1
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Guo R, Adak S, Bellotti P, Gao X, Smith WW, Le SN, Ma J, Houk KN, Glorius F, Chen S, Brown MK. Photochemical Dearomative Cycloadditions of Quinolines and Alkenes: Scope and Mechanism Studies. J Am Chem Soc 2022; 144:17680-17691. [PMID: 36106902 PMCID: PMC9840784 DOI: 10.1021/jacs.2c07726] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Photochemical dearomative cycloaddition has emerged as a useful strategy to rapidly generate molecular complexity. Within this context, stereo- and regiocontrolled intermolecular para-cycloadditions are rare. Herein, a method to achieve photochemical cycloaddition of quinolines and alkenes is shown. Emphasis is placed on generating sterically congested products and reaction of highly substituted alkenes and allenes. In addition, the mechanistic details of the process are studied, which revealed a reversible radical addition and a selectivity-determining radical recombination. The regio- and stereochemical outcome of the reaction is also rationalized.
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Affiliation(s)
- Renyu Guo
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Souvik Adak
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Peter Bellotti
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149Münster, Germany
| | - Xinfeng Gao
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - W Walker Smith
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Sam Ngan Le
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, Ohio44074, United States
| | - Jiajia Ma
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149Münster, Germany
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California90095, United States
| | - Frank Glorius
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149Münster, Germany
| | - Shuming Chen
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, Ohio44074, United States
| | - M Kevin Brown
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
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2
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Wang X, Tong WY, Huang B, Cao S, Li Y, Jiao J, Huang H, Yi Q, Qu S, Wang X. Convergent Synthesis of 1,4-Dicarbonyl Z-Alkenes through Three-Component Coupling of Alkynes, α-Diazo Sulfonium Triflate, and Water. J Am Chem Soc 2022; 144:4952-4965. [PMID: 35274949 DOI: 10.1021/jacs.1c12874] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report a general protocol for the convergent synthesis of 1,4-dicarbonyl Z-alkenes form alkynes using α-diazo sulfonium triflate and water. The C═O, C═C, and C-H bonds are formed under mild conditions with a wide range of functional groups tolerated. The reaction exhibits excellent Z-selectivity and complete regioselectivity. The resulting 1,4-dicarbonyl Z-alkenes can smoothly undergo follow-up conversion to a variety of heteroaromatic scaffolds. Moreover, the reaction also provides a facile access to the corresponding deuterated Z-alkenes and deuterated heteroarenes with a high level of deuterium incorporation (90-97% D-inc.) by directly using D2O, thus rendering the method highly valuable. The comprehensive mechanistic studies indicate that a free carbyne radical intermediate is formed via the photocatalytic single electron transfer process, and KH2PO4 plays a crucial role in significant improvements on yield and selectivity based on density-functional theory calculations, providing a new direction for radical coupling reactions of diazo compounds.
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Affiliation(s)
- Xuyong Wang
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Wen-Yan Tong
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Bing Huang
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Si Cao
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Yunlong Li
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Jingchao Jiao
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Hang Huang
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Qiu Yi
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Shuanglin Qu
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
| | - Xi Wang
- College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha 410082, P. R. China
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3
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Joshi C, Macharia JM, Izzo JA, Wambua V, Kim S, Hirschi JS, Vetticatt MJ. Isotope Effects Reveal the Catalytic Mechanism of the Archetypical Suzuki-Miyaura Reaction. ACS Catal 2022; 12:2959-2966. [PMID: 37168650 PMCID: PMC10168682 DOI: 10.1021/acscatal.1c05802] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental and theoretical 13C kinetic isotope effects (KIEs) are utilized to obtain atomistic insight into the catalytic mechanism of the Pd(PPh3)4-catalyzed Suzuki-Miyaura reaction of aryl halides and aryl boronic acids. Under catalytic conditions, we establish that oxidative addition of aryl bromides occurs to a 12-electron monoligated palladium complex (Pd-(PPh3)). This is based on the congruence of the experimental KIE for the carbon attached to bromine (KIEC-Br = 1.020) and predicted KIEC-Br for the transition state for oxidative addition to the Pd(PPh3) complex (1.021). For aryl iodides, the near-unity KIEC-I of ~1.003 suggests that the first irreversible step in the catalytic cycle precedes oxidative addition and is likely the binding of the iodoarene to Pd(PPh3). Our results suggest that the commonly proposed oxidative addition to the 14-electron Pd(PPh3)2 complex can occur only in the presence of excess added ligand or under stoichiometric conditions; in both cases, experimental KIEC-Br of 1.031 is measured, which is identical to the predicted KIEC-Br for the transition state for oxidative addition to the Pd(PPh3)2 complex (1.031). The transmetalation step, under catalytic conditions, is shown to proceed via a tetracoordinate boronate (8B4) intermediate with a Pd-O-B linkage based on the agreement between an experimental KIE for the carbon atom involved in transmetalation (KIEC-Boron = 1.035) and a predicted KIEC-Boron for the 8B4 transmetalation transition state (1.034).
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Affiliation(s)
- Chetan Joshi
- Department of Chemistry, Binghamton University, Vestal, New York 13850, United States
| | - Juliet M. Macharia
- Department of Chemistry, Binghamton University, Vestal, New York 13850, United States
| | - Joseph A. Izzo
- Department of Chemistry, Binghamton University, Vestal, New York 13850, United States
| | - Victor Wambua
- Department of Chemistry, Binghamton University, Vestal, New York 13850, United States
| | - Sungjin Kim
- Department of Chemistry, Binghamton University, Vestal, New York 13850, United States
| | - Jennifer S. Hirschi
- Department of Chemistry, Binghamton University, Vestal, New York 13850, United States
| | - Mathew J. Vetticatt
- Department of Chemistry, Binghamton University, Vestal, New York 13850, United States
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Gnyawali K, Kirinde Arachchige PT, Yi CS. Synthesis of Flavanone and Quinazolinone Derivatives from the Ruthenium-Catalyzed Deaminative Coupling Reaction of 2'-Hydroxyaryl Ketones and 2-Aminobenzamides with Simple Amines. Org Lett 2021; 24:218-222. [PMID: 34958227 DOI: 10.1021/acs.orglett.1c03870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The cationic Ru-H complex [(C6H6)(PCy3)(CO)RuH]+BF4- (1) with 3,4,5,6-tetrachloro-1,2-benzoquinone (L1) was found to be a highly effective catalyst for the deaminative coupling reaction of 2'-hydroxyaryl ketones with simple amines to form 3-substituted flavanone products. The analogous deaminative coupling reaction of 2-aminobenzamides with branched amines directly formed 3,3-disubstituted quinazolinone products. The catalytic method efficiently installs synthetically useful flavanone and quinazolinone core structures without employing any reactive reagents.
