Jamie Platt

Question 1

Explain what is meant by “TIP3P model” of water.

Answer 1

TIP3P is the “transferable interaction potential: 3 point”, one of the most common molecular
mechanics forcefields used for description of water.

Question 2

TIP3P model, Which degrees of freedom of water molecules are frozen and which are allowed to
change in this model?

Answer 2

O—H bond lengths and H-O-H bond angle are frozen in TIP3P: also, point charges on
atoms are fixed.

Question 3

How are non-covalent interactions described in this model?

Answer 3

As with most molecular mechanics, a combination of electrostatic and van der Waals terms
are used. The former is based on Coulomb’s law using partial charges assigned to O (d-) 
and H (d+). The latter uses the Lennard-Jones potential, with a single centred on O rather
than separate parameters for O and H

Question 4

How might the above factors limit the model’s ability to describe hydration of a solute
such as MVK?

Answer 4

limiting factor is the frozen charge/dipole moment:
H2O in bulk has much larger dipole moment than in gas phase, and the value in solution will
vary depending on the solute. A single set of point charges cannot hope to model all the
intricacies of such a situation

Question 5

How do you estimate the number of conformations of a molecule

Answer 5

Related to the number of conformation and number of rotatable bonds.
e.g pentane has two rotatable bonds and 3 conformations per rotation (or 6 depending on how you argue it)
3^2=9 conformation
or 6^2=36 conformations

Question 6

Which terms from the general molecular mechanics expression given in lectures are most important in determining the relative energy of conformations?

Answer 6

Bond lengths and angles should not change significantly between conformations, and alkanes are non-polar, so only torsional and VDW terms are important here.

Question 7

Forcefields

Answer 7

Electronic structure is not calculated at all but interactions are set up at an atom-atom level

Question 8

What contributes to potential energy of forcefields

Answer 8

Bonded terms:
-stretch
-bend
-torsion
Non Bonded term:
-Electrostatic
-VDW

Question 9

Torsion forcefields approach

Answer 9

• Combine multiple cosine functions of a torsion angle

- Cosine functions are needed as torsional motion is periodic

Question 10

Torsion PE equation

Answer 10

• V(tor) = Torsional Potential energy
• Vn = the barrier to rotation
• n = the multiplicity
• gamma = is the phase angle
• omega = torsional angle

Question 11

Electrostatic forcefield approach

Answer 11

• Coulombs law
• PE of two charges seperated by distance r in a vacuum
• Only counted for remote nuclei

Question 12

Approaches to assign charges to atoms

Answer 12

Electronegativity equalisation:
-electrons flow towards more electronegative atoms and eventually stabilise

Electrostatic potential fitting:
-charges reproduce how the molecule “looks” to other molecules

Question 13

VDW forcefield approach

Answer 13

Lennard-Jones potential:

• combination of attractive and repulsive parts
• written in terms of well depth (epsilon) and separation where the energy is zero (sigma)

Question 14

Limiting approximations of electrostatics

Answer 14

Charges dont change as molecules environment changes (not realistic)
-The need for polarizable forcefields

Question 15

Force

Answer 15

The force acting on atoms is the negative of the first derivative of the potential energy

Question 16

Bond stretch and angle bend forcefields

Answer 16

Both are parametrised as polynomial form

• Taylor expansion
• Harmonic term most useful
• cubic and quartic added to improve on simple harmonic