Molecular Mechanics

Question 1

What is Molecular Mechanics?

Answer 1

Treating molecules as classical objects, and calculating potential energy function typically based on bonded terms; torsions, bond angles, bond energies and non-bonded terms; electrostatic and van Der waal energies

Question 2

What is the formula for:
Ebond (Rab)=
what are the adv and dis

Answer 2

Ebond (Rab)= 1/2 Kab(Rab - R0)^2
adv: simple and accurate for small ΔR
dis: inaccurate as ΔR gets bigger, only as accurate as the parameters used, not as good for delocalised bonding

Question 3

What is the formula for:
Eangle (θabc)=
what are the adv and dis

Answer 3

Eangle (θabc)= 1/2 Kabc (θabc-θ0)^2
adv: simple to apply, generally accurate for small angle displacements
dis: only as accurate as parameters used, often requires cross terms for high strain

Question 4

What is the formula for:
Etorsion(τ) =

Answer 4

Σ Vn/2 (1+ cos(nτ-Υn))
is the sum for all values on n

Question 5

What is the formula for:
Evdw(Rab)
adv and dis

Answer 5

4ε[(σ/Rab)^12-(σ/Rab)^6)]
adv: often uses Lennard-jones potential between atom pairs
energy has a physically correct interpretation
dis: need σ and ε parameters between every pair of atoms in system
number of atom pairs can be very large (cut off over 12Å)

Question 6

What is the formula for:
Eelectrostatic(Rab)=
adv and dis

Answer 6

qAqB/4πεRab
adv. energy has a physically correct interpretation (molecules have unequal charge distribution due to difference in electronegativity)
dis. only as accurate as qA qB values
usually limited to point charges (monopoles) so not good for lone pairs or π systems
most expensive term to evaluate since the number of pairs of atoms can be very large (no cut-off due to R-1 dependence)

Question 7

What does it mean to cross the potential energy barrier?

Answer 7

Going from one stable state to another by crossing the energy barrier between them

Question 8

What is a forcefield?

Answer 8

a force field is a set of parameters and mathematical functions used to model the interactions between atoms and molecules in a system, it converts molecular co-ordinates to PE with the derivative w.r.t co-ordinate changes being the force on each atom

Question 9

What can molecular Mechanics not predict?

Answer 9

Bonding
Because there’s no explicit electrons or nuclei

Question 10

What is an atom type?

Answer 10

Atom typing refers to the classification of atoms in a molecular system into different types based on their chemical identity and environment
examples: hybridisation, functional groups, elemental identification