Molecular Mechanics Flashcards
Principles
- treat molecules as if they follow classical mechanics - Empirical models; fitted to reproduce experimental data
Energies are calculated assuming
- Bonds behave like simple springs - Atoms behave as soft spheres which attract each other but repel when they get too close
Molecular forcefiels and Energy calculations
- forcefield is derived from aproximations of van der waals, bonded and electrostatic interactions.
- a forcefield is a set of classical mechanics equations that let us calculate the total energy of a molecule based on the positions of the atoms
- Forcefields assume that energy can be divided into individual components
Covealent bonds
- strongest interaction
- become longer as you move down the periodic table and shorter as you move to the right
Modelling the potential energy of bonds
At short interatomic distances potential energy increases drasticaly due to repulsion
as they move further apart the energy approaches 0 (bond is broken) (well depth corresponds to energy required to break the bond)
while the curve dues not fit morse potential energy particuarly well, error is reduced as the bonds are unstrained at eq bond length
Ebond = k 2 (r − r0 )^ 2 + C
r0 shidts left/right
K dilates => energy required to stretch
Electrostatic interactions
- proportional to amound of charge on each particle and inversely proportional to the distance between them
- long range…
- 3o= vaccum constant = 8.85*10e12 C^2, J-1M-1
V = potential energy
Q= charge on particles
R = distance
Modellling of charge-charge interactions
- modelled using point charges located at the position of the atom nucleus
- this is inaccurate as in reality charges are spread across the atomic orbitals and can also change in location depending on the environment
Modelling Van Der Valls interactions
attractions short range proportional to 1/r ^6
repulsion is proportional to 1/r^12
- sum of two curves
Calculating interactions between molecules
(N*(n-1))/2