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Affiliation(s)
- Krishna Gnyawali
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | | | - Chae S Yi
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
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5
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Dale HJA, Leach AG, Lloyd-Jones GC. Heavy-Atom Kinetic Isotope Effects: Primary Interest or Zero Point? J Am Chem Soc 2021; 143:21079-21099. [PMID: 34870970 DOI: 10.1021/jacs.1c07351] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemists have many options for elucidating reaction mechanisms. Global kinetic analysis and classic transition-state probes (e.g., LFERs, Eyring) inevitably form the cornerstone of any strategy, yet their application to increasingly sophisticated synthetic methodologies often leads to a wide range of indistinguishable mechanistic proposals. Computational chemistry provides powerful tools for narrowing the field in such cases, yet wholly simulated mechanisms must be interpreted with great caution. Heavy-atom kinetic isotope effects (KIEs) offer an exquisite but underutilized method for reconciling the two approaches, anchoring the theoretician in the world of calculable observables and providing the experimentalist with atomistic insights. This Perspective provides a personal outlook on this synergy. It surveys the computation of heavy-atom KIEs and their measurement by NMR spectroscopy, discusses recent case studies, highlights the intellectual reward that lies in alignment of experiment and theory, and reflects on the changes required in chemical education in the area.
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Affiliation(s)
- Harvey J A Dale
- EaStChem, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Andrew G Leach
- School of Health Sciences, The University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
| | - Guy C Lloyd-Jones
- EaStChem, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
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6
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Kirinde Arachchige PT, Handunneththige S, Talipov MR, Kalutharage N, Yi CS. Scope and Mechanism of the Redox-Active 1,2-Benzoquinone Enabled Ruthenium-Catalyzed Deaminative α-Alkylation of Ketones with Amines. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Suhashini Handunneththige
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Marat R. Talipov
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Nishantha Kalutharage
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Chae S. Yi
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
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7
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Kuan KY, Singleton DA. Isotope Effects and the Mechanism of Photoredox-Promoted [2 + 2] Cycloadditions of Enones. J Org Chem 2021; 86:6305-6313. [PMID: 33890775 DOI: 10.1021/acs.joc.1c00099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
13C kinetic isotope effects (KIEs) for the photoredox-promoted [2 + 2] cycloaddition of enones were determined in homocoupling and heterocoupling examples. The only significant KIEs were observed at the β carbon, indicating that Cβ-Cβ bond formation is irreversible. However, these KIEs were much lower than computational predictions, suggesting that product selectivity is determined in part by a step prior to Cβ-Cβ bond formation. The results are explained as arising from a competition between C-C bond formation and electron exchange between substrate alkenes. This idea is supported by a relatively small substituent effect on substrate selectivity. The possible rates for electron transfer and bond-forming steps are analyzed, and the competition appears plausible, particularly if the mechanism involves a complex between reduced and neutral enone molecules.
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Affiliation(s)
- Kai-Yuan Kuan
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Daniel A Singleton
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
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8
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Wambua V, Hirschi JS, Vetticatt MJ. Rapid Evaluation of the Mechanism of Buchwald-Hartwig Amination and Aldol Reactions Using Intramolecular 13C Kinetic Isotope Effects. ACS Catal 2021; 11:60-67. [PMID: 34659873 DOI: 10.1021/acscatal.0c04752] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A practical approach is introduced for the rapid determination of 13C kinetic isotope effects that utilizes a "designed" reactant with two identical reaction sites. The mechanism of the Buchwald-Hartwig amination of tert-butylbromobenzene with primary and secondary amines is investigated under synthetically relevant catalytic conditions using traditional intermolecular 13C NMR methodology at natural abundance. Switching to 1,4-dibromobenzene, a symmetric bromoarene as the designed reactant, the same experimental 13C KIEs are determined using an intramolecular KIE approach. This rapid methodology for KIE determination requires substantially less material and time compared to traditional approaches. Details of the Buchwald-Hartwig amination mechanism are investigated under varying synthetic conditions, namely a variety of halides and bases. The enantioselectivity-determining step of the l-proline catalyzed aldol reaction is also evaluated using this approach. We expect this mechanistic methodology to gain traction among synthetic chemists as a practical technique to rapidly obtain high-resolution information regarding the transition structure of synthetically relevant reactions under catalytic conditions.
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Affiliation(s)
- Victor Wambua
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Jennifer S. Hirschi
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Mathew J. Vetticatt
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
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9
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Zhuo MH, Wilbur DJ, Kwan EE, Bennett CS. Matching Glycosyl Donor Reactivity to Sulfonate Leaving Group Ability Permits S N2 Glycosylations. J Am Chem Soc 2019; 141:16743-16754. [PMID: 31550879 PMCID: PMC6814073 DOI: 10.1021/jacs.9b07022] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here we demonstrate that highly β-selective glycosylation reactions can be achieved when the electronics of a sulfonyl chloride activator and the reactivity of a glycosyl donor hemiacetal are matched. While these reactions are compatible with the acid- and base-sensitive protecting groups that are commonly used in oligosaccharide synthesis, these protecting groups are not relied upon to control selectivity. Instead, β-selectivity arises from the stereoinversion of an α-glycosyl arylsulfonate in an SN2-like mechanism. Our mechanistic proposal is supported by NMR studies, kinetic isotope effect (KIE) measurements, and DFT calculations.
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Affiliation(s)
- Ming-Hua Zhuo
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
| | - David J Wilbur
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
| | - Eugene E Kwan
- Merck & Co. Inc. , 33 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Clay S Bennett
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
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10
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Roytman VA, Karugu RW, Hong Y, Hirschi JS, Vetticatt MJ. 13 C Kinetic Isotope Effects as a Quantitative Probe To Distinguish between Enol and Enamine Mechanisms in Aminocatalysis. Chemistry 2018; 24:8098-8102. [PMID: 29654709 DOI: 10.1002/chem.201801748] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 01/24/2023]
Abstract
A combination of experimental 13 C kinetic isotope effects (KIEs) and high-level density functional theory (DFT) calculations is used to distinguish between "enamine" and "enol" mechanisms in the Michael addition of acetone to trans-β-nitrostyrene catalyzed by Jacobsen's primary amine thiourea catalyst. In light of the recent findings that the widely used 18 O-incorporation probe for these mechanisms is flawed, the results described in this communication demonstrate an alternative probe to distinguish between these pathways. A key advantage of this probe is that quantitative mechanistic information is obtained without modifying experimental conditions. This approach is expected to find application in resolving mechanistic debates, while providing valuable information about the key transition state of organocatalyzed reactions involving the α-functionalization of carbonyls.
