Density functional theory of biologically relevant metal centers

Recent applications of density functional theory to biologically relevant metal centers are reviewed. The emphasis is on reaction mechanisms, structures, and modeling. The accuracy of different functionals is discussed for standard benchmark tests of first- and second-row molecules and for transition metal systems. Modeling aspects of the protein metal complexes are discussed regarding both the size of the model being treated quantum mechanically and the treatment of the protein surrounding it. To illustrate the effects, structures computed without the effects of the protein are compared with experimental structures from enzymes, and results from simple dielectric models of the protein for electron transfer processes are described. The choice of spin state is discussed for multimetal complexes. Examples of mechanisms studied recently by density functional theory are described, such as O2 and methane activation in methane monooxygenase and O2 formation in photosystem II.

Theoretical models for the oxygen radical mechanism of water oxidation and of the water oxidizing complex of photosystem II

Hybrid density functional theory is used to study reasonably realistic models of the oxygen-evolving manganese complex in photosystem II. Since there is not yet any X-ray structure of the complex, other types of experimental and theoretical information are used to construct the model complexes. In these complexes, three manganese centers are predicted to be closely coupled by mu-oxo bonds in a triangular orientation. Using these models, the previously suggested oxygen radical mechanism for O2 formation is reinvestigated. It is found that the oxygen radical in the S3 state now appears in a bridging position between two manganese atoms. It is still suggested that only one manganese atom is redox-active. Instead, a number of surprisingly large trans-effects are found, which motivate the existence and define the function of the other manganese atoms in the Mn4 cluster. Calcium has a strong chelating effect which helps in the creation of the necessary oxygen radical. In the present model the chemistry preceding the actual O-O bond formation occurs in an incomplete cube with a missing corner and with two manganese and one calcium in three of the corners. The external water providing the second oxygen of O2 enters in the missing corner of the cube. The present findings are in most cases in good agreement with experimental results as given in particular by EXAFS.

O-O bond cleavage and alkane hydroxylation in methane monooxygenase

Several new aspects of the O-O bond cleavage and alkane hydroxylation mechanisms have been studied by hybrid density functional theory in this reinvestigation of methane monooxygenase. As concerning key intermediates in these reactions, a new important low-lying state is found, described either as Fe2(III,V) or as Fe2(III,IV)O. A fully optimized transition state for O-O bond cleavage has been determined. It is suggested that the large difference in optimal size (as determined in gas phase) of the complex, before and after the O-O bond cleavage, leads to an additional driving force for the reaction, not considered previously. The strain of the enzyme is estimated to lead to a driving force in the forward direction of about 5 kcal/mol, which could explain some of the pH dependence found in recent experiments. For the hydroxylation reaction, a clean hydrogen abstraction transition state leading to a substrate radical is again found, in contrast to interpretations of radical clock experiments. An explanation, based on new results, is suggested that could account for both the experimental and theoretical results.

O-O bond splitting mechanism in cytochrome oxidase

Hybrid density functional theory (DFT) calculations have been used to investigate different mechanisms for O-O bond splitting in cytochrome oxidase. It is shown that the requirement for a low activation barrier for the O-O bond splitting is that two protons, apart from the tyrosine hydroxyl proton, are available at the binuclear center. A mechanism is suggested for the transformation from a species with a molecularly coordinated O2, to an O-O cleaved species with an oxo-ferryl group. The mechanism has a calculated activation barrier in reasonable agreement with experimental estimates, and the overall reaction is close to thermoneutral, in line with the requirement that the energy wasted as heat should be minimized. The rate limiting step in the mechanism occurs at the initial Fe-O2 intermediate, consistent with experimental observations that the decay of the oxy intermediate parallels the increase of the oxo product. The formation of a radical at the cross-linked tyrosine-histidine structure is a possible source for one of the electrons required in the bond cleavage process. Possible sources for the two protons are discussed, including a suggested key role for the hydroxyl group on the farnesyl side chain of heme a3.