| 1. |
- Bruschi, Maurizio, et al.
(författare)
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A DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenases active site
- 2008
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Ingår i: Comptes Rendus. Chimie. - : Elsevier BV. - 1631-0748. ; 11:8, s. 834-841
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Tidskriftsartikel (refereegranskat)abstract
- In the present contribution, a density functional theory (DFT) investigation is described regarding a recently synthesized Fe6S6 complex - see C. Tard, X. Liu, S.K. Ibrahim, M. Bruschi, L. De Gioia, S.C. Davies, X. Yang, L.-S. Wang, G. Sawers, C.J. Pickett, Nature 433 (2005) 610 - that is structurally and functionally related to the [FeFe]-hydrogenases active site (the so-called H-cluster, which includes a binuclear subsite directly involved in catalysis and an Fe4S4 cubane). The analysis of relative stabilities and atomic charges of different isomers evidenced that the structural and redox properties of the synthetic assembly are significantly different from those of the enzyme active site. A comparison between the hexanuclear cluster and simpler synthetic diiron models is also described; the results of such a comparison indicated that the cubane moiety can favour the stabilization of the cluster in a structure closely resembling the H-cluster geometry when the synthetic Fe6S6 complex is in its dianionic state. However, the opposite effect is observed when the synthetic cluster is in its monoanionic form.
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| 2. |
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| 3. |
- Chen, Shilu, 1979-
(författare)
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Quantum Chemical Modeling of Binuclear Zinc Enzymes
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In the present thesis, the reaction mechanisms of several di-zinc hydrolases have been explored using quantum chemical modeling of the enzyme active sites. The studied enzymes are phosphotriesterase (PTE), aminopeptidase from Aeromonas proteolytica (AAP), glyoxalase II (GlxII), and alkaline phosphatase (AP). All of them contain a binuclear divalent zinc core in the active site. The density functional theory (DFT) method B3LYP functional was employed in the investigations. The potential energy surfaces (PESs) for various reaction pathways have been mapped and the involved transition states and intermediates have been characterized. The hydrolyses of different types of substrates were examined, including phosphate esters (PTE and AP) and the substrates containing carbonyl group (AAP and GlxII). The roles of zinc ions and individual active-site residues were analyzed and general features of di-zinc enzymes have been characterized. The bridging hydroxide stabilized by two zinc ions has been confirmed to be capable of the nucleophile in the hydrolysis reactions. PTE, AAP, and GlxII all employ the bridging hydroxide as the direct nucleophile. Furthermore, it is shown that either one of or both zinc ions provide the main catalytic power by stabilizing the negative charge developing during the reaction and thereby lowering the barriers. In the cases of GlxII and AP, one of zinc ions also contributes to the catalysis by stabilizing the leaving group. These features perfectly satisfy the two requisites for the hydrolysis, i.e. sufficient nucleophilicity and stabilization of charge. A competing mechanism, in which the bridging hydroxide acts as a base, was shown to have significantly higher barrier in the case of PTE. For phosphate hydrolysis reactions, it is important to characterize the nature of the transition states involved in the reactions. Associative mechanisms were observed for both PTE and AP. The former uses a step-wise associative pathway via a penta-coordinated intermediate, while the latter proceeds through a concerted associative path via penta-coordinated transition states. Finally, with PTE as a test case, systematic evaluation of the computational performance of the quantum chemical modeling approach has been performed. This assessment, coupled with other results of this thesis, provide an effective demonstration of the usefulness and powerfulness of quantum chemical active-site modeling in the exploration of enzyme reaction mechanisms and in the characterization of the transition states involved.
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| 4. |
- Eilers, Gerriet, et al.
