Solution‐Phase Organic Chemistry

The vast majority of chemical reactions occur in solution. Perhaps most critical is that all of biochemistry takes place in an aqueous environment, and so if computational chemistry is to be relevant for biochemical applications, treatment of the solvent is imperative. This chapter presents case studies of aqueous-phase chemistry analyzed using quantum mechanical computations. The computational work of Jorgensen's group was instrumental in bringing critical insight into the nature of the aqueous Diels-Alder reaction. The chapter focuses on the structure of D-glucose and the role that aqueous solvent has in altering its conformational preference. It discusses the structures of the tautomers of each of the four DNA bases and uracil, found in RNA, focusing on the differences in the gas and solution phases. The chapter ends with a discussion on amino acids.