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Per E. M. Siegbahn - One of the best experts on this subject based on the ideXlab platform.
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Theoretical study of the Catalytic Reaction Mechanism of MndD
JBIC Journal of Biological Inorganic Chemistry, 2006Co-Authors: Valentin Georgiev, Tomasz Borowski, Per E. M. SiegbahnAbstract:Manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) is an enzyme taking part in the catabolism of aromatic compounds in the environment. It uses molecular oxygen to perform an extradiol cleavage of the ring of the ortho -dihydroxylated aromatic compound homoprotocatechuate. A theoretical investigation of the Reaction path for MndD was performed using hybrid density functional theory with the B3LYP functional, and a Catalytic Mechanism has been suggested. Models of different size were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the substrate first binds at the active site as a monoanion. Next the dioxygen is bound, forming a hydroperoxo intermediate. The O–O bond, activated in this way undergoes homolytic cleavage leading to an oxyl and then to an extra epoxide radical with subsequent opening of the aromatic ring. The lactone ring is then hydrolyzed by the Mn-bound OH group, and the final product is obtained in the last Reaction steps. Alternative Reaction paths were considered, and their calculated barriers were found to be higher than for the suggested Mechanism. The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state.
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Catalytic Reaction Mechanism of homogentisate dioxygenase a hybrid dft study
Journal of the American Chemical Society, 2005Co-Authors: Tomasz Borowski, Valentin Georgiev, Per E. M. SiegbahnAbstract:Human homogentisate dioxygenase is an FeII-dependent enzyme responsible for aromatic ring cleavage. The Mechanism of its Catalytic Reaction has been investigated with the hybrid density functional method B3LYP. A relatively big model of the active site was first used to determine the substrate binding mode. It was found that binding of the substrate dianion with a vacant position trans to Glu341 is most favorable. The model was then truncated to include only the most relevant parts of the active-site residues involved in iron coordination and substrate binding. Thus, methylimidazole was used to model His292, His335, His365, and His371, while propionate modeled Glu341. The computational results suggest that the Catalytic Reaction of homogentisate dioxygenases involves three major chemical steps: formation of the peroxo intermediate, homolytic cleavage of the O−O bond leading to an arene oxide radical, and finally, cleavage of the six-membered ring. Calculated barriers for alternative Reaction paths are ma...
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Catalytic Reaction Mechanism of Oxalate Oxidase (Germin). A Hybrid DFT Study
Journal of Chemical Theory and Computation, 2005Co-Authors: Tomasz Borowski, Nigel G J Richards, Arianna Bassan, Per E. M. SiegbahnAbstract:The Mechanism of the Catalytic Reaction for oxalate oxidase has been investigated with the hybrid density functional method B3LYP. The models used in the calculations comprise of the manganese ion, three imidazoles, and one acetate, which model the active-site Mn(II) and its first-shell protein ligands. Moreover, the reactants, i.e., singly protonated oxalate and dioxygen, have been explicitly considered. The computational results suggest that the enzyme−oxalate complex can adopt two conformations, one with bidentate oxalate and 6-coordinate manganese and the second one with monodentate substrate and coordinatively unsaturated Mn(II). This second species reacts with dioxygen on the quartet potential energy surface, and in a rate-limiting step yields one CO2 molecule and a reactive intermediate, in which Mn(III) is coordinated by HOO- and a formyl radical anion. A subsequent fast spin transition, from the quartet to the sextet spin state, allows an electron transfer from the formyl radical anion to Mn(III)...