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Affiliation(s)
| | - Rachael W Karugu
- Department of Chemistry, Binghamton University, Binghamton, NY, 13902, USA
| | - Yun Hong
- Department of Chemistry, Binghamton University, Binghamton, NY, 13902, USA
| | - Jennifer S Hirschi
- Department of Chemistry, Binghamton University, Binghamton, NY, 13902, USA
| | - Mathew J Vetticatt
- Department of Chemistry, Binghamton University, Binghamton, NY, 13902, USA
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11
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Moggré GJ, Poulin MB, Tyler PC, Schramm VL, Parker EJ. Transition State Analysis of Adenosine Triphosphate Phosphoribosyltransferase. ACS Chem Biol 2017; 12:2662-2670. [PMID: 28872824 DOI: 10.1021/acschembio.7b00484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first step in histidine biosynthesis, a pathway essential to microorganisms and a validated target for antimicrobial drug design. The ATP-PRT enzyme catalyzes the reversible substitution reaction between phosphoribosyl pyrophosphate and ATP. The enzyme exists in two structurally distinct forms, a short- and a long-form enzyme. These forms share a catalytic core dimer but bear completely different allosteric domains and thus distinct quaternary assemblies. Understanding enzymatic transition states can provide essential information on the reaction mechanisms and insight into how differences in domain structure influence the reaction chemistry, as well as providing a template for inhibitor design. In this study, the transition state structures for ATP-PRT enzymes from Campylobacter jejuni and Mycobacterium tuberculosis (long-form enzymes) and from Lactococcus lactis (short-form) were determined and compared. Intrinsic kinetic isotope effects (KIEs) were obtained at reaction sensitive positions for the reverse reaction using phosphonoacetic acid, an alternative substrate to the natural substrate pyrophosphate. The experimental KIEs demonstrated mechanistic similarities between the three enzymes and provided experimental boundaries for quantum chemical calculations to characterize the transition states. Predicted transition state structures support a dissociative reaction mechanism with a DN*AN‡ transition state. Weak interactions from the incoming nucleophile and a fully dissociated ATP adenine are predicted regardless of the difference in overall structure and quaternary assembly. These studies establish that despite significant differences in the quaternary assembly and regulatory machinery between ATP-PRT enzymes from different sources, the reaction chemistry and catalytic mechanism are conserved.
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Affiliation(s)
- Gert-Jan Moggré
- Maurice
Wilkins Centre, Biomolecular Interaction Centre and Department of
Chemistry, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Myles B. Poulin
- Department
of Chemistry and Biochemistry, University of Maryland College Park, College
Park, Maryland 20742, United States
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Peter C. Tyler
- Ferrier
Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Vern L. Schramm
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Emily J. Parker
- Maurice
Wilkins Centre, Biomolecular Interaction Centre and Department of
Chemistry, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
- Ferrier
Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
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12
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Aziz HR, Singleton DA. Concert along the Edge: Dynamics and the Nature of the Border between General and Specific Acid-Base Catalysis. J Am Chem Soc 2017; 139:5965-5972. [PMID: 28378578 PMCID: PMC5502124 DOI: 10.1021/jacs.7b02148] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Reactions that involve a combination of proton transfer and heavy-atom bonding changes are normally categorized by whether the proton transfer is occurring during the rate-limiting step, as in the distinction between general and specific acid-base catalysis. The experimental and computational study here of a β-ketoacid decarboxylation shows how the distinction between the two mechanisms breaks down near its border due to the differing time scales for proton versus heavy-atom motion. Isotope effects in the decarboxylation of benzoylacetic acid support a transition state in which the proton transfer is complete. In quasiclassical trajectories passing through this transition state, the new O-H bond after proton transfer undergoes several vibrations before heavy-atom motion completes the reaction. The bonding changes are thus temporally separated at a "dynamic intermediate" structure that acts equivalently to an ordinary intermediate in the trajectories, including the reversal of trajectories at the intermediate when the second "step" fails, but the structure is not an energy minimum. The results define a border between mechanisms where the usual energetic definition of intermediates is not meaningful.
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Affiliation(s)
| | - Daniel A. Singleton
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77842, United States
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13
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Żaczek S, Gelman F, Dybala-Defratyka A. A Benchmark Study of Kinetic Isotope Effects and Barrier Heights for the Finkelstein Reaction. J Phys Chem A 2017; 121:2311-2321. [PMID: 28248520 DOI: 10.1021/acs.jpca.7b00230] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we present a combined (experimental and computational) study of the Finkelstein reaction in condensed phase, where bromine is substituted by iodine in 2-bromoethylbenzene, in the presence of either acetone or acetonitrile as a solvent. Performance of various density functional theory and ab initio methods were tested for reaction barrier heights as well as for bromine and carbon kinetic isotope effects (KIEs). Two different implicit solvation models were examined (PCM and SMD). Theoretically predicted KIEs were compared with experimental values, while reaction barrier heights were assessed using the CCSD(T)-level and experimental energies as reference. In general, although the tested parameters (energies and KIEs) do not exhibit any substantial difference upon a change of the solvent, the different behavior of the theoretical methods was observed depending on the solvent. With respect to isotope effects, both PCM and SMD seem to perform very similarly, though results obtained with PCM are slightly closer to the experimental values. For predicting reaction barriers, utilization of either PCM or SMD solvation models yielded different results. Functionals from the ωB97 family: ωB97, ωB97X, and ωB97X-D provide the most accurate results for the studied system.
