In order to study the coordinative behavior of doubly charged metal ions in water, a few representative metals have been chosen for theoretical studies. These are the group 2 metal ions beryllium, magnesium, and calcium and the group 12 zinc ion. The density functional method B3LYP has been used with very large basis sets. It is found that the water dipole moment and polarizabilities, which are critical for the accuracy of the binding energies, are very well reproduced provided that the basis set on the metal is included in the calculations. One of the main points of the present investigation has been to study the boundary between the first and second hydration shells. Trends of binding energies and structures are also discussed.

The oxidation of methane with molecular oxygen using the atomic platinum cation as a catalyst, yielding methanol, formaldehyde, and higher oxidation products, has been studied both computationally and experimentally. The most relevant reaction pathways have been followed in detail. To this end a large number of stationary points, both minima and transition states, have been optimized using a hybrid density functional theory method (B3LYP). At these optimized geometries, energies have been calculated using both an empirical scaling scheme (PCI-80) and the B3LYP method employing extended basis sets with several polarization functions. Good agreement with available experimental data has been obtained. For the parts of the catalytic cycle where detailed experimental results have not been available, the new calculated results have complemented the experimental picture to reach an almost complete understanding of the reaction mechanisms. Spin−orbit effects have been incorporated using an empirical approach, which has lead to improved agreement with experiments. The new FTICR experiments reported in the present study have helped to clarify some of the most complicated reaction sequences.

The communication between the cysteine, Cys439, at the substrate site and the tyrosyl radical, Tyr122, in ribonucleotide reductase is studied by quantum chemical models at the DFT-B3LYP level. Recent theoretical and experimental studies have indicated that an electron transfer between these sites is highly unlikely. Instead, a model based on the hydrogen atom transfer (HAT) mechanism is investigated. In this mechanism both the proton and electron are moved in each step to avoid a costly charge separation. It is found that the hydrogen atom transfer steps required for communication between Cys439 in R1 and Trp48 in the region of the iron dimer in R2 all have quite low energy barriers. The radical transfer between Tyr731 and Tyr730 has a barrier of 4.9 kcal/mol, while the one between Tyr730 to Cys439 has a barrier of 8.1 kcal/mol. An interesting aspect of these transfers is that the dielectric contribution from the protein is very small, indicating very small charge separations. The radical transfer from Tyr122 to Trp48 over the iron dimer is considerably more complicated. A model is suggested where this transfer occurs in essentially one step by a hydrogen atom transfer from a water ligand of the iron dimer to Tyr122. In this process an electron is transferred between Trp48 to the hydroxyl ligand of iron over the Trp48-Asp237-His241 chain leading to a cationic tryptophan radical.

DFT quantum chemical methods are used to probe the mechanism of the nickel−iron hydrogenases. Starting from the experimental X-ray structure, all plausible oxidation states and spin states were investigated. The structure and reactivity pattern of the NiFe cluster are best reproduced by assuming a NiFe(II,III) oxidation state assignment of the resting state of the cluster. In our proposed mechanism of H2 oxidation by the enzyme, H2 first binds to Fe in the form of a molecular hydrogen complex, which then undergoes heterolytic splitting. This process is spin-dependent and does not occur for the high-spin sextet state. In the key step, hydride transfer to iron and proton transfer to the adjacent cysteinethiolate ligand is accompanied by decoordination of the protonated cysteinethiol from Ni while remaining bound to iron. Simultaneously, the cyanide ligand on iron binds with the nickel atom in a rare bridging binding mode. After the H2 dissociation, the hydride bound to Fe can then be transferred to Ni which should be a necessary preliminary for subsequent hydrogen atom or electron transport. The transition state for hydrogen splitting was located, and the resulting calculated energy barrier is in remarkably good agreement with the experimental value.

The catalytic cycle for the heterolytic splitting of H2 by Ni-Fe hydrogenase has been investigated in four recent quantum chemical studies. The mechanisms proposed are described and compared. Although there are clear differences in these mechanisms and in the assignments of the different states observed experimentally, there are also important points of concensus.

ABSTRACT:The density functional theory DFT method B3LYP has been used to investigate the catalytic mechanism of Ni᎐Fe hydrogenases in light of new experimental data on the structure. The reaction pathway suggested in previous theoretical work is now slightly modified. In the reaction mechanism proposed in the present study, one of the hydrogens from H appears as a hydride bridge between Ni and Fe in the reduced 2 form. The bridging hydride brings Ni and Fe closer together, which results in an interatomic distance of 2.56 A, which is a shortening from the calculated oxidized form of 0.28 A. A shortening of the Ni᎐Fe distance in the reduced form as compared to the oxidized form agrees with the recent experimental X-ray structures. Effects on the reaction mechanisms, due to protonation and deprotonation of the terminal cysteine ligands on Ni and coordination of a water molecule on Ni have also been studied. Solvent effects have been included using dielectric cavity methods.

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