Transition State Search Using rPM6: Iron- and Manganese-Catalyzed Oxidation Reactions as a Test Case

Abstract

We present a reparameterization of PM6 (rPM6) for Fe in a similar procedure to that for Mn in our previous work [T. Saito, Y. Takano, Chem. Lett. 2017, 46, 1567]. The performance of the spin unrestricted rPM6 (UrPM6) method has been examined on both energy minimization and transition state (TS) search on the basis of the spin unrestricted density functional theory (UDFT) calculations. For energy minimization, the UrPM6 outperforms the original UPM6 on the basis of the UB3LYP/SVP-optimized geometries. The test set for TS search is comprised of 58 TS structures for oxidation reactions catalyzed by a variety of iron and manganese complexes including active sites of cytochrome P450 and soluble methane monooxygenase as well as their biomimetic complexes. The standard UPM6 method can locate only 21 out of 58 TS structures (36%), whereas an overall success rate is 83% (48 out of 58) by means of UrPM6. Furthermore, the UrPM6-optimized structures can be obtained easily (on the order of several minutes) and 94% of those are found to be utilized for the subsequent refinement by UDFT without any modifications of geometrical parameters.

Quantitative Assessment of rPM6 for Fluorine- and Chlorine-Containing Metal Complexes: Comparison with Experimental, First-Principles, and Other Semiempirical Results

“…It is obvious that the magnitude of the J values obtained with UPM6 were much larger than those obtained with experiments by at most two digits, excluding the case of KASPEC. Our recent study revealed that the UPM6 optimization made a Fe···Fe separation in sMMOQ too short [52], and the same is also true for other diiron complexes. As such, the poor reproducibility in the geometries of the diiron centers is responsible for the overwhelmingly large deviations of J values.…”

“…Fluorine and chlorine both had 12 optimizable core-core parameters, resulting in the 18 and 21 parameters in total for fluorine and chlorine, respectively (for details, see Table 1). During the optimization, the parameters for H, C, N, O, Mn, and Fe remained frozen at the values determined in our previous studies [48,49,52].…”

“…Very recently, we proposed the rPM6 method [48,49,50,51,52], which is a reparameterization variant of PM6 [53], and tested the spin unrestricted PM6 (UrPM6) against organic diradicals and iron– and manganese–catalyzed C–H and C=C bond activation reactions. It turned out that UrPM6 outperforms the original UPM6 and spin unrestricted density functional-based tight binding (UDFTB) methods for calculating J values for organic diradicals.…”

Machine learning and semi-empirical calculations: a synergistic approach to rapid, accurate, and mechanism-based reaction barrier prediction

“…41 Despite some reported disagreements with more accurate ab initio methods, for example in the assignment of Diels-Alder reactions as either step-wise or concerted, 42 SQM methods have been shown to produce reliable geometries for TSs of many reactions, including nucleophilic substitutions, isomerisations, alkene epoxidations, metal-catalysed oxidations, and even some cycloadditions. [43][44][45] However, they require expensive, highaccuracy DFT single point energy (SPE) corrections to give reliable barriers, 43 and thus SQM data alone is not of a sufficient quality for accurate reaction modelling.…”

The most reactive iron and manganese complexes with N-pentadentate ligands for dioxygen activation—synthesis, characteristics, applications

“…Recently, synthesis of low-valent iron and manganese complexes capable of stabilizing intermediates produced in the oxygenation cycles, which show similarity to natural systems, is of great interest. Within the last two decades, a number of mononuclear complexes with oxoiron(IV) [ 3 – 20 ] and oxomanganese(IV) [ 9 , 11 , 18 , 21 ] units supported by polydentate non-heme ligands have been investigated. These complexes serve as models for high-valent intermediates in the catalytic cycles of enzymes that carry out a series of oxidative modifications.…”