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Harris ME, Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1801-8. [PMID: 25936517 DOI: 10.1016/j.bbapap.2015.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/21/2023]
Abstract
The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44118, United States.
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, United States; Department of Chemistry, University of Chicago, Chicago, IL 60637, United States
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, United States; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States
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2
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Kim SI, Kim EH, Um IH. Kinetics and Mechanism of Nucleophilic Displacement Reactions of Y-Substituted Phenyl Benzoates with Cyanide Ion. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.03.689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Feng G, Tanifum EA, Adams H, Hengge AC, Williams NH. Mechanism and transition state structure of aryl methylphosphonate esters doubly coordinated to a dinuclear cobalt(III) center. J Am Chem Soc 2009; 131:12771-9. [PMID: 19673521 DOI: 10.1021/ja904134n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Reactivities of five phosphonate esters each coordinated to a dinuclear Co(III) complex were investigated ([Co(2)(tacn)(2)(OH)(2){O(2)P(Me)OAr}](3+); tacn = 1,4,7-triazacyclononane; substituent = m-F, p-NO(2) (1a); p-NO(2) (1b); m-NO(2) (1c); p-Cl (1d); unsubstituted (1e)). Hydrolysis of the phosphonate esters in 1a to 1e is specific base catalyzed and takes place by intramolecular oxide attack on the bridging phosphonate. These data define a Brønsted beta(lg) of -1.12, considerably more negative than that of the hydrolysis of the uncomplexed phosphonates (-0.69). For 1b, the kinetic isotope effects in the leaving group are (18)k(lg) = 1.0228 and (15)k = 1.0014, at the nonbridging phosphoryl oxygens (18)k(nonbridge) = 0.9954, and at the nucleophilic oxygen(18)k(nuc) = 1.0105. The KIEs and the beta(lg) data point to a transition state for the alkaline hydrolysis of 1b that is similar to that of a phosphate monoester complex with the same leaving group, rather than the isoelectronic diester complex. The data from these model systems parallel the observation that in protein phosphatase-1, which has an active site that resembles the structures of these complexes, the catalyzed hydrolysis of aryl methylphosphonates and aryl phosphates are much more similar to one another than the uncomplexed hydrolysis reactions of the two substrates.
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Affiliation(s)
- Guoqiang Feng
- University of Sheffield, Centre for Chemical Biology, Department of Chemistry, Sheffield, UK S3 7HF
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Li QG, Xue Y. Effects of substituent and leaving group on the gas-phase SN2 reactions of phenoxides with halomethanes: a DFT investigation. J Phys Chem A 2009; 113:10359-66. [PMID: 19711938 DOI: 10.1021/jp905346e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Computational investigations on the gas-phase nucleophilic substitution reactions of p-substituted phenoxides (p-Y-C6H4O-, Y = OH, CH3O, CH3, H, F, Cl, CF3) with halomethanes (CH3X, X = F, Cl, Br, and I) were performed by the B3LYP and MP2 methods with the 6-311+G(d,p) basis set. Calculated results indicate that the reactions are more endothermic only when the substrate is a lighter halide. The complexation enthalpies, the key parameters in the transition state (TS), the central barriers, overall barriers, overall reaction enthalpies, and the charge of the O4 atom in the TSs all present good correlations with the Hammett constants sigma of substituents in the nucleophile. Leffler-Grunwald rate equilibrium relationships predict the degree of bond formation in the transition state suggesting that the reactions have progressed 31%, 24%, 24%, and 21% in the TS for halomethanes (X = F, Cl, Br, and I), respectively. The TS structure with substituents in the nucleophile is not kinetically but thermodynamically controlled, similar to the earlier results. Furthermore, the excellent relationship between the central barrier heights and the looseness of the transition state structure indicates that the stretching of the cleaving bond is one of the major factors determining the central barrier heights. The nucleophilicity of the nucleophile decreases with the increase of the electron-withdrawing power of substituent Y in the nucleophile, while the leaving-group ability of the halogen atom increases with the decrease of its Mulliken electronegativity.
