Molecular Mechanics

Question 1

Molecular Geometry

Answer 1

The relative positions of atoms of a molecule in space

A set {R}eq where the potential energy surface has a local minima

Question 2

Molecular Mechanics (MM)

Answer 2

The use of classical mechanics to describe the potential energy surface
- very fast compared to QM methods
- popular for large molecules, where QM methods would be too costly (time, RAM, diskspace)

Question 3

Classical Mechanics

Answer 3

Since the PES does not contain rotational or translational energy for vibrational motion, the classical harmonic oscillators are good starting models

F(x) = -kx
U(x) = (1/2)kx^2

Question 4

How is an MM model defined?

Answer 4

By it’s force field: the set of chosen equations for:
- bond stretching
- valence angle bending
- torsions
- van der waals interactions
- electrostatic interactions
as well as the parameters in these equations

Question 5

Parametrization

Answer 5

Choosing values for these parameters

This is done by minimizing the errors that the force field makes in trying to reproduce a set of experimentally well-defined data (training set)

eg. if FF is trained on data from amides/esters, it will work well for amides/esters but not as well for azides

Question 6

What is the accuracy of a force field linked to?

Answer 6

The training set used for parametrization

Question 7

Geometry Optimization

Answer 7

An iterative procedure for finding equilibrium and transition-state geometries of molecules

Question 8

Popular MM methods

Answer 8

AMBER
CHARMM
MM3

Question 9

Summary

Answer 9

MM works well for equilibrium properties of molecules which are similar to those of the ‘training set’ used for that particular MM’s original parametrization