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Affiliation(s)
- Szymon Żaczek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology , Żeromskiego 116, 90-924 Łódź, Poland
| | - Faina Gelman
- Geological Survey of Israel , Malkhei Israel Street 30, 95501 Jerusalem, Israel
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology , Żeromskiego 116, 90-924 Łódź, Poland
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14
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West TH, Walden DM, Taylor JE, Brueckner AC, Johnston RC, Cheong PHY, Lloyd-Jones GC, Smith AD. Catalytic Enantioselective [2,3]-Rearrangements of Allylic Ammonium Ylides: A Mechanistic and Computational Study. J Am Chem Soc 2017; 139:4366-4375. [PMID: 28230365 PMCID: PMC5374492 DOI: 10.1021/jacs.6b11851] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A mechanistic study of the isothiourea-catalyzed enantioselective [2,3]-rearrangement of allylic ammonium ylides is described. Reaction kinetic analyses using 19F NMR and density functional theory computations have elucidated a reaction profile and allowed identification of the catalyst resting state and turnover-rate limiting step. A catalytically relevant catalyst-substrate adduct has been observed, and its constitution elucidated unambiguously by 13C and 15N isotopic labeling. Isotopic entrainment has shown the observed catalyst-substrate adduct to be a genuine intermediate on the productive cycle toward catalysis. The influence of HOBt as an additive upon the reaction, catalyst resting state, and turnover-rate limiting step has been examined. Crossover experiments have probed the reversibility of each of the proposed steps of the catalytic cycle. Computations were also used to elucidate the origins of stereocontrol, with a 1,5-S···O interaction and the catalyst stereodirecting group providing transition structure rigidification and enantioselectivity, while preference for cation-π interactions over C-H···π is responsible for diastereoselectivity.
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Affiliation(s)
- Thomas H West
- EaStCHEM, School of Chemistry, University of St Andrews , North Haugh, St. Andrews, KY16 9ST, U.K
| | - Daniel M Walden
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97333, United States
| | - James E Taylor
- EaStCHEM, School of Chemistry, University of St Andrews , North Haugh, St. Andrews, KY16 9ST, U.K
| | - Alexander C Brueckner
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97333, United States
| | - Ryne C Johnston
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97333, United States
| | - Paul Ha-Yeon Cheong
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97333, United States
| | - Guy C Lloyd-Jones
- EaStCHEM, School of Chemistry, University of Edinburgh , Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, U.K
| | - Andrew D Smith
- EaStCHEM, School of Chemistry, University of St Andrews , North Haugh, St. Andrews, KY16 9ST, U.K
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15
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Jézéquel T, Joubert V, Giraudeau P, Remaud GS, Akoka S. The new face of isotopic NMR at natural abundance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:77-90. [PMID: 27921330 DOI: 10.1002/mrc.4548] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/28/2016] [Accepted: 11/02/2016] [Indexed: 05/26/2023]
Abstract
The most widely used method for isotope analysis at natural abundance is isotope ratio monitoring by Mass Spectrometry (irm-MS) which provides bulk isotopic composition in 2 H, 13 C, 15 N, 18 O or 34 S. However, in the 1980s, the direct access to Site-specific Natural Isotope Fractionation by Nuclear Magnetic Resonance (SNIF-NMRTM ) was immediately recognized as a powerful technique to authenticate the origin of natural or synthetic products. The initial - and still most popular - application consisted in detecting the chaptalization of wines by irm-2 H NMR. The approach has been extended to a wide range of methodologies over the last decade, paving the way to a wide range of applications, not only in the field of authentication but also to study metabolism. In particular, the emerging irm-13 C NMR approach delivers direct access to position-specific 13 C isotope content at natural abundance. After highlighting the application scope of irm-NMR (2 H and 13 C), this article describes the major improvements which made possible to reach the required accuracy of 1‰ (0.1%) in irm-13 C NMR. The last part of the manuscript summarizes the different steps to perform isotope analysis as a function of the sample properties (concentration, peak overlap) and the kind of targeted isotopic information (authentication, affiliation). Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Tangi Jézéquel
- Université de Nantes, CNRS, CEISAM UMR 6230, Nantes, France
| | | | - Patrick Giraudeau
- Université de Nantes, CNRS, CEISAM UMR 6230, Nantes, France
- Institut Universitaire de France, Paris, France
| | | | - Serge Akoka
- Université de Nantes, CNRS, CEISAM UMR 6230, Nantes, France
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16
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Kwan EE, Park Y, Besser HA, Anderson TL, Jacobsen EN. Sensitive and Accurate 13C Kinetic Isotope Effect Measurements Enabled by Polarization Transfer. J Am Chem Soc 2017; 139:43-46. [PMID: 28005341 PMCID: PMC5674980 DOI: 10.1021/jacs.6b10621] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polarization transfer is demonstrated as a sensitive technique for the measurement of isotopic fractionation of protonated carbons at natural abundance. This method allows kinetic isotope effects (KIEs) to be determined with substantially less material or shorter acquisition time compared with traditional experiments. Computations quantitatively reproduce the KIEs in a Diels-Alder reaction and a catalytic glycosylation. The glycosylation is shown to occur by an effectively concerted mechanism.
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Affiliation(s)
- Eugene E. Kwan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yongho Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Harrison A. Besser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Thayer L. Anderson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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17
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Measurement of Kinetic Isotope Effects by Continuously Monitoring Isotopologue Ratios Using NMR Spectroscopy. Methods Enzymol 2017. [DOI: 10.1016/bs.mie.2017.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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18
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Linscott JA, Kapilashrami K, Wang Z, Senevirathne C, Bothwell IR, Blum G, Luo M. Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8. Proc Natl Acad Sci U S A 2016; 113:E8369-E8378. [PMID: 27940912 PMCID: PMC5206543 DOI: 10.1073/pnas.1609032114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein lysine methyltransferases (PKMTs) catalyze the methylation of protein substrates, and their dysregulation has been linked to many diseases, including cancer. Accumulated evidence suggests that the reaction path of PKMT-catalyzed methylation consists of the formation of a cofactor(cosubstrate)-PKMT-substrate complex, lysine deprotonation through dynamic water channels, and a nucleophilic substitution (SN2) transition state for transmethylation. However, the molecular characters of the proposed process remain to be elucidated experimentally. Here we developed a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method and corresponding mathematic matrix to determine precisely the ratios of isotopically methylated peptides. This approach may be generally applicable for examining the kinetic isotope effects (KIEs) of posttranslational modifying enzymes. Protein lysine methyltransferase SET8 is the sole PKMT to monomethylate histone 4 lysine 20 (H4K20) and its function has been implicated in normal cell cycle progression and cancer metastasis. We therefore implemented the MS-based method to measure KIEs and binding isotope effects (BIEs) of the cofactor S-adenosyl-l-methionine (SAM) for SET8-catalyzed H4K20 monomethylation. A primary intrinsic 13C KIE of 1.04, an inverse intrinsic α-secondary CD3 KIE of 0.90, and a small but statistically significant inverse CD3 BIE of 0.96, in combination with computational modeling, revealed that SET8-catalyzed methylation proceeds through an early, asymmetrical SN2 transition state with the C-N and C-S distances of 2.35-2.40 Å and 2.00-2.05 Å, respectively. This transition state is further supported by the KIEs, BIEs, and steady-state kinetics with the SAM analog Se-adenosyl-l-selenomethionine (SeAM) as a cofactor surrogate. The distinct transition states between protein methyltransferases present the opportunity to design selective transition-state analog inhibitors.