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4 hydroxyphenylpyruvate dioxygenase a hybrid density functional study of the Catalytic Reaction Mechanism
Biochemistry, 2004Co-Authors: Tomasz Borowski, And Arianna Bassan, Per E. M. SiegbahnAbstract:Density functional calculations using the B3LYP functional has been used to study the Reaction Mechanism of 4-hydroxyphenylpyruvate dioxygenase. The first part of the Catalytic Reaction, dioxygen activation, is found to have the same Mechanism as in α-ketoglutarate-dependent enzymes; the ternary enzyme−substrate−dioxygen complex is first decarboxylated to the iron(II)-peracid intermediate, followed by heterolytic cleavage of the O−O bond yielding an iron(IV)-oxo species. This highly reactive intermediate attacks the aromatic ring at the C1 position and forms a radical σ complex, which can either form an arene oxide or undergo a C1−C2 side-chain migration. The arene oxide is found to have no Catalytic relevance. The side-chain migration is a two-step process; the carbon−carbon bond cleavage first affords a biradical intermediate, followed by a decay of this species forming the new C−C bond. The ketone intermediate formed by a 1,2 shift of an acetic acid group rearomatizes either at the active site of the e...
Tomasz Borowski - One of the best experts on this subject based on the ideXlab platform.
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Theoretical study of the Catalytic Reaction Mechanism of MndD
JBIC Journal of Biological Inorganic Chemistry, 2006Co-Authors: Valentin Georgiev, Tomasz Borowski, Per E. M. SiegbahnAbstract:Manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) is an enzyme taking part in the catabolism of aromatic compounds in the environment. It uses molecular oxygen to perform an extradiol cleavage of the ring of the ortho -dihydroxylated aromatic compound homoprotocatechuate. A theoretical investigation of the Reaction path for MndD was performed using hybrid density functional theory with the B3LYP functional, and a Catalytic Mechanism has been suggested. Models of different size were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the substrate first binds at the active site as a monoanion. Next the dioxygen is bound, forming a hydroperoxo intermediate. The O–O bond, activated in this way undergoes homolytic cleavage leading to an oxyl and then to an extra epoxide radical with subsequent opening of the aromatic ring. The lactone ring is then hydrolyzed by the Mn-bound OH group, and the final product is obtained in the last Reaction steps. Alternative Reaction paths were considered, and their calculated barriers were found to be higher than for the suggested Mechanism. The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state.
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Catalytic Reaction Mechanism of homogentisate dioxygenase a hybrid dft study
Journal of the American Chemical Society, 2005Co-Authors: Tomasz Borowski, Valentin Georgiev, Per E. M. SiegbahnAbstract:Human homogentisate dioxygenase is an FeII-dependent enzyme responsible for aromatic ring cleavage. The Mechanism of its Catalytic Reaction has been investigated with the hybrid density functional method B3LYP. A relatively big model of the active site was first used to determine the substrate binding mode. It was found that binding of the substrate dianion with a vacant position trans to Glu341 is most favorable. The model was then truncated to include only the most relevant parts of the active-site residues involved in iron coordination and substrate binding. Thus, methylimidazole was used to model His292, His335, His365, and His371, while propionate modeled Glu341. The computational results suggest that the Catalytic Reaction of homogentisate dioxygenases involves three major chemical steps: formation of the peroxo intermediate, homolytic cleavage of the O−O bond leading to an arene oxide radical, and finally, cleavage of the six-membered ring. Calculated barriers for alternative Reaction paths are ma...
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Catalytic Reaction Mechanism of Oxalate Oxidase (Germin). A Hybrid DFT Study
Journal of Chemical Theory and Computation, 2005Co-Authors: Tomasz Borowski, Nigel G J Richards, Arianna Bassan, Per E. M. SiegbahnAbstract:The Mechanism of the Catalytic Reaction for oxalate oxidase has been investigated with the hybrid density functional method B3LYP. The models used in the calculations comprise of the manganese ion, three imidazoles, and one acetate, which model the active-site Mn(II) and its first-shell protein ligands. Moreover, the reactants, i.e., singly protonated oxalate and dioxygen, have been explicitly considered. The computational results suggest that the enzyme−oxalate complex can adopt two conformations, one with bidentate oxalate and 6-coordinate manganese and the second one with monodentate substrate and coordinatively unsaturated Mn(II). This second species reacts with dioxygen on the quartet potential energy surface, and in a rate-limiting step yields one CO2 molecule and a reactive intermediate, in which Mn(III) is coordinated by HOO- and a formyl radical anion. A subsequent fast spin transition, from the quartet to the sextet spin state, allows an electron transfer from the formyl radical anion to Mn(III)...