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Affiliation(s)
- Qiang-gen Li
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, People's Republic of China
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Dybala-Defratyka A, Szatkowski L, Kaminski R, Wujec M, Siwek A, Paneth P. Kinetic isotope effects on dehalogenations at an aromatic carbon. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:7744-7750. [PMID: 19031855 DOI: 10.1021/es800276y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In order to interpret the observed isotopic fractionation it is necessaryto understand its relationship with the isotope effect(s) on steps that occur during the conversion of the initial reactant to the final product. We examine this relationship from the biochemical point of view and elaborate on the consequences of the assumptions that it is based on. We illustrate the discrepancies between theoretical and experimental interpretation of kinetic isotope effects on examples of dehalogenation reactions that occur at an aromatic carbon atom. The examples include 4-chlorobenzoyl-CoA dehalogenase-catalyzed conversion of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA, dehaloperoxidase-catalyzed conversion of 2,4,6-trichlorophenol to 2,6-dichloroquinone, and spontaneous hydrolysis of atrazine at pH 12. For this latter reaction we have measured the chlorine kinetic isotope effect and estimated its value theoretically at the DFT level of theory. Results of chlorine kinetic isotope effects suggest that the studied dechlorination reactions proceed in a single step with significant weakening of the carbon-chlorine bond in the transition state.
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Affiliation(s)
- Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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Westaway KC, Fang YR, MacMillar S, Matsson O, Poirier RA, Islam SM. Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory. J Phys Chem A 2008; 112:10264-73. [PMID: 18816038 DOI: 10.1021/jp804237g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found for the reactions with a halogen leaving group. This presumably is found because of the bulky (sterically hindered) leaving group in the tosylate reaction. From every prospective, the tosylate reaction is too different from the halogen reactions to be compared.
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Affiliation(s)
- Kenneth C Westaway
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada, P3E 2C6.
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Iyer S, Hengge AC. The effects of sulfur substitution for the nucleophile and bridging oxygen atoms in reactions of hydroxyalkyl phosphate esters. J Org Chem 2008; 73:4819-29. [PMID: 18533704 PMCID: PMC2575009 DOI: 10.1021/jo8002198] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of sulfur substitution on the reactions of hydroxyalkyl phosphate esters are examined. These compounds are models for the intramolecular phosphoryl transfer reaction involved in the cleavage of the internucleotide bond in RNA. The models studied here lack the ribose ring and their conformational flexibility results in greater stability and the availability of different reaction pathways. Sulfur in the nucleophilic position shows no nucleophilic reaction at phosphorus, instead rapidly attacking at the beta carbon atom, forming thiirane with departure of a phosphomonoester. Sulfur substitution at either of the two bridging positions leads to cleavage of the diester via formation of a cyclic intermediate, but with significant rate acceleration when compared to the oxygen analogues. The bridge-substituted models react substantially slower than the analogous ribose compounds with sulfur substitution at comparable positions. Kinetic isotope effects reveal significant differences in the transition state depending on which bridging position sulfur occupies. When sulfur is in the scissile bridging position, a highly associative transition state is indicated, with a largely formed bond to the nucleophile and the scissile P-S bond is little changed. When sulfur occupies the other bridging position, the isotope effects imply a very early transition state in a concerted reaction.
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Affiliation(s)
- Subashree Iyer
- Utah State University, Department of Chemistry and Biochemistry, Logan, Utah 84322-0300, USA
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Dzierzawska J, Jarota A, Karolak M, Piotrowski L, Placek I, Swiderek K, Szatkowski L, Paneth P. Carbon and secondary deuterium kinetic isotope effects on SN2 methyl transfer reactions. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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9
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Matsson O, MacMillar S. Isotope effects for fluorine-18 and carbon-11 in the study of reaction mechanisms. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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10
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Westaway KC, Fang YR, MacMillar S, Matsson O, Poirier RA, Islam SM. A New Insight into Using Chlorine Leaving Group and Nucleophile Carbon Kinetic Isotope Effects To Determine Substituent Effects on the Structure of SN2 Transition States. J Phys Chem A 2007; 111:8110-20. [PMID: 17663535 DOI: 10.1021/jp0729765] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chlorine leaving group k(35)/k(37), nucleophile carbon k(11)/k(14), and secondary alpha-deuterium [(kH/kD)alpha] kinetic isotope effects (KIEs) have been measured for the SN2 reactions between para-substituted benzyl chlorides and tetrabutylammonium cyanide in tetrahydrofuran at 20 degrees C to determine whether these isotope effects can be used to determine the substituent effect on the structure of the transition state. The secondary alpha-deuterium KIEs indicate that the transition states for these reactions are unsymmetric. The theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion; i.e., they suggest that the transition states for these reactions are unsymmetric with a long NC-C(alpha) and reasonably short C(alpha)-Cl bonds. The chlorine isotope effects suggest that these KIEs can be used to determine the substituent effects on transition state structure with the KIE decreasing when a more electron-withdrawing para-substituent is present. This conclusion is supported by theoretical calculations. The nucleophile carbon k(11)/k(14) KIEs for these reactions, however, do not change significantly with substituent and, therefore, do not appear to be useful for determining how the NC-C(alpha) transition-state bond changes with substituent. The theoretical calculations indicate that the NC-C(alpha) bond also shortens as a more electron-withdrawing substituent is placed on the benzene ring of the substrate but that the changes in the NC-C(alpha) transition-state bond with substituent are very small and may not be measurable. The results also show that using leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is more complicated than previously thought. The implication of using both chlorine leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is discussed.
