Flashcards
Interacting systems- lectures 5 and 6
Cards in this deck (14)
- 1Does using a molecular mechanics force- field give an exact agreement with the radial distribution function?No.
It does provide additional insight, for example velocity auto-correction and the time scale for collisions. - 2Using benzene as an example, what do the force-field simulations also tell you about the molecule.The ensemble of structures populated at a specific temperature tells you about the probability of finding the molecule at a particular angle relative to the neighbouring molecule. This can be calculated as specific orientations of a molecule are formed to give the lowest energy structure.
- 3Describe the water model TI4P and discuss the approximations used in this model.The water simulation in this model is based on the model having four point charges.
Only the oxygen Lenard Jones interactions are taken into account as hydrogen does not have any van der waals forces.
The quantum nature of water makes it complicated to simulate, the TI3P model and the TI4P model assume the H atoms are HEAVIER than reality. Means the 2nd/3rd salvation shell that water has due to having interactions that go beyond its closest neighbours are not formed.
Water is treated as a rigid monomer and the vibration of the bonds are neglected. - 4What are the limitations of the MD?Corresponds to normal weaknesses.
does not account for the full description of the electrostatic properties.
Does not account for polarizabiltiy i.e. changes in molecular environment. - 5What properties are predicted well with the point charge models and what properties are not predicted so well for water?Prperties such as the number of H bonds and the the mean density are reproduced well.
The melting point ( where the gibbs free energy of water and ice are equal)- how density changes in relation to T are not predicted so well. - 6What proof do we have that increasing the numb rod point charges on the water models increases the models ability to reproduce some of water's properties.The more point charges a model has, the more able the radial distribution function is able to formulate peaks for the 2nd and 3rd salvation shell.
As the number of point charges increase, the more easy it is to predict the change of density as function of T. i.e. gets closer to the experimental value FOUR. - 7For the mixing of an organic molecule and water , what is expected according to the lattice model?The lattice model ALWAYS predicts that the entropy of mixing is favoured and positive. The deltaH and delta U values are equal to one another and = KBT XAB NANB/N
Where X AB describes the relative affinity of the interaction between A and B compared to A and A and B and B.
I.e. XAB= Z/KBT ( WAB-(WAA+WBB/2)) - 8Continued..According to this equation, where the interaction between ,molecules of the organic molecule and the organic molecule are GREATER compared to the interactions of the organic molecule and water, chi AB will be positive and unfavourable and should give a positive deltaU and delta H value.
- 9When is the main limitation of the lattice model observed?When studying the mixing of an organic molecule with water. Usually it is a fairly good approximation to neglect the changes of electronic/vibrational/ rotational energy for molecules upon mixing. However this is not the case for the mixing of organic molecules in water due to the network of dynamic H bonds.
- 10How is this reflected in the enthalpy and entropy values for the transferring of an organic molecule from a non-polar organic solvent to water?The entropy value decreases, the water molecules form a cavity around the organic molecule with all the H bonds pointing AWAY from the organic molecule, when originally the H bonds formed randomly. For an average water molecule the number of H bonds formed usually increases and the strength of the bonds increase also. This Explains why the enthalpy value for the transfer is negative, due to the release of energy on strong bond/ increased bond formation.
- 11Why can you also not use the lattice model for proteins?They are very dynamic
- 12How does this affect the binding of substates?Substrate binding is also dynamic so cannot be predicted by the lattice model either.
- 13What is used instead of the lattice model?Molecular Dynamic simulations.
- 14What are the limitations of the molecular mechanic potential energy function ( Any point charge model)Does not give a full account of the electrostatic properties, e.g. the quadruples on benzene not accounted for.
does not respond to changes in molecular environment or structure. This is surprising due to the known importance of polarisability.
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- 2nd year Chemistry (Chemistry 2nd Year) Flashcards on Interacting systems- lectures 5 and 6, created by Charlotte Feldman on 11/05/2016.
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