Ab initio path‐integral calculations of kinetic and equilibrium isotope effects on base‐catalyzed RNA transphosphorylation models

Abstract

Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2′-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This paper significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and non-enzymatic 2′-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a “gold-standard” coupled-cluster level of theory [CCSD(T)]. In addition to the widely-used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently-developed ab initio path-integral method, i.e., automated integration-free path-integral (AIF-PI) method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis.

Elementary isotope effects – Sensitivity to potential energy shape

“…The results of the path integral calculations of the equilibrium isotope effects with ab initio methods [2,24] confirm that the discrepancy between different methods is usually no more than a few percent. Note that different ab initio methods may give different force constants what is excluded form the present research by setting the same force constant for each PEC of a given molecule.…”

Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

“…studies on closely related systems. [23,24,49] As for those reactants with enhanced leaving groups (conjugate acids have lower pK a values, less than ca. 13), the 2'-O KIEs are always large normal while the 5'-O KIEs are mostly normal but much closer to unity.…”

Palladium‐Catalyzed/Norbornene‐Mediated CH Activation/ N‐Tosylhydrazone Insertion Reaction: A Route to Highly Functionalized Vinylarenes

“…[9,18,[24][25][26][27][28][29] This dianion reaction (Scheme 1) in aqueous solution has been studied by using different models for RNA and representing the solventasac ontinuum. [26,27,[29][30][31][32][33] In some of these studies, the geometries of stationaryp oints in the gas phase were used for the calculations in solution. Other calculations in aqueous solution were carried out with the hybrid quantum mechanics/molecular mechanics (QM/MM) method.…”