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Affiliation(s)
- Joshua A Linscott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021
| | - Kanishk Kapilashrami
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Zhen Wang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Chamara Senevirathne
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Ian R Bothwell
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Gil Blum
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021
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19
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Roston D, Cui Q. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects. J Am Chem Soc 2016; 138:11946-57. [PMID: 27541005 PMCID: PMC5705178 DOI: 10.1021/jacs.6b07347] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reaction's transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured values. Our results provide a detailed interpretation of the measured isotope effects and make predictions that can test the proposed model. The model indicates that the substrate is deformed in the ground state (GS) of the reaction and partially resembles the TS. The highly preorganized active site preferentially binds conformations that resemble the TS and not the GS, which induces the substrate to adapt to the enzyme, rather than the other way around-as with classic "induced fit" models. The preferential stabilization of the TS over the GS is what lowers the barrier to the chemical step.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
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20
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Derakhshani-Molayousefi M, Kashefolgheta S, Eilers JE, Lu Y. Computational Replication of the Primary Isotope Dependence of Secondary Kinetic Isotope Effects in Solution Hydride-Transfer Reactions: Supporting the Isotopically Different Tunneling Ready State Conformations. J Phys Chem A 2016; 120:4277-84. [DOI: 10.1021/acs.jpca.6b03571] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Sadra Kashefolgheta
- Department
of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
- Department of Theory & Bio-systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - James E. Eilers
- Department
of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department
of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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21
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Poulin MB, Schneck JL, Matico RE, Hou W, McDevitt PJ, Holbert M, Schramm VL. Nucleosome Binding Alters the Substrate Bonding Environment of Histone H3 Lysine 36 Methyltransferase NSD2. J Am Chem Soc 2016; 138:6699-702. [PMID: 27183271 PMCID: PMC6702673 DOI: 10.1021/jacs.6b01612] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nuclear receptor-binding SET domain protein 2 (NSD2) is a histone H3 lysine 36 (H3K36)-specific methyltransferase enzyme that is overexpressed in a number of cancers, including multiple myeloma. NSD2 binds to S-adenosyl-l-methionine (SAM) and nucleosome substrates to catalyze the transfer of a methyl group from SAM to the ε-amino group of histone H3K36. Equilibrium binding isotope effects and density functional theory calculations indicate that the SAM methyl group is sterically constrained in complex with NSD2, and that this steric constraint is released upon nucleosome binding. Together, these results show that nucleosome binding to NSD2 induces a significant change in the chemical environment of enzyme-bound SAM.
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Affiliation(s)
- Myles B. Poulin
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Jessica L. Schneck
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Rosalie E. Matico
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Wangfang Hou
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Patrick J. McDevitt
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Marc Holbert
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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22
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Colletto C, Islam S, Juliá-Hernández F, Larrosa I. Room-Temperature Direct β-Arylation of Thiophenes and Benzo[b]thiophenes and Kinetic Evidence for a Heck-type Pathway. J Am Chem Soc 2016; 138:1677-83. [PMID: 26788885 PMCID: PMC4774971 DOI: 10.1021/jacs.5b12242] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
The
first example of a regioselective β-arylation of benzo[b]thiophenes and thiophenes at room temperature with aryl
iodides as coupling partners is reported. This methodology stands
out for its operational simplicity: no prefunctionalization of either
starting material is required, the reaction is insensitive to air
and moisture, and it proceeds at room temperature. The mild conditions
afford wide functional group tolerance, often with complete regioselectivity
and high yields, resulting in a highly efficient catalytic system.
Initial mechanistic studies, including 13C and 2H KIEs, suggest that this process occurs via a concerted carbo-palladation
across the thiophene double bond, followed by a base-assisted anti-elimination.
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Affiliation(s)
- Chiara Colletto
- School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom.,School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Saidul Islam
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Francisco Juliá-Hernández
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Igor Larrosa
- School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
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23
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Plata RE, Singleton DA. A case study of the mechanism of alcohol-mediated Morita Baylis-Hillman reactions. The importance of experimental observations. J Am Chem Soc 2015; 137:3811-26. [PMID: 25714789 PMCID: PMC4379969 DOI: 10.1021/ja5111392] [Citation(s) in RCA: 312] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 12/12/2022]
Abstract
The mechanism of the Morita Baylis-Hillman reaction has been heavily studied in the literature, and a long series of computational studies have defined complete theoretical energy profiles in these reactions. We employ here a combination of mechanistic probes, including the observation of intermediates, the independent generation and partitioning of intermediates, thermodynamic and kinetic measurements on the main reaction and side reactions, isotopic incorporation from solvent, and kinetic isotope effects, to define the mechanism and an experimental mechanistic free-energy profile for a prototypical Morita Baylis-Hillman reaction in methanol. The results are then used to critically evaluate the ability of computations to predict the mechanism. The most notable prediction of the many computational studies, that of a proton-shuttle pathway, is refuted in favor of a simple but computationally intractable acid-base mechanism. Computational predictions vary vastly, and it is not clear that any significant accurate information that was not already apparent from experiment could have been garnered from computations. With care, entropy calculations are only a minor contributor to the larger computational error, while literature entropy-correction processes lead to absurd free-energy predictions. The computations aid in interpreting observations but fail utterly as a replacement for experiment.
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Affiliation(s)
- R. Erik Plata
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Daniel A. Singleton
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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24
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Hirsch BM, Burgos ES, Schramm VL. Transition-state analysis of 2-O-acetyl-ADP-ribose hydrolysis by human macrodomain 1. ACS Chem Biol 2014; 9:2255-62. [PMID: 25051211 PMCID: PMC4201351 DOI: 10.1021/cb500485w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Macrodomains, including the human macrodomain 1 (MacroD1), are erasers of the post-translational modification of monoadenosinediphospho-ribosylation and hydrolytically deacetylate the sirtuin product O-acetyl-ADP-ribose (OAADPr). OAADPr has been reported to play a role in cell signaling based on oocyte microinjection studies, and macrodomains affect an array of cell processes including transcription and response to DNA damage. Here, we investigate human MacroD1 by transition-state (TS) analysis based on kinetic isotope effects (KIEs) from isotopically labeled OAADPr substrates. Competitive radiolabeled-isotope effects and mass spectrometry were used to obtain KIE data to yield intrinsic KIE values. Intrinsic KIEs were matched to a quantum chemical structure of the TS that includes the active site residues Asp184 and Asn174 and a structural water molecule. Transition-state analysis supports a concerted mechanism with an early TS involving simultaneous nucleophilic water attack and leaving group bond cleavage where the breaking C-O ester bond=1.60 Å and the C-O bond to the attacking water nucleophile=2.30 Å. The MacroD1 TS provides mechanistic understanding of the OAADPr esterase chemistry.
