The development of a PM3 parameter set to describe iron–sulfur proteins

Understanding rubredoxin redox sites by density functional theory studies of analogues

Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH(3))(4)](0/1-/2-), [Fe(S(2)-o-xyl)(2)](0/1-/2-), and Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) in different conformations. In particular, the study of Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ∼0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.

Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron-containing proteins to be accurately modeled, focussing on iron-sulfur, iron-heme, and iron-only hydrogenases. Data computed at the B3LYP/6-31G* level for a training set of 60 representative complexes have been employed. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure and energetics of molecules both within and outside the training set, and overcome the extensive deficiencies of a B3LYP/STO-3G model. Particularly encouraging is the success of the parameters in describing [4Fe-4S] cubanes. The derived parameter set provides a starting point should greater accuracy for a more restricted range of compounds be required.

Specific parametrisation of a hybrid potential to simulate reactions in phosphatases

Phosphatases are key biomolecules because they regulate many cellular processes. These enzymes have been studied for many years, but there are still doubts about the catalytic mechanism. Computer simulations can be used to shed light on these questions. Here we develop a new and specific parametrisation, and present extensive tests of a hybrid potential that can be used to reliably simulate reactions catalysed by phosphatases. High level ab initio data for phosphate ester thiolysis and alcoholysis is used in the training set. The parametrised quantum mechanical Hamiltonian reproduces ab initio energies with a root mean-squared deviation of 3 kcal mol(-1) for species along the pathway of various phosphate ester reactions. Preliminary results for simulation with the calibrated hybrid potential of catalysis by the phosphatase VHR indicate the calculated reaction barriers are in very good agreement with experiment.

Development of parameter sets for semi-empirical MO calculations of transition metal systems: Iron parameters for iron–sulfur proteins

A semi-empirical parameter set for iron has been developed which is appropriate for the study of iron-sulfur proteins having a single iron atom, by fitting to density-functional theory (DFT) calculations obtained for a series of small models of iron-containing proteins. These parameters are obtained using a modified BFGS optimisation procedure previously used to obtain semi-empirical parameters for the main group elements. The modifications to this procedure for obtaining parameters for transition metal atoms are outlined. In addition to modifications to the semi-empirical core repulsion function, which yield significant improvements in the calculation of molecular structures, compared to the standard core repulsion function, are outlined. The reported parameters are then tested on a set of model complexes containing a variety of ligands and show good agreement with both DFT and experimental data for these species.