Example questions for ‘Molecular Modelling’

Dr. Adrian Mulholland

(1) What approximation leads to the concept of a potential energy surface? What types of points on a potential energy surface are particularly relevant in understanding a chemical reaction?

(2) Two methods that are widely used for the optimization of molecular geometries are the ‘Steepest descents’ and ‘Newton-Raphson’ techniques. Without giving detailed mathematical descriptions, briefly outline the advantages and disadvantages of these two techniques.

(3) Give a typical expression for a ‘molecular mechanics’ potential energy function of the type used for macromolecular simulations. Include intra- and intermolecular terms. Describe what each energy term represents. Also state briefly the physical origin of each of the energy terms.

(4) Describe briefly how parameters may be found for the various different energy terms in a typical molecular mechanics potential function.

(5) Discuss the strengths and its limitations of a typical molecular mechanics potential function. Give brief examples of types of applications for which a molecular mechanics potential function is suitable, and also give examples of applications for which molecular mechanics modelling is not suitable. What improvements could be made to the molecular mechanics potential energy function?

(6) Compare and contrast the Monte Carlo and molecular dynamics simulation methods.

(7) Outline the basic techniques involved in setting up and running (a) a molecular dynamics simulation and (b) a Monte Carlo simulation

(8) Discuss the ‘lattice dynamics’ technique. For what types of problems would lattice dynamics methods typically be used?

(9) Give reasons why calculation and analysis of the harmonic vibrational frequencies of molecules may be useful. Outline the process involved in calculation of harmonic vibrational frequencies.

(10) Outline techniques which could be used to generate models of transition state structures for chemical reactions. How could such transition state models be improved? Describe how you could confirm that a structure really is a transition state structure. Also outline how you could show that the transition state really is the right one for the reaction of interest.

(11) Find the Newton-Raphson step, and the minimum, for the function f(x,y) = 2x² + 2y², starting from the point (x,y) = (3,–2). Show your working.

(12) Briefly describe the following methods for calculating molecular energies and geometries (outline their advantages and disadvantages):

(i) ab initio molecular orbital methods

(ii) semiempirical molecular orbital methods

(iii) molecular mechanics methods

(iv) combined quantum mechanics/molecular mechanics methods

(13) What is meant by the term ‘correlation energy’? What methods can be used to calculate energies including correlation effects?

(14) Briefly describe methods that can be used to include solvent effects in ab initio molecular orbital calculations

(15) Outline how activation free energies can be calculated from (e.g.) ab initio molecular orbital calculations, i.e. how different contributions (vibrational, rotational, etc.) to the activation energy can be found. It is not necessary to give detailed expressions for partition functions.