(författare)
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Ligand versus metal protonation of an iron hydrogenase active site mimic
- 2007
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 13:25, s. 7075-7084
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Tidskriftsartikel (refereegranskat)abstract
- The protonation behavior of the iron hydrogenase active-site mimic [Fe2(u-adt)(CO)4(PMe3)2] (1; adt=N-benzyl-azadithiolate) has been investigated by spectroscopic, electrochemical, and computational methods. The combination of an adt bridge and electron-donating phosphine ligands allows protonation of either the adt nitrogen to give [Fe2(μ-Hadt)(CO)4(PMe3)2]+ ([1H]+), the Fe-Fe bond to give [Fe2-(μ-adt)(μ-H)(CO)4(PMe3)2]+ ([1Hy]+), or both sites simultaneously to give [Fe2(μ-Hadt)(μ-H)(CO)4(PMe3)2]2+ ([1HHy]2+). Complex 1 and its protonation products have been characterized in acetonitrile solution by IR, 1H, and 31PNMR spectroscopy. The solution structures of all protonation states feature a basal/basal orientation of the phosphine ligands, which contrasts with the basal/apical structure of 1 in the solid state. Density functional calculations have been performed on all protonation states and a comparison between calculated and experimental spectra confirms the structural assignments. The ligand protonated complex [1H]+ (pKa =12) is the initial, metastable protonation product while the hydride [1Hy]+ (pKa=15) is the thermodynamically stable singly protonated form. Tautomerization of cation [1H]+ to [1Hy]+ does not occur spontaneously. However, it can be catalyzed by HCl (k=2.2M-1s-1), which results in the selective formation of cation [1Hy]+. The protonations of the two basic sites have strong mutual effects on their basicities such that the hydride (pKa=8) and the ammonium proton (pKa=5) of the doubly protonated cationic complex [1HHy]2+ are considerably more acidic than in the singly protonated analogues. The formation of dication [1HHy]2+ from cation [1H]+ is exceptionally slow with perchloric or trifluoromethanesulfonic acid (k= 0.15 M-1s-1), while the dication is formed substantially faster (k > 102 M-1 s-1) with hydrobromic acid. Electrochemically, 1 undergoes irreversible reduction at -2.2V versus ferrocene, and this potential shifts to -1.6, - 1.1, and -1.0 V for the cationic complexes [1H]+, [1Hy]+, and [1HHy]2+, respectively, upon protonation. The doubly protonated form [1HHy]2+ is reduced at less negative potential than all previously reported hydrogenase models, although catalytic proton reduction at this potential is characterized by slow turnover.
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| 5. |
- Greco, Claudio, et al.
(författare)
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A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases
- 2007
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 46:15, s. 5911-5921
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Tidskriftsartikel (refereegranskat)abstract
- Fe-only hydrogenases are enzymes that catalyze dihydrogen production or oxidation, due to the presence of an unusual Fe6S6 cluster (the so-called H-cluster) in their active site, which is composed of a Fe2S2 subsite, directly involved in catalysis, and a classical Fe4S4 cubane cluster. Here, we present a hybrid quantum mechanical and molecular mechanical (QM/MM) investigation of the Fe-only hydrogenase from Desulfovibrio desulfuricans, in order to unravel key issues regarding the activation of the enzyme from its completely oxidized inactive state (H-ox(inac)) and the influence of the protein environment on the structural and catalytic properties of the H-cluster. Our results show that the Fe2S2 subcluster in the (FeFeII)-Fe-II redox statewhich is experimentally observed for the completely oxidized form of the enzymebinds a water molecule to one of its metal centers. The computed QM/MM energy values for water binding to the diferrous subsite are in fact over 70 kJ mol(-1); however, the affinity toward water decreases by 1 order of magnitude after a one-electron reduction of H-ox(inact), thus leading to the release of coordinated water from the H-cluster. The investigation of a catalytic cycle of the Fe-only hydrogenase that implies formation of a terminal hydride ion and a di(thiomethyl)amine (DTMA) molecule acting as an acid/base catalyst indicates that all steps have reasonable reaction energies and that the influence of the protein on the thermodynamic profile of H-2 production catalysis is not negligible. QM/MM results show that the interactions between the Fe2S2 subsite and the protein environment could give place to structural rearrangements of the H-cluster functional for catalysis, provided that the bidentate ligand that bridges the iron atoms in the binuclear subsite is actually a DTMA residue.
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| 6. |
- Greco, Claudio, et al.
(författare)
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Structural insights into the active-ready form of [FeFe]-Hydrogenase and mechanistic details of its inhibition by carbon monoxide
- 2007
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 46:18, s. 7256-7258
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Tidskriftsartikel (refereegranskat)abstract
- [FeFe]-Hydrogenases harbor a {2Fe3S} assembly bearing two CO and two CN- groups, a mu-CO ligand, and a vacant coordination site trans to the mu-CO group. Recent theoretical results obtained studying the isolated {2Fe3S} subsite indicated that one of the CN- ligands can easily move from the crystallographic position to the coordination site trans to the mu-CO group; such an isomerization would have a major impact on substrates and inhibitors binding regiochemistry and, consequently, on the catalytic mechanism. To shed light on this crucial issue, we have carried out hybrid QM/MM and free energy perturbation calculations on the whole enzyme, which demonstrate that the protein environment plays a crucial role and maintains the CN- group fixed in the position observed in the crystal structure; these results strongly support the hypothesis that the vacant coordination site trans to the mu-CO group has a crucial functional relevance both in the context of CO-mediated inhibition of the enzyme and in dihydrogen oxidation/evolution catalysis.
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