2011
DOI: 10.1002/anie.201104147
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Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

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Cited by 53 publications
(112 citation statements)
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“…Experiment and computation together indicate that RNase A stabilizes a product-like transition state that is very similar to the anionic solution mechanism catalyzed by specific base in solution[12, 34, 36, 60]. Nonetheless, the enzyme significantly alters leaving group bonding attributable to general acid catalysis from His119.…”
Section: Discussionmentioning
confidence: 98%
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“…Experiment and computation together indicate that RNase A stabilizes a product-like transition state that is very similar to the anionic solution mechanism catalyzed by specific base in solution[12, 34, 36, 60]. Nonetheless, the enzyme significantly alters leaving group bonding attributable to general acid catalysis from His119.…”
Section: Discussionmentioning
confidence: 98%
“…Computational studies of nucleophilic attack on diesters including cyclization reactions has consistently illustrated the potential for stepwise mechanism for RNA transphosphorylation with a transient monoanionic phosphorane intermediate[3236]. Recently, density-functional calculations[33] were used to analyze a series of transphosphorylation models with different leaving groups to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state (Fig.…”
Section: Mechanisms and Transition States Of Solution Rna 2’-o-tramentioning
confidence: 99%
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“…Most importantly, KIEs are very sensitive to changes in transition state bonding environment, and ultimately encode information about the transition state that allows validation of predicted pathways that pass through it, which in turn provides insight into enzyme mechanism (Harris & Cassano, 2008; Lassila, Zalatan, & Herschlag, 2011). Nonetheless, a detailed interpretation of KIE data in terms of structure and bonding in the transition state requires the use of computational quantum mechanical models (Wong et al, 2012; H. Chen et al, 2014).…”
Section: Computing Kinetic Isotope Effects To Verify Transition Stamentioning
confidence: 99%
“…[26,27] Subsequently, additional approaches were introduced in the study of enzyme reactions, such as variational TST with the multidimensional tunneling approach of Truhlar and co-workers, [14,70] and wave function based methods of HammesSchiffer and co-workers. [71] Following in the footsteps of the Warshel group, we [29][30][31][32]34,72,73] and others [74][75][76][77][78] further developed the Feynman PI approach for enzyme simulations. PIs are particularly suitable for enzyme simulations because they are readily applicable to multidimensional systems and may be employed in mixed quantumÀclassical systems.…”
Section: The Feynman Path-integral Approach and The Qcpmentioning
confidence: 99%