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4 hydroxyphenylpyruvate dioxygenase a hybrid density functional study of the Catalytic Reaction Mechanism
Biochemistry, 2004Co-Authors: Tomasz Borowski, And Arianna Bassan, Per E. M. SiegbahnAbstract:Density functional calculations using the B3LYP functional has been used to study the Reaction Mechanism of 4-hydroxyphenylpyruvate dioxygenase. The first part of the Catalytic Reaction, dioxygen activation, is found to have the same Mechanism as in α-ketoglutarate-dependent enzymes; the ternary enzyme−substrate−dioxygen complex is first decarboxylated to the iron(II)-peracid intermediate, followed by heterolytic cleavage of the O−O bond yielding an iron(IV)-oxo species. This highly reactive intermediate attacks the aromatic ring at the C1 position and forms a radical σ complex, which can either form an arene oxide or undergo a C1−C2 side-chain migration. The arene oxide is found to have no Catalytic relevance. The side-chain migration is a two-step process; the carbon−carbon bond cleavage first affords a biradical intermediate, followed by a decay of this species forming the new C−C bond. The ketone intermediate formed by a 1,2 shift of an acetic acid group rearomatizes either at the active site of the e...
Qiuhong Ai - One of the best experts on this subject based on the ideXlab platform.
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supported tio2 mcm 41 as an efficient and eco friendly catalyst for highly selective preparation of cyclohexanone oxime from solvent free liquid phase oxidation of cyclohexylamine with molecular oxygen
Applied Catalysis A-general, 2018Co-Authors: Jinyuan Song, Renjie Deng, Fangfang Zhao, Qiuhong AiAbstract:Abstract A green and efficient approach for solvent-free selective Catalytic oxidation of cyclohexylamine to cyclohexanone oxime in liquid phase has been developed. The results showed that the supported 30%TiO2/MCM-41 as efficient and eco-friendly catalyst gave 78.4% of cyclohexylamine conversion with 89.1% of selectivity to cyclohexanone oxime. It has been demonstrated that the Catalytic active sites are the surface titanium hydroxyl groups of catalyst. Moreover, the present catalyst can be easily separated, recycled, regenerated and reused. The probable Catalytic Reaction Mechanism of cyclohexylamine with molecular oxygen over supported TiO2/MCM-41 was suggested. This work affords a new and environmentally friendly route for the synthesis of cyclohexanone oxime, and has important industrial application prospects.
Zhengyi Fu - One of the best experts on this subject based on the ideXlab platform.
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Solvent-free Catalytic synthesis and optical properties of super-hard phase ultrafine carbon nitride nanowires with abundant surface active sites
RSC Advances, 2020Co-Authors: Jilin Wang, Yunle Gu, Shuyi Mo, Lulu Zhang, Fei Long, Weimin Wang, Zhengyi FuAbstract:High-quality ultrafine α/β-carbon nitride (α/β-C3N4) nanowires have been fabricated through a novel hot melt reduction synthetic method using polyvinylchloride ([–C2H3Cl–]n), ammonium chloride (NH4Cl) and ferric oxide (Fe2O3) as raw materials. The purity, structure, morphology, crystallinity and surface state of the as-prepared samples were investigated by FSEM, TEM, HRTEM, SAED, XRD, EDX, FTIR and XPS. The nanowires presented good crystallinity with a length range of 1–4 μm and an average diameter of about 10 nm. Every nanowire possessed a high specific surface area and rough surface with abundant exposed atoms/prominences, indicating that the surface structure will facilitate further surface modification, functionalization and related applications. In addition, UV-vis diffuse reflectance and the corresponding photoluminescence (PL) spectra indicated that the nanowires have a wide band gap (4.38 eV) and obvious ultraviolet luminescence properties at the maximum emission peak of about 340 nm. A Catalytic Reaction Mechanism and the growth model were also proposed to explain the formation process of the C3N4 nanowires.