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Affiliation(s)
- Brett M. Hirsch
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Emmanuel S. Burgos
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Vern L. Schramm
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
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25
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Chen Z, Nieves-Quinones Y, Waas JR, Singleton DA. Isotope effects, dynamic matching, and solvent dynamics in a Wittig reaction. Betaines as bypassed intermediates. J Am Chem Soc 2014; 136:13122-5. [PMID: 25208686 PMCID: PMC4183629 DOI: 10.1021/ja506497b] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
The
mechanism of the Wittig reaction of anisaldehyde with a stabilized
ylide was studied by a combination of 13C kinetic isotope
effects, conventional calculations, and molecular dynamics calculations
in a cluster of 53 THF molecules. The isotope effects support a cycloaddition
mechanism involving two sequential transition states associated with
separate C–C and P–O bond formations. However, the betaine
structure in between the two transition states is bypassed as an equilibrated
intermediate in most trajectories. The role of the dynamics of solvent
equilibration in the nature of mechanistic intermediates is discussed.
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Affiliation(s)
- Zhuo Chen
- Department of Chemistry, Texas A&M University , P.O. Box 30012, College Station, Texas 77842, United States
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26
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Biswas B, Collins SC, Singleton DA. Dynamics and a unified understanding of competitive [2,3]- and [1,2]-sigmatropic rearrangements based on a study of ammonium ylides. J Am Chem Soc 2014; 136:3740-3. [PMID: 24579740 PMCID: PMC3971961 DOI: 10.1021/ja4128289] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The
[2,3]- and [1,2]-sigmatropic rearrangements of ammonium ylides
are studied by a combination of experimental, standard computational,
and dynamic trajectory methods. The mixture of concerted [2,3] rearrangement
and bond cleavage observed experimentally is accounted for by the
outcome of trajectories passing through the formal [2,3] rearrangement
transition state. In this way the bond cleavage is promoted by the
pericyclic stabilization of the [2,3] transition state. It is proposed
that this dynamic effect is responsible for the pervasive co-occurrence
of the two rearrangements.
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Affiliation(s)
- Bibaswan Biswas
- Department of Chemistry, Texas A&M University , P.O. Box 30012, College Station, Texas 77842, United States
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27
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Pellarin KR, Puddephatt RJ. Oxidation of a Dimethylplatinum(II) Complex with Oxaziridines: A Hemiaminal Intermediate but No Oxo Complex. Organometallics 2013. [DOI: 10.1021/om400079b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kyle R. Pellarin
- Department of Chemistry, University of Western Ontario, London, Canada N6A 5B7
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28
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Fong A, Meyer MP, O’Leary DJ. Enthalpy/entropy contributions to conformational KIEs: theoretical predictions and comparison with experiment. Molecules 2013; 18:2281-96. [PMID: 23429344 PMCID: PMC6269852 DOI: 10.3390/molecules18022281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/22/2013] [Accepted: 02/01/2013] [Indexed: 11/16/2022] Open
Abstract
Previous theoretical studies of Mislow’s doubly-bridged biphenyl ketone 1 and dihydrodimethylphenanthrene 2 have determined significant entropic contributions to their normal (1) and inverse (2) conformational kinetic isotope effects (CKIEs). To broaden our investigation, we have used density functional methods to characterize the potential energy surfaces and vibrational frequencies for ground and transition structures of additional systems with measured CKIEs, including [2.2]-metaparacyclophane-d (3), 1,1'-binaphthyl (4), 2,2'-dibromo-[1,1'-biphenyl]-4,4'-dicarboxylic acid (5), and the 2-(N,N,N-trimethyl)-2'-(N,N-dimethyl)-diaminobiphenyl cation (6). We have also computed CKIEs in a number of systems whose experimental CKIEs are unknown. These include analogs of 1 in which the C=O groups have been replaced with CH2 (7), O (8), and S (9) atoms and ring-expanded variants of 2 containing CH2 (10), O (11), S (12), or C=O (13) groups. Vibrational entropy contributes to the CKIEs in all of these systems with the exception of cyclophane 3, whose isotope effect is predicted to be purely enthalpic in origin and whose Bigeleisen-Mayer ZPE term is equivalent to ΔΔH‡. There is variable correspondence between these terms in the other molecules studied, thus identifying additional examples of systems in which the Bigeleisen-Mayer formalism does not correlate with ΔH/ΔS dissections.
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Affiliation(s)
- Aaron Fong
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, CA 91711, USA; E-Mail:
| | - Matthew P. Meyer
- Department of Chemistry, University of California, Merced, Atwater, CA 95301, USA
- Authors to whom correspondence should be addressed; E-Mails: (M.P.M.); (D.J.O.); Tel.: +1-209-228-2982 (M.P.M.); Fax: +1-209-228-4646 (M.P.M.); Tel.: +1-909-621-8444 (D.J.O.); Fax: +1-909-607-7726 (D.J.O.)
| | - Daniel J. O’Leary
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, CA 91711, USA; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (M.P.M.); (D.J.O.); Tel.: +1-209-228-2982 (M.P.M.); Fax: +1-209-228-4646 (M.P.M.); Tel.: +1-909-621-8444 (D.J.O.); Fax: +1-909-607-7726 (D.J.O.)
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29
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Lou M, Gilpin ME, Burger SK, Malik AM, Gawuga V, Popović V, Capretta A, Berti PJ. Transition state analysis of acid-catalyzed hydrolysis of an enol ether, enolpyruvylshikimate 3-phosphate (EPSP). J Am Chem Soc 2012; 134:12947-57. [PMID: 22765168 DOI: 10.1021/ja3043382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton transfer to carbon represents a significant catalytic challenge because of the large intrinsic energetic barrier and the frequently unfavorable thermodynamics. Multiple kinetic isotope effects (KIEs) were measured for acid-catalyzed hydrolysis of the enol ether functionality of enolpyruvylshikimate 3-phosphate (EPSP) as a nonenzymatic analog of the EPSP synthase (AroA) reaction. The large solvent deuterium KIE demonstrated that protonating C3 was the rate-limiting step, and the lack of solvent hydron exchange into EPSP demonstrated that protonation was irreversible. The reaction mechanism was stepwise, with C3, the methylene carbon, being protonated to form a discrete oxacarbenium ion intermediate before water attack at the cationic center, that is, an AH(‡)*AN (or AH(‡) + AN) mechanism. The calculated 3-(14)C and 3,3-(2)H2 KIEs varied as a function of the extent of proton transfer at the transition state, as reflected in the C3-H(+) bond order, nC3-H+. The calculated 3-(14)C KIE was a function primarily of C3 coupling with the movement of the transferring proton, as reflected in the reaction coordinate contribution ((light)ν(‡)/(heavy)ν(‡)), rather than of changes in bonding. Coupling was strongest in early and late transition states, where the reaction coordinate frequency was lower. The other calculated (14)C and (18)O KIEs were more sensitive to interactions with counterions and solvation in the model structures than nC3-H+. The KIEs revealed a moderately late transition state with significant oxacarbenium ion character and with a C3-H(+) bond order ≈0.6.
