The Diels-Alder reaction is one of the most powerful synthetic tools in organic chemistry, and asymmetric Diels-Alder catalysis allows for rapid construction of chiral carbon scaﬀolds. For this reason, considerable eﬀort has been invested in developing eﬃcient and stereoselective organo- and biocatalysts. However, Diels-Alder is a virtually unknown reaction in Nature, and to engineer an enzyme into a Diels-Alderase is therefore a challenging task. Despite several successful designs of catalytic antibodies since the 1980’s, their catalytic activities have remained low, and no true artiﬁcial ’Diels-Alderase’ enzyme was reported before 2010.
In this thesis, we employ state-of-the-art computational tools to study the mechanism of organocatalyzed Diels-Alder in detail, and to redesign existing enzymes into intermolecular Diels-Alder catalysts. Papers I–IV explore the mechanistic variations when employing increasingly activated reactants and the eﬀect of catalysis. In particular, the relation between the traditionally presumed concerted mechanism and a stepwise pathway, forming one bond at a time, is probed. Papers V–X deal with enzyme design and the computational aspects of predicting catalytic activity. Four novel, computationally designed Diels-Alderase candidates are presented in Papers VI–IX. In Paper X, a new parameterization of the Linear Interaction Energy model for predicting protein-ligand aﬃnities is presented.
A general ﬁnding in this thesis is that it is diﬃcult to attain large transition state stabilization eﬀects solely by hydrogen bond catalysis. In addition, water (the preferred solvent of enzymes) is well-known for catalyzing Diels- Alder by itself. Therefore, an eﬃcient Diels-Alderase must rely on large binding aﬃnities for the two substrates and preferential binding conformations close to the transition state geometry. In Papers VI–VIII, we co-designed the enzyme active site and substrates in order to achieve the best possible complementarity and maximize binding aﬃnity and pre-organization. Even so, catalysis is limited by the maximum possible stabilization oﬀered by hydrogen bonds, and by the inherently large energy barrier associated with the [4+2] cycloaddition.
The stepwise Diels-Alder pathway, proceeding via a zwitterionic intermediate, may oﬀer a productive alternative for enzyme catalysis, since an enzyme active site may be more diﬀerentiated towards stabilizing the high-energy states than for the standard mechanism. In Papers I and III, it is demonstrated that a hydrogen bond donor catalyst provides more stabilization of transition states having pronounced charge-transfer character, which shifts the preference towards a stepwise mechanism.
Another alternative, explored in Paper IX, is to use an α,β -unsaturated ketone as a ’pro-diene’, and let the enzyme generate the diene in situ by general acid/base catalysis. The results show that the potential reduction in the reaction barrier with such a mechanism is much larger than for conventional Diels-Alder. Moreover, an acid/base-mediated pathway is a better mimic of how natural enzymes function, since remarkably few catalyze their reactions solely by non-covalent interactions.
Stockholm: KTH Royal Institute of Technology, 2012. , xii, 138 p.
Computational chemistry, density functional theory, enzyme design, molecular modeling, organocatalysis, stepwise Diels-Alder, oxyanion hole