Molecular orbital calculations may be used to predict structures of intermolecular

Chapter 18, Problem 18.20

(choose chapter or problem)

Molecular orbital calculations may be used to predict structures of intermolecular complexes. Hydrogen bonds between purine and pyrimidine bases are responsible for the double helix structure of DNA (see Chapter 19). Consider methyl-adenine (16, with R = CH3) and methyl-thymine (17, with R = CH3) as models of two bases that can form hydrogen bonds in DNA. (a) Using molecular modelling software and the computational method of your choice, calculate the atomic charges of all atoms in methyl-adenine and methyl-thymine. (b) Based on your tabulation of atomic charges, identify the atoms in methyl-adenine and methyl-thymine that are likely to participate in hydrogen bonds. (c) Draw all possible adeninethymine pairs that can be linked by hydrogen bonds, keeping in mind that linear arrangements of the A-HB fragments are preferred in DNA. For this step, you may want to use your molecular modelling software to align the molecules properly. (d) Consult Chapter 19 and determine which of the pairs that you drew in part (c) occur naturally in DNA molecules. (e) Repeat parts (a)(d) for cytosine and guanine, which also form base pairs in DNA (see Chapter 19 for the structures of these bases).