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Affiliation(s)
- Meiyan Lou
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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30
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Lou M, Burger SK, Gilpin ME, Gawuga V, Capretta A, Berti PJ. Transition State Analysis of Enolpyruvylshikimate 3-Phosphate (EPSP) Synthase (AroA)-Catalyzed EPSP Hydrolysis. J Am Chem Soc 2012; 134:12958-69. [PMID: 22765279 DOI: 10.1021/ja304339h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meiyan Lou
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Steven K. Burger
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Meghann E. Gilpin
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Vivian Gawuga
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Alfredo Capretta
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul J. Berti
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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31
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Ruiz Pernía JJ, Williams IH. Ensemble-Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution. Chemistry 2012; 18:9405-14. [DOI: 10.1002/chem.201200443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Indexed: 11/11/2022]
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32
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Vetticatt MJ, Singleton DA. Isotope effects and heavy-atom tunneling in the Roush allylboration of aldehydes. Org Lett 2012; 14:2370-3. [PMID: 22506639 DOI: 10.1021/ol300789a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Intermolecular (13)C kinetic isotope effects (KIEs) for the Roush allylboration of p-anisaldehyde were determined using a novel approach. The experimental (13)C KIEs fit qualitatively with the expected rate-limiting cyclic transition state, but they are far higher than theoretical predictions based on conventional transition state theory. This discrepancy is attributed to a substantial contribution of heavy-atom tunneling to the reaction, and this is supported by multidimensional tunneling calculations that reproduce the observed KIEs.
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Affiliation(s)
- Mathew J Vetticatt
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
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33
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Kamerlin SCL. Theoretical Comparison of p-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer. J Org Chem 2011; 76:9228-38. [DOI: 10.1021/jo201104v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Schramm VL. Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes. Annu Rev Biochem 2011; 80:703-32. [PMID: 21675920 DOI: 10.1146/annurev-biochem-061809-100742] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein's dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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35
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Silva RG, Schramm VL. Uridine phosphorylase from Trypanosoma cruzi: kinetic and chemical mechanisms. Biochemistry 2011; 50:9158-66. [PMID: 21932786 DOI: 10.1021/bi2013382] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reversible phosphorolysis of uridine to generate uracil and ribose 1-phosphate is catalyzed by uridine phosphorylase and is involved in the pyrimidine salvage pathway. We define the reaction mechanism of uridine phosphorylase from Trypanosoma cruzi by steady-state and pre-steady-state kinetics, pH-rate profiles, kinetic isotope effects from uridine, and solvent deuterium isotope effects. Initial rate and product inhibition patterns suggest a steady-state random kinetic mechanism. Pre-steady-state kinetics indicated no rate-limiting step after formation of the enzyme-products ternary complex, as no burst in product formation is observed. The limiting single-turnover rate constant equals the steady-state turnover number; thus, chemistry is partially or fully rate limiting. Kinetic isotope effects with [1'-(3)H]-, [1'-(14)C]-, and [5'-(14)C,1,3-(15)N(2)]uridine gave experimental values of (α-T)(V/K)(uridine) = 1.063, (14)(V/K)(uridine) = 1.069, and (15,β-15)(V/K)(uridine) = 1.018, in agreement with an A(N)D(N) (S(N)2) mechanism where chemistry contributes significantly to the overall rate-limiting step of the reaction. Density functional theory modeling of the reaction in gas phase supports an A(N)D(N) mechanism. Solvent deuterium kinetic isotope effects were unity, indicating that no kinetically significant proton transfer step is involved at the transition state. In this N-ribosyl transferase, proton transfer to neutralize the leaving group is not part of transition state formation, consistent with an enzyme-stabilized anionic uracil as the leaving group. Kinetic analysis as a function of pH indicates one protonated group essential for catalysis and for substrate binding.
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Affiliation(s)
- Rafael G Silva
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, United States
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36
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Silva RG, Vetticatt MJ, Merino EF, Cassera MB, Schramm VL. Transition-state analysis of Trypanosoma cruzi uridine phosphorylase-catalyzed arsenolysis of uridine. J Am Chem Soc 2011; 133:9923-31. [PMID: 21599004 DOI: 10.1021/ja2031294] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Uridine phosphorylase catalyzes the reversible phosphorolysis of uridine and 2'-deoxyuridine to generate uracil and (2-deoxy)ribose 1-phosphate, an important step in the pyrimidine salvage pathway. The coding sequence annotated as a putative nucleoside phosphorylase in the Trypanosoma cruzi genome was overexpressed in Escherichia coli , purified to homogeneity, and shown to be a homodimeric uridine phosphorylase, with similar specificity for uridine and 2'-deoxyuridine and undetectable activity toward thymidine and purine nucleosides. Competitive kinetic isotope effects (KIEs) were measured and corrected for a forward commitment factor using arsenate as the nucleophile. The intrinsic KIEs are: 1'-(14)C = 1.103, 1,3-(15)N(2) = 1.034, 3-(15)N = 1.004, 1-(15)N = 1.030, 1'-(3)H = 1.132, 2'-(2)H = 1.086, and 5'-(3)H(2) = 1.041 for this reaction. Density functional theory was employed to quantitatively interpret the KIEs in terms of transition-state structure and geometry. Matching of experimental KIEs to proposed transition-state structures suggests an almost synchronous, S(N)2-like transition-state model, in which the ribosyl moiety possesses significant bond order to both nucleophile and leaving groups. Natural bond orbital analysis allowed a comparison of the charge distribution pattern between the ground-state and the transition-state models.
