Molecular mechanics geometry optimization

You can often use experimental data, such as Nuclear Overhauser Effect (NOE) signals from 2D NMR studies, as restraints. NOE signals give distances between pairs of hydrogens in a molecule. Use these distances to limit distances during a molecular mechanics geometry optimization or molecular dynamics calculation. Information on dihedral angles, deduced from NMR, can also limit a conformational search. 

In this next section the dipole magnitude and directionality from MM3(2000) is compared to results obtained by MM3(96), Hartree-Fock and Mdller-Plesset minimized structures (calculated using GAUSSIAN94),77 as well as experimental dipole moment measurements.78 For the molecular mechanics geometry optimizations, full matrix energy minimizations were carried out, and ground state structures were verified by the vibrational... 

Maseras F, Morokuma K (1995) IMOMM a new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states. J. Comput. Chem. 

Maseras, F. and Morokuma, K. (in press) A New Integrated Ab Initio + Molecular Mechanics Geometry Optimization Scheme of Equilibrium Structures and Transition States, J. Comp. Chem.. 

Integrated Ab Initio + Molecular Mechanics Geometry Optimization Scheme of Equihbrium Structures and Transition States. 

When you perform an ah initio calculation, it is not always easy to know which basis set to use. Normally you should not use more complexity than is needed to answer your question or solve the problem. In fact, it may be desirable to determine the approximate geometry of the molecule using molecular mechanics. Many programs will allow you to use the result of a molecular mechanics geometry optimization as a starting point for an ah initio calculation. If possible, you should do so to save computational time. 

Pu J, Truhlar DG (2005) Redristributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations J Phys Chem A 109 3991 004 Maseras F, Moiokuma K (1995) IMOMM, a new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structure and transition states. J Comput Chem 16 1170-1179... 

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