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Affiliation(s)
- Kenneth C Westaway
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario P3E 2C6, Canada.
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11
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Westaway KC. Determining transition state structure using kinetic isotope effects. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1434] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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12
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Fang YR, MacMillar S, Eriksson J, Kołodziejska-Huben M, Dybała-Defratyka A, Paneth P, Matsson O, Westaway KC. The Effect of Solvent on the Structure of the Transition State for the SN2 Reaction between Cyanide Ion and Ethyl Chloride in DMSO and THF Probed with Six Different Kinetic Isotope Effects. J Org Chem 2006; 71:4742-7. [PMID: 16776498 DOI: 10.1021/jo052375e] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The secondary alpha- and beta-deuterium, the alpha-carbon, the nucleophile carbon, the nucleophile nitrogen, and the chlorine leaving group kinetic isotope effects for the S(N)2 reaction between cyanide ion and ethyl chloride were determined in the very slightly polar solvent THF at 30 degrees C. A comparison of these KIEs with those reported earlier for the same reaction in the polar solvent DMSO shows that the transition state in THF is only slightly tighter with very slightly shorter NC-C(alpha) and C(alpha)-Cl bonds. This minor change in transition state structure does not account for the different transition structures that were earlier suggested by interpreting the experimental KIEs and the gas-phase calculations, respectively. It therefore seems unlikely that the different transition states suggested by the two methods are due to the lack of appropriate solvent modeling in the theoretical calculations. Previously it was predicted that the transition state of S(N)2 reactions where the nucleophile and the leaving group have the same charge would be unaffected by a change in solvent. The experimental KIEs support this view.
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Affiliation(s)
- Yao-ren Fang
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
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Westaway KC. Using kinetic isotope effects to determine the structure of the transition states of SN2 reactions. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0065-3160(06)41004-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Matsson O, Dybala-Defratyka A, Rostkowski M, Paneth P, Westaway KC. A theoretical investigation of alpha-carbon kinetic isotope effects and their relationship to the transition-state structure of S(N)2 reactions. J Org Chem 2005; 70:4022-7. [PMID: 15876091 DOI: 10.1021/jo047987y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] The transition structures and alpha-carbon 12C/13C kinetic isotope effects for 22 S(N)2 reactions between methyl chloride and a wide variety of nucleophiles have been calculated using the B1LYP/aug-cc-pVDZ level of theory. Anionic, neutral, and radical anion nucleophiles were used to give a wide range of S(N)2 transition states so the relationship between the magnitude of the alpha-carbon kinetic isotope effect and transition-state structure could be determined. The results suggest that the alpha-carbon 12C/13C kinetic isotope effects for S(N)2 reactions will be large (near the experimental maximum) and that the curve relating the magnitude of the KIE to the percent transfer of the alpha-carbon from the nucleophile to the leaving group in the transition state has a broad maximum. This means very similar KIEs will be found for early, symmetric, and late transition states and that one cannot use the magnitude of these KIEs to estimate transition-state structure.
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Affiliation(s)
- O Matsson
- Division of Organic Chemistry, Department of Chemistry, Uppsala University, P.O. Box 599, 75124 Uppsala, Sweden.
