Molecular structure programs atom function

PC Model has some features that are not found in many other molecular mechanics programs. This is one of the few programs that outputs the energy given by the force field and the heat of formation and a strain energy. Atom types for describing transition structures in the MMX force field are included. There is a metal coordination option for setting up calculations with metal atoms. There are also molecular similarity and conformation search functions. 

All electron calculations were carried out with the DFT program suite Turbomole (152,153). The clusters were treated as open-shell systems in the unrestricted Kohn-Sham framework. For the calculations we used the Becke-Perdew exchange-correlation functional dubbed BP86 (154,155) and the hybrid B3LYP functional (156,157). For BP86 we invoked the resolution-of-the-iden-tity (RI) approximation as implemented in Turbomole. For all atoms included in our models we employed Ahlrichs valence triple-C TZVP basis set with polarization functions on all atoms (158). If not noted otherwise, initial guess orbitals were obtained by extended Hiickel theory. Local spin analyses were performed with our local Turbomole version, where either Lowdin (131) or Mulliken (132) pseudo-projection operators were employed. Broken-symmetry determinants were obtained with our restrained optimization tool (136). Pictures of molecular structures were created with Pymol (159). 

I>ensity functional theory (DFT) calculations were also used to confinn the structure of adsorbed enolic species on Ag/AFO using the (iaussian 98 suite of programs. The simulation molecular structure model and FTIR spectrum of the surface enolic species on Ag Al Oi are shown in Fig. 7. In model A. the enolic species (OI <.TI-() ) binided with a silver atom, and the optimized distance between the oxygen and silver atom w as 2.072 A.. Apparently, ihe calculated FTIR spectrum was reasonably similar to the correspimding experimental result. 

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