Oxford University Press | Online Resource Centre

Choose your answer by clicking the radio button next to your choice and then press 'Submit' to get your score.

Question 1

Which of the following terms refers to the molecular modelling computational method that uses equations obeying the laws of classical physics?

a) Quantum mechanics

b) Molecular calculations

c) Molecular mechanics

d) Quantum theory

Question 2

Which of the following terms refers to the molecular modelling computational method that uses quantum physics?

a) Quantum mechanics

b) Molecular calculations

c) Molecular mechanics

d) Quantum theory

Question 3

Which of the following statements is true?

a) Energy minimisation is carried out using quantum mechanics.

b) Energy minimisation is used to find a stable conformation for a molecule.

c) Energy minimisation is carried out by varying only bond angles and bond lengths.

d) Energy minimisation stops when a structure is formed with a much greater stability than the previous one in the process.

Question 4

The following graph shows the stability of a molecule as its structure is varied during conformational analysis.

What term is used to describe the point on the graph marked X?

a) Global energy minimum

b) Transition state

c) Local energy minimum

d) Conformational minimum

Question 5

The following graph shows the stability of a molecule as its structure is varied during conformational analysis.

What term is used to describe the point on the graph marked Z?

a) Global energy minimum

b) Transition state

c) Local energy minimum

d) Conformational minimum

Question 6

The following graph shows the stability of a molecule as its structure is varied during conformational analysis.

If energy minimisation was carried out on a starting structure appearing as shown on the graph, at which point would energy minimisation stop?

a) V

b) X

c) Y

d) Z

Question 7

Which of the following needs to be known before two drugs can be overlaid to compare their structures?

a) The pharmacophore of each drug.

b) The active conformation of each drug.

c) Both of the above.

d) Neither of the above.

Question 8

Which of the following statements is true?

a) The most stable conformation of a drug is also the active conformation.

b) The active conformation is the most reactive conformation of a structure.

c) The active conformation is the conformation adopted by a drug when it binds to its target binding site.

d) The active conformation can be determined by conformational analysis.

Question 9

Which of the following statements is false with regard to cyclic structures?

a) They are normally more rigid than acyclic structures.

b) They are locked into the active conformation.

c) They are useful in determining the active conformation of a series of related compounds.

d) They are normally more difficult to synthesise than acyclic molecules.

Question 10

What is meant by docking?

a) The process by which two different structures are compared by molecular modelling.

b) The process by which a lead compound is simplified by removing excess functional groups.

c) The process by which drugs are fitted into their target binding sites using molecular modelling.

d) The process by which a pharmacophore is identified.

Question 11

What is meant by de novo drug design?

a) The synthesis of a compound from simple starting materials.

b) The design of the synthesis required to generate a novel range of structures.

c) The design of a novel drug based on molecular modelling studies of a binding site.

d) The modification of a drug based on molecular modelling studies into how it binds to its target binding site.

Question 12

Which of the following statements is true in de novo drug design?

a) The design of rigid molecules is superior to flexible ones.

b) Molecules should be designed to fit as snugly as possible into the target binding site.

c) Molecules that have to adopt an unstable conformation in order to bind should be rejected.

d) Desolvation energies can be ignored since they are likely to be the same for different molecules having the same pharmacophore.

Question 13

Which of the following software programmes is used for automated de novo drug design?

a) DOCK

b) LUDI

c) Chem3D

d) CoMFA

Question 14

Which of the following statements is false with regard to using molecular modelling to design a combinatorial library?

a) Pharmacophore triangles can be used to design a library.

b) The aim is to synthesise the minimum number of structures likely to produce the maximum number of pharmacophores.

c) Flexible structures should be analysed before rigid ones.

d) Structures should only be included in the library if they represent at least 10% additional new pharmacophores compared with the total represented by structures already present in the library.

Question 15

Which of the following operations or calculations would generally be carried out using molecular mechanics?

a) Molecular orbital energies

b) Energy minimisation

c) Electrostatic potentials

d) Transition-state geometries

Oxford University Press, Online Resource Centre, Chapter 17.

Chapter 17

Instructions