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Humphry T, Forconi M, Williams NH, Hengge AC. Altered mechanisms of reactions of phosphate esters bridging a dinuclear metal center. J Am Chem Soc 2005; 126:11864-9. [PMID: 15382921 DOI: 10.1021/ja047110g] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic isotope effects in the nucleophile and leaving group were obtained for the reaction of p-nitrophenyl phosphate monoester coordinated to a dinuclear Co(III) complex. The metal complex of the p-nitrophenyl phosphate monoester was found to hydrolyze by a single-step concerted mechanism, with significant nucleophilic participation in the transition state. By contrast, the hydrolysis of uncomplexed p-nitrophenyl phosphate occurs by a very loose transition state with little bond formation to the nucleophile. Previously, the metal complex of the diester methyl-p-nitrophenyl phosphate was found to hydrolyze via a two-step addition-elimination mechanism, in contrast to the concerted hydrolysis mechanism followed by uncomplexed diesters with the p-nitrophenolate leaving group. These results show that coordination to a metal complex can significantly alter the mechanism of phosphoryl transfer.
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Affiliation(s)
- Tim Humphry
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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Dybała-Defratyka A, Rostkowski M, Matsson O, Westaway KC, Paneth P. A new interpretation of chlorine leaving group kinetic isotope effects; a theoretical approach. J Org Chem 2004; 69:4900-5. [PMID: 15255714 DOI: 10.1021/jo049327z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chlorine leaving group kinetic isotope effects (KIEs) for the S(N)2 reactions between methyl chloride and a wide range of anionic, neutral, and radical anion nucleophiles were calculated in the gas phase and, in several cases, using a continuum solvent model. In contrast to the expected linear dependence of the chlorine KIEs on the C(alpha)-Cl bond order in the transition state, the KIEs fell in a very small range (1.0056-1.0091), even though the C(alpha)-Cl transition state bond orders varied widely from approximately 0.32 to 0.78, a range from reactant-like to very product-like. This renders chlorine KIEs, and possibly other leaving-group KIEs, less useful for studies of reaction mechanisms than commonly assumed. A partial explanation for this unexpected relationship between the C(alpha)-Cl transition state bond order and the magnitude of the chlorine KIE is presented.
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Affiliation(s)
- Agnieszka Dybała-Defratyka
- Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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Cassano AG, Anderson VE, Harris ME. Analysis of solvent nucleophile isotope effects: evidence for concerted mechanisms and nucleophilic activation by metal coordination in nonenzymatic and ribozyme-catalyzed phosphodiester hydrolysis. Biochemistry 2004; 43:10547-59. [PMID: 15301552 DOI: 10.1021/bi049188f] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heavy atom isotope effects are a valuable tool for probing chemical and enzymatic reaction mechanisms; yet, they are not widely applied to examine mechanisms of nucleophilic activation. We developed approaches for analyzing solvent (18)O nucleophile isotope effects ((18)k(nuc)) that allow, for the first time, their application to hydrolysis reactions of nucleotides and nucleic acids. Here, we report (18)k(nuc) for phosphodiester hydrolysis catalyzed by Mg(2+) and by the Mg(2+)-dependent RNase P ribozyme and deamination by the Zn(2+)-dependent protein enzyme adenosine deaminase (ADA). Because ADA incorporates a single solvent molecule into the product inosine, this reaction can be used to monitor solvent (18)O/(16)O ratios in complex reaction mixtures. This approach, combined with new methods for analysis of isotope ratios of nucleotide phosphates by whole molecule mass spectrometry, permitted determination of (18)k(nuc) for hydrolysis of thymidine 5'-p-nitrophenyl phosphate and RNA cleavage by the RNase P ribozyme. For ADA, an inverse (18)k(nuc) of 0.986 +/- 0.001 is observed, reflecting coordination of the nucleophile by an active site Zn(2+) ion and a stepwise mechanism. In contrast, the observed (18)k(nuc) for phosphodiester reactions were normal: 1.027 +/- 0.013 and 1.030 +/- 0.012 for the Mg(2+)- and ribozyme-catalyzed reactions, respectively. Such normal effects indicate that nucleophilic attack occurs in the rate-limiting step for these reactions, consistent with concerted mechanisms. However, these magnitudes are significantly less than the (18)k(nuc) observed for nucleophilic attack by hydroxide (1.068 +/- 0.007), indicating a "stiffer" bonding environment for the nucleophile in the transition state. Kinetic analysis of the Mg(2+)-catalyzed reaction indicates that a Mg(2+)-hydroxide complex is the catalytic species; thus, the lower (18)k(nuc), in large part, reflects direct metal ion coordination of the nucleophilic oxygen. A similar value for the RNase P ribozyme catalyzed reaction provides support for nucleophilic activation by metal ion catalysis.