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low temperature synthesis of polycrystalline explosion phase boron nitride submicron powders
Diamond and Related Materials, 2013Co-Authors: Jilin Wang, Yunle Gu, Weimin Wang, Zili Li, Zhengyi FuAbstract:Abstract High purity quasi-octahedral polycrystalline explosion phase boron nitride (e-BN) submicron-powders were synthesized in an autoclave at 600 °C for 6 h using Mg, FeB1.3 and NH4Cl as the raw materials. Samples were characterized by SEM, FSEM, EDX, TEM, HRTEM, SAED, X-ray powder diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy. The as-synthesized e-BN powders demonstrated a face-centered cubic structure with lattice parameter of 8.300 A. Besides the e-BN samples presented a quasi-octahedral morphology with an average diameter of 0.8 μm. The effects of time, temperature, raw materials and possible Catalytic Reaction Mechanism of the growth of quasi-octahedral polycrystalline e-BN were also discussed.
Inaki Tunon - One of the best experts on this subject based on the ideXlab platform.
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Catalytic Reaction Mechanism in Native and Mutant COMT from the Adaptive String Method and Mean Reaction Force Analysis.
2020Co-Authors: David Adrian Saez, Inaki Tunon, Kirill Zinovjev, Esteban Vöhringer-martinezAbstract:Catechol-O-Methyltransferase is an enzyme which catalyzes the methylation Reaction of dopamine by <i>S</i>-Adenosylmethionine increasing the Reaction rate by almost 16 orders of magnitude compared to the Reaction in aqueous solution. Here, we combine the recently introduced adaptive string method and the Mean Reaction Force method in combination with structural and electronic descriptors to characterize the Reaction Mechanism. The Catalytic effect of the enzyme is addressed by comparison of the Reaction Mechanism in the human wild-type enzyme, in the less effective Y68A mutant and in aqueous solution. The influence of these different environments at different stages of the chemical process and the significance of key collective variables describing the Reaction were quantified. Our results show that the native enzyme limits the access of water molecules to the active site, enhancing the interaction between the reactants and providing a more favorable electrostatic environment to assist the S<sub>N</sub>2 methyl transfer Reaction.
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elucidating the Catalytic Reaction Mechanism of orotate phosphoribosyltransferase by means of x ray crystallography and computational simulations
ACS Catalysis, 2020Co-Authors: Maite Roca, Sergio Navasyuste, Kirill Zinovjev, Miguel Lopezestepa, Sara Gomez, Francisco J Fernandez, Cristina M Vega, Inaki TunonAbstract:Orotate phosphoribosyltransferase (OPRTase) catalyzes the Reaction between the ribose donor α-d-5-phosphoribosyl-1-pyrophosphate (PRPP) and orotate (OA) in the presence of Mg2+ ion to obtain pyrophosphate and pyrimidine nucleotide orotidine 5′-monophosphate (OMP), a key precursor in de novo biosynthesis of pyrimidine nucleotides. In this work, several structures of the dimeric Escherichia coli OPRTase (EcOPRTase) have been determined at high resolution, and kinetic measurements have been carried out to obtain the Catalytic rate and Michaelis constants. Molecular dynamics (MD) simulations have been carried out, and structural analysis from the X-ray and MD simulation structures reveals conformational changes related to the flexible Catalytic loop that establishes hydrogen bond interactions with the pyrophosphoryl group of PRPP. It is proposed that the OA substrate can be in equilibrium in its tautomeric forms. Starting from the most stable tautomeric form, all the plausible Mechanisms have been explored by...