ArticlePhysical chemistry chemical physics : PCCP2014
Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations.
Article in Physical chemistry chemical physics : PCCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 20 citations in OpenAlex.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications.The journal of physical chemistry. B · 2025Article
- Multireference Generalization of the Weighted Thermodynamic Perturbation Method.The journal of physical chemistry. A · 2022Article
- Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis.The journal of physical chemistry. A · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Phosphodiester models for cleavage of nucleic acids.Beilstein journal of organic chemistry · 2018Review
- A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.Journal of chemical theory and computation · 2017Article
- Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.Journal of chemical theory and computation · 2016Article
- VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.The Journal of chemical physics · 2016Article
- Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.Biochimica et biophysica acta · 2015Review
- Nucleic acid reactivity: challenges for next-generation semiempirical quantum models.Journal of computational chemistry · 2015Article
- Multipolar Ewald methods, 2: applications using a quantum mechanical force field.Journal of chemical theory and computation · 2015Article
- Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions.Chemistry (Weinheim an der Bergstrasse, Germany) · 2014Article
- Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation.Current opinion in chemical biology · 2014Review
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Authors and funding
2 authors at 2 institutions in 3 countries.
Funding
Abstract
RNA cleavage transesterification is of fundamental reaction in biology that is catalyzed by both protein and RNA enzymes. In this work, a series of RNA transesterification model reactions with a wide range of leaving groups are investigated with density-functional calculations in an aqueous solvation environment in order to study linear free energy relationships (LFERs) and their connection to transition state structure and bonding. Overall, results obtained from the polarizable continuum solvation model with UAKS radii produce the best linear correlations and closest overall agreement with experimental results. Reactions with a poor leaving group are predicted to proceed via a stepwise mechanism with a late transition state that is rate controlling. As leaving group becomes more acidic and labile, the barriers of both early and late transition states decrease. LFERs for each transition state are computed, with the late transition state barrier showing greater sensitivity to leaving group pKa. For sufficiently enhanced leaving groups, the reaction mechanism transits to a concerted mechanism characterized by a single early transition state. Further linear relationships were derived for bond lengths and bond orders as a function of leaving group pKa and rate constant values that can be used for prediction. This work provides important benchmark linear free energy data that allows a molecular-level characterization of the structure and bonding of the transition states for this important class of phosphoryl transfer reactions. The relations reported herein can be used to aid in the interpretation of data obtained from experimental studies of non-catalytic and catalytic mechanisms.
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