Molecular Modelling Equilibrium Geometries

This model has the advantage that the atomic polar tensor elements can be determined at the equilibrium geometry from a single molecular orbital calculation. Coupled with a set of trajectories (3R /3G)o obtained from a normal coordinate analysis, the IR and VCD intensities of all the normal modes of a molecule can be obtained in one calculation. In contrast, the other MO models require a separate MO calculation for each normal mode, since the (3p,/3G)o contributions for each unit are determined by finite displacement of the molecule along each normal coordinate. Both the APT and FPC models are useful in readily assessing how changes in geometry or refinements in the vibrational force field affect the frequencies and intensities of all the vibrational modes of a molecule. 

Molecular modeling, like all other technical disciplines, has its own jargon. Much of this is described in Appendix B (Common Terms and Acronyms), and only one aspect will be addressed here. This concerns specification of theoretical model used for property calculation together with theoretical model used for equilibrium (or transition-state) geometry calculation. 

Calculated equilibrium geometries for hydrogen and main-group hydrides containing one and two heavy (non-hydrogen) atoms are provided in Appendix A5 (Tables A5-1 and A5-10 for molecular mechanics models, A5-2 and A5-11 for Hartree-Fock models, A5-3 and A5-12 for local density models, A5-4 to A5-7 and A5-13 to A5-16 for BP, BLYP, EDFl and B3LYP density functional models, A5-8 and A5-17 for MP2 models and A5-9 and A5-18 for MNDO, AMI and PM3 semi-empirical models). Mean absolute errors in bond lengths are provided in Tables 5-1 and 5-2 for one and two-heavy-atom systems, respectively. 

This chapter addresses the relative cost of molecular mechanics and quantum chemical models for energy and equilibrium geometry calculations as well as for frequency evaluations. Taken together with performance issues addressed in previous chapters, this allows broad recommendations to be made regarding selection of an appropriate model. 

Molecular mechanics models are restricted to the description of molecular equilibrium geometry and conformation. They are the method of choice for conformational searching on complex systems. 

The Spartan 02 04 molecular modeling software packages were used to predict the optimized geometry and the NMR spectra. The H-NMR spectra were predicted at the ab initio level using the Hartree-Fock to obtain the equilibrium geometry with the 3-2IG basis set. In a similar manner, we predicted the proton NMR spectra of the absorbed HCl. 

It turned out that CNDO/1 calculations gave poor predictions of molecular equilibrium geometries, and this failing was analysed as being due to the treatment of the Uu and the penetration terms Vab-The CNDO/2 model came next (Pople and Segal, 1966). It differs from CNDO/1 in the way it handles Uu and Vab- The penetration term Fab is no longer calculated exactly, but taken as —ZbKab- The atomic terms become... 

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