Many researchers have synthesized cytochrome P450 model compounds.
Some of these are discussed in Section 7.4.5. One goal of cytochrome P450
model compound research has been to synthesize an oxoiron(IV) species with
an iron coordination sphere similar to that of the supposed cytochrome P450
catalytic intermediate — that is, four planar nitrogen ligands and axial oxo and
thiolate ligands. This goal has been partially achieved recently by a collabora-
tive effort headed by Jason Halfen, Eckard M ü nck, and Larry Que.^33 The
model compound, [Fe IV (O)(TMCS)] + , is discussed in Section 7.4.5.3 (see Figure
7.23 ). In addition to electronic and M ö ssbauer spectroscopy, along with
extended X - ray absorption fi ne structure (EXAFS) structural data, the
researchers optimized the geometry of the model compound using DFT cal-
culations. The supplement to the 2005 Science paper describes the DFT pro-
cedures used in great detail. Only the fi rst procedural remarks are given here.
The density functional calculations were performed using Becke ’ s three -
parameter hybrid functional (B3LYP) and basis set 6 - 311G provided by the
Gaussian 03 (Revision - B.05) software package.^34 The M ö ssbauer^57 Fe hyper-
fi ne parameter, Δ E Q, was calculated using the properties keyword of the
Gaussian code. The M ö ssbauer^57 Fe isomer shifts, δ , were evaluated from the
DFT charge density at the Fe nucleus using the calibration given by Vraj-
masu.^35 The SCF procedures and geometry optimizations were terminated
upon reaching the default convergence criteria. Geometry optimizations were
performed for theS = 1 and S = 2 states of [FeO(TMCS)] +. The interested
reader should consult reference 33 and its accompanying supplemental mate-
rial for more information.
4.4.4 Semiempirical Methods,
Semiempirical molecular orbital (MO) methods follow from (a) the Hartree –
Fock models with inclusion of additional approximations and (b) the introduc-
tion of empirical parameters. These methods provide acceptable equilibrium
and transition - state geometries but fail to account reliably for known thermo-
chemistry. The single additional approximation used in semiempirical methods,
termed NDDO, eliminates overlap of atomic basis functions on different
atoms, a severe limitation. However, it leads to a great reduction in computa-
tion effort. Most currently used semiempirical models are restricted to a
minimal valence basis set of atomic functions. Because of this, calculations
involving a heavy main - group element (e.g., gallium) take place in the same
time frame as those for a fi rst - row element (e.g., boron). Slater - type basis func-
tions (STOs closely related to exact solutions for the hydrogen atom) are used
in place of Gaussian functions (bell - shaped wavefunctions) employed for ab
initio calculations. The adjustable parameters introduced to reproduce experi-
mental data in semiempirical calculations can improve the model obtained
only if the correct method is chosen for the molecule in question. Three of the
commonly used methods are called AM1 (limited data set of parameters
mostly applicable to organic molecules and ligands),^36 PM3 (larger and more
QUANTUM MECHANICS-BASED COMPUTATIONAL METHODS 173