The use of methods involving semi-empirical molecular orbital theory to study the structure and reactivity of transition metal complexesElectronic supplementary information (ESI) available: Atomic electronic states used for the transition metal parameterisation. See http://www.rsc.org/suppdata/fd/b2/b211791f/

Abstract

The electronic structure of molecular systems containing transition metal atoms is traditionally studied using methods based on density functional theory (DFT). Although such an approach has been quite successful, the treatment of large systems, be they transition metal complexes, bioinorganic molecules or the solid state, is still extremely computationally demanding at this level, and may not be practical for many systems of interest. In this paper we describe how semi-empirical MO methods can be used to overcome these computational bottlenecks, yet still provide predictions of the necessary accuracy. We describe strategies to achieve this by focussing on: (i) obtaining appropriate parameters for transition metal atoms via a genetic algorithm, to be used within a parallelised implementation of neglect of differential diatomic overlap (NDDO) methods, and (ii) the use of multilevel treatments which involve DFT and semi-empirical methods to describe different regions of the molecule. Here we show by reference to histidine and porphyrin complexes, the importance of a correct partitioning of the organic substrate. We illustrate the potential of such a dual level approach by reporting preliminary results showing the catalytic role of the enzyme, dimethyl sulfoxide reductase.

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.…”

“…[11,[13][14][15][16][17][18][19][20][21][22]24,26] We use thirteen different DFT methods to optimize structures along the reaction pathway, both in the gas phase and with a continuum solvent. Accurate energies are obtained by single-point calculations at the coupledcluster level of theory.…”

“…[22,24] were used, and the starting structures for W were obtained by simply replacing Mo with W. The model consisted of two DMDT molecules as models of the pyranopterin dithiolene ligands, CH 3 O -as a model of the serine ligand from the protein, and a DMSO molecule. [10,13,[15][16][17][18][19][20][21][22][23][24] Initially, all the geometries of stationary points along the reaction coordinates were optimized without symmetry constraints in the gas phase at the B3LYP/def2-TZVP level of theory. [29][30][31] The def2-SVP [29] basis set was also tested, but it gave large errors in the calculated energies (although the structures were similar; see Tables S1 and S2 in the Sup-porting Information for details).…”

Semiempirical Molecular Orbital Scheme To Study Lanthanide(III) Complexes: PM3 Parameters for Europium, Gadolinium, and Ytterbium

“…Thus the one-center lanthanide parameters, where the 4f electrons are part of the electronic core can be obtained in essentially the same way as for firstrow transition metals. 48 The remaining parameters (G pp , s , p , d , s , p , d ) were assigned different values for different parametrization runs. The core electron attraction and core repulsion parameters, F, δ Gd-X , and R Gd-X , were set equal to 1.0, 1.5, and 2.0.…”

Synthesis and Characterization of Two Novel Complexes of Cr(III) with Benzilmonoxime

“…Available parameters for Cr metal were implemented in the PM3 semi-empirical method. 41 The parameterized PM3 was used for the geometry optimization of the complexes under study.…”