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Affiliation(s)
- Adam G Cassano
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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Humphry T, Forconi M, Williams NH, Hengge AC. An altered mechanism of hydrolysis for a metal-complexed phosphate diester. J Am Chem Soc 2002; 124:14860-1. [PMID: 12475323 DOI: 10.1021/ja027671c] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isotope effects in the nucleophile and in the leaving group were measured to gain information about the mechanism and transition state of the hydrolysis of methyl p-nitrophenyl phosphate complexed to a dinuclear cobalt complex. The complexed diester undergoes hydrolysis about 1011 times faster than the corresponding uncomplexed diester. The kinetic isotope effects indicate that this rate acceleration is accompanied by a change in mechanism. A large inverse 18O isotope effect in the bridging hydroxide nucleophile (0.937 +/- 0.002) suggests that nucleophilic attack occurs before the rate-determining step. Large isotope effects in the nitrophenyl leaving group (18Olg = 1.029 +/- 0.002, 15N = 1.0026 +/- 0.0002) indicate significant fission of the P-O ester bond in the transition state of the rate-determining step. The data indicate that in contrast to uncomplexed diesters, which undergo hydrolysis by a concerted mechanism, the reaction of the complexed diester likely proceeds via an addition-elimination mechanism. The rate-limiting step is expulsion of the p-nitrophenyl leaving group from the intermediate, which proceeds by a late transition state with extensive bond fission to the leaving group. This represents a substantial change in mechanism from the hydrolysis of uncomplexed aryl phosphate diesters.
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Affiliation(s)
- Tim Humphry
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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Koerner T, Fang YR, Westaway KC. Using Incoming Nucleophile Primary Hydrogen−Deuterium Kinetic Isotope Effects To Model the SN2 Transition State. J Am Chem Soc 2000. [DOI: 10.1021/ja000441i] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Terry Koerner
- Contribution from the Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada P3E 2C6
| | - Yao-ren Fang
- Contribution from the Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada P3E 2C6
| | - Kenneth Charles Westaway
- Contribution from the Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada P3E 2C6
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Westaway KC, Jiang W. Isotope effects in nucleophilic substitution reactions XI. The effect of ion-pairing, substituents, and the solvent on SN2 transition states. CAN J CHEM 1999. [DOI: 10.1139/v99-078] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The secondary alpha deuterium and primary leaving group nitrogen KIEs and Hammett ρ values found for the free ion and ion-pair SN2 reactions between benzyldimethylphenylammonium ion and sodium para-substituted thiophenoxides in methanol at 20.000°C show how (i) ion-pairing of the nucleophile, (ii) a change in substituent in the nucleophile, and (iii) a change in solvent alters the structure of a Type II SN2 transition state. Ion-pairing shortens the weaker sulfur - alpha carbon (SCα) transition state bond significantly but does not alter the stronger alpha carbon - leaving group (CαN) transition state bond as the bond strength hypothesis predicts. However, the effect of ion pairing, i.e., the decrease in the SCα bond on ion-pairing, decreases as a more electron-withdrawing substituent is added to the nucleophile, and the SCα bond actually increases when the nucleophile is the p-chlorothiophenoxide ion. The identical Hammett ρ values of -0.85 and -0.84 for the free ion and ion-pair reactions, respectively, may be observed because, on average, the SCα bonds are identical in the free ion and ion-pair transition states. When a more electron-donating substituent is added to the nucleophile, an earlier transition state is found in both the ion-pair and free ion reactions. However, the substituent effect is smaller in the ion-pair reactions, presumably because the change in the negative charge on the sulfur atom with substituent is greater in the free ion than in the ion-pair. The substituent effect on transition state structure suggested by the KIEs is not predicted by any of the theories that are used to predict substituent effects on SN2 reactions. Both the secondary alpha deuterium and primary leaving group nitrogen KIEs and the Hammett ρ values indicate that the transition state is earlier when the solvent is changed from DMF to methanol as the "solvation rule for SN2 reactions" predicts. This probably occurs because an earlier, more ionic, transition state is more highly solvated (more stable) in methanol.Key words: nucleophilic substitution, SN2, isotope effect, transition state, substituent, ion-pair.
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Secondary Deuterium Kinetic Isotope Effects and Transition State Structure. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0065-3160(08)60194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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