Hydrogen atom embedding function

Molybdopterin has another function besides participating in electron transfer between the site of catalysis and other electron-acceptor groups. It serves as an anchor for the active site where a multitude of hydrogen bonds between the pterin (and, if present, the dinucleotide) and the protein provide a secure tether for the reactive metal site (17). Evidence for the immobility conferred by the pterin(s) embedded in the protein is found in a comparsion of the DMSOR structures from both Rhodobacter sources. Regardless of the Mo coordination environment, the MGD ligands are nearly superimposable (75). This similarity of pterin structure is most clearly observed in the 1.3-A structure, where the Mo atom dissociated and shifted away from one pterin ligand, which otherwise was unaffected. The nucleotide tails on MGD, MCD, and other derivatives of molybdopterin also contribute to locking the molybdenum catalyst in position. 

A fundamental requirement on all of the computational studies on metal surface dynamics is fhe need fo perform simulafions with realistic potentials and in a feasible amounf of fime. To this end, the temperature-accelerated dynamics method [14,74,75] has arisen as a possible approach for reaching the latter limit. With the exception of quanfum simulations, most classical simulations are based on semiempirical potentials derived either from the embedded atom method or effective medium theory [76-78]. However a recent potential energy surface for hydrogen on Cu(l 10) based on density functional theory calculations produced qualitatively different results from those of the embedded atom method including predictions of differenf preferred binding sites [79]. 

Fig. 3. Energy AE " of hydrogen and oxygen embedded in infinite jellium as a function of jellium density The energy zero is the energy of the free atom [16]...

---