Computational modelling of oxygenation processes in enzymes and biomimetic model complexes

Abstract

With computational resources becoming more efficient and more powerful and at the same time cheaper, computational methods have become more and more popular for studies on biochemical and biomimetic systems. Although large efforts from the scientific community have gone into exploring the possibilities of computational methods for studies on large biochemical systems, such studies are not without pitfalls and often cannot be routinely done but require expert execution. In this review we summarize and highlight advances in computational methodology and its application to enzymatic and biomimetic model complexes. In particular, we emphasize on topical and state-of-the-art methodologies that are able to either reproduce experimental findings, e.g., spectroscopic parameters and rate constants, accurately or make predictions of short-lived intermediates and fast reaction processes in nature. Moreover, we give examples of processes where certain computational methods dramatically fail.

Singlet versus Triplet Reactivity in an Mn(V)–Oxo Species: Testing Theoretical Predictions Against Experimental Evidence

“…It should be noted that computational methods that better reproduce experimental crystal structure coordinates are often not the preferred methods for reproducing reaction rates, as found previously. 31 We under-took an extensive benchmarking study of the [Mn(O)(H 8 Cz)-(CN)] − complex using a range of density functional and ab initio methods, particularly aimed at establishing the amount of Hartree–Fock exchange interaction needed in the calculations.…”

A Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulf­oxide Reductase with Mo and W

“…The transition structure corresponded to the (Me) 2 S=O double-bond cleavage and is similar to the crystal structures of the enzyme in both the oxidized and reduced states. [13] Later studies by Thapper, [14] McNamara, [15,16] Hernandez-Marin and Ziegler, [17] Solomon, [18,19] Hofmann, [20,21] and us [22][23][24] have established a two-step associative mechanism, in which DMSO first binds to the reduced active site, and the S-O bond is cleaved in the second step concomitant with the oxidization of the Mo ion to the Mo VI state (see Scheme 1). The second step is rate limiting and has a predicted activation energy of 76, [14] 80, [15] 69, [17] 68, [18,19] 40, [20,21] or 63 kJ/mol.…”

Influence of Ligand Architecture on Oxidation Reactions by High‐Valent Nonheme Manganese Oxo Complexes Using Water as a Source of Oxygen

“…For Mn IV = O, where less thorough bench marking is available, the results therefore are within the error limit also in agreement with the experimental data. [21,22] Importantly, there is a constant shift of relative energies, approximately 2-3 kJ mol À1 , between the two basis sets used. That is, the activation barriers of the two isomers are approximately identical and largely independent of the basis set.…”