Mechanisms of metalloenzymes studied by quantum chemical methods

Siegbahn, Per E. M.

doi:10.1017/s0033583502003827

Cited by 196 publications

(246 citation statements)

References 114 publications

(136 reference statements)

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“…The density fitting and chain of spheres (RIJCOSX) approximations (34) have been employed together with the def2-TZVPP/J auxiliary basis set (35). Following Siegbahn (36), the protein environment was crudely modeled by the COSMO model by taking dielectric constant as 4.0.…”

Section: Methodsmentioning

confidence: 99%

Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C–H bond activation transition state

Neese

2011

Proc. Natl. Acad. Sci. U.S.A.

245

232

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Oxo-iron(IV) species are implicated as key intermediates in the catalytic cycles of heme and nonheme oxygen activating iron enzymes that selectively functionalize aliphatic C-H bonds. Ferryl complexes can exist in either quintet or triplet ground states. Density functional theory calculations predict that the quintet oxo-iron(IV) species is more reactive toward C-H bond activation than its corresponding triplet partner, however; the available experimental data on model complexes suggests that both spin multiplicities display comparable reactivities. To clarify this ambiguity, a detailed electronic structure analysis of alkane hydroxylation by an oxo-iron(IV) species on different spin-state potential energy surfaces is performed. According to our results, the lengthening of the Fe-oxo bond in ferryl reactants, which is the part of the reaction coordinate for H-atom abstraction, leads to the formation of oxyl-iron(III) species that then perform actual C-H bond activation. The differential reactivity stems from the fact that the two spin states have different requirements for the optimal angle at which the substrate should approach the ðFeOÞ 2þ core because distinct electron acceptor orbitals are employed on the two surfaces. The H-atom abstraction on the quintet surface favors the "σ-pathway" that requires an essentially linear attack; by contrast a "π-channel" is operative on the triplet surface that leads to an ideal attack angle near 90°. However, the latter is not possible due to steric crowding; thus, the attenuated orbital interaction and the unavoidably increased Pauli repulsion result in the lower reactivity of the triplet oxo-iron(IV) complexes. density functional calculation | nonheme iron | reaction mechanism O xo-iron(IV) intermediates have attracted much interest in bioinorganic chemistry because they are implicated as key intermediates in the catalytic cycles of heme and nonheme oxygen activating iron enzymes that selectively functionalize unactivated C-H bonds (1). Detailed experimental and theoretical studies on the hydroxylation of saturated hydrocarbons by ferryl species in heme systems, foremost cytochrome P450, have been performed (2). On the other hand a number of nonheme enzymes are able to activate molecular dioxygen to modify alkane or arene substrates as well. So far, nonheme ferryl species have been spectroscopically characterized in four mononuclear iron enzymes and were found to feature high-spin (HS) (S ¼ 2) electronic ground state configurations (3). In parallel, a wide range of synthetic FeðIVÞ¼O complexes were synthesized and characterized (4). In almost all cases they contain intermediate-spin (IS) (S ¼ 1) rather than HS ferryl centers (4). The only exceptions are ½FeðIVÞðOÞðH 2 OÞ 5 2þ (5) and the recently reported model complex ½FeðIVÞðOÞðTMG 3 trenÞ 2þ (TMG 3 tren ¼ N½CH 2 CH 2 N ¼ CðNMe 2 Þ 2 ) (6). Presumably because the ðFeOÞ 2þ core is sheltered by the sterically bulky supporting ligand in ½FeðIVÞðOÞ ðTMG 3 trenÞ 2þ , its reactivity toward C-H bond cleavage is only comparabl...

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Section: Methodsmentioning

confidence: 99%

Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C–H bond activation transition state

Neese

2011

Proc. Natl. Acad. Sci. U.S.A.

245

232

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“…Glutamate and aspartate ligands were modeled as formic acids and the histidines as imidazoles, in line with the modeling of other enzymes. [16] All atoms in the complex were fully optimized, unlike the procedure in previous studies in which some atoms were frozen at their suggested X-ray positions. The reason for this change of strategy is that it was discovered that an unreasonable amount of strain was present in the OEC complex.…”

Section: Methodsmentioning

confidence: 99%

“…[17] The calculations discussed here were obtained by using the DFT hybrid functional B3LYP [8] with procedures very similar to those used in previous studies. [16,10,11,12] Small basis sets for the geometries, large basis sets for energies, and a surrounding dielectric medium with a dielectric constant equal to 4.0 were used. The main difference is that in the present study a larger basis set cc-pvtz(-f) was used for the final energies rather than the lacv3p** basis set used previously.…”

Section: Methodsmentioning

confidence: 99%

OO Bond Formation in the S₄ State of the Oxygen‐Evolving Complex in Photosystem II

Siegbahn

2006

Chemistry A European J

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309

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Based on recent X-ray structures of the oxygen-evolving complex in photosystem II, quantum chemical geometry optimizations of several thousand structures have been performed in order to elucidate the mechanism for dioxygen formation. Many of the results of these calculations have been presented previously. The energetically most stable structure of the S(4) state has been used in the present study to investigate essentially all the possible ways the O--O bond can be formed in this structure. A key feature, emphasized previously, of the S(4) state is that an oxygen radical ligand is present rather than an Mn(V) state. Previous studies have indicated that this oxygen radical can form an O--O bond by an attack from a water molecule in the second coordination shell. The present systematic investigation has led to a new type of mechanism that is significantly favored over the previous one. A calculated transition-state barrier of 12.5 kcal mol(-1) was found for this mechanism, whereas the best previous results gave 18-20 kcal mol(-1). A requirement on the spin alignment for a low barrier is formulated.

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“…The next major step in the development of DFT was the introduction of hybrid functionals, which mix GGA with exact Hartree-Fock exchange (Becke 1993). Nowadays, hybrid DFT with the use of the B3LYP functional (Becke 1988;Lee et al 1988) is the dominant choice for the treatment of transition metal containing molecules (Siegbahn 2003). This method has shown good performance for a truly wide variety of chemical systems and properties, although specific limitations and failures have also been identified.…”

Section: Theoretical Backgroundmentioning

confidence: 99%

The Density Functional Theory

Lipparini¹

2008

Modern Many-Particle Physics

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Density functional theory (DFT) finds increasing use in applications related to biological systems. Advancements in methodology and implementations have reached a point where predicted properties of reasonable to high quality can be obtained. Thus, DFT studies can complement experimental investigations, or even venture with some confidence into experimentally unexplored territory. In the present contribution, we provide an overview of the properties that can be calculated with DFT, such as geometries, energies, reaction mechanisms, and spectroscopic properties. A wide range of spectroscopic parameters is nowadays accessible with DFT, including quantities related to infrared and optical spectra, X-ray absorption and Mössbauer, as well as all of the magnetic properties connected with electron paramagnetic resonance spectroscopy except relaxation times. We highlight each of these fields of application with selected examples from the recent literature and comment on the capabilities and limitations of current methods.

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Mechanisms of metalloenzymes studied by quantum chemical methods

Cited by 196 publications

References 114 publications

Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C–H bond activation transition state

Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C–H bond activation transition state

OO Bond Formation in the S₄ State of the Oxygen‐Evolving Complex in Photosystem II

The Density Functional Theory

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Mechanisms of metalloenzymes studied by quantum chemical methods

Cited by 196 publications

References 114 publications

Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C–H bond activation transition state

Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C–H bond activation transition state

OO Bond Formation in the S4 State of the Oxygen‐Evolving Complex in Photosystem II

The Density Functional Theory

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OO Bond Formation in the S₄ State of the Oxygen‐Evolving Complex in Photosystem II