 42.9 and 39.9 kcal/mol, respectively. These high activation barriers lead us to reconsider the catalytic mechanism of heme oxygenase
Computational Biology↗
Theoretical measurements of conductance in an (AT)12 DNA molecule.
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Adenine↗
A non-radical mechanism for methane hydroxylation at the diiron active site of soluble methane monooxygenase.
We propose a non-radical mechanism for the conversion of methane into methanol by soluble methane monooxygenase (sMMO), the active site of which involves a diiron active center. We assume the active site of the MMOH(Q) intermediate, exhibiting direct reactivity with the methane substrate, to be a bis(mu-oxo)diiron(IV) complex in which one of the iron atoms is coordinatively unsaturated (five-coordinate). Is it reasonable for such a diiron complex to be formed in the catalytic reaction of sMMO? The answer to this important question is positive from the viewpoint of energetics in density functional theory (DFT) calculations. Our model thus has a vacant coordination site for substrate methane. If MMOH(Q) involves a coordinatively unsaturated iron atom at the active center, methane is effectively converted into methanol in the broken-symmetry singlet state by a non-radical mechanism; in the first step a methane C-H bond is dissociated via a four-centered transition state (TS1) resulting in an important intermediate involving a hydroxo ligand and a methyl ligand, and in the second step the binding of the methyl ligand and the hydroxo ligand through a three-centered transition state (TS2) results in the formation of a methanol complex. This mechanism is essentially identical to that of the methane-methanol conversion by the bare FeO(+) complex and relevant transition metal-oxo complexes in the gas phase. Neither radical species nor ionic species are involved in this mechanism. We look in detail at kinetic isotope effects (KIEs) for H atom abstraction from methane on the basis of transition state theory with Wigner tunneling corrections.
Binding Sites↗
A theoretical study of reactivity and regioselectivity in the hydroxylation of adamantane by ferrate(VI).
The conversion of adamantane to adamantanols mediated by ferrate (FeO(4)(2)(-)), monoprotonated ferrate (HFeO(4)(-)), and diprotonated ferrate (H(2)FeO(4)) is discussed with the hybrid B3LYP density functional theory (DFT) method. Diprotonated ferrate is the best mediator for the activation of the C-H bonds of adamantane via two reaction pathways, in which 1-adamantanol is formed by the abstraction of a tertiary hydrogen atom (3 degrees ) and 2-adamantanol by the abstraction of a secondary hydrogen atom (2 degrees ). Each reaction pathway is initiated by a C-H bond cleavage via an H-atom abstraction that leads to a radical intermediate, followed by a C-O bond formation via an oxygen rebound step to lead to an adamantanol complex. The activation energies for the C-H cleavage step are 6.9 kcal/mol in the 1-adamantanol pathway and 8.4 kcal/mol in the 2-adamantanol pathway, respectively, at the B3LYP/6-311++G level of theory, whereas those of the second reaction step corresponding to the rebound step are relatively small. Thus, the rate-determining step in the two pathways is the C-H bond dissociation step, which is relevant to the regioselectivity for adamantane hydroxylation. The relative rate constant (3 degrees )/(2 degrees ) for the competing H-atom abstraction reactions is calculated to be 9.30 at 75 degrees C, which is fully consistent with an experimental value of 10.1.
Journal Article↗