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Affiliation(s)
- Rafael G Silva
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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Silva RG, Hirschi JS, Ghanem M, Murkin AS, Schramm VL. Arsenate and phosphate as nucleophiles at the transition states of human purine nucleoside phosphorylase. Biochemistry 2011; 50:2701-9. [PMID: 21348499 DOI: 10.1021/bi200279s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of 6-oxypurine (2'-deoxy)ribonucleosides, generating (2-deoxy)ribose 1-phosphate and the purine base. Transition-state models for inosine cleavage have been proposed with bovine, human, and malarial PNPs using arsenate as the nucleophile, since kinetic isotope effects (KIEs) are obscured on phosphorolysis due to high commitment factors. The Phe200Gly mutant of human PNP has low forward and reverse commitment factors in the phosphorolytic reaction, permitting the measurement of competitive intrinsic KIEs on both arsenolysis and phosphorolysis of inosine. The intrinsic 1'-(14)C, 1'-(3)H, 2'-(2)H, 9-(15)N, and 5'-(3)H(2) KIEs for inosine were measured for arsenolysis and phosphorolysis. Except for the remote 5'-(3)H(2), and some slight difference between the 2'-(2)H KIEs, all isotope effects originating in the reaction coordinate are the same within experimental error. Hence, arsenolysis and phosphorolysis proceed through closely related transition states. Although electrostatically similar, the volume of arsenate is greater than phosphate and supports a steric influence to explain the differences in the 5'-(3)H(2) KIEs. Density functional theory calculations provide quantitative models of the transition states for Phe200Gly human PNP-catalyzed arsenolysis and phosphorolysis, selected upon matching calculated and experimental KIEs. The models confirm the striking resemblance between the transition states for the two reactions.
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Affiliation(s)
- Rafael G Silva
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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38
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Schwartz PA, Vetticatt MJ, Schramm VL. Transition state analysis of the arsenolytic depyrimidination of thymidine by human thymidine phosphorylase. Biochemistry 2011; 50:1412-20. [PMID: 21222488 DOI: 10.1021/bi101900b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis, promotes angiogenesis, and is involved in metabolic inactivation of antiproliferative agents that inhibit thymidylate synthase. Understanding its transition state structure is on the path to design transition state analogues. Arsenolysis of dT by hTP permits kinetic isotope effect (KIE) analysis of the reaction by forming thymine and the chemically unstable 2-deoxyribose 1-arsenate. The transition state for the arsenolytic reaction was characterized using multiple KIEs and computational analysis. Transition state analysis revealed a concerted bimolecular (A(N)D(N)) mechanism. A transition state constrained to match the intrinsic KIE values was found using density functional theory (B3LYP/6-31G*). An active site histidine is implicated as the catalytic base responsible for activation of the arsenate nucleophile and stabilization of the thymine leaving group during the isotopically sensitive step. At the transition state, the deoxyribose ring exhibits significant oxocarbenium ion character with bond breaking (r(C-N) = 2.45 Å) nearly complete and minimal bond making to the attacking nucleophile (r(C-O) = 2.95 Å). The transition state model predicts a deoxyribose conformation with a 2'-endo ring geometry. Transition state structure for the slow hydrolytic reaction of hTP involves a stepwise mechanism [Schwartz, P. A., Vetticatt, M. J., and Schramm, V. L. (2010) J. Am. Chem. Soc. 132, 13425-13433], in contrast to the concerted mechanism described here for arsenolysis.
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Affiliation(s)
- Phillip A Schwartz
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Abstract
Kinetic isotope effects are exquisitely sensitive probes of transition structure. As such, kinetic isotope effects offer a uniquely useful probe for the symmetry-breaking process that is inherent to stereoselective reactions. In this Concept article, we explore the role of steric and electronic effects in stereocontrol, and we relate these concepts to recent studies carried out in our laboratory. We also explore the way in which kinetic isotope effects serve as useful points of contact with computational models of transition structures. Finally, we discuss future opportunities for kinetic isotope effects to play a role in asymmetric catalyst development.
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Affiliation(s)
- Thomas Giagou
- School of Natural Sciences, University of California Merced, 5200 N. Lake Rd., Merced, CA 95344 (USA)
| | - Matthew P. Meyer
- School of Natural Sciences, University of California Merced, 5200 N. Lake Rd., Merced, CA 95344 (USA)
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40
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Hiller DA, Zhong M, Singh V, Strobel SA. Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects. Biochemistry 2010; 49:3868-78. [PMID: 20359191 PMCID: PMC2864349 DOI: 10.1021/bi901458x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The ester bond of peptidyl-tRNA undergoes nucleophilic attack in solution and when catalyzed by the ribosome. To characterize the uncatalyzed hydrolysis reaction, a model of peptide release, the transition state structure for hydrolysis of a peptidyl-tRNA mimic was determined. Kinetic isotope effects were measured at several atoms that potentially undergo a change in bonding in the transition state. Large kinetic isotope effects of carbonyl (18)O and alpha-deuterium substitutions on uncatalyzed hydrolysis indicate the transition state is nearly tetrahedral. Kinetic isotope effects were also measured for aminolysis by hydroxylamine to study a reaction similar to the formation of a peptide bond. In contrast to hydrolysis, the large leaving group (18)O isotope effect indicates the C-O3' bond has undergone significant scission in the transition state. The smaller carbonyl (18)O and alpha-deuterium effects are consistent with a later transition state. The assay developed here can also be used to measure isotope effects for the ribosome-catalyzed reactions. These uncatalyzed reactions serve as a basis for determining what aspects of the transition states are stabilized by the ribosome to achieve a rate enhancement.
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Affiliation(s)
- David A Hiller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
| | | | - Vipender Singh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
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41
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Greig IR. The analysis of enzymic free energy relationships using kinetic and computational models. Chem Soc Rev 2010; 39:2272-301. [DOI: 10.1039/b902741f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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42
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Litvinas ND, Brodsky BH, Du Bois J. C-H hydroxylation using a heterocyclic catalyst and aqueous H2O2. Angew Chem Int Ed Engl 2009; 48:4513-6. [PMID: 19449353 DOI: 10.1002/anie.200901353] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Substituted benzoxathiazines function as catalysts for the selective hydroxylation of tertiary C-H bonds. Mechanistic studies have revealed an unanticipated disparity between oxaziridine reactivity and catalyst performance and have given way to a new catalyst and an aqueous H(2)O(2) reaction protocol that greatly facilitate such transformations (see scheme).
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Affiliation(s)
- Nichole D Litvinas
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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43
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Litvinas N, Brodsky B, Du Bois J. CH Hydroxylation Using a Heterocyclic Catalyst and Aqueous H2O2. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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