Quantum chemical modeling of reaction mechanism for 2-oxoglutarate dependent enzymes: effect of substitution of iron by nickel and cobalt

Enzymatic hydroxylation reactions carried out by 2-oxoglutarate (2OG) dependent iron-containing oxygenases were recently implicated in oxygen sensing. In addition to oxygen depletion, two metals, cobalt and nickel, are capable of inducing hypoxic stress in cells by inhibiting oxygenase activity. Two possible scenarios have been proposed for the explanation of the hypoxic effects of cobalt and nickel: oxidation of enzyme-bound iron following cobalt or nickel exposure, and substitution of iron by cobalt or nickel. Here, by using density functional theory calculations, we modeled the reaction route from the reaction components to the high-spin metal-oxide intermediate in the activation of oxygen molecule by 2OG-dependent enzymes for three metal ions Fe(II), Ni(II), and Co(II) in the active site. An initial molecular model was constructed based on the crystal structure of iron-containing asparaginyl hydroxylase (FIH-1). Nickel- and cobalt-containing enzymes were modeled by a consequent replacement of the iron in the active center. The energy profiles connecting stationary points on the potential surfaces were computed by using the intrinsic reaction coordinate (IRC) technique from the located transition states. The results of calculations show that the substitution of iron by nickel or cobalt modifies the reaction energy profile; however, qualitatively, the reaction mechanism remains essentially the same. Thus, we would postulate that if the iron ion in the active site were substitutable by nickel and/or cobalt ions enzyme activity would be considerably altered due to high activation barriers.     

(Salen)Mn-catalyzed epoxidation of alkenes: a two-zone process with different spin-state channels as suggested by DFT study

[structure: see text] A novel (two-zone process with different spin-state channels) mechanistic picture for the Jacobsen-Katsuki reaction is presented that provides insight into the still elusive understanding of the epoxidation mechanism. For the first time, we show that the salen moiety of the catalyst can be explicitly involved in the epoxidation process.     

A theoretical study of the molecule of boric oxide B2O3

Conclusion At the present time there is definite experimental material on the geometric configurations and vibrational frequencies for molecules and ions of the type X₂Y₃, namely: B₂O₃, Xe₂F ₃ ⁺ [29], I ₅ ^– [30, 31], H₂F ₃ ⁺ [32], etc. All of them, within the limits of accuracy of the experimental data, have a planar geometric configuration YXYXY, and the angle XYX, with the exception of I ₅ ^– , is close to 135° (137.5, 151.95, and 130–139° in the series given above), the angle YXY is close to 180° (174–178°), and the distance from a terminal atom Y to the neighboring atom X is approximately 10% shorter than the corresponding distance from the central atom Y to the neighboring atoms X. The estimated frequency of the bending vibration has comparatively low values: 70–100 cm^–1 for B₂O₃ in a matrix, and 160 cm^–1 for XeF ₃ ⁺ in the crystal. These data indicate the existence of a class of deformationally nonrigid molecules of the type X₂Y₃, which must contain other molecules in addition to those listed above. The detailed study of this class of compound will make it posible to answer a number of questions which have not yet been resolved, for example those associated with the difference in the composition of the vapor over B₂O₃ and Al₂O₃, etc. The experience of the present work shows that such a study should include, as a natural and necessary component, quantum-mechanical calculations, whose results generally make it possible to resolve disputed problems, to establish a correspondence between different experimental data, and to obtain information on the structure of potential surfaces and the electronic structures of different states of the molecules being studied, which cannot yet be obtained experimentally.All-Union Scientific-Research Institute for the Metrological Service. Chemistry Department, Moscow State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 22, No. 1, pp. 29–38, January–February, 1981.     

Single- and Double-Beam Optical Formation of Relief-Phase Diffraction Microstructures in Carbazole-Containing Azopolymer Films

Optics and Spectroscopy - Single- and double-beam formation of diffraction microstructures in carbazole-containing azopolymer films is presented. The possibility of recording single...     

On a weighted boundary-value problem in an infinite half-strip for a biaxisymmetric Helmholtz equation

We study a boundary-value problem for a generalized biaxisymmetric Helmholtz equation. Boundary conditions in this problem depend on equation parameters. By the method of separation of variables, using the Fourier-Bessel series expansion and the Hankel transform, we prove the unique solvability of the problem and establish explicit formulas for its solution.     

(Salen)Mn(III)-catalyzed epoxidation reaction as a multichannel process with different spin states. Electronic tuning of asymmetric catalysis: a theoretical study

The (salen)Mn(III)-catalyzed epoxidation reaction mechanism has been investigated using density functional theory (DFT). There is considerable interest in and controversy over the mechanism of this reaction. The results of experimental studies have offered some support for three different reaction mechanisms: concerted, stepwise radical, and metallooxetane mediated. In this paper, a theoretical examination of the reaction suggests a novel mechanism that describes the reaction as a multichannel process combining both concerted and stepwise radical pathways. The competing channels have different spin states: the singlet, the triplet, and the quintet. The singlet reaction pathway corresponds to a concerted mechanism and leads exclusively to a cis epoxide product. In contrast, the triplet and quintet reactions follow a stepwise mechanism and lead to a product mixture of cis and trans epoxides. We show that the experimentally observed dependence of isomer product ratios on electronic effects connected with the substitution of the catalyst ligands is due to changing the relative position and, hence, the relative activities of the channels with different cis-trans yields. Because the results and conclusions of the present work dramatically differ from the results and conclusion of the recent DFT theoretical investigation (Linde, C.; Akermark, B; Norrby, P.-O.; Svensson, M. J. Am. Chem. Soc. 1999, 121, 5083.), we studied possible sources for the deep contradictions between the two works. The choice of the DFT functional and a model has been shown to be crucial for accurate results. Using high level ab initio calculations (coupled cluster-CCSD(T)), we show that the computational procedure employed in this study generates significantly more reliable numerical results. It is also shown that the smaller cationic model without a chlorine ligand that was used by Linde et al. is too oversimplified with respect to our larger neutral model. For this reason, using the cationic model led to a qualitatively wrong quintet reaction profile that played a key role in theoretical postulates in the earlier work.